Psyllid ID: psy6094

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-----
Protein Sequence
MKSPHSPKGLTHSVTSWETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRMVMVE
Secondary Structure (PSIPRED)
ccccccccccccccccHHHHHHHccccHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHHHHHHcccEEEEEEEccccccEEEccccccccccccccccHHccccccccccccHHHHHHHHHHHHHccccccccEEEEEEEccccccEEEHHHHHHHHHHHccccccHHHHHHHHcccccccEEEEcccHHHHHHHHHHHHHccccccccEEEEEccccccHHHHHcccccccccccEEEEEccccccccccccEEEEEcccccccccccccccccccccccccHHcccccccccccccccEEEEcccHHHHcccccccccccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccHHHHHHHcccccccccccHHHHHHHcccccHHHHHHHHHHHHHccccccccccccccccccccccccHHHHcccccEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccccHccHHHHHHHHHccccHHHHHHHHHcccccHHcccccHHHHHHcccHHHHHHHHHHHHHcccEEEEEEccccccccEEEHHHHcHHHHHHHccEEHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccccccccEEEEEccccHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHHHHHHHHccccccEEEEEEHccccHHHHHHHcccccccccEEEEEEEEEEEEEEEccEEEEEcccccEEccccccccccEEEEEEccHHHHHHccccccccccccEEEEEcHHHHccccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcccccccccHHcHHHccccccHHHHHHHHHccccHHHHHHHHHccccEEEEEcccccEEEEcccccccEEEEc
Coil and Loop (DISEMBL)
mksphspkglthsVTSWETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKklpsyqmrDAVLDMVRNNQITvisgetgsgpplhlDFITLKrsetqqypndvlnmlkdpelegvnnDVIFSLLQHIcttqrpgaiLVYCTYTfmgvspmkvFFCKNVLQRLMkgvganspKRWVKLLRSMLVVPILVFLPGWDTINSLHRsmcqssffnssrfqiiplhsmlptvsqksifntppegvRKIVLATNiaetsitidDIVYVVdcgktkmsnfdvkdniatlkpEWISLANAKQRrgragrtlkrsetqqypndvlnmlkdpelegvnnDVIFSLLQHIcttqrpgailvflpgwdTINSLHRsmcqssffnSCLLYEFamvdnkpkeiitvrdclsfeckpSTAKIIKELRARLDMLLAHklshpgttawgdpnegnilhccsgfsrmvmve
Flexible Loop (DISEMBL)
mksphspkglthsvtswetrQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLearkklpsyqmRDAVLDMVRNNQITvisgetgsgppLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAtniaetsitiddiVYVVDCGKTKMSNFDVkdniatlkpewislanakqrrgragrtlkrsetqqypndVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHpgttawgdpneGNILHCCSGFSRMVMVE
Low Complexity Region (SEG)
MKSPHSPKGLTHSVTSWETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRMVMVE
Disordered region (IsUnstruct)
**********************LLNDPVLDAAFKKEMI********************YQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLA*************************LNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRM****
Disordered Region (DISOPRED)
*******************************************************LPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLN***********NDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMC****FNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRMVMVE
Disordered Region (DISEMBL)
***************SWETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLAN*************RSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRMVMVE
Disordered Region (DISPRO)
***********************************************EMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANA*********TLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRMVMVE
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKSPHSPKGLTHSVTSWETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAKIIKELRARLDMLLAHKLSHPGTTAWGDPNEGNILHCCSGFSRMVMVE
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

No hits with e-value below 0.001 by BLAST

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	455
380029828	863	PREDICTED: probable ATP-dependent RNA he	0.338	0.178	0.431	3e-40
110755029	964	PREDICTED: probable ATP-dependent RNA he	0.338	0.159	0.431	4e-40
383865235	976	PREDICTED: probable ATP-dependent RNA he	0.345	0.160	0.434	9e-40
350402556	977	PREDICTED: probable ATP-dependent RNA he	0.340	0.158	0.429	3e-39
328711816	1055	PREDICTED: probable ATP-dependent RNA he	0.338	0.145	0.421	3e-39
340711835	977	PREDICTED: probable ATP-dependent RNA he	0.340	0.158	0.429	1e-38
488587119	856	PREDICTED: LOW QUALITY PROTEIN: probable	0.619	0.329	0.364	1e-38
432891825	1050	PREDICTED: probable ATP-dependent RNA he	0.272	0.118	0.620	3e-38
390349687	1040	PREDICTED: probable ATP-dependent RNA he	0.221	0.097	0.634	5e-38
47224961	706	unnamed protein product [Tetraodon nigro	0.254	0.164	0.655	6e-38

>gi|380029828|ref|XP_003698567.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like, partial [Apis florea]

 Score =  172 bits (436), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 88/204 (43%), Positives = 119/204 (58%), Gaps = 50/204 (24%)

Query: 100 QQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCK 159
           ++YP +V++ L++P  E ++ D+I  L++HIC T+ PGA                     
Sbjct: 412 KKYPREVIDQLRNPYSEMMSLDLIEQLIRHICRTKAPGA--------------------- 450

Query: 160 NVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQI 219
                                        ILVFLPG   I  L+R M  +  ++ S + I
Sbjct: 451 -----------------------------ILVFLPGMMDITKLNRMMLDTGCYSQSHYVI 481

Query: 220 IPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKD 279
            PLHS +PT+ QK IF  PP+GVRKI++AT+IAETSITI+D+VYV+DCGK K   FD++ 
Sbjct: 482 YPLHSRMPTIDQKLIFKEPPKGVRKIIIATSIAETSITIEDVVYVIDCGKMKFGKFDIQK 541

Query: 280 NIATLKPEWISLANAKQRRGRAGR 303
           NI TL+PEW+SLANAKQRRGRAGR
Sbjct: 542 NIQTLEPEWVSLANAKQRRGRAGR 565

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110755029|ref|XP_394965.3| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Apis mellifera]

 Score =  172 bits (435), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 88/204 (43%), Positives = 119/204 (58%), Gaps = 50/204 (24%)

Query: 100 QQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCK 159
           ++YP +V++ L++P  E ++ D+I  L++HIC T+ PGA                     
Sbjct: 412 KKYPREVIDQLRNPYSEMMSLDLIEQLIRHICRTKAPGA--------------------- 450

Query: 160 NVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQI 219
                                        ILVFLPG   I  L+R M  +  ++ S + I
Sbjct: 451 -----------------------------ILVFLPGMMDITKLNRMMLDTGCYSQSHYVI 481

Query: 220 IPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKD 279
            PLHS +PT+ QK IF  PP+GVRKI++AT+IAETSITI+D+VYV+DCGK K   FD++ 
Sbjct: 482 YPLHSRMPTIDQKLIFKEPPKGVRKIIIATSIAETSITIEDVVYVIDCGKMKFGKFDIQK 541

Query: 280 NIATLKPEWISLANAKQRRGRAGR 303
           NI TL+PEW+SLANAKQRRGRAGR
Sbjct: 542 NIQTLEPEWVSLANAKQRRGRAGR 565

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383865235|ref|XP_003708080.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Megachile rotundata]

 Score =  171 bits (433), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 90/207 (43%), Positives = 122/207 (58%), Gaps = 50/207 (24%)

Query: 97  SETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVF 156
           +  ++Y   V+  L++PE E ++ ++I  L+++IC TQ PGA                  
Sbjct: 426 ASEKRYSAQVIGQLRNPESEKLSINLIEELIRYICRTQPPGA------------------ 467

Query: 157 FCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSR 216
                                           ILVFLPG   I +L + M +S  +  S+
Sbjct: 468 --------------------------------ILVFLPGMMDIVNLQKRMIESRQYPESQ 495

Query: 217 FQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFD 276
           F I PLHS+LPT+ QK IF+ PP+G+RKI++AT+IAETSITI+D+VYV++CG+TK   FD
Sbjct: 496 FVIYPLHSLLPTIEQKLIFSEPPDGIRKIIIATSIAETSITIEDVVYVINCGRTKFGKFD 555

Query: 277 VKDNIATLKPEWISLANAKQRRGRAGR 303
           VK NI TL+PEWISLANAKQRRGRAGR
Sbjct: 556 VKKNIQTLEPEWISLANAKQRRGRAGR 582

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350402556|ref|XP_003486528.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Bombus impatiens]

 Score =  169 bits (428), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 88/205 (42%), Positives = 119/205 (58%), Gaps = 50/205 (24%)

Query: 99  TQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFC 158
           T++Y  +V+  L++P  E ++ D+I  L+++IC T  PGA                    
Sbjct: 424 TKKYSKEVIEQLRNPNSEKLSLDLIEQLVRYICKTNDPGA-------------------- 463

Query: 159 KNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQ 218
                                         ILVFLPG   I  LH+ M ++  +  +++ 
Sbjct: 464 ------------------------------ILVFLPGMMDIIKLHKIMLENRQYPQNQYV 493

Query: 219 IIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVK 278
           I PLHS +PTV QK +F TPPEGVRKI++AT+IAETSITI+D+VYVVDCGK K   FD++
Sbjct: 494 IYPLHSRMPTVDQKLVFKTPPEGVRKIIIATSIAETSITIEDVVYVVDCGKMKFGKFDLQ 553

Query: 279 DNIATLKPEWISLANAKQRRGRAGR 303
            N+ TL+PEW+SLANAKQRRGRAGR
Sbjct: 554 KNVQTLEPEWVSLANAKQRRGRAGR 578

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328711816|ref|XP_001947767.2| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Acyrthosiphon pisum]

 Score =  169 bits (428), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 86/204 (42%), Positives = 118/204 (57%), Gaps = 50/204 (24%)

Query: 100 QQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCK 159
           ++YP  +LN L++P  E  + ++I  L+ +IC  +  GA                     
Sbjct: 506 KKYPYAILNWLENPTSEDTDYELILELIYYICNNKDDGA--------------------- 544

Query: 160 NVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQI 219
                                        ILVFL GWD I+ L + +    F N+SR+ +
Sbjct: 545 -----------------------------ILVFLSGWDQISKLTKILKDKGFGNTSRYIL 575

Query: 220 IPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKD 279
           IPLHSMLPTVSQKS+F +PP GVRKI+L+TNIAETS+TIDD+VYV++ G+ K+  FD ++
Sbjct: 576 IPLHSMLPTVSQKSVFESPPRGVRKIILSTNIAETSVTIDDVVYVINNGRMKLKGFDAEN 635

Query: 280 NIATLKPEWISLANAKQRRGRAGR 303
           NI TL  EW+SLAN++QRRGRAGR
Sbjct: 636 NIGTLNEEWVSLANSRQRRGRAGR 659

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340711835|ref|XP_003394474.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Bombus terrestris]

 Score =  167 bits (423), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 88/205 (42%), Positives = 119/205 (58%), Gaps = 50/205 (24%)

Query: 99  TQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFC 158
           T++Y  +V+  L++P  E ++ D+I  L+++IC T+  GA                    
Sbjct: 424 TKKYSKEVIEQLRNPNSEKLSLDLIEQLVRYICKTKDSGA-------------------- 463

Query: 159 KNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQ 218
                                         ILVFLPG   I  LH+ M ++  +  +++ 
Sbjct: 464 ------------------------------ILVFLPGMMDIIKLHKIMLENRQYPQNQYV 493

Query: 219 IIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVK 278
           I PLHS +PTV QK +F TPPEGVRKI++AT+IAETSITI+D+VYVVDCGK K   FD++
Sbjct: 494 IYPLHSRMPTVDQKLVFKTPPEGVRKIIIATSIAETSITIEDVVYVVDCGKMKFGKFDLQ 553

Query: 279 DNIATLKPEWISLANAKQRRGRAGR 303
            NI TL+PEW+SLANAKQRRGRAGR
Sbjct: 554 KNIQTLEPEWVSLANAKQRRGRAGR 578

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|488587119|ref|XP_004478889.1| PREDICTED: LOW QUALITY PROTEIN: probable ATP-dependent RNA helicase DHX36 [Dasypus novemcinctus]

 Score =  167 bits (422), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 110/302 (36%), Positives = 163/302 (53%), Gaps = 20/302 (6%)

Query: 21  QKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDA-VLDMVRNNQIT---- 75
           QK   D  +D    +++ +K    RY EM   R+KLPSY M+    LD+  N+ I     
Sbjct: 180 QKNEPDITIDQQLLEDLQKKKTDLRYIEMQHFREKLPSYGMQKIRELDLFLNHSIILLLA 239

Query: 76  ------VISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKD-PELEGVNNDVIFSLLQ 128
                 V S   G+ P +H+   T    E      D++  ++  PE +   + +    +Q
Sbjct: 240 VKIIMFVFSAIIGNCPMIHIPGFTFPVVEY--LLEDIIEKIRYVPEQKEHRSQLKRGFMQ 297

Query: 129 -HICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRL-MKGVGANSPKRWVKLLRSMLV 186
            H+   ++     +Y       V  ++  +  + +  + M           V L+R +++
Sbjct: 298 GHVNRQEKEEKEAIYKERWPDYVRELRRRYSASTVDVMEMMDDDKVDLNLIVALIRHIVL 357

Query: 187 V----PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV 242
                 ILVFLPGWD I++LH  +     F S +F IIPLHS++PTV+Q  +F   P GV
Sbjct: 358 EEEDGAILVFLPGWDNISTLHDLLMSQVMFKSDKFLIIPLHSLMPTVNQTQVFKRTPPGV 417

Query: 243 RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAG 302
           RKIV+ATNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAG
Sbjct: 418 RKIVIATNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAG 477

Query: 303 RT 304
           R 
Sbjct: 478 RV 479

Source: Dasypus novemcinctus

Species: Dasypus novemcinctus

Genus: Dasypus

Family: Dasypodidae

Order: Cingulata

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432891825|ref|XP_004075666.1| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Oryzias latipes]

 Score =  166 bits (419), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 77/124 (62%), Positives = 96/124 (77%)

Query: 180 LLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPP 239
           ++RS     ILVFLPGWD I+ L+  +   + F S RF IIPLHS++PTV+Q  +F  PP
Sbjct: 512 IVRSEEEGAILVFLPGWDNISGLNDLLMAQTMFRSDRFVIIPLHSLMPTVNQTQVFKRPP 571

Query: 240 EGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRG 299
            GVRKIV+ATNIAETSITIDD+VYV+D GK K +NFD  +NI+T+  EW+SLANAKQR+G
Sbjct: 572 PGVRKIVIATNIAETSITIDDVVYVIDGGKIKETNFDTNNNISTMTAEWVSLANAKQRKG 631

Query: 300 RAGR 303
           RAGR
Sbjct: 632 RAGR 635

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|390349687|ref|XP_784575.3| PREDICTED: probable ATP-dependent RNA helicase DHX36-like [Strongylocentrotus purpuratus]

 Score =  165 bits (418), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 73/115 (63%), Positives = 92/115 (80%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
           ILVFLPGWD I+ LH  +   + F+  RF IIPLHSM+PT++Q+ +F  PP GVRKI++A
Sbjct: 454 ILVFLPGWDQISKLHDKLTSQTLFSEERFIIIPLHSMMPTINQRQVFEHPPPGVRKIIIA 513

Query: 249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
           TNIAETSITIDD+VYVV+ G+ K +NFDV +NI T+K EW+S A+A QRRGRAGR
Sbjct: 514 TNIAETSITIDDVVYVVNLGRVKETNFDVANNIRTMKAEWVSKASAHQRRGRAGR 568

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

>gi|47224961|emb|CAF97376.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  165 bits (417), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 76/116 (65%), Positives = 92/116 (79%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
           ILVFLPGWD I+SL+  +     F S RF IIPLHS++PTV+Q  +F  PP GVRKIV+A
Sbjct: 203 ILVFLPGWDGISSLNDLLMAQQMFRSDRFVIIPLHSLMPTVNQTQVFKKPPPGVRKIVIA 262

Query: 249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           TNIAETSITIDD+VYV+D GK K ++FD  +NI+T+  EW+SLANAKQRRGRAGR 
Sbjct: 263 TNIAETSITIDDVVYVIDGGKIKETHFDTNNNISTMTEEWVSLANAKQRRGRAGRV 318

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

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	455
RGD|1308767	1000	Dhx36 "DEAH (Asp-Glu-Ala-His)	0.356	0.162	0.497	4.5e-58
MGI|MGI:1919412	1001	Dhx36 "DEAH (Asp-Glu-Ala-His)	0.356	0.161	0.491	5.9e-58
UNIPROTKB|F6V8H1	1122	DHX36 "Uncharacterized protein	0.356	0.144	0.497	7e-58
UNIPROTKB|Q9H2U1	1008	DHX36 "Probable ATP-dependent	0.356	0.160	0.491	1.3e-57
UNIPROTKB|Q05B79	1010	DHX36 "Uncharacterized protein	0.356	0.160	0.491	2.8e-57
UNIPROTKB|E1C550	985	DHX36 "Uncharacterized protein	0.329	0.152	0.506	3e-57
ZFIN|ZDB-GENE-050419-20	1037	si:dkey-119o24.1 "si:dkey-119o	0.252	0.110	0.588	4.5e-54
UNIPROTKB|E7EWK3	797	DHX36 "Probable ATP-dependent	0.356	0.203	0.491	8e-51
TAIR|locus:2039280	995	AT2G35920 [Arabidopsis thalian	0.362	0.165	0.473	6.9e-45
TAIR|locus:2052841	1299	HVT1 "helicase in vascular tis	0.252	0.088	0.577	9.5e-44

RGD|1308767 Dhx36 "DEAH (Asp-Glu-Ala-His) box polypeptide 36" [Rattus norvegicus (taxid:10116)]

 Score = 397 (144.8 bits), Expect = 4.5e-58, Sum P(4) = 4.5e-58
 Identities = 84/169 (49%), Positives = 111/169 (65%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S RF IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   483 ILVFLPGWDNISTLHDLLMSQVMFKSDRFLIIPLHSLMPTVNQTQVFKKTPPGVRKIVIA 542

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   543 TNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAGRVQPGH 602

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTT---QRPGAILVFL 354
                 Y     ++L D +L     +++ + L+ +C      R G I  FL
Sbjct:   603 CYHLYNGLRASLLDDYQLP----EILRTPLEELCLQIKILRLGGIAYFL 647

GO:0003725 "double-stranded RNA binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GO:0009615 "response to virus" evidence=IEA;ISO

GO:0043330 "response to exogenous dsRNA" evidence=IEA;ISO

MGI|MGI:1919412 Dhx36 "DEAH (Asp-Glu-Ala-His) box polypeptide 36" [Mus musculus (taxid:10090)]

 Score = 394 (143.8 bits), Expect = 5.9e-58, Sum P(4) = 5.9e-58
 Identities = 83/169 (49%), Positives = 111/169 (65%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S +F IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   484 ILVFLPGWDNISTLHDLLMSQVMFKSDKFLIIPLHSLMPTVNQTQVFKKTPPGVRKIVIA 543

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   544 TNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAGRVQPGH 603

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTT---QRPGAILVFL 354
                 Y     ++L D +L     +++ + L+ +C      R G I  FL
Sbjct:   604 CYHLYNGLRASLLDDYQLP----EILRTPLEELCLQIKILRLGGIAYFL 648

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IDA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0009615 "response to virus" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IMP

UNIPROTKB|F6V8H1 DHX36 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 397 (144.8 bits), Expect = 7.0e-58, Sum P(4) = 7.0e-58
 Identities = 84/169 (49%), Positives = 111/169 (65%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S RF IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   605 ILVFLPGWDNISTLHDLLMSQVMFKSDRFLIIPLHSLMPTVNQTQVFKKTPPGVRKIVIA 664

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   665 TNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAGRVQPGH 724

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTT---QRPGAILVFL 354
                 Y     ++L D +L     +++ + L+ +C      R G I  FL
Sbjct:   725 CYHLYNGLRASLLDDYQLP----EILRTPLEELCLQIKILRLGGIAYFL 769

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9H2U1 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]

 Score = 394 (143.8 bits), Expect = 1.3e-57, Sum P(4) = 1.3e-57
 Identities = 83/169 (49%), Positives = 111/169 (65%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S +F IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   491 ILVFLPGWDNISTLHDLLMSQVMFKSDKFLIIPLHSLMPTVNQTQVFKRTPPGVRKIVIA 550

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   551 TNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAGRVQPGH 610

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTT---QRPGAILVFL 354
                 Y     ++L D +L     +++ + L+ +C      R G I  FL
Sbjct:   611 CYHLYNGLRASLLDDYQLP----EILRTPLEELCLQIKILRLGGIAYFL 655

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q05B79 DHX36 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 392 (143.0 bits), Expect = 2.8e-57, Sum P(4) = 2.8e-57
 Identities = 83/169 (49%), Positives = 112/169 (66%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S +F IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   493 ILVFLPGWDNISTLHDLLMSQVMFKSDKFIIIPLHSLMPTVNQTQVFKRTPPGVRKIVIA 552

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   553 TNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAGRVQPGH 612

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTT---QRPGAILVFL 354
                 Y +   ++L D +L     +++ + L+ +C      R G I  FL
Sbjct:   613 CYHLYNSLRASLLDDYQLP----EILRTPLEELCLQIKILRLGGIAHFL 657

GO:0043330 "response to exogenous dsRNA" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|E1C550 DHX36 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 388 (141.6 bits), Expect = 3.0e-57, Sum P(4) = 3.0e-57
 Identities = 78/154 (50%), Positives = 106/154 (68%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S RF IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   472 ILVFLPGWDNISTLHDLLMSQVMFKSDRFIIIPLHSLMPTVNQTQVFKKTPPGVRKIVIA 531

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+V+V+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   532 TNIAETSITIDDVVFVIDGGKIKETHFDTQNNISTMAAEWVSKANAKQRKGRAGRVQPGH 591

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHIC 342
                 Y     ++L D +L     +++ + L+ +C
Sbjct:   592 CYHLYNGLRASLLDDYQLP----EILRTPLEELC 621

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

ZFIN|ZDB-GENE-050419-20 si:dkey-119o24.1 "si:dkey-119o24.1" [Danio rerio (taxid:7955)]

 Score = 368 (134.6 bits), Expect = 4.5e-54, Sum P(4) = 4.5e-54
 Identities = 73/124 (58%), Positives = 93/124 (75%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQ--IIPLHSMLPTVSQKSI-------FNTPP 239
             ILVFLPGWD I++L+  +     F S R++  IIPLHS++PTVSQ  +       F  PP
Sbjct:   505 ILVFLPGWDNISTLNDLLMSDQMFKSGRYRFIIIPLHSLMPTVSQTQVISLFPQVFKKPP 564

Query:   240 EGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRG 299
              GVRKIV+ATNIAETSITIDD+VYV+D GK K ++FD ++NI T+  EW+S+ANAKQR+G
Sbjct:   565 PGVRKIVIATNIAETSITIDDVVYVIDGGKIKETHFDTQNNIRTMTAEWVSIANAKQRKG 624

Query:   300 RAGR 303
             RAGR
Sbjct:   625 RAGR 628

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E7EWK3 DHX36 "Probable ATP-dependent RNA helicase DHX36" [Homo sapiens (taxid:9606)]

 Score = 394 (143.8 bits), Expect = 8.0e-51, Sum P(3) = 8.0e-51
 Identities = 83/169 (49%), Positives = 111/169 (65%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
             ILVFLPGWD I++LH  +     F S +F IIPLHS++PTV+Q  +F   P GVRKIV+A
Sbjct:   405 ILVFLPGWDNISTLHDLLMSQVMFKSDKFLIIPLHSLMPTVNQTQVFKRTPPGVRKIVIA 464

Query:   249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
             TNIAETSITIDD+VYV+D GK K ++FD ++NI+T+  EW+S ANAKQR+GRAGR     
Sbjct:   465 TNIAETSITIDDVVYVIDGGKIKETHFDTQNNISTMSAEWVSKANAKQRKGRAGRVQPGH 524

Query:   309 ETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTT---QRPGAILVFL 354
                 Y     ++L D +L     +++ + L+ +C      R G I  FL
Sbjct:   525 CYHLYNGLRASLLDDYQLP----EILRTPLEELCLQIKILRLGGIAYFL 569

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003725 "double-stranded RNA binding" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0043330 "response to exogenous dsRNA" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

TAIR|locus:2039280 AT2G35920 [Arabidopsis thaliana (taxid:3702)]

 Score = 366 (133.9 bits), Expect = 6.9e-45, Sum P(3) = 6.9e-45
 Identities = 79/167 (47%), Positives = 107/167 (64%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFF-NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL 247
             ILVFL GWD I+ L   +  ++F  +SS+F ++PLH  +PTV+Q+ IF+ PP   RKIVL
Sbjct:   506 ILVFLTGWDEISKLLEKINMNNFLGDSSKFLVLPLHGSMPTVNQREIFDRPPPNKRKIVL 565

Query:   248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR 307
             ATNIAE+SITIDD+VYVVDCGK K +++D  + +A L P WIS A+A QRRGRAGR    
Sbjct:   566 ATNIAESSITIDDVVYVVDCGKAKETSYDALNKVACLLPSWISKASAHQRRGRAGRVQAG 625

Query:   308 SETQQYPNDVLNMLKDPELEGVNNDVIFSLLQHICTTQRPGAILVFL 354
                + YP  + +     +L  +    +  L  HI + Q  G+I  FL
Sbjct:   626 VCYRLYPKVIYDAFPQYQLPEIIRTPLQELCLHIKSLQ-VGSIGSFL 671

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0004386 "helicase activity" evidence=IEA;ISS

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

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2052841 HVT1 "helicase in vascular tissue and tapetum" [Arabidopsis thaliana (taxid:3702)]

 Score = 363 (132.8 bits), Expect = 9.5e-44, Sum P(4) = 9.5e-44
 Identities = 67/116 (57%), Positives = 90/116 (77%)

Query:   189 ILVFLPGWDTINSLHRSMCQSSFF-NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL 247
             ILVFLPGWD IN   + + ++ FF +S++F II LHSM+P   QK +FN PP G RKIVL
Sbjct:   554 ILVFLPGWDDINKTRQRLLENPFFADSAKFDIICLHSMVPAGEQKKVFNRPPPGCRKIVL 613

Query:   248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
             ATNIAE+++TIDD+VYV+D G+ K  ++D  +N++TL+  W+S ANAKQR+GRAGR
Sbjct:   614 ATNIAESAVTIDDVVYVIDSGRMKEKSYDPYNNVSTLQSSWVSKANAKQRQGRAGR 669

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0004386 "helicase activity" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0000226 "microtubule cytoskeleton organization" evidence=RCA

GO:0000911 "cytokinesis by cell plate formation" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	455
COG1643	845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	4e-37
TIGR01970	819	TIGR01970, DEAH_box_HrpB, ATP-dependent helicase H	5e-25
PRK11664	812	PRK11664, PRK11664, ATP-dependent RNA helicase Hrp	1e-20
TIGR01967	1283	TIGR01967, DEAH_box_HrpA, ATP-dependent helicase H	8e-18
PRK11131	1294	PRK11131, PRK11131, ATP-dependent RNA helicase Hrp	3e-16
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	3e-13
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	3e-12
COG1643	845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	1e-07
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	6e-07
TIGR01967	1283	TIGR01967, DEAH_box_HrpA, ATP-dependent helicase H	3e-05
PRK11131	1294	PRK11131, PRK11131, ATP-dependent RNA helicase Hrp	2e-04

>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]

 Score =  144 bits (365), Expect = 4e-37
 Identities = 51/116 (43%), Positives = 64/116 (55%), Gaps = 2/116 (1%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
           ILVFLPG   I      +           +I+PL+  L    Q  +F   P G RK+VLA
Sbjct: 262 ILVFLPGQREIERTAEWL--EKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLA 319

Query: 249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           TNIAETS+TI  I YV+D G  K   +D +  +  L+ E IS A+A QR GRAGRT
Sbjct: 320 TNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRT 375

Length = 845

>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB

 Score =  108 bits (271), Expect = 5e-25
 Identities = 50/116 (43%), Positives = 64/116 (55%), Gaps = 3/116 (2%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
           ILVFLPG   I  +   +        S   I PL+  L   +Q       P+G RK+VLA
Sbjct: 212 ILVFLPGQAEIRRVQEQL-AERL--DSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLA 268

Query: 249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           TNIAETS+TI+ I  V+D G  +++ FD K  I  L+   IS A+A QR GRAGR 
Sbjct: 269 TNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL 324

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 [Unknown function, Enzymes of unknown specificity]. Length = 819

>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional

 Score = 94.6 bits (236), Expect = 1e-20
 Identities = 49/116 (42%), Positives = 67/116 (57%), Gaps = 5/116 (4%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLP-TVSQKSIFNTPPEGVRKIVL 247
           +L+FLPG   +  + R   Q +   +S   + PL+  L     QK+I   P  G RK+VL
Sbjct: 215 LLLFLPG---VGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPA-GRRKVVL 270

Query: 248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
           ATNIAETS+TI+ I  VVD G  +++ FD K  +  L  + IS A+  QR GRAGR
Sbjct: 271 ATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGR 326

Length = 812

>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA

 Score = 86.4 bits (214), Expect = 8e-18
 Identities = 46/119 (38%), Positives = 66/119 (55%), Gaps = 13/119 (10%)

Query: 189 ILVFLPG----WDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRK 244
           IL+FLPG     D    L +        N    +I+PL++ L    Q+ +F   P   R+
Sbjct: 282 ILIFLPGEREIRDAAEILRKR-------NLRHTEILPLYARLSNKEQQRVFQ--PHSGRR 332

Query: 245 IVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
           IVLATN+AETS+T+  I YV+D G  ++S +  +  +  L  E IS A+A QR+GR GR
Sbjct: 333 IVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGR 391

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 [Unknown function, Enzymes of unknown specificity]. Length = 1283

>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional

 Score = 81.3 bits (201), Expect = 3e-16
 Identities = 44/120 (36%), Positives = 67/120 (55%), Gaps = 13/120 (10%)

Query: 189 ILVFLPG----WDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRK 244
           IL+F+ G     DT ++L++        N    +I+PL++ L    Q  +F       R+
Sbjct: 289 ILIFMSGEREIRDTADALNKL-------NLRHTEILPLYARLSNSEQNRVFQ--SHSGRR 339

Query: 245 IVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           IVLATN+AETS+T+  I YV+D G  ++S +  +  +  L  E IS A+A QR+GR GR 
Sbjct: 340 IVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV 399

Length = 1294

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 18/93 (19%)

Query: 211 FFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKT 270
                  ++  LH  L    ++ I +    G  K+++AT++AE  + +  +  V+     
Sbjct: 6   LLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI----- 60

Query: 271 KMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
               +D+            S A+  QR GRAGR
Sbjct: 61  ---IYDL----------PWSPASYIQRIGRAGR 80

Length = 82

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

 Score = 61.4 bits (150), Expect = 3e-12
 Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 18/93 (19%)

Query: 211 FFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKT 270
                  ++  LH  L    ++ I      G  K+++AT++A   I + D+  V+     
Sbjct: 2   LLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVI----- 56

Query: 271 KMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
              N+D+            + A+  QR GRAGR
Sbjct: 57  ---NYDL----------PWNPASYIQRIGRAGR 76

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

>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]

 Score = 53.9 bits (130), Expect = 1e-07
 Identities = 19/49 (38%), Positives = 28/49 (57%)

Query: 36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSG 84
           M  + +S    ++LE R  LP   +RD +L  +  NQ+ +I GETGSG
Sbjct: 29 GMDARSRSANVPDILEYRSGLPVTAVRDEILKAIEQNQVVIIVGETGSG 77

Length = 845

>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 = 48.0 bits (115), Expect = 6e-07
 Identities = 22/116 (18%), Positives = 44/116 (37%), Gaps = 24/116 (20%)

Query: 188 PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL 247
            +L+F P    ++ L               ++  LH       ++ +     EG   +++
Sbjct: 30  KVLIFCPSKKMLDELAE------LLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLV 83

Query: 248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR 303
           AT++    I + ++  V+        N+D+            S ++  QR GRAGR
Sbjct: 84  ATDVIARGIDLPNVSVVI--------NYDL----------PWSPSSYLQRIGRAGR 121

Length = 131

>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA

 Score = 46.3 bits (110), Expect = 3e-05
 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 18/98 (18%)

Query: 1   MKSPHSPKGLTHSVTSWETRQKLLNDPVLDAAFKKEMIRKLQSR---RYQEMLEARKKLP 57
           ++  H       ++  +  R        +DAA  K   R  Q+    RY +       LP
Sbjct: 23  LRKDHDQDRAIAALAKFRER--------IDAACDKVEAR-RQAVPEIRYPD------NLP 67

Query: 58  SYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLK 95
               R+ + + +  NQ+ +I+GETGSG    L  I L+
Sbjct: 68  VSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLE 105

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 [Unknown function, Enzymes of unknown specificity]. Length = 1283

>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 14/50 (28%), Positives = 28/50 (56%)

Query: 35  KEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSG 84
           +   R L     +  +   + LP  Q +  +L+ +R++Q+ +++GETGSG
Sbjct: 52  QAAQRVLLREAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSG 101

Length = 1294

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	455
KOG0923|consensus	902		100.0
KOG0922|consensus	674		100.0
KOG0924|consensus	1042		100.0
KOG0925|consensus	699		100.0
KOG0920|consensus	924		100.0
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
KOG0926|consensus	1172		100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
KOG0921|consensus	1282		100.0
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.97
KOG0328|consensus	400		99.97
PRK01172	674	ski2-like helicase; Provisional	99.97
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.97
PTZ00110	545	helicase; Provisional	99.97
KOG0340|consensus	442		99.97
KOG0345|consensus	567		99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.96
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.96
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.96
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.96
PTZ00424	401	helicase 45; Provisional	99.96
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.96
PRK02362	737	ski2-like helicase; Provisional	99.96
KOG0333|consensus	673		99.96
KOG0342|consensus	543		99.96
KOG0343|consensus	758		99.95
KOG0338|consensus	691		99.95
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.94
PRK00254	720	ski2-like helicase; Provisional	99.94
KOG0332|consensus	477		99.94
KOG0347|consensus	731		99.94
KOG0326|consensus	459		99.93
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.93
KOG0341|consensus	610		99.93
KOG0336|consensus	629		99.93
KOG0339|consensus	731		99.93
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.93
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.92
KOG0335|consensus	482		99.92
KOG0348|consensus	708		99.92
KOG0334|consensus	997		99.91
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.91
KOG0327|consensus	397		99.9
KOG0346|consensus	569		99.9
PRK13767	876	ATP-dependent helicase; Provisional	99.9
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.89
PRK10689	1147	transcription-repair coupling factor; Provisional	99.87
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.87
KOG0344|consensus	593		99.87
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.86
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.86
KOG0350|consensus	620		99.86
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.84
KOG4284|consensus	980		99.84
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.83
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.83
KOG0337|consensus	529		99.82
COG1202	830	Superfamily II helicase, archaea-specific [General	99.82
KOG0349|consensus	725		99.81
PRK09401	1176	reverse gyrase; Reviewed	99.76
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.76
COG1204	766	Superfamily II helicase [General function predicti	99.74
COG1205	851	Distinct helicase family with a unique C-terminal	99.74
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.73
PHA02558	501	uvsW UvsW helicase; Provisional	99.72
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.7
PRK14701	1638	reverse gyrase; Provisional	99.69
KOG0354|consensus	746		99.68
PRK13766	773	Hef nuclease; Provisional	99.65
KOG0352|consensus	641		99.64
PRK09694	878	helicase Cas3; Provisional	99.63
KOG0351|consensus	941		99.62
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.62
KOG0952|consensus	1230		99.62
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.6
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.56
PRK05580	679	primosome assembly protein PriA; Validated	99.53
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.53
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.52
KOG0921|consensus	1282		99.48
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.47
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.46
KOG0950|consensus	1008		99.46
KOG0329|consensus	387		99.45
KOG0951|consensus	1674		99.44
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.43
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.42
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.42
PRK05298	652	excinuclease ABC subunit B; Provisional	99.42
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.41
KOG0353|consensus	695		99.4
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.37
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.32
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.3
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.29
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.25
PRK04914	956	ATP-dependent helicase HepA; Validated	99.23
PF04408	102	HA2: Helicase associated domain (HA2); InterPro: I	99.22
KOG0948|consensus	1041		99.21
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.16
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.15
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.13
KOG0947|consensus	1248		99.08
KOG4150|consensus	1034		99.02
smart00847	92	HA2 Helicase associated domain (HA2) Add an annota	98.99
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.82
KOG0953|consensus	700		98.82
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.76
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.73
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.73
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.49
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.39
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.37
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	98.32
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.21
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.17
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.75
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.65
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.61
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.6
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.55
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.01
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	96.83
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.77
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	96.75
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.66
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	96.58
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.42
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	96.42
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.31
KOG0949|consensus	1330		96.3
KOG0391|consensus	1958		96.14
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	96.09
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	95.91
smart00487	201	DEXDc DEAD-like helicases superfamily.	95.89
COG4096	875	HsdR Type I site-specific restriction-modification	95.81
KOG0392|consensus	1549		95.81
KOG0385|consensus	971		95.79
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	95.61
PF13245	76	AAA_19: Part of AAA domain	95.57
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.39
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	95.33
KOG0951|consensus	1674		95.3
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.27
KOG1123|consensus	776		95.24
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	95.24
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	95.24
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.18
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	95.11
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	95.11
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.04
PF13555	62	AAA_29: P-loop containing region of AAA domain	94.98
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.95
PRK10536	262	hypothetical protein; Provisional	94.94
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	94.91
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	94.84
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.74
KOG0384|consensus	1373		94.64
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	94.6
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.6
PRK13851	344	type IV secretion system protein VirB11; Provision	94.6
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	94.46
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	94.39
KOG1802|consensus	935		94.16
KOG0389|consensus	941		94.0
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	93.92
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.91
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	93.81
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	93.78
KOG0387|consensus	923		93.65
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	93.58
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.55
smart00382	148	AAA ATPases associated with a variety of cellular	93.5
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	93.48
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	93.46
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	92.98
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.98
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	92.78
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	92.75
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	92.68
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	92.53
KOG0390|consensus	776		92.51
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.5
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	92.43
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	92.41
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.37
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	92.35
PRK05580	679	primosome assembly protein PriA; Validated	92.3
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	92.2
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	92.16
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	92.14
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	92.05
KOG2373|consensus	514		91.94
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	91.88
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	91.86
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	91.76
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	91.57
KOG1000|consensus	689		91.48
COG4525	259	TauB ABC-type taurine transport system, ATPase com	91.44
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	91.38
PRK10436	462	hypothetical protein; Provisional	91.31
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	91.29
PF00005	137	ABC_tran: ABC transporter This structure is on hol	91.28
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	91.23
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.2
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	91.17
TIGR00595	505	priA primosomal protein N'. All proteins in this f	91.13
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	91.12
PF05729	166	NACHT: NACHT domain	91.11
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	91.06
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	90.98
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	90.93
PRK14974	336	cell division protein FtsY; Provisional	90.68
PRK14873	665	primosome assembly protein PriA; Provisional	90.68
PRK00300	205	gmk guanylate kinase; Provisional	90.64
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	90.62
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	90.57
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	90.43
PF13173	128	AAA_14: AAA domain	90.18
PRK13764	602	ATPase; Provisional	90.16
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	90.16
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	90.12
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	90.09
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	90.01
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	89.93
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	89.91
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	89.9
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	89.83
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	89.81
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	89.73
PRK08233	182	hypothetical protein; Provisional	89.68
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	89.63
KOG0388|consensus	1185		89.57
TIGR00235	207	udk uridine kinase. Model contains a number of lon	89.54
PF12846	304	AAA_10: AAA-like domain	89.44
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	89.41
PF00004	132	AAA: ATPase family associated with various cellula	89.4
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	89.35
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	89.35
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	89.3
PRK10875	615	recD exonuclease V subunit alpha; Provisional	89.26
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	89.22
PRK09200	790	preprotein translocase subunit SecA; Reviewed	89.04
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	88.99
COG3910	233	Predicted ATPase [General function prediction only	88.94
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	88.91
KOG1970|consensus	634		88.89
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	88.88
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	88.87
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	88.84
cd03269	210	ABC_putative_ATPase This subfamily is involved in	88.77
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	88.74
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	88.74
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	88.72
PRK14530	215	adenylate kinase; Provisional	88.7
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	88.69
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	88.63
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	88.61
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	88.6
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	88.59
PHA02244	383	ATPase-like protein	88.58
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	88.58
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	88.53
PRK06526	254	transposase; Provisional	88.52
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	88.42
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	88.36
PRK09183	259	transposase/IS protein; Provisional	88.36
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	88.36
PRK05541	176	adenylylsulfate kinase; Provisional	88.32
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	88.29
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	88.27
PRK07261	171	topology modulation protein; Provisional	88.27
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	88.23
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	88.21
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	88.21
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	88.12
PLN02165	334	adenylate isopentenyltransferase	88.08
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	87.99
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	87.98
TIGR00376	637	DNA helicase, putative. The gene product may repre	87.94
COG4136	213	ABC-type uncharacterized transport system, ATPase	87.93
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	87.9
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	87.9
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	87.87
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	87.82
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	87.8
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	87.8
PF03668	284	ATP_bind_2: P-loop ATPase protein family; InterPro	87.8
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	87.79
PRK14527	191	adenylate kinase; Provisional	87.76
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	87.76
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	87.71
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	87.69
cd03246	173	ABCC_Protease_Secretion This family represents the	87.68
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	87.68
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	87.66
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	87.61
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	87.61
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	87.6
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	87.58
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	87.58
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	87.57
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	87.56
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	87.55
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	87.54
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	87.52
PRK12402	337	replication factor C small subunit 2; Reviewed	87.48
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	87.48
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	87.47
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	87.43
TIGR01978	243	sufC FeS assembly ATPase SufC. SufC is part of the	87.39
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	87.36
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	87.31
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	87.28
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	87.27
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	87.23
PRK14531	183	adenylate kinase; Provisional	87.2
PRK00698	205	tmk thymidylate kinase; Validated	87.16
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	87.16
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	87.15
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	87.14
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	87.13
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	87.12
PRK14247	250	phosphate ABC transporter ATP-binding protein; Pro	87.12
PRK10908	222	cell division protein FtsE; Provisional	87.08
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	87.07
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	87.06
cd03279	213	ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complex	87.03
KOG1803|consensus	649		87.01
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	86.95
COG1127	263	Ttg2A ABC-type transport system involved in resist	86.88
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	86.88
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	86.86
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	86.79
PRK14262	250	phosphate ABC transporter ATP-binding protein; Pro	86.78
PRK10744	260	pstB phosphate transporter ATP-binding protein; Pr	86.73
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	86.71
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	86.69
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	86.69
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	86.69
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	86.66
PRK08118	167	topology modulation protein; Reviewed	86.65
TIGR02324	224	CP_lyasePhnL phosphonate C-P lyase system protein	86.65
PRK09825	176	idnK D-gluconate kinase; Provisional	86.64
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	86.63
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	86.56
TIGR02770	230	nickel_nikD nickel import ATP-binding protein NikD	86.55
TIGR02323	253	CP_lyasePhnK phosphonate C-P lyase system protein	86.54
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	86.51
cd03216	163	ABC_Carb_Monos_I This family represents the domain	86.47
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	86.46
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	86.45
COG1135	339	AbcC ABC-type metal ion transport system, ATPase c	86.45
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	86.4
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	86.33
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	86.32
TIGR00972	247	3a0107s01c2 phosphate ABC transporter, ATP-binding	86.29
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	86.26
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	86.23
PRK13646	286	cbiO cobalt transporter ATP-binding subunit; Provi	86.22
PRK05480	209	uridine/cytidine kinase; Provisional	86.2
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	86.19
cd03215	182	ABC_Carb_Monos_II This family represents domain II	86.16
PRK14248	268	phosphate ABC transporter ATP-binding protein; Pro	86.12
cd03270	226	ABC_UvrA_I The excision repair protein UvrA domain	86.12
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	86.11
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	86.1
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	86.02
PRK14738	206	gmk guanylate kinase; Provisional	86.01
PRK14273	254	phosphate ABC transporter ATP-binding protein; Pro	86.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	85.99
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	85.98
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	85.97
PRK14239	252	phosphate transporter ATP-binding protein; Provisi	85.8
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	85.78
KOG0060|consensus	659		85.72
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	85.69
PRK11264	250	putative amino-acid ABC transporter ATP-binding pr	85.68
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	85.65
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	85.65
PRK13548	258	hmuV hemin importer ATP-binding subunit; Provision	85.61
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	85.56
COG4133	209	CcmA ABC-type transport system involved in cytochr	85.52
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	85.5
PRK14237	267	phosphate transporter ATP-binding protein; Provisi	85.48
cd03294	269	ABC_Pro_Gly_Bertaine This family comprises the gly	85.46
KOG0347|consensus	731		85.43
PRK06762	166	hypothetical protein; Provisional	85.42
PRK00131	175	aroK shikimate kinase; Reviewed	85.41
PRK13638	271	cbiO cobalt transporter ATP-binding subunit; Provi	85.37
PRK13648	269	cbiO cobalt transporter ATP-binding subunit; Provi	85.31
COG4152	300	ABC-type uncharacterized transport system, ATPase	85.3
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	85.28
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	85.24
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	85.24
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	85.22
KOG1533|consensus	290		85.21
PRK14240	250	phosphate transporter ATP-binding protein; Provisi	85.2
PRK14269	246	phosphate ABC transporter ATP-binding protein; Pro	85.19
PRK14259	269	phosphate ABC transporter ATP-binding protein; Pro	85.17
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	85.17
PRK14737	186	gmk guanylate kinase; Provisional	85.15
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	85.12
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	85.11
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	85.09
PRK14244	251	phosphate ABC transporter ATP-binding protein; Pro	85.06
PRK03695	248	vitamin B12-transporter ATPase; Provisional	85.05
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	85.04
PRK14274	259	phosphate ABC transporter ATP-binding protein; Pro	85.03
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	84.95
PRK10771	232	thiQ thiamine transporter ATP-binding subunit; Pro	84.94
PRK14532	188	adenylate kinase; Provisional	84.93
PRK14256	252	phosphate ABC transporter ATP-binding protein; Pro	84.91
PRK14255	252	phosphate ABC transporter ATP-binding protein; Pro	84.91
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	84.91
PRK13547	272	hmuV hemin importer ATP-binding subunit; Provision	84.88
COG4619	223	ABC-type uncharacterized transport system, ATPase	84.84
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	84.84
cd03234	226	ABCG_White The White subfamily represents ABC tran	84.82
PRK14267	253	phosphate ABC transporter ATP-binding protein; Pro	84.82
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	84.81
PRK14241	258	phosphate transporter ATP-binding protein; Provisi	84.8
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	84.78
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	84.77
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	84.75
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	84.75
PRK14261	253	phosphate ABC transporter ATP-binding protein; Pro	84.74
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	84.73
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	84.73
PRK15056	272	manganese/iron transporter ATP-binding protein; Pr	84.71
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	84.71
PRK08356	195	hypothetical protein; Provisional	84.69
cd03290	218	ABCC_SUR1_N The SUR domain 1. The sulfonylurea rec	84.67
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	84.67
PRK08181	269	transposase; Validated	84.66
PRK13645	289	cbiO cobalt transporter ATP-binding subunit; Provi	84.66
PRK04296	190	thymidine kinase; Provisional	84.59
PRK11614	237	livF leucine/isoleucine/valine transporter ATP-bin	84.59
PRK06217	183	hypothetical protein; Validated	84.58
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	84.58
PRK14528	186	adenylate kinase; Provisional	84.56
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	84.53
PRK14245	250	phosphate ABC transporter ATP-binding protein; Pro	84.52
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	84.51
PRK13649	280	cbiO cobalt transporter ATP-binding subunit; Provi	84.48
PRK14253	249	phosphate ABC transporter ATP-binding protein; Pro	84.42
PRK11231	255	fecE iron-dicitrate transporter ATP-binding subuni	84.42
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	84.39
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	84.37
PRK11701	258	phnK phosphonate C-P lyase system protein PhnK; Pr	84.36
TIGR03771	223	anch_rpt_ABC anchored repeat-type ABC transporter,	84.35
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	84.35
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	84.34
PRK11831	269	putative ABC transporter ATP-binding protein YrbF;	84.32
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	84.3
COG3973	747	Superfamily I DNA and RNA helicases [General funct	84.29
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	84.29
PRK14238	271	phosphate transporter ATP-binding protein; Provisi	84.29
PRK09984	262	phosphonate/organophosphate ester transporter subu	84.28
PRK10253	265	iron-enterobactin transporter ATP-binding protein;	84.25
PRK13975	196	thymidylate kinase; Provisional	84.23
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	84.16
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	84.15
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	84.13
PRK14268	258	phosphate ABC transporter ATP-binding protein; Pro	84.13
CHL00131	252	ycf16 sulfate ABC transporter protein; Validated	84.12
PRK07667	193	uridine kinase; Provisional	84.09
PRK09087	226	hypothetical protein; Validated	84.02
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	84.0
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	84.0
PRK14265	274	phosphate ABC transporter ATP-binding protein; Pro	83.98
PRK14251	251	phosphate ABC transporter ATP-binding protein; Pro	83.98
PRK13651	305	cobalt transporter ATP-binding subunit; Provisiona	83.97
PRK15112	267	antimicrobial peptide ABC system ATP-binding prote	83.96
TIGR02769	265	nickel_nikE nickel import ATP-binding protein NikE	83.91
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	83.88
PRK13635	279	cbiO cobalt transporter ATP-binding subunit; Provi	83.87
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	83.85
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	83.85
PRK13643	288	cbiO cobalt transporter ATP-binding subunit; Provi	83.84
TIGR00968	237	3a0106s01 sulfate ABC transporter, ATP-binding pro	83.83
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	83.83
PRK14257	329	phosphate ABC transporter ATP-binding protein; Pro	83.82
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	83.79
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	83.79
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	83.73
PRK13633	280	cobalt transporter ATP-binding subunit; Provisiona	83.69
PRK03839	180	putative kinase; Provisional	83.69
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	83.68
PRK14249	251	phosphate ABC transporter ATP-binding protein; Pro	83.65
PRK01184	184	hypothetical protein; Provisional	83.65
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	83.64

>KOG0923|consensus

Probab=100.00  E-value=2.9e-93  Score=721.73  Aligned_cols=392  Identities=28%  Similarity=0.402  Sum_probs=354.9

Q ss_pred             HHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh-----------------------------
Q psy6094          45 RYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL-----------------------------   94 (455)
Q Consensus        45 ~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~-----------------------------   94 (455)
                      +-.++.+.|+.||+|.++++++.+|.++||+||.|+||||||||+| ||.+                             
T Consensus       253 ~~~~iee~RksLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPRRVAAmSVAaRVA~  332 (902)
T KOG0923|consen  253 RRESIEEVRKSLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPRRVAAMSVAARVAE  332 (902)
T ss_pred             HHHHHHHHHhcCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhcccccCCceEeecCcchHHHHHHHHHHHH
Confidence            4556778899999999999999999999999999999999999999 9987                             


Q ss_pred             hh----cCCCCC-hH-----------------HHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCC
Q psy6094          95 KR----SETQQY-PN-----------------DVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGA  138 (455)
Q Consensus        95 e~----~~~vg~-p~-----------------~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~  138 (455)
                      |+    |..||| +|                 -|||++ .+|+|..|+             +|+|++++|++. +.||++
T Consensus       333 EMgvkLG~eVGYsIRFEdcTSekTvlKYMTDGmLlREfL~epdLasYSViiiDEAHERTL~TDILfgLvKDIa-r~RpdL  411 (902)
T KOG0923|consen  333 EMGVKLGHEVGYSIRFEDCTSEKTVLKYMTDGMLLREFLSEPDLASYSVIIVDEAHERTLHTDILFGLVKDIA-RFRPDL  411 (902)
T ss_pred             HhCcccccccceEEEeccccCcceeeeeecchhHHHHHhccccccceeEEEeehhhhhhhhhhHHHHHHHHHH-hhCCcc
Confidence            22    223332 11                 189998 999999999             999999999999 999999


Q ss_pred             eEEEEccCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHH
Q psy6094         139 ILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTIN  200 (455)
Q Consensus       139 k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~  200 (455)
                      |++++|||+                 ||+ |||+++|.+.+.-+|+.....+   .+..|+. .+.|+||||++|+++|+
T Consensus       412 KllIsSAT~DAekFS~fFDdapIF~iPGRRyPVdi~Yt~~PEAdYldAai~t---VlqIH~t-qp~GDILVFltGQeEIE  487 (902)
T KOG0923|consen  412 KLLISSATMDAEKFSAFFDDAPIFRIPGRRYPVDIFYTKAPEADYLDAAIVT---VLQIHLT-QPLGDILVFLTGQEEIE  487 (902)
T ss_pred             eEEeeccccCHHHHHHhccCCcEEeccCcccceeeecccCCchhHHHHHHhh---heeeEec-cCCccEEEEeccHHHHH
Confidence            999999999                 999 9999999988877776544321   2333333 77899999999999999


Q ss_pred             HHHHHHHhcCCC---CCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCccccccc
Q psy6094         201 SLHRSMCQSSFF---NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDV  277 (455)
Q Consensus       201 ~l~~~L~~~~~~---~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~  277 (455)
                      .+.+.|.+....   ....+.++|+|+.||.+.|.+||++.|+|.||||+|||||||||||+||.||||+|++|++.|||
T Consensus       488 t~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynp  567 (902)
T KOG0923|consen  488 TVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNP  567 (902)
T ss_pred             HHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCC
Confidence            999888865322   34578999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccccccccchhhHHhhhcccCCCCCCeEEecCC----hhhhccCCCCcccccC-hHHHHHHHh---------hhcC
Q psy6094         278 KDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP----NDVLNMLKDPELEGVN-NDVIFSLLQ---------HICT  343 (455)
Q Consensus       278 ~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t----~~~~~~~~~PEi~r~~-~~~~L~~l~---------~~~~  343 (455)
                      ++||+.|..+|||||+|.||+|||||+|||+||||||    ..+++..+.|||+|.| ..++|.+++         +|++
T Consensus       568 rtGmesL~v~piSKAsA~QRaGRAGRtgPGKCfRLYt~~aY~~eLE~~t~PEIqRtnL~nvVL~LkSLGI~Dl~~FdFmD  647 (902)
T KOG0923|consen  568 RTGMESLLVTPISKASANQRAGRAGRTGPGKCFRLYTAWAYEHELEEMTVPEIQRTNLGNVVLLLKSLGIHDLIHFDFLD  647 (902)
T ss_pred             CcCceeEEEeeechhhhhhhccccCCCCCCceEEeechhhhhhhhccCCCcceeeccchhHHHHHHhcCcchhcccccCC
Confidence            9999999999999999999999999999999999999    5678899999999999 999997765         8999


Q ss_pred             CCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhc-----CcCC
Q psy6094         344 TQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLS-----FECK  403 (455)
Q Consensus       344 ~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~ls-----f~~p  403 (455)
                      ||+.+++..||+.|+.||||+..|+|     |.+|+.|++||+||               ++|++||||||     |+.|
T Consensus       648 pPp~etL~~aLE~LyaLGALn~~GeL-----Tk~GrrMaEfP~dPmlsKmi~as~ky~cs~EiitiaamlS~~~svfyrp  722 (902)
T KOG0923|consen  648 PPPTETLLKALEQLYALGALNHLGEL-----TKLGRRMAEFPVDPMLSKMIVASEKYKCSEEIITIAAMLSVGASVFYRP  722 (902)
T ss_pred             CCChHHHHHHHHHHHHhhccccccch-----hhhhhhhhhcCCCHHHHhHHhhhccccchHHHHHHHHHHhcCchheecc
Confidence            99999999999999999999999999     99999999999999               79999999999     8899


Q ss_pred             cChHHHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCCCchHhHHHhh
Q psy6094         404 PSTAKIIKELRARLD-MLLAHKLSHPGTTAWGDPNEGNILHCCSGF  448 (455)
Q Consensus       404 ~~~~~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~~~~~~~c~~~  448 (455)
                      .++.-.++.+++.|. +.|||++++++|++|...+.+  .+||.++
T Consensus       723 k~~~v~ad~a~~~f~~~~gDhi~~L~vyn~w~es~~s--~~wC~e~  766 (902)
T KOG0923|consen  723 KDKQVHADNARKNFEEPVGDHIVLLNVYNQWKESKYS--TQWCYEN  766 (902)
T ss_pred             hhhhhhhhhhhhccCCCCcchhhhhHHHHHHhhcchh--hHHHHHh
Confidence            999999999999999 999999999999999999886  8999873

>KOG0922|consensus

Probab=100.00  E-value=3.1e-91  Score=714.48  Aligned_cols=395  Identities=28%  Similarity=0.380  Sum_probs=352.8

Q ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------------
Q psy6094          42 QSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------------   94 (455)
Q Consensus        42 ~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------------   94 (455)
                      ......++.++|+.||+|+++++|+.++++|+++||.|+||||||||+| |+++                          
T Consensus        36 ~~~~~~~i~~qR~~LPI~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RV  115 (674)
T KOG0922|consen   36 GKSTNLSIQEQRESLPIYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRV  115 (674)
T ss_pred             ccccccCHHHhhccCCHHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHHHHHHHHHH
Confidence            4456677889999999999999999999999999999999999999999 8877                          


Q ss_pred             --h----hcCCCCC-hH-----------------HHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCC
Q psy6094          95 --K----RSETQQY-PN-----------------DVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRP  136 (455)
Q Consensus        95 --e----~~~~vg~-p~-----------------~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~  136 (455)
                        |    .|+.||| .|                 -|||++ .||.|+.|+             ||+||++||+++ +.|+
T Consensus       116 AeE~~~~lG~~VGY~IRFed~ts~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~-~~R~  194 (674)
T KOG0922|consen  116 AEEMGCQLGEEVGYTIRFEDSTSKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLHTDILLGLLKKIL-KKRP  194 (674)
T ss_pred             HHHhCCCcCceeeeEEEecccCCCceeEEEecchHHHHHHhcCCccccccEEEEechhhhhhHHHHHHHHHHHHH-hcCC
Confidence              2    2344443 11                 199999 999999999             999999999999 9999


Q ss_pred             CCeEEEEccCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHH
Q psy6094         137 GAILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDT  198 (455)
Q Consensus       137 ~~k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~e  198 (455)
                      ++|+|+||||+                 +|| |||+++|++.+..+|+.....   ..+..|.. .++|+|||||+|++|
T Consensus       195 ~LklIimSATlda~kfS~yF~~a~i~~i~GR~fPVei~y~~~p~~dYv~a~~~---tv~~Ih~~-E~~GDILvFLtGqeE  270 (674)
T KOG0922|consen  195 DLKLIIMSATLDAEKFSEYFNNAPILTIPGRTFPVEILYLKEPTADYVDAALI---TVIQIHLT-EPPGDILVFLTGQEE  270 (674)
T ss_pred             CceEEEEeeeecHHHHHHHhcCCceEeecCCCCceeEEeccCCchhhHHHHHH---HHHHHHcc-CCCCCEEEEeCCHHH
Confidence            99999999999                 899 999999999887777643321   11223333 889999999999999


Q ss_pred             HHHHHHHHHhcCCCC--CCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccc
Q psy6094         199 INSLHRSMCQSSFFN--SSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFD  276 (455)
Q Consensus       199 i~~l~~~L~~~~~~~--~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd  276 (455)
                      |+.+++.|.+.....  .....++|+||.||.++|.+||.+.|.|.||||+||||||||||||+|.||||+|++|.+.||
T Consensus       271 Ie~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~  350 (674)
T KOG0922|consen  271 IEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYN  350 (674)
T ss_pred             HHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeec
Confidence            999999999764321  112378999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh---hhccCCCCcccccC-hHHHHHHHh---------hhcC
Q psy6094         277 VKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND---VLNMLKDPELEGVN-NDVIFSLLQ---------HICT  343 (455)
Q Consensus       277 ~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~---~~~~~~~PEi~r~~-~~~~L~~l~---------~~~~  343 (455)
                      +++|++.|..+||||++|.||+|||||++||+|||||+++   .|++.+.|||+|++ ...+|++++         +|++
T Consensus       351 p~~g~~~L~v~~ISkasA~QRaGRAGRt~pGkcyRLYte~~~~~~~~~~~PEI~R~~Ls~~vL~Lkalgi~d~l~F~f~d  430 (674)
T KOG0922|consen  351 PRTGLDSLIVVPISKASANQRAGRAGRTGPGKCYRLYTESAYDKMPLQTVPEIQRVNLSSAVLQLKALGINDPLRFPFID  430 (674)
T ss_pred             cccCccceeEEechHHHHhhhcccCCCCCCceEEEeeeHHHHhhcccCCCCceeeechHHHHHHHHhcCCCCcccCCCCC
Confidence            9999999999999999999999999999999999999965   45678899999999 999998876         7999


Q ss_pred             CCChhhHHhHHhhhhhcccccCCCCCCcccCCh-HHHHHhhCCCCh---------------hHHHHHHHhhc----CcCC
Q psy6094         344 TQRPGAILVFLPGWDTINSLHRSMCQSSFFNSC-LLYEFAMVDNKP---------------KEIITVRDCLS----FECK  403 (455)
Q Consensus       344 ~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~-lG~~l~~lp~~p---------------~~~l~iaa~ls----f~~p  403 (455)
                      ||+++++..|++.|..+||||++|.+     |. +|+.|+.||++|               +++++|||+||    |..|
T Consensus       431 ~P~~~~l~~AL~~L~~lgald~~g~l-----t~p~G~~ma~~Pl~p~lsk~ll~s~~~gc~~e~l~i~a~Lsv~~~f~~p  505 (674)
T KOG0922|consen  431 PPPPEALEEALEELYSLGALDDRGKL-----TSPLGRQMAELPLEPHLSKMLLKSSELGCSEEILTIAAMLSVQSVFSRP  505 (674)
T ss_pred             CCChHHHHHHHHHHHhcCcccCcCCc-----CchHHhhhhhcCCCcchhhhhhhccccCCcchhhhheeeeeccceecCc
Confidence            99999999999999999999999999     87 999999999999               89999999999    8889


Q ss_pred             cChHHH-HHHHHhhhC-CCCcHHHHHHHHHHHhcCCCCchHhHHHhh
Q psy6094         404 PSTAKI-IKELRARLD-MLLAHKLSHPGTTAWGDPNEGNILHCCSGF  448 (455)
Q Consensus       404 ~~~~~~-~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~~~~~~~c~~~  448 (455)
                      ...+.+ ++..|++|. .+|||+|++|+|+.|.+.+..  .+||.+|
T Consensus       506 ~~~~~~~a~~~~~kf~~~eGDh~tlL~vy~~~~~~~~~--~~wC~en  550 (674)
T KOG0922|consen  506 KDKKAEDADRKRAKFANPEGDHLTLLNVYESWKENGTS--KKWCKEN  550 (674)
T ss_pred             cchhhhhhhHHHHhhcCcccCHHHHHHHHHHHHhcCCh--hhHHHHh
Confidence            888877 889999999 999999999999999985543  7999984

>KOG0924|consensus

Probab=100.00  E-value=8.9e-89  Score=689.72  Aligned_cols=389  Identities=26%  Similarity=0.362  Sum_probs=352.9

Q ss_pred             HHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh----------------------------hh--
Q psy6094          48 EMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL----------------------------KR--   96 (455)
Q Consensus        48 ~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~----------------------------e~--   96 (455)
                      .+.++|+.||+|.++++++..|..|++|||.|+||||||||+| ||++                            |+  
T Consensus       347 ~i~eqrq~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~  426 (1042)
T KOG0924|consen  347 SIREQRQYLPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYADNGMIGCTQPRRVAAISVAKRVAEEMGV  426 (1042)
T ss_pred             hHHHHHhhcchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcccccCCeeeecCchHHHHHHHHHHHHHHhCC
Confidence            4779999999999999999999999999999999999999999 9987                            33  


Q ss_pred             --cCCCCC-hH-----------------HHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEE
Q psy6094          97 --SETQQY-PN-----------------DVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVY  142 (455)
Q Consensus        97 --~~~vg~-p~-----------------~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~il  142 (455)
                        |..||| +|                 -|||+. .|..|..|+             +|+|+++||.++ ..|.|+|+|+
T Consensus       427 ~lG~~VGYsIRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~l-arRrdlKliV  505 (1042)
T KOG0924|consen  427 TLGDTVGYSIRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVL-ARRRDLKLIV  505 (1042)
T ss_pred             ccccccceEEEeeecCCCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHH-HhhccceEEE
Confidence              555663 22                 188988 999999999             999999999999 8888999999


Q ss_pred             EccCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHH
Q psy6094         143 CTYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHR  204 (455)
Q Consensus       143 mSAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~  204 (455)
                      +|||+                 ||| |||++.|.+.+.++|+......   .+..|+. ..+|+||||++|+++|+..+.
T Consensus       506 tSATm~a~kf~nfFgn~p~f~IpGRTyPV~~~~~k~p~eDYVeaavkq---~v~Ihl~-~~~GdilIfmtGqediE~t~~  581 (1042)
T KOG0924|consen  506 TSATMDAQKFSNFFGNCPQFTIPGRTYPVEIMYTKTPVEDYVEAAVKQ---AVQIHLS-GPPGDILIFMTGQEDIECTCD  581 (1042)
T ss_pred             eeccccHHHHHHHhCCCceeeecCCccceEEEeccCchHHHHHHHHhh---heEeecc-CCCCCEEEecCCCcchhHHHH
Confidence            99999                 899 9999999999999887654332   1223333 678999999999999999888


Q ss_pred             HHHhcCCC----CCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCC
Q psy6094         205 SMCQSSFF----NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDN  280 (455)
Q Consensus       205 ~L~~~~~~----~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~  280 (455)
                      .+...-..    ....+.|+|+||+||+.-|.++|++.+.|.|||||||||||||+|||+|.||||||++|.++||++.|
T Consensus       582 ~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G  661 (1042)
T KOG0924|consen  582 IIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIG  661 (1042)
T ss_pred             HHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccccc
Confidence            87754221    23479999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccchhhHHhhhcccCCCCCCeEEecCCh----hhhccCCCCcccccC-hHHHHHHHh---------hhcCCCC
Q psy6094         281 IATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN----DVLNMLKDPELEGVN-NDVIFSLLQ---------HICTTQR  346 (455)
Q Consensus       281 ~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~----~~~~~~~~PEi~r~~-~~~~L~~l~---------~~~~~P~  346 (455)
                      ++.|+.+|||+|+|.||+|||||++||.||||||+    ++|-..+.|||+|+| ..++|.+++         +|+|||+
T Consensus       662 ~D~L~~~pIS~AnA~QRaGRAGRt~pG~cYRlYTe~ay~~eml~stvPEIqRTNl~nvVLlLkslgV~dll~FdFmD~Pp  741 (1042)
T KOG0924|consen  662 MDALQIVPISQANADQRAGRAGRTGPGTCYRLYTEDAYKNEMLPSTVPEIQRTNLSNVVLLLKSLGVDDLLKFDFMDPPP  741 (1042)
T ss_pred             cceeEEEechhccchhhccccCCCCCcceeeehhhhHHHhhcccCCCchhhhcchhhHHHHHHhcChhhhhCCCcCCCCH
Confidence            99999999999999999999999999999999996    456678999999999 999887665         7999999


Q ss_pred             hhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhc----CcCCcChH
Q psy6094         347 PGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLS----FECKPSTA  407 (455)
Q Consensus       347 ~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~ls----f~~p~~~~  407 (455)
                      .+.+..|+..|..||||+..|.|     |++|+.|++||+||               ++|++|++|||    |+.|.+.+
T Consensus       742 ed~~~~sly~Lw~LGAl~~~g~L-----T~lG~~MvefpLDP~lsKmll~a~~~Gc~dEilsIvSmLSvp~VF~rpker~  816 (1042)
T KOG0924|consen  742 EDNLLNSLYQLWTLGALDNTGQL-----TPLGRKMVEFPLDPPLSKMLLMAARMGCSDEILSIVSMLSVPAVFYRPKERE  816 (1042)
T ss_pred             HHHHHHHHHHHHHhhccccCCcc-----chhhHHhhhCCCCchHHHHHHHHhccCcHHHHHHHHHHhcccceeeccccch
Confidence            99999999999999999999999     99999999999999               99999999999    99999999


Q ss_pred             HHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCCCchHhHHHhh
Q psy6094         408 KIIKELRARLD-MLLAHKLSHPGTTAWGDPNEGNILHCCSGF  448 (455)
Q Consensus       408 ~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~~~~~~~c~~~  448 (455)
                      ++++.+|.+|. +.|||||++|+|++|..++++  ..||.+|
T Consensus       817 eead~ar~Kf~~~~sDhLTlLNVf~qw~~~~~~--~~WCnd~  856 (1042)
T KOG0924|consen  817 EEADAAREKFQVPESDHLTLLNVFNQWRKNKYS--SMWCNDH  856 (1042)
T ss_pred             hhhhhHHhhhcCCCCchhhHHHHHHHHHhcCCc--hhhhhhh
Confidence            99999999999 999999999999999998876  7899873

>KOG0925|consensus

Probab=100.00  E-value=1.8e-85  Score=646.01  Aligned_cols=408  Identities=27%  Similarity=0.382  Sum_probs=362.2

Q ss_pred             cCCcchHHHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------
Q psy6094          24 LNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------   94 (455)
Q Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------   94 (455)
                      ...........+.|...-.+++|++++++|..||+|.+++++++.+.+||.+|++|+||||||||+| |+++        
T Consensus        14 ~~~~~~~~k~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~~~   93 (699)
T KOG0925|consen   14 ISGAEENAKAINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHLTG   93 (699)
T ss_pred             cccccchhhhcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhccc
Confidence            3334444455778889999999999999999999999999999999999999999999999999999 7776        


Q ss_pred             ------------------------hhcCCCCC---------hHH---------HHHhc-cCCCCcCcc------------
Q psy6094          95 ------------------------KRSETQQY---------PND---------VLNML-KDPELEGVN------------  119 (455)
Q Consensus        95 ------------------------e~~~~vg~---------p~~---------ll~~l-~d~~L~~~~------------  119 (455)
                                              ..|..|||         |++         |+|+. +||.|..|+            
T Consensus        94 v~CTQprrvaamsva~RVadEMDv~lG~EVGysIrfEdC~~~~T~Lky~tDgmLlrEams~p~l~~y~viiLDeahERtl  173 (699)
T KOG0925|consen   94 VACTQPRRVAAMSVAQRVADEMDVTLGEEVGYSIRFEDCTSPNTLLKYCTDGMLLREAMSDPLLGRYGVIILDEAHERTL  173 (699)
T ss_pred             eeecCchHHHHHHHHHHHHHHhccccchhccccccccccCChhHHHHHhcchHHHHHHhhCcccccccEEEechhhhhhH
Confidence                                    34666774         222         77887 999999999            


Q ss_pred             -hHHHHHHHHHHHHhcCCCCeEEEEccCC-----------------CCCccceEEeehhhhhhhhccCCCCChHHHHHHH
Q psy6094         120 -NDVIFSLLQHICTTQRPGAILVYCTYTF-----------------MGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLL  181 (455)
Q Consensus       120 -~D~ll~~lk~il~~~~~~~k~ilmSAT~-----------------~g~~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i  181 (455)
                       +|+|+++||+++ ..|+|+|+|+||||.                 ||.|||+.+|.+++..+|+.....   ..+..|.
T Consensus       174 ATDiLmGllk~v~-~~rpdLk~vvmSatl~a~Kfq~yf~n~Pll~vpg~~PvEi~Yt~e~erDylEaair---tV~qih~  249 (699)
T KOG0925|consen  174 ATDILMGLLKEVV-RNRPDLKLVVMSATLDAEKFQRYFGNAPLLAVPGTHPVEIFYTPEPERDYLEAAIR---TVLQIHM  249 (699)
T ss_pred             HHHHHHHHHHHHH-hhCCCceEEEeecccchHHHHHHhCCCCeeecCCCCceEEEecCCCChhHHHHHHH---HHHHHHh
Confidence             999999999999 778999999999999                 788999999999887776644322   1244444


Q ss_pred             HccCCCCEEEEcCCHHHHHHHHHHHHhcCCC---CCCCeEEEeecCCCChhhHhhhhcCCCCC-----ceEEEEeCCCCc
Q psy6094         182 RSMLVVPILVFLPGWDTINSLHRSMCQSSFF---NSSRFQIIPLHSMLPTVSQKSIFNTPPEG-----VRKIVLATNIAE  253 (455)
Q Consensus       182 ~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~---~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-----~~kVivaTniae  253 (455)
                      + +.+|+|||||+|.+||+.+++.+......   ..+.+.|+|||    +.+|.++|++.+..     .|||+|+||+||
T Consensus       250 ~-ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniae  324 (699)
T KOG0925|consen  250 C-EEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAE  324 (699)
T ss_pred             c-cCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchh
Confidence            4 66999999999999999999999865432   35679999999    77788999988753     589999999999


Q ss_pred             cCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh----hhccCCCCccccc
Q psy6094         254 TSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND----VLNMLKDPELEGV  329 (455)
Q Consensus       254 ~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~----~~~~~~~PEi~r~  329 (455)
                      +|+||++|.||||.|+.|+++|||+.+.+++...||||++|.||+|||||+.||+||||||++    +|.+.+.|||+|.
T Consensus       325 tsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt~pGkcfrLYte~~~~~em~~~typeilrs  404 (699)
T KOG0925|consen  325 TSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFEKEMQPQTYPEILRS  404 (699)
T ss_pred             eeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCCCCCceEEeecHHhhhhcCCCCCcHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999964    5667899999999


Q ss_pred             C-hHHHHHHHh---------hhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh-----------
Q psy6094         330 N-NDVIFSLLQ---------HICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP-----------  388 (455)
Q Consensus       330 ~-~~~~L~~l~---------~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p-----------  388 (455)
                      | .+++|++..         +|++||.|+++++|++.|..++|||++|+|     |++|..|++||+||           
T Consensus       405 NL~s~VL~LKklgI~dlvhfdfmDpPAPEtLMrALE~LnYLaaLdDdGnL-----T~lG~imSEFPLdPqLAkmLi~S~e  479 (699)
T KOG0925|consen  405 NLSSTVLQLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLAALDDDGNL-----TSLGEIMSEFPLDPQLAKMLIGSCE  479 (699)
T ss_pred             hhHHHHHHHHhcCcccccCCcCCCCCChHHHHHHHHHhhhhhhhCCCccc-----chhhhhhhcCCCChHHHHHHhhcCC
Confidence            9 999998764         899999999999999999999999999999     99999999999999           


Q ss_pred             ----hHHHHHHHhhc----CcCCc-ChHHHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCCCchHhHHHh
Q psy6094         389 ----KEIITVRDCLS----FECKP-STAKIIKELRARLD-MLLAHKLSHPGTTAWGDPNEGNILHCCSG  447 (455)
Q Consensus       389 ----~~~l~iaa~ls----f~~p~-~~~~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~~~~~~~c~~  447 (455)
                          +++++|+||||    |..|. ..++.++++++.|+ ..|||+|++|+|++|++...  ..+||++
T Consensus       480 fnCsnEiLsisAMLsvPncFvRp~~~a~kaAdeak~~faH~dGDHlTLlnVYhAfkq~~~--~~~WC~~  546 (699)
T KOG0925|consen  480 FNCSNEILSISAMLSVPNCFVRPTSSASKAADEAKETFAHIDGDHLTLLNVYHAFKQNNE--DPNWCYD  546 (699)
T ss_pred             CCchHHHHHHHhcccCCccccCCChhHHHHHHHHHHHhccCCcchHHHHHHHHHHHhcCC--ChhHHHH
Confidence                89999999999    99998 66778899999999 99999999999999999884  4799998

>KOG0920|consensus

Probab=100.00  E-value=1.3e-83  Score=689.86  Aligned_cols=413  Identities=31%  Similarity=0.492  Sum_probs=364.9

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .+.....+++|+++++.|++||+|.++++|+++|++++|++|+|+||||||||+| |||+                    
T Consensus       152 ~~~~~~~s~~~~~~~~~R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIs  231 (924)
T KOG0920|consen  152 RQSEPKKSESYKEMLRFRESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRIS  231 (924)
T ss_pred             hhchhhhhhHHHHHHHHHHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHH
Confidence            6667778899999999999999999999999999999999999999999999999 9998                    


Q ss_pred             ----------hhcCC----CCC------------------hHHHHHhc-cCCCCcCcc-------------hHHHHHHHH
Q psy6094          95 ----------KRSET----QQY------------------PNDVLNML-KDPELEGVN-------------NDVIFSLLQ  128 (455)
Q Consensus        95 ----------e~~~~----vg~------------------p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk  128 (455)
                                ||++.    |||                  .+.|||.| .|+.+.+++             +|+||.++|
T Consensus       232 AIsvAeRVa~ER~~~~g~~VGYqvrl~~~~s~~t~L~fcTtGvLLr~L~~~~~l~~vthiivDEVHER~i~~DflLi~lk  311 (924)
T KOG0920|consen  232 AISVAERVAKERGESLGEEVGYQVRLESKRSRETRLLFCTTGVLLRRLQSDPTLSGVTHIIVDEVHERSINTDFLLILLK  311 (924)
T ss_pred             HHHHHHHHHHHhccccCCeeeEEEeeecccCCceeEEEecHHHHHHHhccCcccccCceeeeeeEEEccCCcccHHHHHH
Confidence                      44333    332                  11299999 999999998             999999999


Q ss_pred             HHHHhcCCCCeEEEEccCC-----------------CCC-ccceEEeehhhhhhhh--ccCC-----C--C---------
Q psy6094         129 HICTTQRPGAILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLM--KGVG-----A--N---------  172 (455)
Q Consensus       129 ~il~~~~~~~k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~--~~~~-----~--~---------  172 (455)
                      .++ ..+|++|+||||||+                 +|+ |||..+|++|++....  ....     +  .         
T Consensus       312 ~lL-~~~p~LkvILMSAT~dae~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~  390 (924)
T KOG0920|consen  312 DLL-PRNPDLKVILMSATLDAELFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKL  390 (924)
T ss_pred             HHh-hhCCCceEEEeeeecchHHHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchh
Confidence            999 889999999999999                 899 9999999999875321  1000     0  0         


Q ss_pred             ----ChH----HHHHHHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC-CCCeEEEeecCCCChhhHhhhhcCCCCCc
Q psy6094         173 ----SPK----RWVKLLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFN-SSRFQIIPLHSMLPTVSQKSIFNTPPEGV  242 (455)
Q Consensus       173 ----~~~----~l~~~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~-~~~~~v~~lhs~l~~~~r~~v~~~~~~g~  242 (455)
                          .+.    .+..+|+. ...|.|||||||+++|..+.+.|.....+. ..++.++|+||.|+..+|+.||.++|.|.
T Consensus       391 ~~~~id~~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~  470 (924)
T KOG0920|consen  391 WEPEIDYDLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGT  470 (924)
T ss_pred             ccccccHHHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCc
Confidence                011    14555655 558999999999999999999998765443 35799999999999999999999999999


Q ss_pred             eEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh---h-hh
Q psy6094         243 RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN---D-VL  318 (455)
Q Consensus       243 ~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~---~-~~  318 (455)
                      ||||+||||||+|||||||.||||+|+.|++.||+..++..+...|+|||++.||+|||||+.+|+||+||+.   + .+
T Consensus       471 RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv~~G~cy~L~~~~~~~~~~  550 (924)
T KOG0920|consen  471 RKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRVRPGICYHLYTRSRYEKLM  550 (924)
T ss_pred             chhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCccCCeeEEeechhhhhhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999993   3 33


Q ss_pred             ccCCCCcccccC-hHHHH-----------HHHhhhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCC
Q psy6094         319 NMLKDPELEGVN-NDVIF-----------SLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDN  386 (455)
Q Consensus       319 ~~~~~PEi~r~~-~~~~L-----------~~l~~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~  386 (455)
                      ..++.|||+|.+ .++||           .|++.+++||+.+++..|+..|..+|||+.+++|     |+||++|+.||+
T Consensus       551 ~~~q~PEilR~pL~~l~L~iK~l~~~~~~~fLskaldpP~~~~v~~a~~~L~~igaL~~~e~L-----T~LG~~la~lPv  625 (924)
T KOG0920|consen  551 LAYQLPEILRTPLEELCLHIKVLEQGSIKAFLSKALDPPPADAVDLAIERLKQIGALDESEEL-----TPLGLHLASLPV  625 (924)
T ss_pred             cccCChHHHhChHHHhhheeeeccCCCHHHHHHHhcCCCChHHHHHHHHHHHHhccccCcccc-----hHHHHHHHhCCC
Confidence            459999999999 99999           6788999999999999999999999999999999     999999999999


Q ss_pred             Ch---------------hHHHHHHHhhc----CcCCcChHHHHHHHHhhhC--CCCcHHHHHHHHHHHhcCCCC--c-hH
Q psy6094         387 KP---------------KEIITVRDCLS----FECKPSTAKIIKELRARLD--MLLAHKLSHPGTTAWGDPNEG--N-IL  442 (455)
Q Consensus       387 ~p---------------~~~l~iaa~ls----f~~p~~~~~~~~~~~~~~~--~~sD~~~~~~~~~~~~~~~~~--~-~~  442 (455)
                      ||               ||+++|||+|+    |..|.++++.+++++..|+  ..|||+|++++|+.|.....+  . ..
T Consensus       626 d~~igK~ll~g~if~cLdp~l~iaa~Ls~k~PF~~~~~~~~~~~~~~~~~~~~~~SD~la~~~ay~~w~~~~~~~~~~~~  705 (924)
T KOG0920|consen  626 DVRIGKLLLFGAIFGCLDPALTIAAALSFKSPFVSPLGKREEADKAKKLLALDSISDHLAVVRAYAGWREILRSGPSAEK  705 (924)
T ss_pred             ccccchhheehhhccccchhhhHHHHhccCCCcccCCCchhHHHHHHHHhccCCcchHHHHHHHHHHHHHHHhccchHHH
Confidence            99               99999999999    8888899999999999998  669999999999999998776  2 44


Q ss_pred             hHHHhh----hcCccc
Q psy6094         443 HCCSGF----SRMVMV  454 (455)
Q Consensus       443 ~~c~~~----~~~~m~  454 (455)
                      +||++|    ..|.|+
T Consensus       706 ~fc~~~fLs~~~l~~i  721 (924)
T KOG0920|consen  706 DFCEENFLSSNTLQEI  721 (924)
T ss_pred             HHHHHhhccHHHHHHH
Confidence            999984    445554

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

Probab=100.00  E-value=2.2e-78  Score=652.24  Aligned_cols=406  Identities=27%  Similarity=0.345  Sum_probs=345.1

Q ss_pred             hHHHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh-------------
Q psy6094          29 LDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL-------------   94 (455)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~-------------   94 (455)
                      ........+.....++++..+++.|..||+|..+++|+.+|.+|+++||.|+||||||||+| |+++             
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~LPv~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQ  101 (845)
T COG1643          22 KNQVRGSGMDARSRSANVPDILEYRSGLPVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQ  101 (845)
T ss_pred             hhhhhhhhhhhhhcccccchhhhccccCCcHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecC
Confidence            34445556677778888999999999999999999999999999999999999999999999 8887             


Q ss_pred             ---------------hh----cCCCCC-h--------H---------HHHHhc-cCCCCcCcc-------------hHHH
Q psy6094          95 ---------------KR----SETQQY-P--------N---------DVLNML-KDPELEGVN-------------NDVI  123 (455)
Q Consensus        95 ---------------e~----~~~vg~-p--------~---------~ll~~l-~d~~L~~~~-------------~D~l  123 (455)
                                     ++    |+.||| .        +         -|++++ .|+.|++|+             +|++
T Consensus       102 PRRlAArsvA~RvAeel~~~~G~~VGY~iRfe~~~s~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDil  181 (845)
T COG1643         102 PRRLAARSVAERVAEELGEKLGETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDIL  181 (845)
T ss_pred             chHHHHHHHHHHHHHHhCCCcCceeeEEEEeeccCCCCceeEEeccHHHHHHHhhCcccccCCEEEEcchhhhhHHHHHH
Confidence                           23    334553 1        1         199999 999999999             9999


Q ss_pred             HHHHHHHHHhcCCCCeEEEEccCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHH---
Q psy6094         124 FSLLQHICTTQRPGAILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLR---  182 (455)
Q Consensus       124 l~~lk~il~~~~~~~k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~---  182 (455)
                      |+++|+++...|+|+|+|+||||+                 +|+ |||+++|.+.....+.      .+..+...+.   
T Consensus       182 Lgllk~~~~~rr~DLKiIimSATld~~rfs~~f~~apvi~i~GR~fPVei~Y~~~~~~d~~------l~~ai~~~v~~~~  255 (845)
T COG1643         182 LGLLKDLLARRRDDLKLIIMSATLDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEADYI------LLDAIVAAVDIHL  255 (845)
T ss_pred             HHHHHHHHhhcCCCceEEEEecccCHHHHHHHcCCCCEEEecCCccceEEEecCCCCcchh------HHHHHHHHHHHhc
Confidence            999999996667799999999999                 899 9999999876543331      1111222222   


Q ss_pred             ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee
Q psy6094         183 SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       183 ~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~  262 (455)
                      ....|+|||||||.+||+.+++.|++..  ....+.++||||.|+.++|.++|++.+.|+||||+||||||||||||||+
T Consensus       256 ~~~~GdILvFLpG~~EI~~~~~~L~~~~--l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr  333 (845)
T COG1643         256 REGSGSILVFLPGQREIERTAEWLEKAE--LGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIR  333 (845)
T ss_pred             cCCCCCEEEECCcHHHHHHHHHHHHhcc--ccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeE
Confidence            2779999999999999999999999821  12469999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh---hhccCCCCcccccC-hHHHHHHH
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND---VLNMLKDPELEGVN-NDVIFSLL  338 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~---~~~~~~~PEi~r~~-~~~~L~~l  338 (455)
                      ||||+|+.|.+.||+.+|++.|.++|||||+|.||+|||||+++|+|||||+++   .|.+++.|||+|+| ..++|++.
T Consensus       334 ~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~pGicyRLyse~~~~~~~~~t~PEIlrtdLs~~vL~l~  413 (845)
T COG1643         334 YVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICYRLYSEEDFLAFPEFTLPEILRTDLSGLVLQLK  413 (845)
T ss_pred             EEecCCcccccccccccCceeeeEEEechhhhhhhccccccCCCceEEEecCHHHHHhcccCCChhhhhcchHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999964   56788999999999 99999876


Q ss_pred             h----------hhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh---------------hHHHH
Q psy6094         339 Q----------HICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEIIT  393 (455)
Q Consensus       339 ~----------~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~  393 (455)
                      +          .|+|||+..++..|++.|..+||||.++.|     |++|+.|+.||+||               +++++
T Consensus       414 ~~G~~~d~~~f~fld~P~~~~i~~A~~~L~~LGAld~~g~L-----T~lG~~ms~lpldprLA~mLl~a~~~g~~~e~~~  488 (845)
T COG1643         414 SLGIGQDIAPFPFLDPPPEAAIQAALTLLQELGALDDSGKL-----TPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAAT  488 (845)
T ss_pred             hcCCCCCcccCccCCCCChHHHHHHHHHHHHcCCcCCCCCC-----CHHHHHHHhCCCChHHHHHHHhccccCcHHHHHH
Confidence            4          689999999999999999999999999999     99999999999999               78999


Q ss_pred             HHHhhcCcC-------CcChHH---HHHHHH-hhhC----CCCcHHHHHHHHHHHhcCCCCc----hHhHHHh
Q psy6094         394 VRDCLSFEC-------KPSTAK---IIKELR-ARLD----MLLAHKLSHPGTTAWGDPNEGN----ILHCCSG  447 (455)
Q Consensus       394 iaa~lsf~~-------p~~~~~---~~~~~~-~~~~----~~sD~~~~~~~~~~~~~~~~~~----~~~~c~~  447 (455)
                      |||+||+..       +.+.++   ..+.++ .++.    +.+||++++++|..|...+...    ..+||..
T Consensus       489 Ias~Ls~~~~~s~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~d~~~ll~~~~~~i~~~~~~~~~~~~~~~~~  561 (845)
T COG1643         489 IASMLSEQDRESDFSRDVKLRKQRTAQDLLKRLKRRNAADPRGDHLLLLEAFPDRIARKRAKGEYLRANGCRA  561 (845)
T ss_pred             HHHhhccCCCcchhccccchhhHHHHHHHHHHHHhccCCCcchHHHHHHHHHHHHHHhhhccchhhHhcChhh
Confidence            999999655       222222   222222 2222    5799999999999999876311    3489986

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=1.1e-73  Score=635.35  Aligned_cols=383  Identities=23%  Similarity=0.303  Sum_probs=329.0

Q ss_pred             HHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh----------------------------hh----
Q psy6094          50 LEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL----------------------------KR----   96 (455)
Q Consensus        50 l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~----------------------------e~----   96 (455)
                      +..|..||+|.++++|+++|.+|+++||+|+||||||||+| ++++                            ++    
T Consensus        67 ~~~~~~LPi~~~r~~Il~ai~~~~VviI~GeTGSGKTTqlPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~l  146 (1294)
T PRK11131         67 ITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETEL  146 (1294)
T ss_pred             cCCCCCCCHHHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhh
Confidence            56678899999999999999999999999999999999999 6664                            22    


Q ss_pred             cCCCC------------------ChHHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEc
Q psy6094          97 SETQQ------------------YPNDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCT  144 (455)
Q Consensus        97 ~~~vg------------------~p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmS  144 (455)
                      |..||                  +|+.|++++ .++.|.+|+             +|+++++|+.++ ..++++|+|+||
T Consensus       147 G~~VGY~vrf~~~~s~~t~I~v~TpG~LL~~l~~d~~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL-~~rpdlKvILmS  225 (1294)
T PRK11131        147 GGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELL-PRRPDLKVIITS  225 (1294)
T ss_pred             cceeceeecCccccCCCCCEEEEChHHHHHHHhcCCccccCcEEEecCccccccccchHHHHHHHhh-hcCCCceEEEee
Confidence            33344                  345588988 888898888             889999999998 778899999999


Q ss_pred             cCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHH---H---HHHHHccCCCCEEEEcCCHHHHH
Q psy6094         145 YTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKR---W---VKLLRSMLVVPILVFLPGWDTIN  200 (455)
Q Consensus       145 AT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~---l---~~~i~~~~~g~iLVFlp~~~ei~  200 (455)
                      ||+                 +|+ |||+.+|.+.....     .......   +   +..++...+|+|||||||.++|+
T Consensus       226 ATid~e~fs~~F~~apvI~V~Gr~~pVei~y~p~~~~~-----~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe  300 (1294)
T PRK11131        226 ATIDPERFSRHFNNAPIIEVSGRTYPVEVRYRPIVEEA-----DDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIR  300 (1294)
T ss_pred             CCCCHHHHHHHcCCCCEEEEcCccccceEEEeeccccc-----chhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHH
Confidence            999                 688 99999887532110     0000111   1   22233467899999999999999


Q ss_pred             HHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCC
Q psy6094         201 SLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDN  280 (455)
Q Consensus       201 ~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~  280 (455)
                      .+++.|...+   ...+.+++|||+|++++|.++|++  .|.+||||||||||||||||+|+||||+|++|.+.||+++|
T Consensus       301 ~lae~L~~~~---~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~  375 (1294)
T PRK11131        301 DTADALNKLN---LRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTK  375 (1294)
T ss_pred             HHHHHHHhcC---CCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCccccccccccC
Confidence            9999998754   224679999999999999999996  57899999999999999999999999999999999999999


Q ss_pred             cccccccccchhhHHhhhcccCCCCCCeEEecCChhh---hccCCCCcccccC-hHHHHHHHh---------hhcCCCCh
Q psy6094         281 IATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV---LNMLKDPELEGVN-NDVIFSLLQ---------HICTTQRP  347 (455)
Q Consensus       281 ~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~---~~~~~~PEi~r~~-~~~~L~~l~---------~~~~~P~~  347 (455)
                      ++.+...|+|+++|.||+|||||+++|+||+||+++.   +++++.|||+|++ .++||++++         .|++||+.
T Consensus       376 ~~~Lp~~~iSkasa~QRaGRAGR~~~G~c~rLyte~d~~~~~~~~~PEIlR~~L~~viL~lk~lgl~di~~F~fldpP~~  455 (1294)
T PRK11131        376 VQRLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAFPFVEAPDK  455 (1294)
T ss_pred             cccCCeeecCHhhHhhhccccCCCCCcEEEEeCCHHHHHhhhcccCCccccCCHHHHHHHHHHcCCCCcceeeCCCCCCH
Confidence            9999999999999999999999999999999999654   5678999999999 999998765         68999999


Q ss_pred             hhHHhHHhhhhhcccccCC-----CCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhc----CcCC
Q psy6094         348 GAILVFLPGWDTINSLHRS-----MCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLS----FECK  403 (455)
Q Consensus       348 ~~i~~al~~L~~lgald~~-----~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~ls----f~~p  403 (455)
                      ++|..|++.|..+||||.+     ++|     |++|+.|++||+||               +++++|||+||    |..|
T Consensus       456 ~~i~~al~~L~~LgAld~~~~~~~~~L-----T~lG~~la~LPldPrlakmLl~a~~~~c~~evl~IaA~Lsv~dpf~~p  530 (1294)
T PRK11131        456 RNIQDGVRLLEELGAITTDEQASAYKL-----TPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERP  530 (1294)
T ss_pred             HHHHHHHHHHHHCCCCCccccCCCccC-----cHHHHHHHhCCCChHHHHHHHHhhhcCCHHHHHHHHHHHcCCCcccCC
Confidence            9999999999999999864     357     99999999999999               89999999999    7788


Q ss_pred             cChHHHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCC----CchHhHHHhh
Q psy6094         404 PSTAKIIKELRARLD-MLLAHKLSHPGTTAWGDPNE----GNILHCCSGF  448 (455)
Q Consensus       404 ~~~~~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~----~~~~~~c~~~  448 (455)
                      .+++++++.+|++|. ..|||++++|+|+.|.+...    +..++||++|
T Consensus       531 ~~~~~~a~~~~~~f~~~~sD~lt~ln~~~~~~~~~~~~s~~~~~~~C~~~  580 (1294)
T PRK11131        531 MDKQQASDEKHRRFADKESDFLAFVNLWNYLQEQQKALSSNQFRRLCRTD  580 (1294)
T ss_pred             chhHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHh
Confidence            888889999999999 99999999999999986432    2245899983

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=100.00  E-value=1.9e-72  Score=627.53  Aligned_cols=386  Identities=24%  Similarity=0.319  Sum_probs=329.5

Q ss_pred             HHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh----------------------------hhcCC
Q psy6094          49 MLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL----------------------------KRSET   99 (455)
Q Consensus        49 ~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~----------------------------e~~~~   99 (455)
                      .+..+..||++.++++|+++|.+|+++||+|+||||||||+| ++++                            ++|..
T Consensus        59 ~~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~  138 (1283)
T TIGR01967        59 EIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTP  138 (1283)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCCC
Confidence            456778899999999999999999999999999999999999 7765                            33333


Q ss_pred             ----CCC------------------hHHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEE
Q psy6094         100 ----QQY------------------PNDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYC  143 (455)
Q Consensus       100 ----vg~------------------p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilm  143 (455)
                          |||                  ++.|++++ .|+.|.+|+             +|++++++++++ ..++++|+|+|
T Consensus       139 lG~~VGY~vR~~~~~s~~T~I~~~TdGiLLr~l~~d~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il-~~rpdLKlIlm  217 (1283)
T TIGR01967       139 LGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLL-PRRPDLKIIIT  217 (1283)
T ss_pred             cceEEeeEEcCCcccCCCceeeeccccHHHHHhhhCcccccCcEEEEcCcchhhccchhHHHHHHHHH-hhCCCCeEEEE
Confidence                331                  33488998 899999998             899999999998 78899999999


Q ss_pred             ccCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHHH---HHHHHccCCCCEEEEcCCHHHHHHH
Q psy6094         144 TYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRW---VKLLRSMLVVPILVFLPGWDTINSL  202 (455)
Q Consensus       144 SAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l---~~~i~~~~~g~iLVFlp~~~ei~~l  202 (455)
                      |||+                 +|+ |||+.+|........  .........+   +..+....+|+|||||||..+|+.+
T Consensus       218 SATld~~~fa~~F~~apvI~V~Gr~~PVev~Y~~~~~~~~--~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l  295 (1283)
T TIGR01967       218 SATIDPERFSRHFNNAPIIEVSGRTYPVEVRYRPLVEEQE--DDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDA  295 (1283)
T ss_pred             eCCcCHHHHHHHhcCCCEEEECCCcccceeEEeccccccc--chhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHH
Confidence            9999                 688 999998865321000  0000001112   2222335679999999999999999


Q ss_pred             HHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcc
Q psy6094         203 HRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIA  282 (455)
Q Consensus       203 ~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~  282 (455)
                      ++.|.+..   ..++.+++|||+|++++|.++|+++  +.+||||||||||||||||+|+||||+|++|.+.||+.+|++
T Consensus       296 ~~~L~~~~---~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~  370 (1283)
T TIGR01967       296 AEILRKRN---LRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQ  370 (1283)
T ss_pred             HHHHHhcC---CCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCcc
Confidence            99998753   2357899999999999999999875  358999999999999999999999999999999999999999


Q ss_pred             cccccccchhhHHhhhcccCCCCCCeEEecCChhh---hccCCCCcccccC-hHHHHHHHh---------hhcCCCChhh
Q psy6094         283 TLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV---LNMLKDPELEGVN-NDVIFSLLQ---------HICTTQRPGA  349 (455)
Q Consensus       283 ~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~---~~~~~~PEi~r~~-~~~~L~~l~---------~~~~~P~~~~  349 (455)
                      .+.+.|||+++|.||+|||||+++|+||+||+++.   +.+++.|||+|++ .+++|++.+         .|++||+.++
T Consensus       371 ~L~~~~ISkasa~QRaGRAGR~~~G~cyRLyte~~~~~~~~~~~PEIlR~~L~~viL~l~~lg~~di~~f~fldpP~~~~  450 (1283)
T TIGR01967       371 RLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRA  450 (1283)
T ss_pred             ccCCccCCHHHHHHHhhhhCCCCCceEEEecCHHHHHhhhhccCcccccccHHHHHHHHHhcCCCCcccccCCCCCCHHH
Confidence            99999999999999999999999999999999654   5678999999999 999997764         5899999999


Q ss_pred             HHhHHhhhhhcccccCCC---CCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhc----CcCCcChH
Q psy6094         350 ILVFLPGWDTINSLHRSM---CQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLS----FECKPSTA  407 (455)
Q Consensus       350 i~~al~~L~~lgald~~~---~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~ls----f~~p~~~~  407 (455)
                      +..|++.|..+||||.++   +|     |++|+.|+.||+||               +++++|||+||    |..|.+++
T Consensus       451 i~~A~~~L~~LGAld~~~~~~~L-----T~lGr~ma~LPldPrlarmLl~a~~~gcl~e~l~IaA~Ls~~dp~~~p~~~~  525 (1283)
T TIGR01967       451 IRDGFRLLEELGALDDDEAEPQL-----TPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPMEKQ  525 (1283)
T ss_pred             HHHHHHHHHHCCCCCCCCCCccc-----cHHHHHHhhcCCChHHHHHHHHhhhcCCHHHHHHHHHHHcCCCcCCCcchhH
Confidence            999999999999999988   68     99999999999999               88999999999    66778888


Q ss_pred             HHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCC----CchHhHHHh
Q psy6094         408 KIIKELRARLD-MLLAHKLSHPGTTAWGDPNE----GNILHCCSG  447 (455)
Q Consensus       408 ~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~----~~~~~~c~~  447 (455)
                      ++++.++++|. ..|||++++|+|+.|.+...    +..++||++
T Consensus       526 ~~a~~~~~~f~~~~sD~l~~L~~~~~~~~~~~~~~~~~~~~~C~~  570 (1283)
T TIGR01967       526 QAADQAHARFKDPRSDFLSRVNLWRHIEEQRQALSANQFRNACRK  570 (1283)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHHhhhhccchHHHHHHHH
Confidence            89999999999 99999999999999986432    224589997

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.

>KOG0926|consensus

Probab=100.00  E-value=5.7e-73  Score=582.68  Aligned_cols=391  Identities=25%  Similarity=0.345  Sum_probs=328.2

Q ss_pred             HHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhhh--------hcCCCC--ChHH--------
Q psy6094          45 RYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITLK--------RSETQQ--YPND--------  105 (455)
Q Consensus        45 ~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~e--------~~~~vg--~p~~--------  105 (455)
                      +-.++.+.|..||++....+|+++|+.|.+|||+|+||||||||+| ||++.        .+..+|  +|||        
T Consensus       244 R~~EIQ~sR~~LPI~aeEq~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAk  323 (1172)
T KOG0926|consen  244 RPAEIQESRLDLPIVAEEQRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAK  323 (1172)
T ss_pred             CcHHHHHHHhcCchhHHHHHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHH
Confidence            3457788999999999999999999999999999999999999999 99871        111233  2443        


Q ss_pred             ------------------------------------HHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcC
Q psy6094         106 ------------------------------------VLNML-KDPELEGVN-------------NDVIFSLLQHICTTQR  135 (455)
Q Consensus       106 ------------------------------------ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~  135 (455)
                                                          ||+++ .|-.|..|+             ||+|+++|.+++ ..|
T Consensus       324 RVa~EL~~~~~eVsYqIRfd~ti~e~T~IkFMTDGVLLrEi~~DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV-~LR  402 (1172)
T KOG0926|consen  324 RVAFELGVLGSEVSYQIRFDGTIGEDTSIKFMTDGVLLREIENDFLLTKYSVIILDEAHERSVNTDILIGMLSRIV-PLR  402 (1172)
T ss_pred             HHHHHhccCccceeEEEEeccccCCCceeEEecchHHHHHHHHhHhhhhceeEEechhhhccchHHHHHHHHHHHH-HHH
Confidence                                                89999 999999999             999999998887 443


Q ss_pred             ----------CCCeEEEEccCC---------------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHc
Q psy6094         136 ----------PGAILVYCTYTF---------------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRS  183 (455)
Q Consensus       136 ----------~~~k~ilmSAT~---------------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~  183 (455)
                                +.+|+|+||||+                     +.| |||.++|-+....+|+..+-     .-.+-|++
T Consensus       403 ~k~~ke~~~~kpLKLIIMSATLRVsDFtenk~LFpi~pPlikVdARQfPVsIHF~krT~~DYi~eAf-----rKtc~IH~  477 (1172)
T KOG0926|consen  403 QKYYKEQCQIKPLKLIIMSATLRVSDFTENKRLFPIPPPLIKVDARQFPVSIHFNKRTPDDYIAEAF-----RKTCKIHK  477 (1172)
T ss_pred             HHHhhhhcccCceeEEEEeeeEEecccccCceecCCCCceeeeecccCceEEEeccCCCchHHHHHH-----HHHHHHhh
Confidence                      368999999999                     567 99999987654444432211     12233443


Q ss_pred             -cCCCCEEEEcCCHHHHHHHHHHHHhcCC---------------------------------------------------
Q psy6094         184 -MLVVPILVFLPGWDTINSLHRSMCQSSF---------------------------------------------------  211 (455)
Q Consensus       184 -~~~g~iLVFlp~~~ei~~l~~~L~~~~~---------------------------------------------------  211 (455)
                       .++|.||||++|+.||+.+++.|++...                                                   
T Consensus       478 kLP~G~ILVFvTGQqEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~  557 (1172)
T KOG0926|consen  478 KLPPGGILVFVTGQQEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELV  557 (1172)
T ss_pred             cCCCCcEEEEEeChHHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhh
Confidence             7899999999999999999999986500                                                   


Q ss_pred             ------------------------------------------CCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC
Q psy6094         212 ------------------------------------------FNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT  249 (455)
Q Consensus       212 ------------------------------------------~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT  249 (455)
                                                                +..+.+.|+||||-|+.++|.+||...|.|.|-|||||
T Consensus       558 ~~~~~~~raa~~~~~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaT  637 (1172)
T KOG0926|consen  558 DSGFASLRAAFNALADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVAT  637 (1172)
T ss_pred             cccchhhhhhhhccccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEec
Confidence                                                      00125789999999999999999999999999999999


Q ss_pred             CCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC----hhhhccCCCCc
Q psy6094         250 NIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP----NDVLNMLKDPE  325 (455)
Q Consensus       250 niae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t----~~~~~~~~~PE  325 (455)
                      ||||||+|||+|+||||||+.|+..||..+|+..+...|||||++.||+|||||+++|+|||||+    .+.|+++..||
T Consensus       638 NVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtgpGHcYRLYSSAVf~~~Fe~fS~PE  717 (1172)
T KOG0926|consen  638 NVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTGPGHCYRLYSSAVFSNDFEEFSLPE  717 (1172)
T ss_pred             cchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCCCCceeehhhhHHhhcchhhhccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999    45788999999


Q ss_pred             ccccC-hHHHHHHHh---------hhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh-------
Q psy6094         326 LEGVN-NDVIFSLLQ---------HICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP-------  388 (455)
Q Consensus       326 i~r~~-~~~~L~~l~---------~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p-------  388 (455)
                      |++.| ++++|++.+         .|+.||+..++..|...|..|||||.+|.+     |+||+.|+.||+.|       
T Consensus       718 Ilk~Pve~lvLqMKsMnI~kVvnFPFPtpPd~~~L~~Aer~L~~LgALd~~g~l-----T~lGk~mS~FPlsPrfsKmL~  792 (1172)
T KOG0926|consen  718 ILKKPVESLVLQMKSMNIDKVVNFPFPTPPDRSALEKAERRLKALGALDSNGGL-----TKLGKAMSLFPLSPRFSKMLA  792 (1172)
T ss_pred             HhhCcHHHHHHHHHhcCccceecCCCCCCccHHHHHHHHHHHHHhccccccCCc-----ccccchhcccccChhHHHHHH
Confidence            99999 999999876         688999999999999999999999999999     99999999999999       


Q ss_pred             --------hHHHHHHHhhc----Cc-------CCcC------h-------------------HHHHHHHHhhhC-CCCcH
Q psy6094         389 --------KEIITVRDCLS----FE-------CKPS------T-------------------AKIIKELRARLD-MLLAH  423 (455)
Q Consensus       389 --------~~~l~iaa~ls----f~-------~p~~------~-------------------~~~~~~~~~~~~-~~sD~  423 (455)
                              ..++.++++||    |.       +|..      .                   ++...+++.+|. ..||-
T Consensus       793 ~~~Q~~~lpy~i~lvsaLsv~e~~i~~~~ll~n~~~r~~~~eE~d~~~~de~~~d~~~K~~rr~~~~aa~~rf~~l~sd~  872 (1172)
T KOG0926|consen  793 TSDQHNLLPYNIALVSALSVYEVLIVAASLLPNPLIREFEPEEKDLIKDDETVEDKELKKRRREKSKAARSRFSNLDSDA  872 (1172)
T ss_pred             HHHhhcchhHHHHHHHHHhccchhhhhhhcccccccccCCcchhhccccccccccHHHHHHHHHHHHHHHhhhccCCccH
Confidence                    34566777787    11       1111      0                   011234566787 77999


Q ss_pred             HHHHHHHHHHhcCCCCchHhHHHhh
Q psy6094         424 KLSHPGTTAWGDPNEGNILHCCSGF  448 (455)
Q Consensus       424 ~~~~~~~~~~~~~~~~~~~~~c~~~  448 (455)
                      ++++.+..++..+.++  ..||.++
T Consensus       873 l~Ll~Av~a~ey~~~~--~rfc~~n  895 (1172)
T KOG0926|consen  873 LVLLSAVSAAEYAENG--MRFCEAN  895 (1172)
T ss_pred             HHHHHHHHHHHhhhhc--chhHHhc
Confidence            9999999999888775  4599985

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=6.9e-65  Score=554.98  Aligned_cols=336  Identities=25%  Similarity=0.303  Sum_probs=289.4

Q ss_pred             CCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------------hhcC----CCC--
Q psy6094          56 LPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------------KRSE----TQQ--  101 (455)
Q Consensus        56 lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------------e~~~----~vg--  101 (455)
                      ||++.+.++|+++|.+|+++||+|+|||||||++| ++++                           +++.    .||  
T Consensus         1 LPi~~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~   80 (819)
T TIGR01970         1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYR   80 (819)
T ss_pred             CCchHHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEE
Confidence            79999999999999999999999999999999999 7774                           2222    233  


Q ss_pred             ----------------ChHHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCC----
Q psy6094         102 ----------------YPNDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTF----  147 (455)
Q Consensus       102 ----------------~p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~----  147 (455)
                                      +++.|++++ .++.|.+|+             +|+++++++++....++++|+|+||||+    
T Consensus        81 vr~~~~~s~~t~I~v~T~G~Llr~l~~d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~  160 (819)
T TIGR01970        81 VRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGER  160 (819)
T ss_pred             EccccccCCCCcEEEECCcHHHHHHhhCcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHH
Confidence                            245588988 888899888             6788888888875678999999999999    


Q ss_pred             -------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCC
Q psy6094         148 -------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFN  213 (455)
Q Consensus       148 -------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~  213 (455)
                                   +|+ |||+.+|++.....++...   ....+..++. ..+|+|||||||+++|+.+++.|.+..   
T Consensus       161 l~~~l~~~~vI~~~gr~~pVe~~y~~~~~~~~~~~~---v~~~l~~~l~-~~~g~iLVFlpg~~eI~~l~~~L~~~~---  233 (819)
T TIGR01970       161 LSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDA---VSRAVEHALA-SETGSILVFLPGQAEIRRVQEQLAERL---  233 (819)
T ss_pred             HHHHcCCCcEEEecCcceeeeeEEeecchhhhHHHH---HHHHHHHHHH-hcCCcEEEEECCHHHHHHHHHHHHhhc---
Confidence                         578 8999888754221111000   0011222332 457999999999999999999998742   


Q ss_pred             CCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhh
Q psy6094         214 SSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLAN  293 (455)
Q Consensus       214 ~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~  293 (455)
                      ..++.+++|||+|++++|.++|++|++|++||||||||||||||||+|+||||+|++|...||+.+|++.|.++||||++
T Consensus       234 ~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkas  313 (819)
T TIGR01970       234 DSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQAS  313 (819)
T ss_pred             CCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHH
Confidence            13589999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcccCCCCCCeEEecCChh---hhccCCCCcccccC-hHHHHHHHh---------hhcCCCChhhHHhHHhhhhhc
Q psy6094         294 AKQRRGRAGRTLKRSETQQYPND---VLNMLKDPELEGVN-NDVIFSLLQ---------HICTTQRPGAILVFLPGWDTI  360 (455)
Q Consensus       294 ~~QR~GRaGR~~~G~c~~L~t~~---~~~~~~~PEi~r~~-~~~~L~~l~---------~~~~~P~~~~i~~al~~L~~l  360 (455)
                      |.||+|||||+++|.||+||+++   .|.+++.|||+|++ ++++|+++.         .|++||+.+++..|++.|..+
T Consensus       314 a~QR~GRAGR~~~G~cyrL~t~~~~~~l~~~~~PEI~r~~L~~~~L~l~~~g~~~~~~~~~l~~P~~~~i~~a~~~L~~l  393 (819)
T TIGR01970       314 ATQRAGRAGRLEPGVCYRLWSEEQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLLQRL  393 (819)
T ss_pred             HHhhhhhcCCCCCCEEEEeCCHHHHHhhhcCCCcceeccCcHHHHHHHHHcCCCChhhCCCCCCcCHHHHHHHHHHHHHC
Confidence            99999999999999999999954   46789999999999 999997654         689999999999999999999


Q ss_pred             ccccCCCCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhcCcCC
Q psy6094         361 NSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLSFECK  403 (455)
Q Consensus       361 gald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~lsf~~p  403 (455)
                      ||||.+++|     |++|+.|+.||++|               +++++|||+|+-..+
T Consensus       394 gald~~~~l-----T~~G~~~~~lp~~p~l~~~ll~~~~~~~~~~~~~iaa~ls~~~~  446 (819)
T TIGR01970       394 GALDAQGRL-----TAHGKAMAALGCHPRLAAMLLSAHSTGLAALACDLAALLEERGL  446 (819)
T ss_pred             CCCCCCCCc-----CHHHHHHHhcCCCHHHHHHHHHhhhcCCHHHHHHHHHHHcCCCC
Confidence            999999999     99999999999999               778999999995443

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=9.3e-64  Score=547.13  Aligned_cols=322  Identities=26%  Similarity=0.350  Sum_probs=279.0

Q ss_pred             cCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------------hhcCC----CC-
Q psy6094          55 KLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------------KRSET----QQ-  101 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------------e~~~~----vg-  101 (455)
                      .||+|.+.++|++++.+++++|++|+|||||||++| ++++                           ++++.    || 
T Consensus         3 ~LPi~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy   82 (812)
T PRK11664          3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGY   82 (812)
T ss_pred             CCCHHHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEE
Confidence            499999999999999999999999999999999999 7775                           22222    22 


Q ss_pred             -----------------ChHHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCC---
Q psy6094         102 -----------------YPNDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTF---  147 (455)
Q Consensus       102 -----------------~p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~---  147 (455)
                                       +|+.|++++ .|+.|.+|+             +|+++++++++++..++++|+|+||||+   
T Consensus        83 ~vr~~~~~~~~t~I~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~~~  162 (812)
T PRK11664         83 RMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDND  162 (812)
T ss_pred             EecCccccCCCCcEEEEChhHHHHHHhhCCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCCHH
Confidence                             355688988 888888888             7889999998886678999999999999   


Q ss_pred             --------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCC
Q psy6094         148 --------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFF  212 (455)
Q Consensus       148 --------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~  212 (455)
                                    +|+ |||+.+|++.....++...   ....+...+. ...|+|||||||.++|+.+++.|++..  
T Consensus       163 ~l~~~~~~~~~I~~~gr~~pV~~~y~~~~~~~~~~~~---v~~~l~~~l~-~~~g~iLVFlpg~~ei~~l~~~L~~~~--  236 (812)
T PRK11664        163 RLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEA---VARATAELLR-QESGSLLLFLPGVGEIQRVQEQLASRV--  236 (812)
T ss_pred             HHHHhcCCCCEEEecCccccceEEeccCchhhhHHHH---HHHHHHHHHH-hCCCCEEEEcCCHHHHHHHHHHHHHhc--
Confidence                          578 8998888754322111000   0001223333 457999999999999999999998632  


Q ss_pred             CCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchh
Q psy6094         213 NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLA  292 (455)
Q Consensus       213 ~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka  292 (455)
                       ..++.+++|||+|++++|.++|+++++|++||||||||||||||||+|+||||+|++|...||+.+|++.|.++||||+
T Consensus       237 -~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSka  315 (812)
T PRK11664        237 -ASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQA  315 (812)
T ss_pred             -cCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechh
Confidence             1258899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHhhhcccCCCCCCeEEecCChh---hhccCCCCcccccC-hHHHHHHHh---------hhcCCCChhhHHhHHhhhhh
Q psy6094         293 NAKQRRGRAGRTLKRSETQQYPND---VLNMLKDPELEGVN-NDVIFSLLQ---------HICTTQRPGAILVFLPGWDT  359 (455)
Q Consensus       293 ~~~QR~GRaGR~~~G~c~~L~t~~---~~~~~~~PEi~r~~-~~~~L~~l~---------~~~~~P~~~~i~~al~~L~~  359 (455)
                      +|.||+|||||+++|.||+||+++   .+.+++.|||+|++ ++++|.+++         .|++||++.++..|++.|..
T Consensus       316 sa~QR~GRaGR~~~G~cyrL~t~~~~~~l~~~~~PEI~r~dL~~~~L~l~~~g~~~~~~~~~ld~P~~~~~~~A~~~L~~  395 (812)
T PRK11664        316 SMTQRAGRAGRLEPGICLHLYSKEQAERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRLLQQ  395 (812)
T ss_pred             hhhhhccccCCCCCcEEEEecCHHHHhhCccCCCCceeccchHHHHHHHHHcCCCCHHhCCCCCCCCHHHHHHHHHHHHH
Confidence            999999999999999999999954   46789999999999 999997654         68999999999999999999


Q ss_pred             cccccCCCCCCcccCChHHHHHhhCCCCh
Q psy6094         360 INSLHRSMCQSSFFNSCLLYEFAMVDNKP  388 (455)
Q Consensus       360 lgald~~~~l~~~~~T~lG~~l~~lp~~p  388 (455)
                      +||||++++|     |++|+.|+.||++|
T Consensus       396 lgald~~g~l-----T~~G~~m~~lp~~P  419 (812)
T PRK11664        396 LGALDGQGRL-----TARGRKMAALGNDP  419 (812)
T ss_pred             CCCCCCCCCc-----CHHHHHHHhcCCch
Confidence            9999999999     99999999999999

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=1.2e-46  Score=403.17  Aligned_cols=293  Identities=17%  Similarity=0.223  Sum_probs=219.0

Q ss_pred             HHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhhh---------h--------cCCCC--ChHH---------HHH---
Q psy6094          61 MRDAVLDMVRNNQITVISGETGSGPPLHLD-FITLK---------R--------SETQQ--YPND---------VLN---  108 (455)
Q Consensus        61 ~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~e---------~--------~~~vg--~p~~---------ll~---  108 (455)
                      .|+++++.+.+|+++|++|+||||||+|+| ++++.         .        +.++.  .|++         +.+   
T Consensus       168 iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg  247 (675)
T PHA02653        168 VQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLG  247 (675)
T ss_pred             HHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhC
Confidence            588999999999999999999999999999 55420         0        01122  3554         111   


Q ss_pred             -----------------------------hc------cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeE
Q psy6094         109 -----------------------------ML------KDPELEGVN-------------NDVIFSLLQHICTTQRPGAIL  140 (455)
Q Consensus       109 -----------------------------~l------~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~  140 (455)
                                                   .+      .++.|.+++             +|+++++++++. .  ...|+
T Consensus       248 ~~~~~g~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L~l~~L~~v~~VVIDEaHEr~~~~DllL~llk~~~-~--~~rq~  324 (675)
T PHA02653        248 FDEIDGSPISLKYGSIPDELINTNPKPYGLVFSTHKLTLNKLFDYGTVIIDEVHEHDQIGDIIIAVARKHI-D--KIRSL  324 (675)
T ss_pred             ccccCCceEEEEECCcchHHhhcccCCCCEEEEeCcccccccccCCEEEccccccCccchhHHHHHHHHhh-h--hcCEE
Confidence                                         01      111233333             888888888765 2  22489


Q ss_pred             EEEccCC-------------------CCC--ccceEEeehhhhh-----hhhccCCCCChHHHHHHHHc---cCCCCEEE
Q psy6094         141 VYCTYTF-------------------MGV--SPMKVFFCKNVLQ-----RLMKGVGANSPKRWVKLLRS---MLVVPILV  191 (455)
Q Consensus       141 ilmSAT~-------------------~g~--~pv~~~~l~~~~~-----~~~~~~~~~~~~~l~~~i~~---~~~g~iLV  191 (455)
                      ++||||+                   +|+  |||+.+|+++...     .+..    .....+...+..   ..+|++||
T Consensus       325 ILmSATl~~dv~~l~~~~~~p~~I~I~grt~~pV~~~yi~~~~~~~~~~~y~~----~~k~~~l~~L~~~~~~~~g~iLV  400 (675)
T PHA02653        325 FLMTATLEDDRDRIKEFFPNPAFVHIPGGTLFPISEVYVKNKYNPKNKRAYIE----EEKKNIVTALKKYTPPKGSSGIV  400 (675)
T ss_pred             EEEccCCcHhHHHHHHHhcCCcEEEeCCCcCCCeEEEEeecCcccccchhhhH----HHHHHHHHHHHHhhcccCCcEEE
Confidence            9999999                   455  7888888765321     1110    001112222322   34689999


Q ss_pred             EcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCC-CCCceEEEEeCCCCccCCCCCCeeEEEeCCCC
Q psy6094         192 FLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTP-PEGVRKIVLATNIAETSITIDDIVYVVDCGKT  270 (455)
Q Consensus       192 Flp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~-~~g~~kVivaTniae~gitI~~V~~VID~g~~  270 (455)
                      ||||+.+++.+++.|.+..    +++.+.+|||++++.++  +++.+ ++|+++|||||||||||||||||++|||+|++
T Consensus       401 Flpg~~ei~~l~~~L~~~~----~~~~v~~LHG~Lsq~eq--~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~  474 (675)
T PHA02653        401 FVASVSQCEEYKKYLEKRL----PIYDFYIIHGKVPNIDE--ILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRV  474 (675)
T ss_pred             EECcHHHHHHHHHHHHhhc----CCceEEeccCCcCHHHH--HHHHHhccCceeEEeccChhhccccccCeeEEEECCCc
Confidence            9999999999999998752    24889999999998643  33343 67999999999999999999999999999988


Q ss_pred             cccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhhhccCCCCcccccC----hHHHHHHHh-------
Q psy6094         271 KMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVLNMLKDPELEGVN----NDVIFSLLQ-------  339 (455)
Q Consensus       271 k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~~~~~~~PEi~r~~----~~~~L~~l~-------  339 (455)
                      |.+.  +..|+    ..|+|+++|.||+|||||+++|.||+||+++.+    .| |.|.+    .+++|.+.+       
T Consensus       475 k~p~--~~~g~----~~~iSkasa~QRaGRAGR~~~G~c~rLyt~~~~----~p-I~ri~~~~L~~~vL~lk~~g~~~~~  543 (675)
T PHA02653        475 YVPE--PFGGK----EMFISKSMRTQRKGRVGRVSPGTYVYFYDLDLL----KP-IKRIDSEFLHNYILYAKYFNLTLPE  543 (675)
T ss_pred             cCCC--cccCc----ccccCHHHHHHhccCcCCCCCCeEEEEECHHHh----HH-HHHHhHHHHHHHHHHHHHcCCCCcc
Confidence            7663  34443    469999999999999999999999999998875    24 66655    567775543       


Q ss_pred             -hhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChH--HHHHhhC
Q psy6094         340 -HICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCL--LYEFAMV  384 (455)
Q Consensus       340 -~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~l--G~~l~~l  384 (455)
                       .|++||+++++..|++.|..+||+|+  +|     |.|  |+.|+.+
T Consensus       544 ~~~ldpP~~~~l~~A~~~L~~lga~~~--~l-----~~l~~~~~~~~~  584 (675)
T PHA02653        544 DLFVIPSNLDRLRKTEEYIDSFNISIE--KW-----YEILSNYYVNML  584 (675)
T ss_pred             cccCCCCCHHHHHHHHHHHHHcCCCch--hh-----hhhhccccHHHH
Confidence             58999999999999999999998865  68     999  9999998

>KOG0921|consensus

Probab=100.00  E-value=1.7e-46  Score=390.71  Aligned_cols=401  Identities=25%  Similarity=0.385  Sum_probs=314.0

Q ss_pred             HHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh-----------------------
Q psy6094          39 RKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL-----------------------   94 (455)
Q Consensus        39 ~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~-----------------------   94 (455)
                      +......+...+++|..||+-.++.+|++++..|++++|.|+||||||||+. |||+                       
T Consensus       360 ~~~~d~e~~~~~a~re~lpva~~~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisa  439 (1282)
T KOG0921|consen  360 RFKRDEALDKITAQREELPVAQYRSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISA  439 (1282)
T ss_pred             hhhcccchhhhhhhhhhCcHHHHHHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccch
Confidence            3345678889999999999999999999999999999999999999999999 9998                       


Q ss_pred             ---------h----hcCCCCC-hHH------------------HHHhccCCCCcCc-------------chHHHHHHHHH
Q psy6094          95 ---------K----RSETQQY-PND------------------VLNMLKDPELEGV-------------NNDVIFSLLQH  129 (455)
Q Consensus        95 ---------e----~~~~vg~-p~~------------------ll~~l~d~~L~~~-------------~~D~ll~~lk~  129 (455)
                               +    .|+.+|| ||.                  +++++.+ .+...             .+|+++.+++.
T Consensus       440 isiaerva~er~e~~g~tvgy~vRf~Sa~prpyg~i~fctvgvllr~~e~-glrg~sh~i~deiherdv~~dfll~~lr~  518 (1282)
T KOG0921|consen  440 ISLAERVANERGEEVGETCGYNVRFDSATPRPYGSIMFCTVGVLLRMMEN-GLRGISHVIIDEIHERDVDTDFVLIVLRE  518 (1282)
T ss_pred             HHHHHHHHHhhHHhhcccccccccccccccccccceeeeccchhhhhhhh-cccccccccchhhhhhccchHHHHHHHHh
Confidence                     2    2444443 332                  5555511 11111             19999999999


Q ss_pred             HHHhcCCCCeEEEEccCC-----------------CCC-ccceEEeehhhhhhhhccCCC---------------CCh--
Q psy6094         130 ICTTQRPGAILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGA---------------NSP--  174 (455)
Q Consensus       130 il~~~~~~~k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~---------------~~~--  174 (455)
                      +. ..-++++++|||||+                 +|+ ||+..+|++++.+........               ..+  
T Consensus       519 m~-~ty~dl~v~lmsatIdTd~f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK  597 (1282)
T KOG0921|consen  519 MI-STYRDLRVVLMSATIDTDLFTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDK  597 (1282)
T ss_pred             hh-ccchhhhhhhhhcccchhhhhhhhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhc
Confidence            98 778899999999999                 788 999999988876432211100               000  


Q ss_pred             -HH----------------------------H----HHHHH-ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCC-CCCeEE
Q psy6094         175 -KR----------------------------W----VKLLR-SMLVVPILVFLPGWDTINSLHRSMCQSSFFN-SSRFQI  219 (455)
Q Consensus       175 -~~----------------------------l----~~~i~-~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~-~~~~~v  219 (455)
                       +.                            +    ..++. ...+|.||||+|++++|..|+..|.....++ ...+.+
T Consensus       598 ~~n~n~~~dd~~~~~~~~am~~~se~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~i  677 (1282)
T KOG0921|consen  598 GRNMNILCDPSYNESTRTAMSRLSEKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEI  677 (1282)
T ss_pred             ccccccccChhhcchhhhhhhcchhhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhccc
Confidence             00                            1    11111 1568999999999999999999998876653 557899


Q ss_pred             EeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhc
Q psy6094         220 IPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRG  299 (455)
Q Consensus       220 ~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~G  299 (455)
                      +|+|+.++.++|.+||++.+.|.+|+|++||+||++|||++++||||.++.+.+.|-..+++..+.++|.||-+..||+|
T Consensus       678 lp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~g  757 (1282)
T KOG0921|consen  678 LPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKG  757 (1282)
T ss_pred             ccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCeEEecCCh---hhhccCCCCcccccC-hHHHH-----------HHHhhhcCCCChhhHHhHHhhhhhccccc
Q psy6094         300 RAGRTLKRSETQQYPN---DVLNMLKDPELEGVN-NDVIF-----------SLLQHICTTQRPGAILVFLPGWDTINSLH  364 (455)
Q Consensus       300 RaGR~~~G~c~~L~t~---~~~~~~~~PEi~r~~-~~~~L-----------~~l~~~~~~P~~~~i~~al~~L~~lgald  364 (455)
                      |+||+++|.||++.+.   +.++++..|||.|.+ .++.|           .|+...+.||+..++..+-..|..++++|
T Consensus       758 r~grvR~G~~f~lcs~arF~~l~~~~t~em~r~plhemalTikll~l~SI~~fl~kal~~~p~dav~e~e~~l~~m~~ld  837 (1282)
T KOG0921|consen  758 RAGRVRPGFCFHLCSRARFEALEDHGTAEMFRTPLHEIALTIKLLRLGSIGEFLGKALQPPPYDAVIEAEAVLREMGALD  837 (1282)
T ss_pred             cCceecccccccccHHHHHHHHHhcCcHhhhcCccHHHHhhHHHHHhhhHHHHHhhccCCCchhhccCchHHHHHhhhhh
Confidence            9999999999999994   445677788888888 66655           56668999999999999999999999999


Q ss_pred             CCCCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhcCcCCcChH----HHHHHHHhhhC--CCCcH
Q psy6094         365 RSMCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLSFECKPSTA----KIIKELRARLD--MLLAH  423 (455)
Q Consensus       365 ~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~lsf~~p~~~~----~~~~~~~~~~~--~~sD~  423 (455)
                      .++.+     |+||+.++.+|+.|               +-|...|+..+|..|+...    ......++.|+  ..|||
T Consensus       838 ~n~el-----t~lg~~la~l~iep~~~k~~~lg~~~g~~~~m~~~as~~s~~~~~~~~~~~~~rl~g~q~~~~g~kfsdh  912 (1282)
T KOG0921|consen  838 ANDEL-----TPLGRMLARLPIEPRIGKMMILGTALGAGSVMCDVASAMSFPTPFVPREKHHSRLSGTQRKFAGNKFSDH  912 (1282)
T ss_pred             ccCcc-----cchhhhhhhccCcccccceeeechhhccchhhhhhhcccccccccccccccccccccchhhccccccccc
Confidence            99999     99999999999999               4455566666655443321    12222344454  44555


Q ss_pred             HHHH-----HHHHHHhcCCCCchHhHHHhh
Q psy6094         424 KLSH-----PGTTAWGDPNEGNILHCCSGF  448 (455)
Q Consensus       424 ~~~~-----~~~~~~~~~~~~~~~~~c~~~  448 (455)
                      .+..     ..++.|..+-.  -++||..|
T Consensus       913 va~~~v~q~~r~~~q~ga~~--e~efc~r~  940 (1282)
T KOG0921|consen  913 VAIVSVIQGYREAVQMGAAA--EREFCERY  940 (1282)
T ss_pred             hhhhhhhhhhHHHhhhhhhh--hhhHhHhh
Confidence            5554     44555544421  13666654

>KOG0330|consensus

Probab=100.00  E-value=8.6e-36  Score=288.42  Aligned_cols=264  Identities=18%  Similarity=0.207  Sum_probs=210.9

Q ss_pred             HHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchh---hhhh-----------
Q psy6094          31 AAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLD---FITL-----------   94 (455)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp---~ll~-----------   94 (455)
                      ..-+.+|.+...++..-+..+.-+..-...+|.+.|+.+.+|+++|+.|+||||||  +++|   .+++           
T Consensus        57 ~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLt  136 (476)
T KOG0330|consen   57 DESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLT  136 (476)
T ss_pred             hhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEec
Confidence            44566888999999999999988888888999999999999999999999999999  3444   2332           


Q ss_pred             --------------hhcCC----------------------------CCChHHHHHhcc-CC--CCcCcc------hHHH
Q psy6094          95 --------------KRSET----------------------------QQYPNDVLNMLK-DP--ELEGVN------NDVI  123 (455)
Q Consensus        95 --------------e~~~~----------------------------vg~p~~ll~~l~-d~--~L~~~~------~D~l  123 (455)
                                    ..|..                            |++|++|.++|. ..  .|...+      +|.+
T Consensus       137 PtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrl  216 (476)
T KOG0330|consen  137 PTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRL  216 (476)
T ss_pred             CcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhh
Confidence                          11111                            225777888772 22  222322      7777


Q ss_pred             HHH-----HHHHHHhcCCCCeEEEEccCCCCC----------ccceEE----e--ehhhhhhhhccCCCCChHHHHHHHH
Q psy6094         124 FSL-----LQHICTTQRPGAILVYCTYTFMGV----------SPMKVF----F--CKNVLQRLMKGVGANSPKRWVKLLR  182 (455)
Q Consensus       124 l~~-----lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~----~--l~~~~~~~~~~~~~~~~~~l~~~i~  182 (455)
                      |.+     |..+++..+.+.|.+||||||+..          -|+++.    |  ++...+.|+......++..|+.++.
T Consensus       217 Ld~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~  296 (476)
T KOG0330|consen  217 LDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLVYLLN  296 (476)
T ss_pred             hhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchhHHHHHH
Confidence            743     677776788999999999999321          233222    2  4455567777777777778999998


Q ss_pred             ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee
Q psy6094         183 SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       183 ~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~  262 (455)
                      ...+++++|||+++...+.++-.|+..+      +.+++|||+|++..|...|+.|++|.+.|+||||||+||+|||.|+
T Consensus       297 e~~g~s~iVF~~t~~tt~~la~~L~~lg------~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd  370 (476)
T KOG0330|consen  297 ELAGNSVIVFCNTCNTTRFLALLLRNLG------FQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVD  370 (476)
T ss_pred             hhcCCcEEEEEeccchHHHHHHHHHhcC------cceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCce
Confidence            8888999999999999999999999885      8999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhhh
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDVL  318 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~~  318 (455)
                      +|||        ||.          |.+-..|+||+||+||+|. |.++.|.|+.+.
T Consensus       371 ~VVN--------yDi----------P~~skDYIHRvGRtaRaGrsG~~ItlVtqyDv  409 (476)
T KOG0330|consen  371 VVVN--------YDI----------PTHSKDYIHRVGRTARAGRSGKAITLVTQYDV  409 (476)
T ss_pred             EEEe--------cCC----------CCcHHHHHHHcccccccCCCcceEEEEehhhh
Confidence            9999        553          3344568899999999998 999999996544

>KOG0331|consensus

Probab=100.00  E-value=4.7e-35  Score=299.44  Aligned_cols=257  Identities=18%  Similarity=0.251  Sum_probs=203.7

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchh---hhhh----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLD---FITL----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp---~ll~----------------   94 (455)
                      .|....+++....++..++.--.+++|.+.++.+..|+++|.+|.||||||  +++|   .+..                
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            678888999999999999999999999999999999999999999999999  4566   2221                


Q ss_pred             -----------------------------------------hhcC--CCCChHHHHHhc--cCCCCcCcc------hHHH
Q psy6094          95 -----------------------------------------KRSE--TQQYPNDVLNML--KDPELEGVN------NDVI  123 (455)
Q Consensus        95 -----------------------------------------e~~~--~vg~p~~ll~~l--~d~~L~~~~------~D~l  123 (455)
                                                               ++|.  .+|+|++|+++|  ..-.|..++      +|.|
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrM  251 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRM  251 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhh
Confidence                                                     1222  133688899988  566777777      9999


Q ss_pred             HHH-----HHHHHHhc-CCCCeEEEEccCCCCC-ccceEEeehhhhhhhhcc-----------------CCCCChHHHHH
Q psy6094         124 FSL-----LQHICTTQ-RPGAILVYCTYTFMGV-SPMKVFFCKNVLQRLMKG-----------------VGANSPKRWVK  179 (455)
Q Consensus       124 l~~-----lk~il~~~-~~~~k~ilmSAT~~g~-~pv~~~~l~~~~~~~~~~-----------------~~~~~~~~l~~  179 (455)
                      |++     ++.++... +++.|++++|||+|+. +.+...|+.++.+..+..                 ....+...+..
T Consensus       252 ldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~  331 (519)
T KOG0331|consen  252 LDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGK  331 (519)
T ss_pred             hccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHH
Confidence            965     88888777 6777899999999877 666555555443211100                 00001111223


Q ss_pred             HHH---ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         180 LLR---SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       180 ~i~---~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      .+.   ...+|.+||||.++..++++.+.|+..+      +.+.+|||+++|.+|..+++.|++|+..|+||||||+|||
T Consensus       332 lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~------~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGL  405 (519)
T KOG0331|consen  332 LLEDISSDSEGKVIIFCETKRTCDELARNLRRKG------WPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGL  405 (519)
T ss_pred             HHHHHhccCCCcEEEEecchhhHHHHHHHHHhcC------cceeeecccccHHHHHHHHHhcccCCcceEEEcccccccC
Confidence            332   3578899999999999999999999864      7899999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |||||++|||        ||++.++          +.|.||.||+||.+. |.+|.+|+.+
T Consensus       406 Di~dV~lVIn--------ydfP~~v----------EdYVHRiGRTGRa~~~G~A~tfft~~  448 (519)
T KOG0331|consen  406 DVPDVDLVIN--------YDFPNNV----------EDYVHRIGRTGRAGKKGTAITFFTSD  448 (519)
T ss_pred             CCccccEEEe--------CCCCCCH----------HHHHhhcCccccCCCCceEEEEEeHH
Confidence            9999999999        7666554          456699999999776 9999999954

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.97  E-value=2.1e-31  Score=279.03  Aligned_cols=257  Identities=14%  Similarity=0.147  Sum_probs=188.0

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|....+++...+.++.-+.-..+++|.++++.+.++++++++|+||||||+.+. .++.                    
T Consensus         5 ~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreL   84 (460)
T PRK11776          5 AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTREL   84 (460)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHH
Confidence            3666678888888888888888999999999999999999999999999995532 2222                    


Q ss_pred             ---------hh-----cC------------------------CCCChHHHHHhc--cCCCCcCcc------hHHHH----
Q psy6094          95 ---------KR-----SE------------------------TQQYPNDVLNML--KDPELEGVN------NDVIF----  124 (455)
Q Consensus        95 ---------e~-----~~------------------------~vg~p~~ll~~l--~d~~L~~~~------~D~ll----  124 (455)
                               ..     +.                        .||+|.++++++  ....+.+++      +|.++    
T Consensus        85 a~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g~  164 (460)
T PRK11776         85 ADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGF  164 (460)
T ss_pred             HHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcCc
Confidence                     00     00                        112455566666  223344554      66655    


Q ss_pred             -HHHHHHHHhcCCCCeEEEEccCCCCC----------ccceEEeehh-----hhhhhhccCCCCChHHHHHHHHccCCCC
Q psy6094         125 -SLLQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFCKN-----VLQRLMKGVGANSPKRWVKLLRSMLVVP  188 (455)
Q Consensus       125 -~~lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l~~-----~~~~~~~~~~~~~~~~l~~~i~~~~~g~  188 (455)
                       ..++.++...+++.|+++||||++..          .|........     +.+.+.......+...+...+....++.
T Consensus       165 ~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~  244 (460)
T PRK11776        165 QDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVSPDERLPALQRLLLHHQPES  244 (460)
T ss_pred             HHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCCCCCCeeEEEEEeCcHHHHHHHHHHHHhcCCCc
Confidence             23666776677889999999999432          1221111000     0011111111112223455555566788


Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCC
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCG  268 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g  268 (455)
                      +||||+++.+++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|||||+|++|||++
T Consensus       245 ~lVF~~t~~~~~~l~~~L~~~~------~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d  318 (460)
T PRK11776        245 CVVFCNTKKECQEVADALNAQG------FSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYE  318 (460)
T ss_pred             eEEEECCHHHHHHHHHHHHhCC------CcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEec
Confidence            9999999999999999998874      7899999999999999999999999999999999999999999999999966


Q ss_pred             CCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         269 KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       269 ~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ++                  -+..+|.||+|||||.+. |.||.|++.+
T Consensus       319 ~p------------------~~~~~yiqR~GRtGR~g~~G~ai~l~~~~  349 (460)
T PRK11776        319 LA------------------RDPEVHVHRIGRTGRAGSKGLALSLVAPE  349 (460)
T ss_pred             CC------------------CCHhHhhhhcccccCCCCcceEEEEEchh
Confidence            53                  345678899999999887 9999999954

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

Probab=99.97  E-value=1.2e-31  Score=282.80  Aligned_cols=257  Identities=18%  Similarity=0.252  Sum_probs=195.8

Q ss_pred             HHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh---hhh--h-------------
Q psy6094          35 KEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD---FIT--L-------------   94 (455)
Q Consensus        35 ~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp---~ll--~-------------   94 (455)
                      ..|.+..+++...+.+...+..-..++|.+.++.+..|++++++|+||||||.+  +|   .+.  .             
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            457777799999999999999999999999999999999999999999999933  44   221  1             


Q ss_pred             ---------------------------------------hhc--CCCCChHHHHHhc--cCCCCcCcc------hHHHHH
Q psy6094          95 ---------------------------------------KRS--ETQQYPNDVLNML--KDPELEGVN------NDVIFS  125 (455)
Q Consensus        95 ---------------------------------------e~~--~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~  125 (455)
                                                             +.|  ..||+|+||++++  ..-.+.++.      +|.||+
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd  188 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLD  188 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhc
Confidence                                                   111  1133677888888  333455555      888885


Q ss_pred             H-----HHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhh-----------------hhhhhccCCCC-ChHHHHHHH
Q psy6094         126 L-----LQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNV-----------------LQRLMKGVGAN-SPKRWVKLL  181 (455)
Q Consensus       126 ~-----lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~-----------------~~~~~~~~~~~-~~~~l~~~i  181 (455)
                      +     +..++...+++.|+++||||++.. -.....|+.++                 .+.|+...... +...+...+
T Consensus       189 ~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll  268 (513)
T COG0513         189 MGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLL  268 (513)
T ss_pred             CCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHH
Confidence            4     666776677899999999999442 11111222211                 12222222222 233355555


Q ss_pred             HccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCe
Q psy6094         182 RSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDI  261 (455)
Q Consensus       182 ~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V  261 (455)
                      .....+.+|||++++..++.++..|...+      +.+..|||+|+|++|.++++.|++|..+|+||||||+||||||+|
T Consensus       269 ~~~~~~~~IVF~~tk~~~~~l~~~l~~~g------~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v  342 (513)
T COG0513         269 KDEDEGRVIVFVRTKRLVEELAESLRKRG------FKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDV  342 (513)
T ss_pred             hcCCCCeEEEEeCcHHHHHHHHHHHHHCC------CeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCcccc
Confidence            55666789999999999999999999875      899999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      .+|||        ||.+.          +...|.||+||+||.|. |.++.|++.
T Consensus       343 ~~Vin--------yD~p~----------~~e~yvHRiGRTgRaG~~G~ai~fv~~  379 (513)
T COG0513         343 SHVIN--------YDLPL----------DPEDYVHRIGRTGRAGRKGVAISFVTE  379 (513)
T ss_pred             ceeEE--------ccCCC----------CHHHheeccCccccCCCCCeEEEEeCc
Confidence            99999        55443          34556699999999988 999999984

>KOG0328|consensus

Probab=99.97  E-value=8.5e-31  Score=244.28  Aligned_cols=279  Identities=16%  Similarity=0.262  Sum_probs=198.1

Q ss_pred             CCCCCccccchhhhccc-cCCcchHHHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCc
Q psy6094           7 PKGLTHSVTSWETRQKL-LNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGP   85 (455)
Q Consensus         7 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGK   85 (455)
                      -....|+...+++..++ ....++++.|.++..+...+-.|.         .....|...+..|..|++||++++.|+||
T Consensus         7 ~~~~~~~~~~feTs~~~~v~~~F~~Mgl~edlLrgiY~yGfe---------kPS~IQqrAi~~IlkGrdViaQaqSGTGK   77 (400)
T KOG0328|consen    7 FTMEDMDTVEFETSEKVKVIPTFDDMGLKEDLLRGIYAYGFE---------KPSAIQQRAIPQILKGRDVIAQAQSGTGK   77 (400)
T ss_pred             cccccccceeEeeccCcccccchhhcCchHHHHHHHHHhccC---------CchHHHhhhhhhhhcccceEEEecCCCCc
Confidence            33445666667776655 344556666666666655444333         33455667777788999999999999999


Q ss_pred             ccchh-hhhh------------------------------------------hhcCC---------------CCChHHHH
Q psy6094          86 PLHLD-FITL------------------------------------------KRSET---------------QQYPNDVL  107 (455)
Q Consensus        86 Ttqlp-~ll~------------------------------------------e~~~~---------------vg~p~~ll  107 (455)
                      |..+. -+|.                                          -.|..               .|+|++++
T Consensus        78 Ta~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~  157 (400)
T KOG0328|consen   78 TATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVL  157 (400)
T ss_pred             eEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHH
Confidence            95554 3332                                          01122               22588888


Q ss_pred             HhccCCCC--cCcc------hHHHHHH-----HHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhhhhhhccCCCCC
Q psy6094         108 NMLKDPEL--EGVN------NDVIFSL-----LQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVLQRLMKGVGANS  173 (455)
Q Consensus       108 ~~l~d~~L--~~~~------~D~ll~~-----lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~~~~~~~~~~~~  173 (455)
                      +++.-..|  ..+.      +|.||.-     +-++.+..+|+.|++++|||+|.. .....+|+.+++..+++...-..
T Consensus       158 dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltl  237 (400)
T KOG0328|consen  158 DMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTL  237 (400)
T ss_pred             HHHHhccccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCch
Confidence            87722222  2222      8888843     455665678999999999999665 55555555555544333222111


Q ss_pred             ------------hHH----HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcC
Q psy6094         174 ------------PKR----WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNT  237 (455)
Q Consensus       174 ------------~~~----l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~  237 (455)
                                  ++.    |.++.....-.+.++||+|++.+++|.+.|+..      +|.|.++||+|++++|.+++..
T Consensus       238 EgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm~~~------nftVssmHGDm~qkERd~im~d  311 (400)
T KOG0328|consen  238 EGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA------NFTVSSMHGDMEQKERDKIMND  311 (400)
T ss_pred             hhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHHHhh------CceeeeccCCcchhHHHHHHHH
Confidence                        111    222222244568999999999999999999986      4999999999999999999999


Q ss_pred             CCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         238 PPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       238 ~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+.|+.+|+++|||-+||+|++.|..|||        ||.          |..+..|.||.||+||.|. |.++.+...+
T Consensus       312 FRsg~SrvLitTDVwaRGiDv~qVslviN--------YDL----------P~nre~YIHRIGRSGRFGRkGvainFVk~~  373 (400)
T KOG0328|consen  312 FRSGKSRVLITTDVWARGIDVQQVSLVIN--------YDL----------PNNRELYIHRIGRSGRFGRKGVAINFVKSD  373 (400)
T ss_pred             hhcCCceEEEEechhhccCCcceeEEEEe--------cCC----------CccHHHHhhhhccccccCCcceEEEEecHH
Confidence            99999999999999999999999999999        553          3445778899999999988 9999999865


Q ss_pred             hh
Q psy6094         317 VL  318 (455)
Q Consensus       317 ~~  318 (455)
                      ++
T Consensus       374 d~  375 (400)
T KOG0328|consen  374 DL  375 (400)
T ss_pred             HH
Confidence            43

>PRK01172 ski2-like helicase; Provisional

Probab=99.97  E-value=6.8e-30  Score=279.21  Aligned_cols=342  Identities=13%  Similarity=0.104  Sum_probs=212.7

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITLK--------------------   95 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~e--------------------   95 (455)
                      |.+..+.+.+.+.++.+.. ..|++|.++++.+.++++++++||||||||++.. .++..                    
T Consensus         3 ~~~~~l~~~~~~~~~~~~~-~l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~~k~v~i~P~raLa~q~   81 (674)
T PRK01172          3 ISDLGYDDEFLNLFTGNDF-ELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEK   81 (674)
T ss_pred             HhhcCCCHHHHHHHhhCCC-CCCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhCCcEEEEechHHHHHHH
Confidence            4455677888888877665 4799999999999999999999999999997654 33320                    


Q ss_pred             ---------hcCCCC---------------------ChHHHHHhc-cCC-CCcCcc------hHH---------HHHHHH
Q psy6094          96 ---------RSETQQ---------------------YPNDVLNML-KDP-ELEGVN------NDV---------IFSLLQ  128 (455)
Q Consensus        96 ---------~~~~vg---------------------~p~~ll~~l-~d~-~L~~~~------~D~---------ll~~lk  128 (455)
                               .|..++                     +|.++...+ .++ .+.+++      .+.         +-.++.
T Consensus        82 ~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le~ll~  161 (674)
T PRK01172         82 YEELSRLRSLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLS  161 (674)
T ss_pred             HHHHHHHhhcCCeEEEEeCCCCCChhhhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHHHHHH
Confidence                     011111                     122211111 111 122222      121         112233


Q ss_pred             HHHHhcCCCCeEEEEccCCCC-----------------C-ccceEE--eehhhhhhhhccCCCCChHHHHHHHHc--cCC
Q psy6094         129 HICTTQRPGAILVYCTYTFMG-----------------V-SPMKVF--FCKNVLQRLMKGVGANSPKRWVKLLRS--MLV  186 (455)
Q Consensus       129 ~il~~~~~~~k~ilmSAT~~g-----------------~-~pv~~~--~l~~~~~~~~~~~~~~~~~~l~~~i~~--~~~  186 (455)
                      .+. ..+++.|+|+||||++.                 + .|+...  |.+..   +....... ...+...+..  ..+
T Consensus       162 ~~~-~~~~~~riI~lSATl~n~~~la~wl~~~~~~~~~r~vpl~~~i~~~~~~---~~~~~~~~-~~~~~~~i~~~~~~~  236 (674)
T PRK01172        162 SAR-YVNPDARILALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRL---ILDGYERS-QVDINSLIKETVNDG  236 (674)
T ss_pred             HHH-hcCcCCcEEEEeCccCCHHHHHHHhCCCccCCCCCCCCeEEEEEecCee---eecccccc-cccHHHHHHHHHhCC
Confidence            322 45678999999999831                 2 232211  11110   00000000 0012222221  467


Q ss_pred             CCEEEEcCCHHHHHHHHHHHHhcCCCCC-------------------CCeEEEeecCCCChhhHhhhhcCCCCCceEEEE
Q psy6094         187 VPILVFLPGWDTINSLHRSMCQSSFFNS-------------------SRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL  247 (455)
Q Consensus       187 g~iLVFlp~~~ei~~l~~~L~~~~~~~~-------------------~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViv  247 (455)
                      +++||||+++++++.+++.|........                   -..-+..+||+|++++|..+++.|++|..+|||
T Consensus       237 ~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLv  316 (674)
T PRK01172        237 GQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIV  316 (674)
T ss_pred             CcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEE
Confidence            8999999999999999998876421000                   012377889999999999999999999999999


Q ss_pred             eCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCC-hhh------
Q psy6094         248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYP-NDV------  317 (455)
Q Consensus       248 aTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t-~~~------  317 (455)
                      ||+++++|+|+|+..+||+ +.   ..|+.      ....++|.+++.||+|||||.+   .|.++.+.. .+.      
T Consensus       317 aT~~la~Gvnipa~~VII~-~~---~~~~~------~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~~~~~~~  386 (674)
T PRK01172        317 ATPTLAAGVNLPARLVIVR-DI---TRYGN------GGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKK  386 (674)
T ss_pred             ecchhhccCCCcceEEEEc-Cc---eEeCC------CCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcccHHHHHH
Confidence            9999999999999887775 22   12321      1235799999999999999987   476666533 221      


Q ss_pred             -hccCCCC--------cccccC--hHHHH----------HHHh-hhc--CCC-C--hhhHHhHHhhhhhcccccCCCCCC
Q psy6094         318 -LNMLKDP--------ELEGVN--NDVIF----------SLLQ-HIC--TTQ-R--PGAILVFLPGWDTINSLHRSMCQS  370 (455)
Q Consensus       318 -~~~~~~P--------Ei~r~~--~~~~L----------~~l~-~~~--~~P-~--~~~i~~al~~L~~lgald~~~~l~  370 (455)
                       +...+.|        ++.+.+  ..+..          .|+. .|+  ..+ +  .+.++.+++.|.+.|+|+.++.  
T Consensus       387 ~l~~~~~pi~S~l~~~~~~~~~~l~~i~~g~~~~~~d~~~~l~~tf~~~~~~~~~l~~~v~~~l~~L~~~~~i~~~~~--  464 (674)
T PRK01172        387 YLSGEPEPVISYMGSQRKVRFNTLAAISMGLASSMEDLILFYNETLMAIQNGVDEIDYYIESSLKFLKENGFIKGDVT--  464 (674)
T ss_pred             HHcCCCCceeecCCCcccHHHHHHHHHHhcccCCHHHHHHHHHhhhhHhcCchHHHHHHHHHHHHHHHHCCCcccCCc--
Confidence             2122222        233332  11111          2221 122  222 2  4678999999999999986543  


Q ss_pred             cccCChHHHHHhhCCCChhHHHHHHHh
Q psy6094         371 SFFNSCLLYEFAMVDNKPKEIITVRDC  397 (455)
Q Consensus       371 ~~~~T~lG~~l~~lp~~p~~~l~iaa~  397 (455)
                       +.+|++|+.++.+|++|+.+..+...
T Consensus       465 -~~~t~lG~~~s~~~l~~~t~~~~~~~  490 (674)
T PRK01172        465 -LRATRLGKLTSDLYIDPESALILKSA  490 (674)
T ss_pred             -EeECHHHHHHHHhCCCHHHHHHHHHH
Confidence             35599999999999999555544433

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.97  E-value=1.7e-30  Score=279.42  Aligned_cols=255  Identities=15%  Similarity=0.153  Sum_probs=191.0

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------   94 (455)
                      |.+..+++...+.++..+....+++|.++++.+.+++++|++|+||||||.++. .+++                     
T Consensus         8 f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa   87 (629)
T PRK11634          8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELA   87 (629)
T ss_pred             HhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHH
Confidence            667778888899999999999999999999999999999999999999996543 2221                     


Q ss_pred             --------hh-----c------------------------CCCCChHHHHHhc--cCCCCcCcc------hHHHHH----
Q psy6094          95 --------KR-----S------------------------ETQQYPNDVLNML--KDPELEGVN------NDVIFS----  125 (455)
Q Consensus        95 --------e~-----~------------------------~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~----  125 (455)
                              ..     +                        ..||+|.++++++  ....+.++.      +|.++.    
T Consensus        88 ~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~gf~  167 (629)
T PRK11634         88 VQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFI  167 (629)
T ss_pred             HHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcccH
Confidence                    00     0                        1123566677766  223345544      666553    


Q ss_pred             -HHHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhh---------------hhhhccCCCCChHHHHHHHHccCCCC
Q psy6094         126 -LLQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVL---------------QRLMKGVGANSPKRWVKLLRSMLVVP  188 (455)
Q Consensus       126 -~lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~---------------~~~~~~~~~~~~~~l~~~i~~~~~g~  188 (455)
                       .+..++...+++.|+++||||+|.. ..+...|+.++.               +.|+......+...+..++.......
T Consensus       168 ~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~~~~~  247 (629)
T PRK11634        168 EDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDA  247 (629)
T ss_pred             HHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHHHHHHHhcCCCC
Confidence             2455565667889999999999654 222222222111               11111111122233556666566788


Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCC
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCG  268 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g  268 (455)
                      +||||+++..++.+++.|...+      +.+..+||++++.+|.++++.|++|+.+||||||++++|||||+|++|||++
T Consensus       248 ~IVF~~tk~~a~~l~~~L~~~g------~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d  321 (629)
T PRK11634        248 AIIFVRTKNATLEVAEALERNG------YNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYD  321 (629)
T ss_pred             EEEEeccHHHHHHHHHHHHhCC------CCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeC
Confidence            9999999999999999999864      7899999999999999999999999999999999999999999999999944


Q ss_pred             CCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         269 KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       269 ~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      +                  |.+.++|.||+|||||.+. |.|+.+++.
T Consensus       322 ~------------------P~~~e~yvqRiGRtGRaGr~G~ai~~v~~  351 (629)
T PRK11634        322 I------------------PMDSESYVHRIGRTGRAGRAGRALLFVEN  351 (629)
T ss_pred             C------------------CCCHHHHHHHhccccCCCCcceEEEEech
Confidence            3                  3456788999999999987 999999984

>PTZ00110 helicase; Provisional

Probab=99.97  E-value=3.5e-30  Score=274.01  Aligned_cols=257  Identities=18%  Similarity=0.198  Sum_probs=188.2

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFIT--------------------   93 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll--------------------   93 (455)
                      .|.+..+.+.+.+.+...+....+++|.+.++.+.+++++|++|+||||||.+  +|.+.                    
T Consensus       131 ~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~  210 (545)
T PTZ00110        131 SFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLA  210 (545)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEEC
Confidence            46667788888888998899999999999999999999999999999999953  45111                    


Q ss_pred             h-------------hh----------------------------cCCCCChHHHHHhc--cCCCCcCcc------hHHHH
Q psy6094          94 L-------------KR----------------------------SETQQYPNDVLNML--KDPELEGVN------NDVIF  124 (455)
Q Consensus        94 ~-------------e~----------------------------~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll  124 (455)
                      +             ..                            ...|++|.+|++.|  ....|..++      +|.++
T Consensus       211 PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~ml  290 (545)
T PTZ00110        211 PTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRML  290 (545)
T ss_pred             ChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhh
Confidence            0             00                            01122566677766  223455555      77766


Q ss_pred             HH-----HHHHHHhcCCCCeEEEEccCCCCC-----------ccceEEe--eh-----hhhhhhhccCCCCChHHHHHHH
Q psy6094         125 SL-----LQHICTTQRPGAILVYCTYTFMGV-----------SPMKVFF--CK-----NVLQRLMKGVGANSPKRWVKLL  181 (455)
Q Consensus       125 ~~-----lk~il~~~~~~~k~ilmSAT~~g~-----------~pv~~~~--l~-----~~~~~~~~~~~~~~~~~l~~~i  181 (455)
                      ..     ++.++...+++.|+++||||++..           .|+....  .+     .+.+.+.......+...+...+
T Consensus       291 d~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll  370 (545)
T PTZ00110        291 DMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLL  370 (545)
T ss_pred             hcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHH
Confidence            43     677776778999999999998432           1211110  00     0000000001111122244444


Q ss_pred             Hc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         182 RS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       182 ~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      ..  ...+.+||||++++.++.+++.|...+      +.+..+||++++++|..+++.|++|..+||||||++++|||||
T Consensus       371 ~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g------~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~  444 (545)
T PTZ00110        371 QRIMRDGDKILIFVETKKGADFLTKELRLDG------WPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVK  444 (545)
T ss_pred             HHhcccCCeEEEEecChHHHHHHHHHHHHcC------CcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcc
Confidence            43  257899999999999999999998754      7789999999999999999999999999999999999999999


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|++||++++                  |-+.++|.||+||+||.+. |.||.+++.+
T Consensus       445 ~v~~VI~~d~------------------P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~  484 (545)
T PTZ00110        445 DVKYVINFDF------------------PNQIEDYVHRIGRTGRAGAKGASYTFLTPD  484 (545)
T ss_pred             cCCEEEEeCC------------------CCCHHHHHHHhcccccCCCCceEEEEECcc
Confidence            9999999554                  3456778999999999877 9999999954

>KOG0340|consensus

Probab=99.97  E-value=7e-30  Score=244.89  Aligned_cols=259  Identities=16%  Similarity=0.148  Sum_probs=188.0

Q ss_pred             HHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhhhh-----------------
Q psy6094          35 KEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITLKR-----------------   96 (455)
Q Consensus        35 ~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~e~-----------------   96 (455)
                      +.|+...+++-..+-+++-+.--..++|...++.|.+|++.|..|.||||||+++. .+++..                 
T Consensus         7 ~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrE   86 (442)
T KOG0340|consen    7 KPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRE   86 (442)
T ss_pred             CchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHH
Confidence            34666667776666666666666777899999999999999999999999998877 666511                 


Q ss_pred             ------------cCCC--------C--------------------ChHHHHHhc-cCCCCcCcc-----------hHHHH
Q psy6094          97 ------------SETQ--------Q--------------------YPNDVLNML-KDPELEGVN-----------NDVIF  124 (455)
Q Consensus        97 ------------~~~v--------g--------------------~p~~ll~~l-~d~~L~~~~-----------~D~ll  124 (455)
                                  |...        |                    +|+++..++ +++.-....           +|.+|
T Consensus        87 LA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL  166 (442)
T KOG0340|consen   87 LALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVL  166 (442)
T ss_pred             HHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhh
Confidence                        1111        1                    233344444 332111111           77777


Q ss_pred             -----HHHHHHHHhcCCCCeEEEEccCCC-----CC-ccceE--Ee-ehh---------hhhhhhccCCCCChHHHHHHH
Q psy6094         125 -----SLLQHICTTQRPGAILVYCTYTFM-----GV-SPMKV--FF-CKN---------VLQRLMKGVGANSPKRWVKLL  181 (455)
Q Consensus       125 -----~~lk~il~~~~~~~k~ilmSAT~~-----g~-~pv~~--~~-l~~---------~~~~~~~~~~~~~~~~l~~~i  181 (455)
                           ..|+.+.+..++..|.++||||+.     -. +|+..  .| ++.         ..+.|+......++..++..+
T Consensus       167 ~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~~L  246 (442)
T KOG0340|consen  167 AGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYLVHLL  246 (442)
T ss_pred             ccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHHHHHH
Confidence                 346666655666789999999991     11 33332  12 111         113344444333444455555


Q ss_pred             Hc---cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         182 RS---MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       182 ~~---~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                      ..   ...+++++|+++..+++.+...|+..      ++.+..|||.|+|++|...+.+|+.+..+|++|||||+||+||
T Consensus       247 r~~~~~~~~simIFvnttr~cQ~l~~~l~~l------e~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDI  320 (442)
T KOG0340|consen  247 RDFENKENGSIMIFVNTTRECQLLSMTLKNL------EVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDI  320 (442)
T ss_pred             hhhhhccCceEEEEeehhHHHHHHHHHHhhh------ceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCC
Confidence            44   36899999999999999999999987      4999999999999999999999999999999999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      |.|..|||..+|+.+                  ..|.||.||+.|+|. |.++.++++.+
T Consensus       321 P~V~LVvN~diPr~P------------------~~yiHRvGRtARAGR~G~aiSivt~rD  362 (442)
T KOG0340|consen  321 PTVELVVNHDIPRDP------------------KDYIHRVGRTARAGRKGMAISIVTQRD  362 (442)
T ss_pred             CceeEEEecCCCCCH------------------HHHHHhhcchhcccCCcceEEEechhh
Confidence            999999996665443                  246799999999998 99999998653

>KOG0345|consensus

Probab=99.96  E-value=6.8e-30  Score=252.64  Aligned_cols=267  Identities=17%  Similarity=0.239  Sum_probs=197.3

Q ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------------
Q psy6094          42 QSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------------   94 (455)
Q Consensus        42 ~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------------   94 (455)
                      +++...+.+..-+.--..++|...++.+.++++|++.++||||||.++- .+++                          
T Consensus        13 L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa   92 (567)
T KOG0345|consen   13 LSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELA   92 (567)
T ss_pred             ccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHH
Confidence            4567777777777777888999999999999999999999999994322 2222                          


Q ss_pred             -------------------------------------hh-cCCCCChHHHHHhc-c-CCCCc--Ccc------hHHHHHH
Q psy6094          95 -------------------------------------KR-SETQQYPNDVLNML-K-DPELE--GVN------NDVIFSL  126 (455)
Q Consensus        95 -------------------------------------e~-~~~vg~p~~ll~~l-~-d~~L~--~~~------~D~ll~~  126 (455)
                                                           +. ..-||+|+||++++ . -..++  +.+      +|.|+++
T Consensus        93 ~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldm  172 (567)
T KOG0345|consen   93 RQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDM  172 (567)
T ss_pred             HHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhcc
Confidence                                                 11 12355788888877 3 22333  222      8999865


Q ss_pred             -----HHHHHHhcCCCCeEEEEccCC---------CCC-ccceEEeehhh-------hh-hhhccCCCCChHHHHHHHHc
Q psy6094         127 -----LQHICTTQRPGAILVYCTYTF---------MGV-SPMKVFFCKNV-------LQ-RLMKGVGANSPKRWVKLLRS  183 (455)
Q Consensus       127 -----lk~il~~~~~~~k~ilmSAT~---------~g~-~pv~~~~l~~~-------~~-~~~~~~~~~~~~~l~~~i~~  183 (455)
                           +..|+...++..+.=|||||.         .|- .||.+..-..-       +. .|+.+....+-..++..+++
T Consensus       173 gFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~  252 (567)
T KOG0345|consen  173 GFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNN  252 (567)
T ss_pred             cHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhc
Confidence                 777887788899999999999         344 56553332111       11 12222222223346677777


Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ...+.++||+||+..++.....+...-    ....++++||.|.+..|.++++.|.+....|++|||||+||||||||++
T Consensus       253 ~~~kK~iVFF~TCasVeYf~~~~~~~l----~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~  328 (567)
T KOG0345|consen  253 NKDKKCIVFFPTCASVEYFGKLFSRLL----KKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDL  328 (567)
T ss_pred             cccccEEEEecCcchHHHHHHHHHHHh----CCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceE
Confidence            788999999999999999998888652    2588999999999999999999999988999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC--hhh----hccCCCCcccccC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP--NDV----LNMLKDPELEGVN  330 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t--~~~----~~~~~~PEi~r~~  330 (455)
                      ||.        |||+...+          ++.||+||+||.|. |.++.+..  ++.    |.-...|++.+..
T Consensus       329 VvQ--------~DpP~~~~----------~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl~i~~~v~le~~~  384 (567)
T KOG0345|consen  329 VVQ--------FDPPKDPS----------SFVHRCGRTARAGREGNAIVFLNPREEAYVEFLRIKGKVELERID  384 (567)
T ss_pred             EEe--------cCCCCChh----------HHHhhcchhhhccCccceEEEecccHHHHHHHHHhcCccchhhhc
Confidence            998        77766644          45699999999888 88877766  222    3334567776655

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=1.6e-29  Score=262.03  Aligned_cols=257  Identities=12%  Similarity=0.098  Sum_probs=181.6

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh---hhh-----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD---FIT-----------------   93 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp---~ll-----------------   93 (455)
                      .|++..+++...+.+...+.....++|.++++.+.++++++++|+||||||..  +|   .++                 
T Consensus         9 ~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~li   88 (423)
T PRK04837          9 KFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALI   88 (423)
T ss_pred             CHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEE
Confidence            46677788888888888888888999999999999999999999999999943  22   111                 


Q ss_pred             --h-------------hh----c------------------------CCCCChHHHHHhc--cCCCCcCcc------hHH
Q psy6094          94 --L-------------KR----S------------------------ETQQYPNDVLNML--KDPELEGVN------NDV  122 (455)
Q Consensus        94 --~-------------e~----~------------------------~~vg~p~~ll~~l--~d~~L~~~~------~D~  122 (455)
                        +             ..    +                        .-||+|.+|++.+  ..-.+..++      +|.
T Consensus        89 l~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~  168 (423)
T PRK04837         89 MAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADR  168 (423)
T ss_pred             ECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHH
Confidence              1             00    0                        1122455566665  223344444      666


Q ss_pred             HHH-----HHHHHHHhcC--CCCeEEEEccCCCCC-c---------cceEEeehhh------hhhhhccCCCCChHHHHH
Q psy6094         123 IFS-----LLQHICTTQR--PGAILVYCTYTFMGV-S---------PMKVFFCKNV------LQRLMKGVGANSPKRWVK  179 (455)
Q Consensus       123 ll~-----~lk~il~~~~--~~~k~ilmSAT~~g~-~---------pv~~~~l~~~------~~~~~~~~~~~~~~~l~~  179 (455)
                      ++.     .++.++...+  ...+.++||||++.. .         |.........      .+.+.......+...+..
T Consensus       169 l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l~~  248 (423)
T PRK04837        169 MFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQT  248 (423)
T ss_pred             HhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHHHH
Confidence            653     2445553333  245678999999432 1         1111110000      000000001111112444


Q ss_pred             HHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         180 LLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       180 ~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      .+.....+.+||||+++..++.+++.|...+      +.+..+||++++++|..+++.|++|..+||||||++++|||||
T Consensus       249 ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g------~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip  322 (423)
T PRK04837        249 LIEEEWPDRAIIFANTKHRCEEIWGHLAADG------HRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIP  322 (423)
T ss_pred             HHHhcCCCeEEEEECCHHHHHHHHHHHHhCC------CcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCcc
Confidence            4554567889999999999999999998764      7899999999999999999999999999999999999999999


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|++||++++                  |.|.++|.||+|||||.|. |.|+.|++++
T Consensus       323 ~v~~VI~~d~------------------P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~  362 (423)
T PRK04837        323 AVTHVFNYDL------------------PDDCEDYVHRIGRTGRAGASGHSISLACEE  362 (423)
T ss_pred             ccCEEEEeCC------------------CCchhheEeccccccCCCCCeeEEEEeCHH
Confidence            9999999444                  3355677899999999987 9999999954

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.96  E-value=2.6e-29  Score=262.77  Aligned_cols=256  Identities=14%  Similarity=0.146  Sum_probs=182.9

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh---hhhh-----------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD---FITL-----------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp---~ll~-----------------   94 (455)
                      |++..+++...+.+...+.--.+++|.++++.+.+++++|++|+||||||..  +|   .+..                 
T Consensus         3 f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~   82 (456)
T PRK10590          3 FDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILT   82 (456)
T ss_pred             HHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEe
Confidence            5677788888888988888899999999999999999999999999999943  33   1110                 


Q ss_pred             ---hh---------------------------------------cCCCCChHHHHHhc--cCCCCcCcc------hHHHH
Q psy6094          95 ---KR---------------------------------------SETQQYPNDVLNML--KDPELEGVN------NDVIF  124 (455)
Q Consensus        95 ---e~---------------------------------------~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll  124 (455)
                         ++                                       ...|++|.+|++.+  ....+..++      +|.++
T Consensus        83 PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll  162 (456)
T PRK10590         83 PTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRML  162 (456)
T ss_pred             CcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHh
Confidence               00                                       00122455555554  222344444      66655


Q ss_pred             H-----HHHHHHHhcCCCCeEEEEccCCCCC----------ccceEEeeh------hhhhhhhccCCCCChHHHHHHHHc
Q psy6094         125 S-----LLQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFCK------NVLQRLMKGVGANSPKRWVKLLRS  183 (455)
Q Consensus       125 ~-----~lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l~------~~~~~~~~~~~~~~~~~l~~~i~~  183 (455)
                      .     .++.++...+++.|+++||||++..          .|.......      .+.+.+.......+...+...+..
T Consensus       163 ~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~l~~~  242 (456)
T PRK10590        163 DMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGK  242 (456)
T ss_pred             ccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHHHHHc
Confidence            3     3566665667888999999999431          111111000      000000000001111223344444


Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      .....+||||+++.+++.+++.|...+      +.+..+||++++++|.++++.|++|..+|||||+++++|||||+|++
T Consensus       243 ~~~~~~lVF~~t~~~~~~l~~~L~~~g------~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~  316 (456)
T PRK10590        243 GNWQQVLVFTRTKHGANHLAEQLNKDG------IRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPH  316 (456)
T ss_pred             CCCCcEEEEcCcHHHHHHHHHHHHHCC------CCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCE
Confidence            556789999999999999999998764      78999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||++++                  |.+..+|.||+|||||.+. |.|+.|++.+
T Consensus       317 VI~~~~------------------P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~  352 (456)
T PRK10590        317 VVNYEL------------------PNVPEDYVHRIGRTGRAAATGEALSLVCVD  352 (456)
T ss_pred             EEEeCC------------------CCCHHHhhhhccccccCCCCeeEEEEecHH
Confidence            999554                  3455678899999999887 9999999854

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

Probab=99.96  E-value=2.2e-29  Score=266.85  Aligned_cols=257  Identities=13%  Similarity=0.142  Sum_probs=182.4

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc--chhhh---hh----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPL--HLDFI---TL----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt--qlp~l---l~----------------   94 (455)
                      .|.+..+++...+.+...+..-.+++|.+.++++.+|++++++|+||||||.  .+|.+   +.                
T Consensus       122 ~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLI  201 (518)
T PLN00206        122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMV  201 (518)
T ss_pred             CHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEE
Confidence            5677778999999998888988999999999999999999999999999993  34411   10                


Q ss_pred             -----h-----------hc----------------------------CCCCChHHHHHhc--cCCCCcCcc------hHH
Q psy6094          95 -----K-----------RS----------------------------ETQQYPNDVLNML--KDPELEGVN------NDV  122 (455)
Q Consensus        95 -----e-----------~~----------------------------~~vg~p~~ll~~l--~d~~L~~~~------~D~  122 (455)
                           +           .+                            ..|++|.+|++.+  ....+..+.      +|.
T Consensus       202 L~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~  281 (518)
T PLN00206        202 LTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDC  281 (518)
T ss_pred             EeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHH
Confidence                 0           00                            0012455566665  333444444      666


Q ss_pred             HHH-----HHHHHHHhcCCCCeEEEEccCCCCC-c---------cceEEeeh--h----hhhhhhccCCCCChHHHHHHH
Q psy6094         123 IFS-----LLQHICTTQRPGAILVYCTYTFMGV-S---------PMKVFFCK--N----VLQRLMKGVGANSPKRWVKLL  181 (455)
Q Consensus       123 ll~-----~lk~il~~~~~~~k~ilmSAT~~g~-~---------pv~~~~l~--~----~~~~~~~~~~~~~~~~l~~~i  181 (455)
                      +++     .+..++ ..-++.|+++||||++.. .         ++....-.  .    +.+.+.......+...+...+
T Consensus       282 ml~~gf~~~i~~i~-~~l~~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l  360 (518)
T PLN00206        282 MLERGFRDQVMQIF-QALSQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDIL  360 (518)
T ss_pred             HhhcchHHHHHHHH-HhCCCCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHH
Confidence            653     244555 334678999999999422 1         11100000  0    000000001111112244444


Q ss_pred             Hc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         182 RS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       182 ~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      ..  ...+++|||++++..++.+++.|....     .+.+..+||++++++|..+++.|+.|..+|||||+++++|||||
T Consensus       361 ~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~-----g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip  435 (518)
T PLN00206        361 KSKQHFKPPAVVFVSSRLGADLLANAITVVT-----GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLL  435 (518)
T ss_pred             HhhcccCCCEEEEcCCchhHHHHHHHHhhcc-----CcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcc
Confidence            32  234689999999999999999997642     47899999999999999999999999999999999999999999


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|++||++++                  |.|..+|.||+|||||.+. |.|+.+++.+
T Consensus       436 ~v~~VI~~d~------------------P~s~~~yihRiGRaGR~g~~G~ai~f~~~~  475 (518)
T PLN00206        436 RVRQVIIFDM------------------PNTIKEYIHQIGRASRMGEKGTAIVFVNEE  475 (518)
T ss_pred             cCCEEEEeCC------------------CCCHHHHHHhccccccCCCCeEEEEEEchh
Confidence            9999999543                  4567889999999999986 9999999854

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=3.7e-29  Score=263.00  Aligned_cols=257  Identities=16%  Similarity=0.164  Sum_probs=183.8

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhh---hhh----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDF---ITL----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~---ll~----------------   94 (455)
                      .|....+++...+.+...+..-.+++|.++++.+.+|+++|++++||||||..  +|.   ++.                
T Consensus        88 ~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLi  167 (475)
T PRK01297         88 RFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALI  167 (475)
T ss_pred             CHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEE
Confidence            46777889999999999999999999999999999999999999999999933  331   110                


Q ss_pred             ----------------hh----c-------------------------CCCCChHHHHHhc--cCCCCcCcc------hH
Q psy6094          95 ----------------KR----S-------------------------ETQQYPNDVLNML--KDPELEGVN------ND  121 (455)
Q Consensus        95 ----------------e~----~-------------------------~~vg~p~~ll~~l--~d~~L~~~~------~D  121 (455)
                                      +.    +                         ..+++|.+|++.+  ....+.+++      .|
T Consensus       168 l~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah  247 (475)
T PRK01297        168 IAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEAD  247 (475)
T ss_pred             EeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHH
Confidence                            00    0                         0011344455444  233444444      55


Q ss_pred             HHHH-----HHHHHHHhc--CCCCeEEEEccCCCCC-c---------cceEEeeh------hhhhhhhccCCCCChHHHH
Q psy6094         122 VIFS-----LLQHICTTQ--RPGAILVYCTYTFMGV-S---------PMKVFFCK------NVLQRLMKGVGANSPKRWV  178 (455)
Q Consensus       122 ~ll~-----~lk~il~~~--~~~~k~ilmSAT~~g~-~---------pv~~~~l~------~~~~~~~~~~~~~~~~~l~  178 (455)
                      .+++     .++.++...  ..+.|++++|||++.. .         |+......      .+.+.+.......+...+.
T Consensus       248 ~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~l~  327 (475)
T PRK01297        248 RMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLY  327 (475)
T ss_pred             HHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchhHHHHHH
Confidence            5553     255565333  2367999999998432 1         11110000      0000011111111122244


Q ss_pred             HHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         179 KLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       179 ~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                      ..+.....+.+||||+++.+++.+++.|...+      +.+..+||++++++|.++++.|++|..+||||||++++||||
T Consensus       328 ~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~------~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi  401 (475)
T PRK01297        328 NLVTQNPWERVMVFANRKDEVRRIEERLVKDG------INAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHI  401 (475)
T ss_pred             HHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcC------CCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcc
Confidence            45554556789999999999999999998764      678999999999999999999999999999999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+|++||++|+                  |.|.++|.||+|||||.+. |.++.+++++
T Consensus       402 ~~v~~VI~~~~------------------P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~  442 (475)
T PRK01297        402 DGISHVINFTL------------------PEDPDDYVHRIGRTGRAGASGVSISFAGED  442 (475)
T ss_pred             cCCCEEEEeCC------------------CCCHHHHHHhhCccCCCCCCceEEEEecHH
Confidence            99999999664                  4577899999999999887 9999999965

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.96  E-value=4.7e-29  Score=259.44  Aligned_cols=257  Identities=16%  Similarity=0.184  Sum_probs=184.8

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh---hhhh----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD---FITL----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp---~ll~----------------   94 (455)
                      .|++..+++...+.++..+....+++|.+.++++.++++++++|+||||||..  +|   .+++                
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~P   81 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTP   81 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECC
Confidence            36777788999999999999999999999999999999999999999999954  33   1111                


Q ss_pred             -------------hh----------------------------cCCCCChHHHHHhc-cC-CCCcCcc------hHHHH-
Q psy6094          95 -------------KR----------------------------SETQQYPNDVLNML-KD-PELEGVN------NDVIF-  124 (455)
Q Consensus        95 -------------e~----------------------------~~~vg~p~~ll~~l-~d-~~L~~~~------~D~ll-  124 (455)
                                   ..                            ...|++|.+|++.+ .. -.+..+.      +|.++ 
T Consensus        82 t~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~  161 (434)
T PRK11192         82 TRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLD  161 (434)
T ss_pred             cHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhC
Confidence                         00                            01122455566665 22 1234444      56555 


Q ss_pred             ----HHHHHHHHhcCCCCeEEEEccCCCCC-----------ccceEEeehh------hhhhhhccCC-CCChHHHHHHHH
Q psy6094         125 ----SLLQHICTTQRPGAILVYCTYTFMGV-----------SPMKVFFCKN------VLQRLMKGVG-ANSPKRWVKLLR  182 (455)
Q Consensus       125 ----~~lk~il~~~~~~~k~ilmSAT~~g~-----------~pv~~~~l~~------~~~~~~~~~~-~~~~~~l~~~i~  182 (455)
                          ..+..+....+...|+++||||+++.           .|+.......      +.+.+..... ..+...+...+.
T Consensus       162 ~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~  241 (434)
T PRK11192        162 MGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLK  241 (434)
T ss_pred             CCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHh
Confidence                23555554566778999999999532           1221111100      0000000100 111122344444


Q ss_pred             ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee
Q psy6094         183 SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       183 ~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~  262 (455)
                      ....+.+||||+++++++.+++.|...+      +.+..+||++++.+|..+++.|++|..+||||||++++|||||+|+
T Consensus       242 ~~~~~~~lVF~~s~~~~~~l~~~L~~~~------~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~  315 (434)
T PRK11192        242 QPEVTRSIVFVRTRERVHELAGWLRKAG------INCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVS  315 (434)
T ss_pred             cCCCCeEEEEeCChHHHHHHHHHHHhCC------CCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCC
Confidence            3467899999999999999999998753      7899999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +||++++                  |.|...|.||+||+||.|. |.|+.+++..
T Consensus       316 ~VI~~d~------------------p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~  352 (434)
T PRK11192        316 HVINFDM------------------PRSADTYLHRIGRTGRAGRKGTAISLVEAH  352 (434)
T ss_pred             EEEEECC------------------CCCHHHHhhcccccccCCCCceEEEEecHH
Confidence            9999554                  3466788999999999876 9999999844

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=2.1e-29  Score=259.35  Aligned_cols=263  Identities=11%  Similarity=0.141  Sum_probs=185.0

Q ss_pred             HHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------
Q psy6094          31 AAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------   94 (455)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------   94 (455)
                      ..+...|.+...++...+.+...+..-.+++|.++++.+.++++++++|+||||||.... .++.               
T Consensus        24 ~~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~  103 (401)
T PTZ00424         24 DEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILA  103 (401)
T ss_pred             ccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEEC
Confidence            335667888888888888888778888899999999999999999999999999995422 1111               


Q ss_pred             --------------hhc----------------------------CCCCChHHHHHhc-c-CCCCcCcc------hHHHH
Q psy6094          95 --------------KRS----------------------------ETQQYPNDVLNML-K-DPELEGVN------NDVIF  124 (455)
Q Consensus        95 --------------e~~----------------------------~~vg~p~~ll~~l-~-d~~L~~~~------~D~ll  124 (455)
                                    ..+                            ..+|+|..+.+.+ . ...+..++      .|.++
T Consensus       104 Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~  183 (401)
T PTZ00424        104 PTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEML  183 (401)
T ss_pred             CCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHH
Confidence                          000                            0112344455444 2 22344444      45444


Q ss_pred             -----HHHHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhh---------------hhhhccCC-CCChHHHHHHHH
Q psy6094         125 -----SLLQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVL---------------QRLMKGVG-ANSPKRWVKLLR  182 (455)
Q Consensus       125 -----~~lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~---------------~~~~~~~~-~~~~~~l~~~i~  182 (455)
                           ..+..++....++.|++++|||++.. ......|+.++.               +.+..... ......+...+.
T Consensus       184 ~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  263 (401)
T PTZ00424        184 SRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYE  263 (401)
T ss_pred             hcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHH
Confidence                 23455555667889999999999542 111111111000               00000000 001111333343


Q ss_pred             ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee
Q psy6094         183 SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       183 ~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~  262 (455)
                      ......+||||++++.++.+++.|...+      +.+..+||++++++|..+++.|++|+.+|||||+++++|||||+++
T Consensus       264 ~~~~~~~ivF~~t~~~~~~l~~~l~~~~------~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~  337 (401)
T PTZ00424        264 TLTITQAIIYCNTRRKVDYLTKKMHERD------FTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVS  337 (401)
T ss_pred             hcCCCeEEEEecCcHHHHHHHHHHHHCC------CcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCC
Confidence            3456789999999999999999998763      7899999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      +||+.+.                  |.|..+|.||+|||||.+. |.||.|++.+.
T Consensus       338 ~VI~~~~------------------p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~  375 (401)
T PTZ00424        338 LVINYDL------------------PASPENYIHRIGRSGRFGRKGVAINFVTPDD  375 (401)
T ss_pred             EEEEECC------------------CCCHHHEeecccccccCCCCceEEEEEcHHH
Confidence            9998553                  4577788899999999876 99999999553

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=6.5e-29  Score=265.38  Aligned_cols=256  Identities=14%  Similarity=0.142  Sum_probs=181.7

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh---hhh------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD---FIT------------------   93 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp---~ll------------------   93 (455)
                      |.++.+++.+.+.++.-+..-.+++|.+.|+.+.+++++|++|+||||||..  +|   .++                  
T Consensus        11 f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl   90 (572)
T PRK04537         11 FSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALIL   90 (572)
T ss_pred             hhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEE
Confidence            5666788888888888888889999999999999999999999999999943  33   111                  


Q ss_pred             -h-------------hhc----------------------------CCCCChHHHHHhc-cCC--CCcCcc------hHH
Q psy6094          94 -L-------------KRS----------------------------ETQQYPNDVLNML-KDP--ELEGVN------NDV  122 (455)
Q Consensus        94 -~-------------e~~----------------------------~~vg~p~~ll~~l-~d~--~L~~~~------~D~  122 (455)
                       +             ..+                            ..|++|.+|++.+ ...  .+..++      +|.
T Consensus        91 ~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~  170 (572)
T PRK04537         91 APTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADR  170 (572)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHH
Confidence             0             000                            1122455566655 221  233333      565


Q ss_pred             HHH-----HHHHHHHhcCC--CCeEEEEccCCCCC-ccceEEeehhh---------------hhhhhccCCCCChHHHHH
Q psy6094         123 IFS-----LLQHICTTQRP--GAILVYCTYTFMGV-SPMKVFFCKNV---------------LQRLMKGVGANSPKRWVK  179 (455)
Q Consensus       123 ll~-----~lk~il~~~~~--~~k~ilmSAT~~g~-~pv~~~~l~~~---------------~~~~~~~~~~~~~~~l~~  179 (455)
                      ++.     .++.++...+.  +.|+++||||++.. ......++.++               .+.+.......+...+..
T Consensus       171 lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~~~L~~  250 (572)
T PRK04537        171 MFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLG  250 (572)
T ss_pred             HhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHHHHHHHHH
Confidence            553     23444433333  68999999999442 11111111110               000111111111122444


Q ss_pred             HHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         180 LLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       180 ~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      ++....+..+||||+++..++.+++.|...+      +.+..+||++++.+|.++++.|++|..+||||||++++|||||
T Consensus       251 ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g------~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip  324 (572)
T PRK04537        251 LLSRSEGARTMVFVNTKAFVERVARTLERHG------YRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHID  324 (572)
T ss_pred             HHhcccCCcEEEEeCCHHHHHHHHHHHHHcC------CCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCcc
Confidence            5554567899999999999999999998764      7899999999999999999999999999999999999999999


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|++||++++                  |.|..+|.||+||+||.+. |.|+.|++..
T Consensus       325 ~V~~VInyd~------------------P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~  364 (572)
T PRK04537        325 GVKYVYNYDL------------------PFDAEDYVHRIGRTARLGEEGDAISFACER  364 (572)
T ss_pred             CCCEEEEcCC------------------CCCHHHHhhhhcccccCCCCceEEEEecHH
Confidence            9999999543                  4566788999999999887 9999999854

>PRK02362 ski2-like helicase; Provisional

Probab=99.96  E-value=3e-28  Score=268.36  Aligned_cols=345  Identities=13%  Similarity=0.082  Sum_probs=217.8

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHH-HHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDM-VRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~-i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      |++..+.+...+.+..++.--.|++|.++++. +.+++++++++|||||||...- .++.                    
T Consensus         3 ~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raLa~q   82 (737)
T PRK02362          3 IAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALASE   82 (737)
T ss_pred             hhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHH
Confidence            44555778888888888888899999999988 8899999999999999995532 2221                    


Q ss_pred             ------hh---cCCCC---------------------ChHHHHHhc--cCCCCcCcc------hHHH---------HHHH
Q psy6094          95 ------KR---SETQQ---------------------YPNDVLNML--KDPELEGVN------NDVI---------FSLL  127 (455)
Q Consensus        95 ------e~---~~~vg---------------------~p~~ll~~l--~d~~L~~~~------~D~l---------l~~l  127 (455)
                            +.   |..++                     +|.++...+  ....+..++      .|.+         -.++
T Consensus        83 ~~~~~~~~~~~g~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~le~il  162 (737)
T PRK02362         83 KFEEFERFEELGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTLEVTL  162 (737)
T ss_pred             HHHHHHHhhcCCCEEEEEeCCcCccccccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHHHHHH
Confidence                  00   11111                     233322222  111222233      2211         1223


Q ss_pred             HHHHHhcCCCCeEEEEccCCCC----------C------ccce--E--Eeehhhh--hhhhccCCCCChHHHHHHHHc--
Q psy6094         128 QHICTTQRPGAILVYCTYTFMG----------V------SPMK--V--FFCKNVL--QRLMKGVGANSPKRWVKLLRS--  183 (455)
Q Consensus       128 k~il~~~~~~~k~ilmSAT~~g----------~------~pv~--~--~~l~~~~--~~~~~~~~~~~~~~l~~~i~~--  183 (455)
                      .++. ...++.|+|+||||++.          .      -|+.  .  ++-+...  ........... ......+..  
T Consensus       163 ~rl~-~~~~~~qii~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  240 (737)
T PRK02362        163 AKLR-RLNPDLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSK-DDTLNLVLDTL  240 (737)
T ss_pred             HHHH-hcCCCCcEEEEcccCCCHHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccc-hHHHHHHHHHH
Confidence            3333 45678999999999832          1      1221  1  1111100  00000000111 111111211  


Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCC--------------------CCC----------CeEEEeecCCCChhhHhh
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFF--------------------NSS----------RFQIIPLHSMLPTVSQKS  233 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--------------------~~~----------~~~v~~lhs~l~~~~r~~  233 (455)
                      ..++++||||+++.+++.+++.|......                    ...          ..-+..+||+|++.+|..
T Consensus       241 ~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~  320 (737)
T PRK02362        241 EEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHREL  320 (737)
T ss_pred             HcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHH
Confidence            46789999999999999999888754210                    000          135788999999999999


Q ss_pred             hhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEE
Q psy6094         234 IFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSET  310 (455)
Q Consensus       234 v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~  310 (455)
                      +++.|++|..+||+||+++++|||+|++++||+.    ...||+..|.     .|+|.+++.||+|||||.+.   |.|+
T Consensus       321 ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~----~~~yd~~~g~-----~~~s~~~y~Qm~GRAGR~g~d~~G~~i  391 (737)
T PRK02362        321 VEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRD----YRRYDGGAGM-----QPIPVLEYHQMAGRAGRPGLDPYGEAV  391 (737)
T ss_pred             HHHHHHcCCCeEEEechhhhhhcCCCceEEEEec----ceeecCCCCc-----eeCCHHHHHHHhhcCCCCCCCCCceEE
Confidence            9999999999999999999999999999999974    2357765442     58999999999999999764   9999


Q ss_pred             ecCChh-----hhccC--CCCcccccC-------hHHHH---------------HHHh-hhcCCC------ChhhHHhHH
Q psy6094         311 QQYPND-----VLNML--KDPELEGVN-------NDVIF---------------SLLQ-HICTTQ------RPGAILVFL  354 (455)
Q Consensus       311 ~L~t~~-----~~~~~--~~PEi~r~~-------~~~~L---------------~~l~-~~~~~P------~~~~i~~al  354 (455)
                      -+....     .+..+  ..||-..+.       .+.++               .|+. .|...+      -.+.++.++
T Consensus       392 i~~~~~~~~~~~~~~~l~~~~~~i~S~l~~~~~l~~~lla~I~~~~~~~~~d~~~~l~~Tf~~~~~~~~~~l~~~v~~~l  471 (737)
T PRK02362        392 LLAKSYDELDELFERYIWADPEDVRSKLATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQTDDTGRLERVVDDVL  471 (737)
T ss_pred             EEecCchhHHHHHHHHHhCCCCceeecCCChhhHHHHHHHHHHhCccCCHHHHHHHHHhChHHhhccchHHHHHHHHHHH
Confidence            988631     12211  122222211       11122               1221 122222      134588999


Q ss_pred             hhhhhcccccCCCCCCcccCChHHHHHhhCCCChhHHHHH
Q psy6094         355 PGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITV  394 (455)
Q Consensus       355 ~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p~~~l~i  394 (455)
                      +.|.+.|+|+.++..  +.+|++|+.++.++++|..+..+
T Consensus       472 ~~L~~~~~i~~~~~~--~~~t~lG~~~s~~~l~~~t~~~~  509 (737)
T PRK02362        472 DFLERNGMIEEDGET--LEATELGHLVSRLYIDPLSAAEI  509 (737)
T ss_pred             HHHHHCCCeeecCCe--EeEChHHHHHHHhcCCHHHHHHH
Confidence            999999999977642  56799999999999999444433

>KOG0333|consensus

Probab=99.96  E-value=3e-29  Score=250.65  Aligned_cols=257  Identities=16%  Similarity=0.205  Sum_probs=182.9

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|++..+..+..+++..=+..-..++|.+.++....++++|..++||||||.+++ .|+.                    
T Consensus       246 nwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpya  325 (673)
T KOG0333|consen  246 NWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYA  325 (673)
T ss_pred             ChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCcee
Confidence            3555566778888888878877888899999999999999999999999996655 3322                    


Q ss_pred             --------------------------------------hhcC--------CCCChHHHHHhc--cCCCCcCcc------h
Q psy6094          95 --------------------------------------KRSE--------TQQYPNDVLNML--KDPELEGVN------N  120 (455)
Q Consensus        95 --------------------------------------e~~~--------~vg~p~~ll~~l--~d~~L~~~~------~  120 (455)
                                                            +.|.        .+++|++|++-|  .+-.|.+..      +
T Consensus       326 iilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldea  405 (673)
T KOG0333|consen  326 IILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEA  405 (673)
T ss_pred             eeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccch
Confidence                                                  1111        122577777665  333333333      5


Q ss_pred             HHHHHH-----HHHHHH-------------------------hcCCCCeEEEEccCCCCC-ccceEEeehhhhhh-----
Q psy6094         121 DVIFSL-----LQHICT-------------------------TQRPGAILVYCTYTFMGV-SPMKVFFCKNVLQR-----  164 (455)
Q Consensus       121 D~ll~~-----lk~il~-------------------------~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~~~-----  164 (455)
                      |.++++     +..++.                         ..+.-.|.+.||||+|-. -.+...|+.++.-.     
T Consensus       406 drmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~  485 (673)
T KOG0333|consen  406 DRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSA  485 (673)
T ss_pred             hhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccC
Confidence            555422     111111                         112237899999999432 22222222222111     


Q ss_pred             ----------hhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhh
Q psy6094         165 ----------LMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSI  234 (455)
Q Consensus       165 ----------~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v  234 (455)
                                +.......+...|...+......+|+||++++..++.+++.|.+.+      +.+..|||+-++++|..+
T Consensus       486 gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g------~~~~tlHg~k~qeQRe~a  559 (673)
T KOG0333|consen  486 GKPTPRVEQKVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAG------YKVTTLHGGKSQEQRENA  559 (673)
T ss_pred             CCCccchheEEEEecchHHHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhcc------ceEEEeeCCccHHHHHHH
Confidence                      0001111122236666665667899999999999999999999985      899999999999999999


Q ss_pred             hcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecC
Q psy6094         235 FNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQY  313 (455)
Q Consensus       235 ~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~  313 (455)
                      ++.|++|...|+||||||.||||||||.+|||+.+.                  -|-..|.||.||+||+|. |.++.+|
T Consensus       560 L~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydma------------------ksieDYtHRIGRTgRAGk~GtaiSfl  621 (673)
T KOG0333|consen  560 LADFREGTGDILVATDVAGRGIDIPNVSLVINYDMA------------------KSIEDYTHRIGRTGRAGKSGTAISFL  621 (673)
T ss_pred             HHHHHhcCCCEEEEecccccCCCCCccceeeecchh------------------hhHHHHHHHhccccccccCceeEEEe
Confidence            999999999999999999999999999999994443                  234567799999999998 9999999


Q ss_pred             Chh
Q psy6094         314 PND  316 (455)
Q Consensus       314 t~~  316 (455)
                      |.+
T Consensus       622 t~~  624 (673)
T KOG0333|consen  622 TPA  624 (673)
T ss_pred             ccc
Confidence            954

>KOG0342|consensus

Probab=99.96  E-value=1.3e-28  Score=245.06  Aligned_cols=260  Identities=14%  Similarity=0.136  Sum_probs=194.8

Q ss_pred             HHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchhhhhh----------------
Q psy6094          31 AAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITL----------------   94 (455)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp~ll~----------------   94 (455)
                      ......|....+|+...+.++.-+..-+.++|+..++.+..|+++++.|.||||||  ++|+++                
T Consensus        78 ~~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKT--lAFLiPaie~l~k~~~~~r~~~  155 (543)
T KOG0342|consen   78 ITTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKT--LAFLLPAIELLRKLKFKPRNGT  155 (543)
T ss_pred             hhhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCce--eeehhHHHHHHHhcccCCCCCe
Confidence            33455677888999999999999999999999999999999999999999999999  444443                


Q ss_pred             -----------------------hh------cCCCC--------------------ChHHHHHhc-cCCC-CcCc-c---
Q psy6094          95 -----------------------KR------SETQQ--------------------YPNDVLNML-KDPE-LEGV-N---  119 (455)
Q Consensus        95 -----------------------e~------~~~vg--------------------~p~~ll~~l-~d~~-L~~~-~---  119 (455)
                                             ..      +..+|                    +|+||+++| ..+. +... .   
T Consensus       156 ~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lv  235 (543)
T KOG0342|consen  156 GVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLV  235 (543)
T ss_pred             eEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeE
Confidence                                   00      01111                    588899999 4332 1111 1   


Q ss_pred             ---hHHHHHH-----HHHHHHhcCCCCeEEEEccCCCCC-ccc-------eEEeehh-----------hhhhhhccCCCC
Q psy6094         120 ---NDVIFSL-----LQHICTTQRPGAILVYCTYTFMGV-SPM-------KVFFCKN-----------VLQRLMKGVGAN  172 (455)
Q Consensus       120 ---~D~ll~~-----lk~il~~~~~~~k~ilmSAT~~g~-~pv-------~~~~l~~-----------~~~~~~~~~~~~  172 (455)
                         +|.+|++     ++.++...+...|..|||||++.. -.+       +..|++-           +.+.|+......
T Consensus       236 lDEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~  315 (543)
T KOG0342|consen  236 LDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDS  315 (543)
T ss_pred             eecchhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccc
Confidence               8999865     777776778899999999999321 000       1112110           112233222222


Q ss_pred             ChHHHHHHHHccCC-CCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         173 SPKRWVKLLRSMLV-VPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       173 ~~~~l~~~i~~~~~-g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      .-..+..++.+... ..|+|||+|+.-+..+++.|+..      ++.|.-+||+.+|..|..+|..|.+...-|+|||||
T Consensus       316 ~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~------dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDV  389 (543)
T KOG0342|consen  316 RFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYI------DLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDV  389 (543)
T ss_pred             hHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhc------CCchhhhhcCCcccccchHHHHHhhcccceEEecch
Confidence            22224455554333 78999999999999999999965      488999999999999999999999999999999999


Q ss_pred             CccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         252 AETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       252 ae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+||+|||+|+.||.        ||++.+          ..+|+||.||+||.|. |..+-+...+
T Consensus       390 aARGlD~P~V~~VvQ--------~~~P~d----------~~~YIHRvGRTaR~gk~G~alL~l~p~  437 (543)
T KOG0342|consen  390 AARGLDIPDVDWVVQ--------YDPPSD----------PEQYIHRVGRTAREGKEGKALLLLAPW  437 (543)
T ss_pred             hhccCCCCCceEEEE--------eCCCCC----------HHHHHHHhccccccCCCceEEEEeChh
Confidence            999999999999998        554443          4678899999999887 9999988844

>KOG0343|consensus

Probab=99.95  E-value=3.7e-28  Score=243.95  Aligned_cols=257  Identities=15%  Similarity=0.185  Sum_probs=204.7

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|.+.-++.+..+-|+.-+..-+..+|.+.|+.-..|++|+..|.||||||.++- .+++                    
T Consensus        70 kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISP  149 (758)
T KOG0343|consen   70 KFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISP  149 (758)
T ss_pred             hHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecc
Confidence            4566677888888888888888899999999999999999999999999994433 3333                    


Q ss_pred             ----------------------------------------hhcCCCCChHHHHHhc-cCCCCcCcc--------hHHHHH
Q psy6094          95 ----------------------------------------KRSETQQYPNDVLNML-KDPELEGVN--------NDVIFS  125 (455)
Q Consensus        95 ----------------------------------------e~~~~vg~p~~ll~~l-~d~~L~~~~--------~D~ll~  125 (455)
                                                              .++.-|++|+|||++| .+|.++.-+        +|.+|+
T Consensus       150 TRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LD  229 (758)
T KOG0343|consen  150 TRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLD  229 (758)
T ss_pred             hHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHH
Confidence                                                    1122233799999999 888776655        898886


Q ss_pred             H-----HHHHHHhcCCCCeEEEEccCCCC----------CccceEE-e-------ehhhhhhhhccCCCCChHHHHHHHH
Q psy6094         126 L-----LQHICTTQRPGAILVYCTYTFMG----------VSPMKVF-F-------CKNVLQRLMKGVGANSPKRWVKLLR  182 (455)
Q Consensus       126 ~-----lk~il~~~~~~~k~ilmSAT~~g----------~~pv~~~-~-------l~~~~~~~~~~~~~~~~~~l~~~i~  182 (455)
                      +     |..++...++..|.+|||||...          .-|+-+- +       .....+.|+......+.+.|..+|.
T Consensus       230 MGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~  309 (758)
T KOG0343|consen  230 MGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIK  309 (758)
T ss_pred             HhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHH
Confidence            5     77788788999999999999911          1122111 1       0112234444455555556777888


Q ss_pred             ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee
Q psy6094         183 SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       183 ~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~  262 (455)
                      ......+|||+.++.++..+++..+...    ++..++.|||.|+|..|..++..|-..+.-|++|||||+||+|.|.|+
T Consensus       310 shlk~K~iVF~SscKqvkf~~e~F~rlr----pg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVd  385 (758)
T KOG0343|consen  310 SHLKKKSIVFLSSCKQVKFLYEAFCRLR----PGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVD  385 (758)
T ss_pred             hccccceEEEEehhhHHHHHHHHHHhcC----CCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccc
Confidence            7888999999999999999999999864    368999999999999999999999888889999999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      +||.        ||          +|...++|+||+||+.|... |.|+.+.+
T Consensus       386 wViQ--------~D----------CPedv~tYIHRvGRtAR~~~~G~sll~L~  420 (758)
T KOG0343|consen  386 WVIQ--------VD----------CPEDVDTYIHRVGRTARYKERGESLLMLT  420 (758)
T ss_pred             eEEE--------ec----------CchhHHHHHHHhhhhhcccCCCceEEEEc
Confidence            9997        54          56667788999999999877 99998888

>KOG0338|consensus

Probab=99.95  E-value=3.1e-28  Score=242.60  Aligned_cols=267  Identities=13%  Similarity=0.159  Sum_probs=206.7

Q ss_pred             CcchHHHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh----------
Q psy6094          26 DPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL----------   94 (455)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~----------   94 (455)
                      ..+.+.+....|....+|.-..+.+..-+.--..++|.+.|+.-+-|++++.+|.||||||.++. .+|+          
T Consensus       172 g~s~~~~~~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~  251 (691)
T KOG0338|consen  172 GVSADTQMNESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVA  251 (691)
T ss_pred             hhhhhhHHhhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCc
Confidence            44455666778999999998888888888888888999999998999999999999999995544 4443          


Q ss_pred             ------------------------------hhcCCCC--------------------ChHHHHHhc-cCCC--CcCcc--
Q psy6094          95 ------------------------------KRSETQQ--------------------YPNDVLNML-KDPE--LEGVN--  119 (455)
Q Consensus        95 ------------------------------e~~~~vg--------------------~p~~ll~~l-~d~~--L~~~~--  119 (455)
                                                    ..|--||                    +|+|++++| ..|.  |+++.  
T Consensus       252 ~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVL  331 (691)
T KOG0338|consen  252 ATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVL  331 (691)
T ss_pred             ceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEE
Confidence                                          1111222                    688899999 5553  44443  


Q ss_pred             ----hHHHH-----HHHHHHHHhcCCCCeEEEEccCCC---------CC-ccceEEeehh------hhhhhhccCC---C
Q psy6094         120 ----NDVIF-----SLLQHICTTQRPGAILVYCTYTFM---------GV-SPMKVFFCKN------VLQRLMKGVG---A  171 (455)
Q Consensus       120 ----~D~ll-----~~lk~il~~~~~~~k~ilmSAT~~---------g~-~pv~~~~l~~------~~~~~~~~~~---~  171 (455)
                          +|.||     ..++.++...+++.|.+||||||.         .- .||.++.-+.      ..+.|+..+.   .
T Consensus       332 vlDEADRMLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~  411 (691)
T KOG0338|consen  332 VLDEADRMLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREG  411 (691)
T ss_pred             EechHHHHHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheecccccc
Confidence                88888     347888877789999999999991         12 5666544221      2344554331   1


Q ss_pred             CChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         172 NSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       172 ~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      ..+..+..+++..-...++||+.++..+.++.=+|--.+      +.+.-|||+|+|++|...++.|+++...|+||||+
T Consensus       412 dRea~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGLlg------l~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDv  485 (691)
T KOG0338|consen  412 DREAMLASLITRTFQDRTIVFVRTKKQAHRLRILLGLLG------LKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDV  485 (691)
T ss_pred             ccHHHHHHHHHHhcccceEEEEehHHHHHHHHHHHHHhh------chhhhhcccccHHHHHHHHHHHHhccCCEEEEech
Confidence            223335555555567889999999999999876665554      78889999999999999999999999999999999


Q ss_pred             CccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         252 AETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       252 ae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+||+||++|..|||+.                  .|.+...|.||+||+.|.|. |..+.|..+.
T Consensus       486 AsRGLDI~gV~tVINy~------------------mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~  533 (691)
T KOG0338|consen  486 ASRGLDIEGVQTVINYA------------------MPKTIEHYLHRVGRTARAGRAGRSVTLVGES  533 (691)
T ss_pred             hhccCCccceeEEEecc------------------CchhHHHHHHHhhhhhhcccCcceEEEeccc
Confidence            99999999999999944                  46677789999999999988 9999999854

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

Probab=99.94  E-value=6e-26  Score=248.65  Aligned_cols=253  Identities=15%  Similarity=0.103  Sum_probs=167.1

Q ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc--chh---hhhh----------------------
Q psy6094          42 QSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPL--HLD---FITL----------------------   94 (455)
Q Consensus        42 ~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt--qlp---~ll~----------------------   94 (455)
                      .++...+.++.++....|++|.+.++++.+|++++++++||||||.  ++|   .++.                      
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~  100 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRA  100 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHH
Confidence            5677788888888989999999999999999999999999999993  344   1111                      


Q ss_pred             --hhc---CCCC-----------------------ChHHHHHhc-cC-----CCCcCcc------hHH-----------H
Q psy6094          95 --KRS---ETQQ-----------------------YPNDVLNML-KD-----PELEGVN------NDV-----------I  123 (455)
Q Consensus        95 --e~~---~~vg-----------------------~p~~ll~~l-~d-----~~L~~~~------~D~-----------l  123 (455)
                        +.+   ..++                       +|..|...+ .+     ..+.+++      +|.           +
T Consensus       101 l~~l~~~~i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g~fg~~~~~i  180 (742)
T TIGR03817       101 VRELTLRGVRPATYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRGVFGSHVALV  180 (742)
T ss_pred             HHHhccCCeEEEEEeCCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccCccHHHHHHH
Confidence              111   0110                       122121111 00     0122222      232           2


Q ss_pred             HHHHHHHHHhcCCCCeEEEEccCCCCC---------ccceEEeehhh-h--hh--hhccC-----C-------CC----C
Q psy6094         124 FSLLQHICTTQRPGAILVYCTYTFMGV---------SPMKVFFCKNV-L--QR--LMKGV-----G-------AN----S  173 (455)
Q Consensus       124 l~~lk~il~~~~~~~k~ilmSAT~~g~---------~pv~~~~l~~~-~--~~--~~~~~-----~-------~~----~  173 (455)
                      +..|+++......++|+|++|||++..         .|+...--+.. .  ..  ++...     .       ..    .
T Consensus       181 l~rL~ri~~~~g~~~q~i~~SATi~n~~~~~~~l~g~~~~~i~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~  260 (742)
T TIGR03817       181 LRRLRRLCARYGASPVFVLASATTADPAAAASRLIGAPVVAVTEDGSPRGARTVALWEPPLTELTGENGAPVRRSASAEA  260 (742)
T ss_pred             HHHHHHHHHhcCCCCEEEEEecCCCCHHHHHHHHcCCCeEEECCCCCCcCceEEEEecCCccccccccccccccchHHHH
Confidence            233444443445788999999999321         12111000000 0  00  00000     0       00    0


Q ss_pred             hHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCC--CCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         174 PKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFF--NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       174 ~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      ...+...+  ..+..+||||++++.++.+++.|......  ......+..+||++++++|.++++.|++|+.+||||||+
T Consensus       261 ~~~l~~l~--~~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~  338 (742)
T TIGR03817       261 ADLLADLV--AEGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNA  338 (742)
T ss_pred             HHHHHHHH--HCCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECch
Confidence            01122223  34689999999999999999988753110  011357889999999999999999999999999999999


Q ss_pred             CccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         252 AETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       252 ae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      +|+||||++|++||++|+                  |-|.++|.||+|||||.+. |.++.+.+
T Consensus       339 lerGIDI~~vd~VI~~~~------------------P~s~~~y~qRiGRaGR~G~~g~ai~v~~  384 (742)
T TIGR03817       339 LELGVDISGLDAVVIAGF------------------PGTRASLWQQAGRAGRRGQGALVVLVAR  384 (742)
T ss_pred             HhccCCcccccEEEEeCC------------------CCCHHHHHHhccccCCCCCCcEEEEEeC
Confidence            999999999999999664                  4567899999999999887 99998876

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.94  E-value=9.4e-26  Score=248.04  Aligned_cols=343  Identities=15%  Similarity=0.073  Sum_probs=209.3

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHH-HHcCCeEEEEcCCCCCcccchh-hhhhh-------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDM-VRNNQITVISGETGSGPPLHLD-FITLK-------------------   95 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~-i~~~~~vii~~~TGSGKTtqlp-~ll~e-------------------   95 (455)
                      |.+...++...+.++.++.--.+++|.++++. +.+++++++++|||||||.... .++..                   
T Consensus         3 ~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa~   82 (720)
T PRK00254          3 VDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAE   82 (720)
T ss_pred             HHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHHH
Confidence            44556788899999999999999999999986 8899999999999999995432 22210                   


Q ss_pred             -----------hcCCCC---------------------ChHHHHHhc--cCCCCcCcc------hHHHH-----HHHHHH
Q psy6094          96 -----------RSETQQ---------------------YPNDVLNML--KDPELEGVN------NDVIF-----SLLQHI  130 (455)
Q Consensus        96 -----------~~~~vg---------------------~p~~ll~~l--~d~~L~~~~------~D~ll-----~~lk~i  130 (455)
                                 .|..++                     +|..+...+  ....+.+++      .+.+.     ..+..+
T Consensus        83 q~~~~~~~~~~~g~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~le~i  162 (720)
T PRK00254         83 EKYREFKDWEKLGLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLEMI  162 (720)
T ss_pred             HHHHHHHHHhhcCCEEEEEeCCCCCchhhhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHHHHH
Confidence                       011111                     222222221  111222222      11111     223444


Q ss_pred             HHhcCCCCeEEEEccCCCC---------------C-ccceE--E-eehhhhhhhhccCCC-C-C---hHHHHHHHHccCC
Q psy6094         131 CTTQRPGAILVYCTYTFMG---------------V-SPMKV--F-FCKNVLQRLMKGVGA-N-S---PKRWVKLLRSMLV  186 (455)
Q Consensus       131 l~~~~~~~k~ilmSAT~~g---------------~-~pv~~--~-~l~~~~~~~~~~~~~-~-~---~~~l~~~i~~~~~  186 (455)
                      +.....+.|+|+||||++.               . .|+..  . +....  .+...... . .   ...+...+  ..+
T Consensus       163 l~~l~~~~qiI~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~i--~~~  238 (720)
T PRK00254        163 LTHMLGRAQILGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVFYQGF--LFWEDGKIERFPNSWESLVYDAV--KKG  238 (720)
T ss_pred             HHhcCcCCcEEEEEccCCCHHHHHHHhCCccccCCCCCCcceeeEecCCe--eeccCcchhcchHHHHHHHHHHH--HhC
Confidence            4455678999999999821               0 12211  0 00000  00000000 0 0   01122233  357


Q ss_pred             CCEEEEcCCHHHHHHHHHHHHhcCC-C-------------------CC-------CCeEEEeecCCCChhhHhhhhcCCC
Q psy6094         187 VPILVFLPGWDTINSLHRSMCQSSF-F-------------------NS-------SRFQIIPLHSMLPTVSQKSIFNTPP  239 (455)
Q Consensus       187 g~iLVFlp~~~ei~~l~~~L~~~~~-~-------------------~~-------~~~~v~~lhs~l~~~~r~~v~~~~~  239 (455)
                      +++|||++++.+++.++..|..... +                   ..       -...+..+||+|++++|..+++.|+
T Consensus       239 ~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~  318 (720)
T PRK00254        239 KGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFR  318 (720)
T ss_pred             CCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHH
Confidence            8999999999999988877743210 0                   00       0124889999999999999999999


Q ss_pred             CCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCChh
Q psy6094         240 EGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYPND  316 (455)
Q Consensus       240 ~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t~~  316 (455)
                      +|..+|||||+++++|+|+|++++||....    .|+ ..|     ..+.+.+++.||+|||||.+   .|.|+-+.+.+
T Consensus       319 ~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~----~~~-~~~-----~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~  388 (720)
T PRK00254        319 EGLIKVITATPTLSAGINLPAFRVIIRDTK----RYS-NFG-----WEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTE  388 (720)
T ss_pred             CCCCeEEEeCcHHhhhcCCCceEEEECCce----EcC-CCC-----ceeCCHHHHHHhhhccCCCCcCCCceEEEEecCc
Confidence            999999999999999999999999996442    243 112     23456788999999999964   49999887622


Q ss_pred             h----hccC--CCCcccccC---hH----HHH---------------HHHh---hhcCCCC----hhhHHhHHhhhhhcc
Q psy6094         317 V----LNML--KDPELEGVN---ND----VIF---------------SLLQ---HICTTQR----PGAILVFLPGWDTIN  361 (455)
Q Consensus       317 ~----~~~~--~~PEi~r~~---~~----~~L---------------~~l~---~~~~~P~----~~~i~~al~~L~~lg  361 (455)
                      .    +..+  ..||-....   ++    .++               .++.   .+...|+    .+.++.++..|.+.|
T Consensus       389 ~~~~~~~~~~~~~pe~l~s~l~~es~l~~~ll~~i~~~~~~~~~~~~~~l~~Tf~~~~~~~~~~~~~~v~~~l~~L~~~~  468 (720)
T PRK00254        389 EPSKLMERYIFGKPEKLFSMLSNESAFRSQVLALITNFGVSNFKELVNFLERTFYAHQRKDLYSLEEKAKEIVYFLLENE  468 (720)
T ss_pred             chHHHHHHHHhCCchhhhccCCchHHHHHHHHHHHHhCCCCCHHHHHHHHHhCHHHHhhcChHhHHHHHHHHHHHHHHCC
Confidence            1    2222  122221111   11    111               1222   1112244    245678888999999


Q ss_pred             cccCCCCCCcccCChHHHHHhhCCCChhHHHHH
Q psy6094         362 SLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITV  394 (455)
Q Consensus       362 ald~~~~l~~~~~T~lG~~l~~lp~~p~~~l~i  394 (455)
                      .++.+++ ..+.+|++|+.++.++++|+.+..+
T Consensus       469 ~i~~~~~-~~~~~t~lG~~~s~~~i~~~t~~~~  500 (720)
T PRK00254        469 FIDIDLE-DRFIPLPLGIRTSQLYIDPLTAKKF  500 (720)
T ss_pred             CeEEcCC-CCEeeChHHHHHHHHhCCHHHHHHH
Confidence            9876432 1356799999999999999444333

>KOG0332|consensus

Probab=99.94  E-value=1.7e-26  Score=222.84  Aligned_cols=262  Identities=18%  Similarity=0.170  Sum_probs=184.8

Q ss_pred             HHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHc--CCeEEEEcCCCCCcccchh-hhhh-----------------
Q psy6094          35 KEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRN--NQITVISGETGSGPPLHLD-FITL-----------------   94 (455)
Q Consensus        35 ~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~--~~~vii~~~TGSGKTtqlp-~ll~-----------------   94 (455)
                      +.|++..++|+..+-+-.-+.--...+|+..++.+..  .+++|.++..|||||+++. -+|.                 
T Consensus        90 ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPt  169 (477)
T KOG0332|consen   90 KSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPT  169 (477)
T ss_pred             ccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCch
Confidence            4678888888887766556666677889999999885  4789999999999997765 3332                 


Q ss_pred             ------------hhc-------------------C------CCCChHHHHHhc-c----CCCCcCc----chHHHHHH--
Q psy6094          95 ------------KRS-------------------E------TQQYPNDVLNML-K----DPELEGV----NNDVIFSL--  126 (455)
Q Consensus        95 ------------e~~-------------------~------~vg~p~~ll~~l-~----d~~L~~~----~~D~ll~~--  126 (455)
                                  ++|                   .      .+|+|+.+++++ .    |+....+    .+|.++.-  
T Consensus       170 rELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG~~i~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG  249 (477)
T KOG0332|consen  170 RELAPQTGEVVEEMGKFTELTASYAIRGSKAKRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQG  249 (477)
T ss_pred             HHHHHHHHHHHHHhcCceeeeEEEEecCcccccCCcchhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhccc
Confidence                        111                   1      122455555544 1    2211111    16666632  


Q ss_pred             ----HHHHHHhcCCCCeEEEEccCCCCC----------------ccceEEeehhhhhhhhccCCCCChHH-HHHHHHccC
Q psy6094         127 ----LQHICTTQRPGAILVYCTYTFMGV----------------SPMKVFFCKNVLQRLMKGVGANSPKR-WVKLLRSML  185 (455)
Q Consensus       127 ----lk~il~~~~~~~k~ilmSAT~~g~----------------~pv~~~~l~~~~~~~~~~~~~~~~~~-l~~~i~~~~  185 (455)
                          --.+....+++.|+++||||....                ..-+..-++.+.+-|+.+........ +..+..-..
T Consensus       250 ~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~t  329 (477)
T KOG0332|consen  250 FQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLT  329 (477)
T ss_pred             ccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhh
Confidence                111222446799999999999111                11112224444455555554433322 222221245


Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV  265 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI  265 (455)
                      -|+.+|||.+++.+.+++..|...+      +.|..|||.|..++|..++..|+.|+.||+|+|||.+||||++.|..||
T Consensus       330 igqsiIFc~tk~ta~~l~~~m~~~G------h~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~Vv  403 (477)
T KOG0332|consen  330 IGQSIIFCHTKATAMWLYEEMRAEG------HQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVV  403 (477)
T ss_pred             hhheEEEEeehhhHHHHHHHHHhcC------ceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEE
Confidence            7899999999999999999999886      7899999999999999999999999999999999999999999999999


Q ss_pred             eCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         266 DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       266 D~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |++++-...            .-..-+.|.||.||+||.|. |.+|.|..
T Consensus       404 NydlP~~~~------------~~pD~etYlHRiGRtGRFGkkG~a~n~v~  441 (477)
T KOG0332|consen  404 NYDLPVKYT------------GEPDYETYLHRIGRTGRFGKKGLAINLVD  441 (477)
T ss_pred             ecCCccccC------------CCCCHHHHHHHhcccccccccceEEEeec
Confidence            966652211            11455789999999999998 99999987

>KOG0347|consensus

Probab=99.94  E-value=1.7e-27  Score=239.28  Aligned_cols=259  Identities=16%  Similarity=0.151  Sum_probs=181.1

Q ss_pred             HHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC-CeEEEEcCCCCCcccchh-hhhh----------------
Q psy6094          33 FKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN-QITVISGETGSGPPLHLD-FITL----------------   94 (455)
Q Consensus        33 ~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~-~~vii~~~TGSGKTtqlp-~ll~----------------   94 (455)
                      =...|.+..+++.....|++-+..-..++|...+++...+ .+++..|+||||||.++. .+++                
T Consensus       179 DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~  258 (731)
T KOG0347|consen  179 DVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTS  258 (731)
T ss_pred             ChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHH
Confidence            3457888889999999999999988888898888876666 899999999999996644 3332                


Q ss_pred             -----------------------------------------------------hh-cCCCCChHHHHHhc--cCCCCcCc
Q psy6094          95 -----------------------------------------------------KR-SETQQYPNDVLNML--KDPELEGV  118 (455)
Q Consensus        95 -----------------------------------------------------e~-~~~vg~p~~ll~~l--~d~~L~~~  118 (455)
                                                                           .+ ...|.+|+||...+  .+-.|.++
T Consensus       259 ~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~  338 (731)
T KOG0347|consen  259 AKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNF  338 (731)
T ss_pred             hccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhh
Confidence                                                                 00 01112466666655  33334444


Q ss_pred             c---------hHHHH---------HHHHHHH-HhcCCCCeEEEEccCCCCC--ccce--------EEeehhhhhhhhc--
Q psy6094         119 N---------NDVIF---------SLLQHIC-TTQRPGAILVYCTYTFMGV--SPMK--------VFFCKNVLQRLMK--  167 (455)
Q Consensus       119 ~---------~D~ll---------~~lk~il-~~~~~~~k~ilmSAT~~g~--~pv~--------~~~l~~~~~~~~~--  167 (455)
                      .         +|.|+         .+|+.+. .......|.++||||+.-.  -|+.        ..-++..++.++.  
T Consensus       339 k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~i  418 (731)
T KOG0347|consen  339 KKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKI  418 (731)
T ss_pred             hhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHh
Confidence            4         78887         2344443 1234678999999999110  1110        0001111222111  


Q ss_pred             ---------------------------cCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEE
Q psy6094         168 ---------------------------GVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQII  220 (455)
Q Consensus       168 ---------------------------~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~  220 (455)
                                                 +....++..+.++|. .-+|..||||++.+.|.+++-.|....      +..+
T Consensus       419 g~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~-ryPGrTlVF~NsId~vKRLt~~L~~L~------i~p~  491 (731)
T KOG0347|consen  419 GFRGKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLT-RYPGRTLVFCNSIDCVKRLTVLLNNLD------IPPL  491 (731)
T ss_pred             CccCCCeeEecCcchhHHHHHHHHhhcCCccccceeEEEEEe-ecCCceEEEechHHHHHHHHHHHhhcC------CCCc
Confidence                                       100000000111111 569999999999999999999998864      7789


Q ss_pred             eecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcc
Q psy6094         221 PLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGR  300 (455)
Q Consensus       221 ~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GR  300 (455)
                      +||+.|.|++|.+.+++|.....-|+||||||+||+|||+|.+||++..++                  +-..|.||+||
T Consensus       492 ~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPr------------------tseiYVHRSGR  553 (731)
T KOG0347|consen  492 PLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPR------------------TSEIYVHRSGR  553 (731)
T ss_pred             hhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCC------------------ccceeEecccc
Confidence            999999999999999999999999999999999999999999999955543                  33446699999


Q ss_pred             cCCCCC-CeEEecCChh
Q psy6094         301 AGRTLK-RSETQQYPND  316 (455)
Q Consensus       301 aGR~~~-G~c~~L~t~~  316 (455)
                      +.|++. |...-|....
T Consensus       554 TARA~~~Gvsvml~~P~  570 (731)
T KOG0347|consen  554 TARANSEGVSVMLCGPQ  570 (731)
T ss_pred             cccccCCCeEEEEeChH
Confidence            999887 9999998844

>KOG0326|consensus

Probab=99.93  E-value=1.3e-26  Score=219.63  Aligned_cols=259  Identities=12%  Similarity=0.138  Sum_probs=188.8

Q ss_pred             HHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh-----------------
Q psy6094          33 FKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL-----------------   94 (455)
Q Consensus        33 ~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~-----------------   94 (455)
                      --.+|++..+.++...-+-..+.--..++|++.++....|+++++.|..|+|||.+.- .+++                 
T Consensus        83 kG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPt  162 (459)
T KOG0326|consen   83 KGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPT  162 (459)
T ss_pred             cCccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeec
Confidence            3346777777766555445556666778899999999999999999999999994422 3333                 


Q ss_pred             ------------hhc----------------------------CCCCChHHHHHhc--cCCCCcCcc------hHHHHH-
Q psy6094          95 ------------KRS----------------------------ETQQYPNDVLNML--KDPELEGVN------NDVIFS-  125 (455)
Q Consensus        95 ------------e~~----------------------------~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~-  125 (455)
                                  +++                            ..||+|+|+++.+  .-..++...      +|-||+ 
T Consensus       163 relALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~  242 (459)
T KOG0326|consen  163 RELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSV  242 (459)
T ss_pred             chhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhch
Confidence                        111                            1133577777766  222344443      777774 


Q ss_pred             ----HHHHHHHhcCCCCeEEEEccCCCCC----------ccceEEeehhh-----hhhhhccCCCCChHHHHHHHHccCC
Q psy6094         126 ----LLQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFCKNV-----LQRLMKGVGANSPKRWVKLLRSMLV  186 (455)
Q Consensus       126 ----~lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l~~~-----~~~~~~~~~~~~~~~l~~~i~~~~~  186 (455)
                          .+.+++...+++.|++++|||+|-.          .|..+..+++.     .+.|.......+.-.+..++....-
T Consensus       243 ~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV~e~qKvhCLntLfskLqI  322 (459)
T KOG0326|consen  243 DFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFVEERQKVHCLNTLFSKLQI  322 (459)
T ss_pred             hhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeeechhhhhhhHHHHHHHhcc
Confidence                3666666788999999999999532          22232233221     2222211111111123333333556


Q ss_pred             CCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEe
Q psy6094         187 VPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVD  266 (455)
Q Consensus       187 g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID  266 (455)
                      .+.+|||++...++.+++.+.+.+      +.++.+|+.|.++.|.+||..|++|..+.+||||..-|||||+.|.+|||
T Consensus       323 NQsIIFCNS~~rVELLAkKITelG------yscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVIN  396 (459)
T KOG0326|consen  323 NQSIIFCNSTNRVELLAKKITELG------YSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVIN  396 (459)
T ss_pred             cceEEEeccchHhHHHHHHHHhcc------chhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEe
Confidence            789999999999999999999886      88999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         267 CGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       267 ~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      ++++|.                  -++|.||.||+||.|- |.++.|.+.
T Consensus       397 FDfpk~------------------aEtYLHRIGRsGRFGhlGlAInLity  428 (459)
T KOG0326|consen  397 FDFPKN------------------AETYLHRIGRSGRFGHLGLAINLITY  428 (459)
T ss_pred             cCCCCC------------------HHHHHHHccCCccCCCcceEEEEEeh
Confidence            776543                  3468899999999998 999999994

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.93  E-value=1.6e-25  Score=241.42  Aligned_cols=118  Identities=14%  Similarity=0.116  Sum_probs=105.0

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+..++....++.+||||+++++++.+++.|...+      +.+.++||+|++++|.++++.|..|..+|||||+++++|
T Consensus       226 ~l~~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~g------~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~G  299 (607)
T PRK11057        226 QLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRG------ISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG  299 (607)
T ss_pred             HHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCC------CCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhcc
Confidence            35566665677899999999999999999999864      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      ||+|+|++||+++.                  |.|.++|.||+|||||.|. |.|+.+|+..+
T Consensus       300 IDip~V~~VI~~d~------------------P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d  344 (607)
T PRK11057        300 INKPNVRFVVHFDI------------------PRNIESYYQETGRAGRDGLPAEAMLFYDPAD  344 (607)
T ss_pred             CCCCCcCEEEEeCC------------------CCCHHHHHHHhhhccCCCCCceEEEEeCHHH
Confidence            99999999999554                  3467889999999999886 99999999543

>KOG0341|consensus

Probab=99.93  E-value=2.8e-26  Score=222.05  Aligned_cols=252  Identities=18%  Similarity=0.238  Sum_probs=185.8

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchh---hhhh----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLD---FITL----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp---~ll~----------------   94 (455)
                      .|.+..+.....+.++..++.-..++|-+-++.+.+|++.|.+|-||||||  +.+|   |.|+                
T Consensus       171 sF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gL  250 (610)
T KOG0341|consen  171 SFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGL  250 (610)
T ss_pred             hhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeE
Confidence            567777888888889999998888899999999999999999999999999  4455   4444                


Q ss_pred             -------------------------------------------------hhcC--CCCChHHHHHhc--cCCCCcCcc--
Q psy6094          95 -------------------------------------------------KRSE--TQQYPNDVLNML--KDPELEGVN--  119 (455)
Q Consensus        95 -------------------------------------------------e~~~--~vg~p~~ll~~l--~d~~L~~~~--  119 (455)
                                                                       .+|.  .|.+|++|.++|  .--.|+...  
T Consensus       251 iicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL  330 (610)
T KOG0341|consen  251 IICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYL  330 (610)
T ss_pred             EEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHh
Confidence                                                             0010  011355555555  111222211  


Q ss_pred             ----hHHHHHH-----HHHHHHhcCCCCeEEEEccCCCCC----------ccceEEeeh------hhhhh--hhccCCCC
Q psy6094         120 ----NDVIFSL-----LQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFCK------NVLQR--LMKGVGAN  172 (455)
Q Consensus       120 ----~D~ll~~-----lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l~------~~~~~--~~~~~~~~  172 (455)
                          +|.|+++     +|.+........|.+|||||+|..          .||.+..-.      ++++.  |++..   
T Consensus       331 ~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqE---  407 (610)
T KOG0341|consen  331 TLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQE---  407 (610)
T ss_pred             hhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhh---
Confidence                7777754     777776667788999999999543          344332211      11111  11111   


Q ss_pred             ChHHHHHHHH--ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCC
Q psy6094         173 SPKRWVKLLR--SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATN  250 (455)
Q Consensus       173 ~~~~l~~~i~--~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTn  250 (455)
                        ..+++++.  +....++|||+..+.+++...+.|--.+      +.++.+||+-.+++|...++.|+.|+..|+||||
T Consensus       408 --aKiVylLeCLQKT~PpVLIFaEkK~DVD~IhEYLLlKG------VEavaIHGGKDQedR~~ai~afr~gkKDVLVATD  479 (610)
T KOG0341|consen  408 --AKIVYLLECLQKTSPPVLIFAEKKADVDDIHEYLLLKG------VEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATD  479 (610)
T ss_pred             --hhhhhHHHHhccCCCceEEEeccccChHHHHHHHHHcc------ceeEEeecCcchhHHHHHHHHHhcCCCceEEEec
Confidence              11233322  2567889999999999999999998765      8999999999999999999999999999999999


Q ss_pred             CCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         251 IAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       251 iae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||..|+|.|+|.+|||+++                  |-..++|.||.||+||.+. |++-.++...
T Consensus       480 VASKGLDFp~iqHVINyDM------------------P~eIENYVHRIGRTGRsg~~GiATTfINK~  528 (610)
T KOG0341|consen  480 VASKGLDFPDIQHVINYDM------------------PEEIENYVHRIGRTGRSGKTGIATTFINKN  528 (610)
T ss_pred             chhccCCCccchhhccCCC------------------hHHHHHHHHHhcccCCCCCcceeeeeeccc
Confidence            9999999999999999443                  3445678899999999988 9988887643

>KOG0336|consensus

Probab=99.93  E-value=1.4e-26  Score=225.45  Aligned_cols=251  Identities=16%  Similarity=0.237  Sum_probs=177.5

Q ss_pred             CHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchh-hhhh-----hhcCCCC-------------
Q psy6094          43 SRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLD-FITL-----KRSETQQ-------------  101 (455)
Q Consensus        43 ~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp-~ll~-----e~~~~vg-------------  101 (455)
                      -++..+-+.+-+.-...++|.+..+.++.|+++|.+|+||+|||  ..+| ++.-     .++...|             
T Consensus       228 ~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLa  307 (629)
T KOG0336|consen  228 YPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELA  307 (629)
T ss_pred             hHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHH
Confidence            34455555555556666779999999999999999999999999  3344 2221     1111111             


Q ss_pred             ------------------------------------------ChHHHHHhc--cCCCCcCcc------hHHHHHH-----
Q psy6094         102 ------------------------------------------YPNDVLNML--KDPELEGVN------NDVIFSL-----  126 (455)
Q Consensus       102 ------------------------------------------~p~~ll~~l--~d~~L~~~~------~D~ll~~-----  126 (455)
                                                                +|++|.+..  .--.|..++      +|.||++     
T Consensus       308 lqie~e~~kysyng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpq  387 (629)
T KOG0336|consen  308 LQIEGEVKKYSYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQ  387 (629)
T ss_pred             HHHHhHHhHhhhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccccHH
Confidence                                                      344444433  112344433      8888865     


Q ss_pred             HHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhhhhhhccC------------CCCChHH---HHH-HHHc-cCCCC
Q psy6094         127 LQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVLQRLMKGV------------GANSPKR---WVK-LLRS-MLVVP  188 (455)
Q Consensus       127 lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~~~~~~~~------------~~~~~~~---l~~-~i~~-~~~g~  188 (455)
                      +++++-..|||.|+++.|||.|.. ......|++++...|+..-            ....+..   ++. ++.. .+...
T Consensus       388 IrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndK  467 (629)
T KOG0336|consen  388 IRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDK  467 (629)
T ss_pred             HHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCce
Confidence            666655889999999999999655 5555566666543322110            0011111   222 2222 56778


Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCC
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCG  268 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g  268 (455)
                      ++|||..+.-++.|...+.-.      ++..-.|||+-.|.+|+..++.|+.|..+|+||||+|.||+|++||++|+|  
T Consensus       468 vIiFv~~K~~AD~LSSd~~l~------gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~N--  539 (629)
T KOG0336|consen  468 VIIFVSRKVMADHLSSDFCLK------GISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYN--  539 (629)
T ss_pred             EEEEEechhhhhhccchhhhc------ccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeec--
Confidence            999999998888777666544      478889999999999999999999999999999999999999999999999  


Q ss_pred             CCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         269 KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       269 ~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                            ||.+.++          +.|.||.||+||+|. |..+.+++.+.
T Consensus       540 ------yDFP~nI----------eeYVHRvGrtGRaGr~G~sis~lt~~D  573 (629)
T KOG0336|consen  540 ------YDFPRNI----------EEYVHRVGRTGRAGRTGTSISFLTRND  573 (629)
T ss_pred             ------cCCCccH----------HHHHHHhcccccCCCCcceEEEEehhh
Confidence                  5544443          467799999999998 99999999553

>KOG0339|consensus

Probab=99.93  E-value=1.4e-26  Score=230.60  Aligned_cols=258  Identities=16%  Similarity=0.225  Sum_probs=189.7

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh--hhhh-------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD--FITL-------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp--~ll~-------------------   94 (455)
                      .|....++..+......-.....++.|.++++....+++||.+|.||||||-++.  .+..                   
T Consensus       224 sfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilv  303 (731)
T KOG0339|consen  224 SFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILV  303 (731)
T ss_pred             hhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEe
Confidence            4455555665565565666677888899999999999999999999999995543  2221                   


Q ss_pred             ----------------------------------h--hcCC------CCChHHHHHhc--cCCCCcCcc------hHHHH
Q psy6094          95 ----------------------------------K--RSET------QQYPNDVLNML--KDPELEGVN------NDVIF  124 (455)
Q Consensus        95 ----------------------------------e--~~~~------vg~p~~ll~~l--~d~~L~~~~------~D~ll  124 (455)
                                                        +  .+-+      |.+|+||++++  .--.+.+++      +|.|+
T Consensus       304 PTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmf  383 (731)
T KOG0339|consen  304 PTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMF  383 (731)
T ss_pred             ccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhh
Confidence                                              0  0011      22688899888  555666666      77777


Q ss_pred             HH-----HHHHHHhcCCCCeEEEEccCCCCC-c---------cceEEee------hhhhhhhhccCCC-CChHHHHHHHH
Q psy6094         125 SL-----LQHICTTQRPGAILVYCTYTFMGV-S---------PMKVFFC------KNVLQRLMKGVGA-NSPKRWVKLLR  182 (455)
Q Consensus       125 ~~-----lk~il~~~~~~~k~ilmSAT~~g~-~---------pv~~~~l------~~~~~~~~~~~~~-~~~~~l~~~i~  182 (455)
                      .+     +|.|....||+.|.++||||++.+ -         ||.+.--      +++.+....+... .+-..+.+++.
T Consensus       384 dmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~  463 (731)
T KOG0339|consen  384 DMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLV  463 (731)
T ss_pred             ccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhh
Confidence            44     788887889999999999999332 1         2221111      0111111111111 11112445554


Q ss_pred             c-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCe
Q psy6094         183 S-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDI  261 (455)
Q Consensus       183 ~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V  261 (455)
                      . ...|.+|+|+.-..+.++++..|...+      +.+..|||++.|.+|.+++..|+.+...|++|||+|++|+||+++
T Consensus       464 ~f~S~gkvlifVTKk~~~e~i~a~Lklk~------~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~i  537 (731)
T KOG0339|consen  464 EFSSEGKVLIFVTKKADAEEIAANLKLKG------FNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSI  537 (731)
T ss_pred             hhccCCcEEEEEeccCCHHHHHHHhcccc------ceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCcccc
Confidence            4 678999999999999999999998764      899999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      +-|||        ||.-..++.          +.||.||+||.+. |..|.|.|+++
T Consensus       538 kTVvn--------yD~ardIdt----------hthrigrtgRag~kGvayTlvTeKD  576 (731)
T KOG0339|consen  538 KTVVN--------YDFARDIDT----------HTHRIGRTGRAGEKGVAYTLVTEKD  576 (731)
T ss_pred             ceeec--------ccccchhHH----------HHHHhhhcccccccceeeEEechhh
Confidence            99999        554444433          4599999999998 99999999654

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.93  E-value=2.5e-25  Score=233.55  Aligned_cols=117  Identities=16%  Similarity=0.192  Sum_probs=102.1

Q ss_pred             HHHHHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         177 WVKLLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       177 l~~~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      +..++.. ..+..+||||+++++++.+++.|+..+      +.+..+||+|++++|..+++.|..|..+|||||+++++|
T Consensus       216 l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g------~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~G  289 (470)
T TIGR00614       216 LLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLG------IAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG  289 (470)
T ss_pred             HHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcC------CCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhcc
Confidence            5555543 344566999999999999999998764      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      ||+|+|++||+++.+                  -|.++|.||+|||||.|. |.|+.+|+..+
T Consensus       290 ID~p~V~~VI~~~~P------------------~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d  334 (470)
T TIGR00614       290 INKPDVRFVIHYSLP------------------KSMESYYQESGRAGRDGLPSECHLFYAPAD  334 (470)
T ss_pred             CCcccceEEEEeCCC------------------CCHHHHHhhhcCcCCCCCCceEEEEechhH
Confidence            999999999996653                  356788999999999886 99999999543

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=99.92  E-value=1.2e-24  Score=239.07  Aligned_cols=116  Identities=15%  Similarity=0.126  Sum_probs=101.8

Q ss_pred             HHHHHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         177 WVKLLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       177 l~~~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      +..++.. ..++..||||.++.+++.+++.|...+      +.+.++||+|++++|..+++.|..|..+|||||+++++|
T Consensus       670 L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~G------ika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMG  743 (1195)
T PLN03137        670 IDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFG------HKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG  743 (1195)
T ss_pred             HHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCC------CCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcC
Confidence            4445543 335689999999999999999999864      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||+|||++||+++++                  -|-++|.||+|||||.|. |.|+.+|+..
T Consensus       744 IDkPDVR~VIHydlP------------------kSiEsYyQriGRAGRDG~~g~cILlys~~  787 (1195)
T PLN03137        744 INKPDVRFVIHHSLP------------------KSIEGYHQECGRAGRDGQRSSCVLYYSYS  787 (1195)
T ss_pred             CCccCCcEEEEcCCC------------------CCHHHHHhhhcccCCCCCCceEEEEecHH
Confidence            999999999996654                  355678899999999886 9999999943

>KOG0335|consensus

Probab=99.92  E-value=1.2e-25  Score=226.87  Aligned_cols=241  Identities=15%  Similarity=0.260  Sum_probs=168.2

Q ss_pred             HHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchh---hhhhhh----cCCC--C-----------------
Q psy6094          50 LEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLD---FITLKR----SETQ--Q-----------------  101 (455)
Q Consensus        50 l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp---~ll~e~----~~~v--g-----------------  101 (455)
                      ++.++..-..++|.-.++.|.+|++++++|+||||||  +.+|   +++++.    +..-  +                 
T Consensus        89 i~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi  168 (482)
T KOG0335|consen   89 IKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQI  168 (482)
T ss_pred             cccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHH
Confidence            4455556666779999999999999999999999999  4455   333311    0000  1                 


Q ss_pred             ----------------------------------------ChHHHHHhc--cCCCCcCcc------hHHHHH-H-----H
Q psy6094         102 ----------------------------------------YPNDVLNML--KDPELEGVN------NDVIFS-L-----L  127 (455)
Q Consensus       102 ----------------------------------------~p~~ll~~l--~d~~L~~~~------~D~ll~-~-----l  127 (455)
                                                              +|++|.+.+  ..-.|....      +|.|++ +     +
T Consensus       169 ~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~I  248 (482)
T KOG0335|consen  169 YNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQI  248 (482)
T ss_pred             HHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccH
Confidence                                                    122233333  222222222      899988 2     7


Q ss_pred             HHHHHhcC----CCCeEEEEccCCCCC-ccceEEeehh----------------hhhhhhccCCCCChHHHHHHHHcc--
Q psy6094         128 QHICTTQR----PGAILVYCTYTFMGV-SPMKVFFCKN----------------VLQRLMKGVGANSPKRWVKLLRSM--  184 (455)
Q Consensus       128 k~il~~~~----~~~k~ilmSAT~~g~-~pv~~~~l~~----------------~~~~~~~~~~~~~~~~l~~~i~~~--  184 (455)
                      ++++....    ...|.++||||.|-. -...-+|+.+                +.+.........+...|...+...  
T Consensus       249 r~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~  328 (482)
T KOG0335|consen  249 RKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNKDDG  328 (482)
T ss_pred             HHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchhhHHHHHHHhhcccC
Confidence            77764332    368999999999543 1111112221                001111111122233355555532  


Q ss_pred             --CCC-----CEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCC
Q psy6094         185 --LVV-----PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSIT  257 (455)
Q Consensus       185 --~~g-----~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~git  257 (455)
                        ..+     .+|||+.+.+.+..++..|...+      +.+.++||..++.+|.+.++.|+.|+..|+||||||+||+|
T Consensus       329 ~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~------~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlD  402 (482)
T KOG0335|consen  329 PPSDGEPKWEKTLVFVETKRGADELAAFLSSNG------YPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLD  402 (482)
T ss_pred             CcccCCcccceEEEEeeccchhhHHHHHHhcCC------CCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCC
Confidence              244     79999999999999999999875      88999999999999999999999999999999999999999


Q ss_pred             CCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         258 IDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       258 I~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ||+|++||+        ||-+...          ..|.||.||+||.|. |.+..||.
T Consensus       403 i~~V~hVIn--------yDmP~d~----------d~YvHRIGRTGR~Gn~G~atsf~n  442 (482)
T KOG0335|consen  403 IPNVKHVIN--------YDMPADI----------DDYVHRIGRTGRVGNGGRATSFFN  442 (482)
T ss_pred             CCCCceeEE--------eecCcch----------hhHHHhccccccCCCCceeEEEec
Confidence            999999999        5544333          356799999999998 99999998

>KOG0348|consensus

Probab=99.92  E-value=2.4e-24  Score=216.11  Aligned_cols=258  Identities=15%  Similarity=0.192  Sum_probs=175.1

Q ss_pred             HHHHHhcCHHHHHHHHHHcc-CCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchhhhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKK-LPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~-lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp~ll~--------------------   94 (455)
                      .|....+++...+-++.+.. --...+|.+.|+.|.++++++|.++||||||  ++|+++                    
T Consensus       137 ~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKT--LAYllPiVq~Lq~m~~ki~Rs~G~~A  214 (708)
T KOG0348|consen  137 AFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKT--LAYLLPIVQSLQAMEPKIQRSDGPYA  214 (708)
T ss_pred             cchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCccc--HHHHHHHHHHHHhcCccccccCCceE
Confidence            56788889998888866544 4556778999999999999999999999999  444443                    


Q ss_pred             ---------------------------------------------hhc--CCCCChHHHHHhc-cCCCC--cCcc-----
Q psy6094          95 ---------------------------------------------KRS--ETQQYPNDVLNML-KDPEL--EGVN-----  119 (455)
Q Consensus        95 ---------------------------------------------e~~--~~vg~p~~ll~~l-~d~~L--~~~~-----  119 (455)
                                                                   ..|  .-+|+|+||+++| ....+  ....     
T Consensus       215 LVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlD  294 (708)
T KOG0348|consen  215 LVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLD  294 (708)
T ss_pred             EEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEec
Confidence                                                         112  2355899999998 33322  2222     


Q ss_pred             -hHHHHHH-----HHHHHHhc-------------CCCCeEEEEccCCC-C------C---ccceEEeehhhh--------
Q psy6094         120 -NDVIFSL-----LQHICTTQ-------------RPGAILVYCTYTFM-G------V---SPMKVFFCKNVL--------  162 (455)
Q Consensus       120 -~D~ll~~-----lk~il~~~-------------~~~~k~ilmSAT~~-g------~---~pv~~~~l~~~~--------  162 (455)
                       +|.||++     +..|+...             ++.++-+|+|||+. |      .   -|+-+- ++...        
T Consensus       295 EaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~-ld~s~~~~~p~~~  373 (708)
T KOG0348|consen  295 EADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYIS-LDKSHSQLNPKDK  373 (708)
T ss_pred             chhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeee-ccchhhhcCcchh
Confidence             7888854     33333211             12367789999991 1      0   122111 11100        


Q ss_pred             ------------------------hhhhccCCCCChHHHHHHHH----ccCCCCEEEEcCCHHHHHHHHHHHHhcCCC--
Q psy6094         163 ------------------------QRLMKGVGANSPKRWVKLLR----SMLVVPILVFLPGWDTINSLHRSMCQSSFF--  212 (455)
Q Consensus       163 ------------------------~~~~~~~~~~~~~~l~~~i~----~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--  212 (455)
                                              +.|......-..-.|...+.    ......++||+.+.+.++.-+.++......  
T Consensus       374 a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~  453 (708)
T KOG0348|consen  374 AVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHL  453 (708)
T ss_pred             hhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhccc
Confidence                                    01100000000000222222    245568999999999999988777642110  


Q ss_pred             --------C------CCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccC
Q psy6094         213 --------N------SSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVK  278 (455)
Q Consensus       213 --------~------~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~  278 (455)
                              .      ..+..++-|||+|+|++|..+|+.|....+-|++|||||+||+|+|+|+.||.        ||+ 
T Consensus       454 e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQ--------Yd~-  524 (708)
T KOG0348|consen  454 EGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQ--------YDP-  524 (708)
T ss_pred             ccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEE--------eCC-
Confidence                    0      12567999999999999999999999999999999999999999999999997        774 


Q ss_pred             CCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         279 DNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       279 ~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                               |-|-+.|.||+||+.|.|. |...-+..
T Consensus       525 ---------P~s~adylHRvGRTARaG~kG~alLfL~  552 (708)
T KOG0348|consen  525 ---------PFSTADYLHRVGRTARAGEKGEALLFLL  552 (708)
T ss_pred             ---------CCCHHHHHHHhhhhhhccCCCceEEEec
Confidence                     5677899999999999988 87766655

>KOG0334|consensus

Probab=99.91  E-value=5.7e-25  Score=236.21  Aligned_cols=256  Identities=18%  Similarity=0.278  Sum_probs=190.9

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh-hhhh------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD-FITL------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp-~ll~------------------   94 (455)
                      .|.++..++.....+++-+.-+..++|.+.+++|..|++||.+|.||||||..  +| +.+.                  
T Consensus       366 sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~a  445 (997)
T KOG0334|consen  366 SWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILA  445 (997)
T ss_pred             hHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEc
Confidence            67888899999998888888899999999999999999999999999999933  34 2111                  


Q ss_pred             ----------------------------------------hhcCC--CCChHHHHHhc--cCCCCcCcc---------hH
Q psy6094          95 ----------------------------------------KRSET--QQYPNDVLNML--KDPELEGVN---------ND  121 (455)
Q Consensus        95 ----------------------------------------e~~~~--vg~p~~ll~~l--~d~~L~~~~---------~D  121 (455)
                                                              .+|..  |++|++.++.+  +...+.+..         +|
T Consensus       446 Ptrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaD  525 (997)
T KOG0334|consen  446 PTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEAD  525 (997)
T ss_pred             CCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhh
Confidence                                                    11211  11455555555  222222222         78


Q ss_pred             HHHHH-----HHHHHHhcCCCCeEEEEccCCCC---------C-ccceEEee------hhhhhhhhccC-CCCChHHHHH
Q psy6094         122 VIFSL-----LQHICTTQRPGAILVYCTYTFMG---------V-SPMKVFFC------KNVLQRLMKGV-GANSPKRWVK  179 (455)
Q Consensus       122 ~ll~~-----lk~il~~~~~~~k~ilmSAT~~g---------~-~pv~~~~l------~~~~~~~~~~~-~~~~~~~l~~  179 (455)
                      .|+.+     +-.|+++.+++.|++++|||+|-         . .||.+.+.      +++.+.+..+. .+.+...|..
T Consensus       526 rmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~e  605 (997)
T KOG0334|consen  526 RMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLE  605 (997)
T ss_pred             hhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHH
Confidence            87743     22267688999999999999931         1 45554332      22222222222 1222222444


Q ss_pred             HHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         180 LLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       180 ~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                      +|.. ...++++||+..+..++.|.+.|.+.+      +.+..|||+.++.+|..+++.|+.|..+++|||+++++|+++
T Consensus       606 Ll~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag------~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv  679 (997)
T KOG0334|consen  606 LLGERYEDGKTIIFVDKQEKADALLRDLQKAG------YNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDV  679 (997)
T ss_pred             HHHHHhhcCCEEEEEcCchHHHHHHHHHHhcC------cchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhccccc
Confidence            4443 568999999999999999999999765      778889999999999999999999999999999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      .++..|||        ||.+++...          |.||.||+||+++ |.||.+.++
T Consensus       680 ~~l~Lvvn--------yd~pnh~ed----------yvhR~gRTgragrkg~AvtFi~p  719 (997)
T KOG0334|consen  680 KELILVVN--------YDFPNHYED----------YVHRVGRTGRAGRKGAAVTFITP  719 (997)
T ss_pred             ccceEEEE--------cccchhHHH----------HHHHhcccccCCccceeEEEeCh
Confidence            99999999        666666443          7799999999999 999999995

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.91  E-value=1.8e-23  Score=225.47  Aligned_cols=118  Identities=15%  Similarity=0.129  Sum_probs=103.7

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+..++....+++.||||+++.+++.+++.|...+      +.+.++||+|+.++|..+++.|..|..+|||||+++++|
T Consensus       214 ~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~g------~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~G  287 (591)
T TIGR01389       214 FLLDYLKKHRGQSGIIYASSRKKVEELAERLESQG------ISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG  287 (591)
T ss_pred             HHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCC------CCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhcc
Confidence            46666665567889999999999999999998764      778999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      ||+|+|++||+++.                  |-|.++|.||+|||||.|. |.|+.+|+..+
T Consensus       288 ID~p~v~~VI~~~~------------------p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d  332 (591)
T TIGR01389       288 IDKPNVRFVIHYDM------------------PGNLESYYQEAGRAGRDGLPAEAILLYSPAD  332 (591)
T ss_pred             CcCCCCCEEEEcCC------------------CCCHHHHhhhhccccCCCCCceEEEecCHHH
Confidence            99999999999554                  3456778899999999885 99999999543

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.

>KOG0327|consensus

Probab=99.90  E-value=6.4e-24  Score=206.54  Aligned_cols=267  Identities=16%  Similarity=0.266  Sum_probs=190.1

Q ss_pred             ccchhhhccccCCcchHHHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hh
Q psy6094          14 VTSWETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FI   92 (455)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~l   92 (455)
                      ...+++++....++++++.|++++.+....-.+        .-|...+|.+|++.| .|.++++++++|||||..+- .+
T Consensus        14 ~~~iesn~~evvdsfddm~L~e~LLrgiy~yGF--------ekPSaIQqraI~p~i-~G~dv~~qaqsgTgKt~af~i~i   84 (397)
T KOG0327|consen   14 EGVIESNWNEVVDSFDDMNLKESLLRGIYAYGF--------EKPSAIQQRAILPCI-KGHDVIAQAQSGTGKTAAFLISI   84 (397)
T ss_pred             cccccccHHHHhhhhhhcCCCHHHHhHHHhhcc--------CCchHHHhccccccc-cCCceeEeeeccccchhhhHHHH
Confidence            457788888888888888888887776644333        345555566666555 56679999999999994433 22


Q ss_pred             hh--------------------------------------------------------h--hcCCCCChHHHHHhc-cCC
Q psy6094          93 TL--------------------------------------------------------K--RSETQQYPNDVLNML-KDP  113 (455)
Q Consensus        93 l~--------------------------------------------------------e--~~~~vg~p~~ll~~l-~d~  113 (455)
                      +.                                                        .  ....+|+|+++++++ .. 
T Consensus        85 Lq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~-  163 (397)
T KOG0327|consen   85 LQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRG-  163 (397)
T ss_pred             HhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccc-
Confidence            21                                                        0  011234577777777 22 


Q ss_pred             CCcC--cc------hHHHH-----HHHHHHHHhcCCCCeEEEEccCCCCC----------ccceEEee------hhhhhh
Q psy6094         114 ELEG--VN------NDVIF-----SLLQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFC------KNVLQR  164 (455)
Q Consensus       114 ~L~~--~~------~D~ll-----~~lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l------~~~~~~  164 (455)
                      .|..  ..      +|.+|     +.+..+....+++.|++++|||+|-.          +|+.+..-      +.+.+.
T Consensus       164 ~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~  243 (397)
T KOG0327|consen  164 SLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQF  243 (397)
T ss_pred             cccccceeEEeecchHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeee
Confidence            2222  22      67777     44777777889999999999999432          33332221      111122


Q ss_pred             hhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceE
Q psy6094         165 LMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRK  244 (455)
Q Consensus       165 ~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~k  244 (455)
                      |.......+-..+.....  .-.+.+|||+|++.+..+...|..++      +.+..+||.+.+.+|..++..|+.|..+
T Consensus       244 ~i~v~k~~k~~~l~dl~~--~~~q~~if~nt~r~v~~l~~~L~~~~------~~~s~~~~d~~q~~R~~~~~ef~~gssr  315 (397)
T KOG0327|consen  244 YINVEKEEKLDTLCDLYR--RVTQAVIFCNTRRKVDNLTDKLRAHG------FTVSAIHGDMEQNERDTLMREFRSGSSR  315 (397)
T ss_pred             eeeccccccccHHHHHHH--hhhcceEEecchhhHHHHHHHHhhCC------ceEEEeecccchhhhhHHHHHhhcCCce
Confidence            222222222222333332  67789999999999999999997664      8999999999999999999999999999


Q ss_pred             EEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         245 IVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       245 VivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+|+|+.+++|+||-++..|||        ||.          |.-+++|.||+||+||.|. |....+.++.
T Consensus       316 vlIttdl~argidv~~~slvin--------ydl----------P~~~~~yihR~gr~gr~grkg~~in~v~~~  370 (397)
T KOG0327|consen  316 VLITTDLLARGIDVQQVSLVVN--------YDL----------PARKENYIHRIGRAGRFGRKGVAINFVTEE  370 (397)
T ss_pred             EEeeccccccccchhhcceeee--------ecc----------ccchhhhhhhcccccccCCCceeeeeehHh
Confidence            9999999999999999999999        553          3456788899999999887 9999999954

>KOG0346|consensus

Probab=99.90  E-value=3.1e-23  Score=203.99  Aligned_cols=260  Identities=16%  Similarity=0.145  Sum_probs=191.5

Q ss_pred             HHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchh---hhhh-----------
Q psy6094          31 AAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLD---FITL-----------   94 (455)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp---~ll~-----------   94 (455)
                      ++-.+.|++..+.++..+.+.+-+.--...+|...|+.+.+|++++..|.||||||  +.+|   -|+.           
T Consensus        15 e~~~ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~   94 (569)
T KOG0346|consen   15 ESKEKTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGP   94 (569)
T ss_pred             hhhhccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccc
Confidence            33447899999999999999999999999999999999999999999999999999  3344   2222           


Q ss_pred             -------------------------------------------------h-hcCCCCChHHHHHhc-cCC--CCcCcc--
Q psy6094          95 -------------------------------------------------K-RSETQQYPNDVLNML-KDP--ELEGVN--  119 (455)
Q Consensus        95 -------------------------------------------------e-~~~~vg~p~~ll~~l-~d~--~L~~~~--  119 (455)
                                                                       + -...||+|.++++++ ..+  .+...+  
T Consensus        95 sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~L  174 (569)
T KOG0346|consen   95 SAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFL  174 (569)
T ss_pred             eeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeE
Confidence                                                             0 011233455577776 332  333333  


Q ss_pred             ----hHHHHHH-----HHHHHHhcCCCCeEEEEccCCCC----------CccceEEeehh-------hhhhhhccCCCCC
Q psy6094         120 ----NDVIFSL-----LQHICTTQRPGAILVYCTYTFMG----------VSPMKVFFCKN-------VLQRLMKGVGANS  173 (455)
Q Consensus       120 ----~D~ll~~-----lk~il~~~~~~~k~ilmSAT~~g----------~~pv~~~~l~~-------~~~~~~~~~~~~~  173 (455)
                          +|++|.+     ++.+....++..|-++||||+..          +.||...+-++       ..+.++.+...++
T Consensus       175 VvDEADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DK  254 (569)
T KOG0346|consen  175 VVDEADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDK  254 (569)
T ss_pred             EechhhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchh
Confidence                8999854     78887788899999999999911          13443222211       1112223332111


Q ss_pred             hHHHHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         174 PKRWVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       174 ~~~l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      -. +...+-+  --.|.+|+|+++.+.+-++.-.|+..+      +..+.|.|.||..-|..+++.|..|...||+|||.
T Consensus       255 fl-llyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFG------iksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~  327 (569)
T KOG0346|consen  255 FL-LLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFG------IKSCILNSELPANSRCHIIEQFNKGLYDIVIATDD  327 (569)
T ss_pred             HH-HHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhC------cHhhhhcccccccchhhHHHHhhCcceeEEEEccC
Confidence            11 2221111  457999999999999999999998875      77888999999999999999999999999999992


Q ss_pred             C-----------------------------------ccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHh
Q psy6094         252 A-----------------------------------ETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQ  296 (455)
Q Consensus       252 a-----------------------------------e~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~Q  296 (455)
                      -                                   .||||..+|..|||+++|                  -+..+|+|
T Consensus       328 s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P------------------~t~~sYIH  389 (569)
T KOG0346|consen  328 SADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFP------------------ETVTSYIH  389 (569)
T ss_pred             ccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCC------------------CchHHHHH
Confidence            1                                   289999999999996653                  44557889


Q ss_pred             hhcccCCCCC-CeEEecCCh
Q psy6094         297 RRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       297 R~GRaGR~~~-G~c~~L~t~  315 (455)
                      |+||+||.+. |.+..+...
T Consensus       390 RvGRTaRg~n~GtalSfv~P  409 (569)
T KOG0346|consen  390 RVGRTARGNNKGTALSFVSP  409 (569)
T ss_pred             hccccccCCCCCceEEEecc
Confidence            9999999877 999988883

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.90  E-value=3.5e-22  Score=223.01  Aligned_cols=113  Identities=22%  Similarity=0.113  Sum_probs=94.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ...+++||||+++..++.++..|............+..+||+|++++|..+++.|++|..+|||||+++|+|||||+|++
T Consensus       282 ~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~  361 (876)
T PRK13767        282 KEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDL  361 (876)
T ss_pred             hcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcE
Confidence            34678999999999999999999874210011356899999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC----CCeEEecCC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL----KRSETQQYP  314 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~----~G~c~~L~t  314 (455)
                      ||+.|.                  |.|.+++.||+|||||..    .|.+|.+..
T Consensus       362 VI~~~~------------------P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~~  398 (876)
T PRK13767        362 VVLLGS------------------PKSVSRLLQRIGRAGHRLGEVSKGRIIVVDR  398 (876)
T ss_pred             EEEeCC------------------CCCHHHHHHhcccCCCCCCCCCcEEEEEcCc
Confidence            998553                  456788999999999852    377776544

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.89  E-value=2.4e-22  Score=222.98  Aligned_cols=112  Identities=20%  Similarity=0.233  Sum_probs=96.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+|+++||+|+.++++.+++.|++..    +++.+..+||+|++++|.++++.|++|+.+|+|||+++|+|||||++++
T Consensus       658 ~~g~qv~if~n~i~~~e~l~~~L~~~~----p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~  733 (926)
T TIGR00580       658 LRGGQVFYVHNRIESIEKLATQLRELV----PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANT  733 (926)
T ss_pred             HcCCeEEEEECCcHHHHHHHHHHHHhC----CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCE
Confidence            457899999999999999999998752    2478999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||.        ||...         -+-+++.||+||+||.+. |.||.+++..
T Consensus       734 VIi--------~~a~~---------~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       734 III--------ERADK---------FGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             EEE--------ecCCC---------CCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            997        33221         122467799999999886 9999999743

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.87  E-value=1.2e-21  Score=221.68  Aligned_cols=111  Identities=17%  Similarity=0.174  Sum_probs=94.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+|.++||+|+.+.++.+++.|.+..    +++.+..+||+|++++|.+++..|++|+.+|+|||+++|+|||||+|++
T Consensus       807 ~r~gqv~vf~n~i~~ie~la~~L~~~~----p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~  882 (1147)
T PRK10689        807 LRGGQVYYLYNDVENIQKAAERLAELV----PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  882 (1147)
T ss_pred             hcCCeEEEEECCHHHHHHHHHHHHHhC----CCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCE
Confidence            347899999999999999999998763    2467889999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      ||-        +++..         -+-+++.||+||+||.+. |.||-+++.
T Consensus       883 VIi--------~~ad~---------fglaq~~Qr~GRvGR~g~~g~a~ll~~~  918 (1147)
T PRK10689        883 III--------ERADH---------FGLAQLHQLRGRVGRSHHQAYAWLLTPH  918 (1147)
T ss_pred             EEE--------ecCCC---------CCHHHHHHHhhccCCCCCceEEEEEeCC
Confidence            993        11100         012458899999999887 999998863

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.87  E-value=2.5e-21  Score=211.24  Aligned_cols=110  Identities=17%  Similarity=0.200  Sum_probs=90.9

Q ss_pred             cCCCCEEEEcCCH--------HHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         184 MLVVPILVFLPGW--------DTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       184 ~~~g~iLVFlp~~--------~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      ..+++++||||..        ..++.+++.|....    +.+.+..+||+|++++|.++++.|++|+.+|+|||+++|+|
T Consensus       469 ~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~----~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~G  544 (681)
T PRK10917        469 AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAF----PELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVG  544 (681)
T ss_pred             HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHC----CCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeC
Confidence            4577999999954        44566777777642    13789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ||||++++||+.+.++       .|          -+++.||+||+||.+. |.||.+++
T Consensus       545 iDip~v~~VIi~~~~r-------~g----------ls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        545 VDVPNATVMVIENAER-------FG----------LAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             cccCCCcEEEEeCCCC-------CC----------HHHHHHHhhcccCCCCceEEEEEEC
Confidence            9999999999843321       12          3567899999999875 99999986

>KOG0344|consensus

Probab=99.87  E-value=1.1e-21  Score=199.83  Aligned_cols=256  Identities=17%  Similarity=0.202  Sum_probs=175.4

Q ss_pred             HhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhhh---hh---cCCCC----------
Q psy6094          40 KLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFITL---KR---SETQQ----------  101 (455)
Q Consensus        40 ~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll~---e~---~~~vg----------  101 (455)
                      ...+++..+-+...+.--....|.+.++.+.++++++.+|+||||||..  +| ++.   ..   -..+|          
T Consensus       141 ~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~P-il~~L~~~~~~~~~~gl~a~Il~ptr  219 (593)
T KOG0344|consen  141 YSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLP-ILQHLKDLSQEKHKVGLRALILSPTR  219 (593)
T ss_pred             hhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhH-HHHHHHHhhcccCccceEEEEecchH
Confidence            4445555555555566555566889999999999999999999999933  33 222   00   00111          


Q ss_pred             -------------------------------------------------ChHHHHHhc-cCC---CCcCcc------hHH
Q psy6094         102 -------------------------------------------------YPNDVLNML-KDP---ELEGVN------NDV  122 (455)
Q Consensus       102 -------------------------------------------------~p~~ll~~l-~d~---~L~~~~------~D~  122 (455)
                                                                       +|.++...+ ..+   .+.++.      +|.
T Consensus       220 eLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~  299 (593)
T KOG0344|consen  220 ELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADL  299 (593)
T ss_pred             HHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHh
Confidence                                                             233455555 222   333333      676


Q ss_pred             HHHH------HHHHHH-hcCCCCeEEEEccCCCC---------C-ccceEEee------hhhhhhhhccCCC-CChHHHH
Q psy6094         123 IFSL------LQHICT-TQRPGAILVYCTYTFMG---------V-SPMKVFFC------KNVLQRLMKGVGA-NSPKRWV  178 (455)
Q Consensus       123 ll~~------lk~il~-~~~~~~k~ilmSAT~~g---------~-~pv~~~~l------~~~~~~~~~~~~~-~~~~~l~  178 (455)
                      |+.-      +-+++. ...++.++=+||||++-         . .++.+.+-      +.+.+.++.+... .+.-.+.
T Consensus       300 lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~r  379 (593)
T KOG0344|consen  300 LFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALR  379 (593)
T ss_pred             hhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheeeecchhHHHHHH
Confidence            6633      333332 23488899999999921         1 22222221      1111222212111 1111244


Q ss_pred             HHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         179 KLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       179 ~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                      ..+...-..++|||+-+.+.+..|...|...     ++..+-.+||..++.+|..++++|+.|+..|++|||+.+||+|+
T Consensus       380 q~v~~g~~PP~lIfVQs~eRak~L~~~L~~~-----~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf  454 (593)
T KOG0344|consen  380 QLVASGFKPPVLIFVQSKERAKQLFEELEIY-----DNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDF  454 (593)
T ss_pred             HHHhccCCCCeEEEEecHHHHHHHHHHhhhc-----cCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccc
Confidence            5555567789999999999999999988532     25789999999999999999999999999999999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhhhc
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDVLN  319 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~~~  319 (455)
                      .||..|||        ||          .|-|.-+|.||.||+||.++ |.+|.+||.+.++
T Consensus       455 ~gvn~VIn--------yD----------~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~  498 (593)
T KOG0344|consen  455 KGVNLVIN--------YD----------FPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMP  498 (593)
T ss_pred             cCcceEEe--------cC----------CCchhHHHHHHhhccCCCCCCcceEEEeccccch
Confidence            99999999        55          35667789999999999998 9999999986654

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

Probab=99.86  E-value=2.3e-21  Score=210.15  Aligned_cols=94  Identities=21%  Similarity=0.194  Sum_probs=79.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHh-----hhhcCCCC----Cc-------eEEEE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQK-----SIFNTPPE----GV-------RKIVL  247 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~-----~v~~~~~~----g~-------~kViv  247 (455)
                      ..++++||||+|+++++.+++.|.+.+      +  ..|||+|++.+|.     ++++.|++    |.       .+|+|
T Consensus       270 e~g~~vLVF~NTv~~Aq~L~~~L~~~g------~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILV  341 (844)
T TIGR02621       270 DSGGAILVFCRTVKHVRKVFAKLPKEK------F--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLV  341 (844)
T ss_pred             hCCCcEEEEECCHHHHHHHHHHHHhcC------C--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEe
Confidence            567899999999999999999998753      3  8899999999999     77887876    43       68999


Q ss_pred             eCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC
Q psy6094         248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK  306 (455)
Q Consensus       248 aTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~  306 (455)
                      ||+++|+||||+. ++||+        ++            ...++|.||+||+||.+.
T Consensus       342 ATdVaerGLDId~-d~VI~--------d~------------aP~esyIQRiGRtgR~G~  379 (844)
T TIGR02621       342 CTSAGEVGVNISA-DHLVC--------DL------------APFESMQQRFGRVNRFGE  379 (844)
T ss_pred             ccchhhhcccCCc-ceEEE--------CC------------CCHHHHHHHhcccCCCCC
Confidence            9999999999987 77775        21            123789999999999876

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.86  E-value=4.5e-21  Score=207.78  Aligned_cols=110  Identities=18%  Similarity=0.238  Sum_probs=90.9

Q ss_pred             cCCCCEEEEcCCH--------HHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         184 MLVVPILVFLPGW--------DTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       184 ~~~g~iLVFlp~~--------~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      ..++.++||||..        ..++.+++.|....    +++.+..+||+|++++|..+++.|++|+.+|||||+++|+|
T Consensus       446 ~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~----~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~G  521 (630)
T TIGR00643       446 AKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAF----PKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVG  521 (630)
T ss_pred             HhCCcEEEEEccccccccchHHHHHHHHHHHHhhC----CCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecC
Confidence            4577899999975        44566777776532    25789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ||+|++++||..+.        +.         -+-+++.||+||+||.+. |.||.++.
T Consensus       522 vDiP~v~~VIi~~~--------~r---------~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       522 VDVPNATVMVIEDA--------ER---------FGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             cccCCCcEEEEeCC--------Cc---------CCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            99999999997433        21         123578899999999875 99999984

>KOG0350|consensus

Probab=99.86  E-value=2.6e-21  Score=193.12  Aligned_cols=120  Identities=16%  Similarity=0.214  Sum_probs=102.2

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      +...|.......+|+|.++.+.+.+++..|+-..  ...++.+-.+.|++..+.|.+.++.|..|...|+||||+.+|||
T Consensus       420 ~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~--~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGi  497 (620)
T KOG0350|consen  420 VYALITSNKLNRTLCFVNSVSSANRLAHVLKVEF--CSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGI  497 (620)
T ss_pred             HHHHHHHhhcceEEEEecchHHHHHHHHHHHHHh--ccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCC
Confidence            4445555677889999999999999999998321  13456677789999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+.||+.|||        ||++          .|--+|.||+||+||+|. |.||.|.+..
T Consensus       498 Dv~~v~~VIN--------Yd~P----------~~~ktyVHR~GRTARAgq~G~a~tll~~~  540 (620)
T KOG0350|consen  498 DVNDVDNVIN--------YDPP----------ASDKTYVHRAGRTARAGQDGYAITLLDKH  540 (620)
T ss_pred             cccccceEee--------cCCC----------chhhHHHHhhcccccccCCceEEEeeccc
Confidence            9999999999        7754          455567799999999998 9999999843

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.84  E-value=3.2e-20  Score=188.37  Aligned_cols=108  Identities=15%  Similarity=0.124  Sum_probs=89.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhh----hhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKS----IFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~----v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      ..++++||||++.++++.+++.|.+...    ...+..+||++++.+|.+    +++.|++|..+|||||+++|+|+||+
T Consensus       220 ~~~~~~lVf~~t~~~~~~~~~~L~~~~~----~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~  295 (358)
T TIGR01587       220 KKGGKIAIIVNTVDRAQEFYQQLKENAP----EEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS  295 (358)
T ss_pred             hCCCeEEEEECCHHHHHHHHHHHHhhcC----CCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC
Confidence            4578999999999999999999987642    357999999999999976    48889999999999999999999996


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-----CeEEecCChh
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-----RSETQQYPND  316 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-----G~c~~L~t~~  316 (455)
                       +++||+        |            +.+-+++.||+||+||.+.     |..|.++...
T Consensus       296 -~~~vi~--------~------------~~~~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       296 -ADVMIT--------E------------LAPIDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             -CCEEEE--------c------------CCCHHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence             778886        2            2234678999999999764     3677776643

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.

>KOG4284|consensus

Probab=99.84  E-value=9.7e-21  Score=193.56  Aligned_cols=254  Identities=13%  Similarity=0.140  Sum_probs=177.2

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------   94 (455)
                      |+...+......-|+.-..--..++|.+.|+++..+-++||++..|+|||..+. ..++                     
T Consensus        27 fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREia  106 (980)
T KOG4284|consen   27 FEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIA  106 (980)
T ss_pred             HHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhh
Confidence            444444444444444435555567799999999999999999999999994433 2222                     


Q ss_pred             ------------------------------------hhcCCCCChHHHHHhc--cCCCCcCcc------hHHHHH-----
Q psy6094          95 ------------------------------------KRSETQQYPNDVLNML--KDPELEGVN------NDVIFS-----  125 (455)
Q Consensus        95 ------------------------------------e~~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~-----  125 (455)
                                                          +-...+|+|+|+++..  .--+...+.      +|-|+.     
T Consensus       107 VQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq  186 (980)
T KOG4284|consen  107 VQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQ  186 (980)
T ss_pred             hHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhhceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHH
Confidence                                                1123355788877655  111222222      677663     


Q ss_pred             -HHHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhh--------------hhhhcc--CCCCChHH-------HHHH
Q psy6094         126 -LLQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVL--------------QRLMKG--VGANSPKR-------WVKL  180 (455)
Q Consensus       126 -~lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~--------------~~~~~~--~~~~~~~~-------l~~~  180 (455)
                       -+..++...+...|++.+|||-|.. -..-..|++++.              ..|+..  ..+...+.       |...
T Consensus       187 ~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~v  266 (980)
T KOG4284|consen  187 DDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHV  266 (980)
T ss_pred             HHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHH
Confidence             3566666778899999999998432 111111111110              122211  11121111       2333


Q ss_pred             HHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCC
Q psy6094         181 LRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDD  260 (455)
Q Consensus       181 i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~  260 (455)
                      +..-+-.+.||||.....++.++..|...+      +.+..+.|.|.|.+|..+|...+.-..+|+||||.-+||||-++
T Consensus       267 f~~ipy~QAlVF~~~~sra~~~a~~L~ssG------~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~  340 (980)
T KOG4284|consen  267 FKSIPYVQALVFCDQISRAEPIATHLKSSG------LDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADN  340 (980)
T ss_pred             HhhCchHHHHhhhhhhhhhhHHHHHhhccC------CCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccc
Confidence            333566789999999999999999999875      88999999999999999999999999999999999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |..|||        .|          .|.....|.||.|||||.|. |.++.+.-
T Consensus       341 vNLVVN--------iD----------~p~d~eTY~HRIGRAgRFG~~G~aVT~~~  377 (980)
T KOG4284|consen  341 VNLVVN--------ID----------APADEETYFHRIGRAGRFGAHGAAVTLLE  377 (980)
T ss_pred             cceEEe--------cC----------CCcchHHHHHHhhhcccccccceeEEEec
Confidence            999999        44          34556778899999999998 99988876

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

Probab=99.83  E-value=1.3e-19  Score=189.34  Aligned_cols=110  Identities=17%  Similarity=0.176  Sum_probs=100.4

Q ss_pred             ccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee
Q psy6094         183 SMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       183 ~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~  262 (455)
                      ....++.+|||.|+.+++.+++.|+..+      +.+.++||+|+.++|..+.+.|.++..+|||||+....|||.|||+
T Consensus       227 ~~~~~~GIIYc~sRk~~E~ia~~L~~~g------~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVR  300 (590)
T COG0514         227 PQLSKSGIIYCLTRKKVEELAEWLRKNG------ISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVR  300 (590)
T ss_pred             cccCCCeEEEEeeHHhHHHHHHHHHHCC------CceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCce
Confidence            3667889999999999999999999874      8999999999999999999999999999999999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +||++++                  |-|-++|.|-+|||||.|. ..|+-||+..
T Consensus       301 fViH~~l------------------P~s~EsYyQE~GRAGRDG~~a~aill~~~~  337 (590)
T COG0514         301 FVIHYDL------------------PGSIESYYQETGRAGRDGLPAEAILLYSPE  337 (590)
T ss_pred             EEEEecC------------------CCCHHHHHHHHhhccCCCCcceEEEeeccc
Confidence            9999554                  4566788899999999886 9999999943

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

Probab=99.83  E-value=2.5e-19  Score=193.51  Aligned_cols=107  Identities=25%  Similarity=0.158  Sum_probs=91.7

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      +....+|||.||+...+.++..|....     ...+..+||+++.++|..+.+.+++|..|++|||.-.|-||||.+|+.
T Consensus       251 ~~~~ttLIF~NTR~~aE~l~~~L~~~~-----~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdl  325 (814)
T COG1201         251 KKHRTTLIFTNTRSGAERLAFRLKKLG-----PDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDL  325 (814)
T ss_pred             hhcCcEEEEEeChHHHHHHHHHHHHhc-----CCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceE
Confidence            344599999999999999999999875     267888999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCC----CCCCeEEecC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR----TLKRSETQQY  313 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR----~~~G~c~~L~  313 (455)
                      ||..|                  .|-|.+...||.||+|+    +..|..|...
T Consensus       326 VIq~~------------------SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         326 VIQLG------------------SPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             EEEeC------------------CcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            99844                  34566677899999996    2346666555

>KOG0337|consensus

Probab=99.82  E-value=2.7e-20  Score=182.66  Aligned_cols=255  Identities=15%  Similarity=0.142  Sum_probs=178.8

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhhh-hhcCCCC------ChHH--
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFITL-KRSETQQ------YPND--  105 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll~-e~~~~vg------~p~~--  105 (455)
                      |....++......+.+...--..++|...++.|+++++++..|.||||||-+  +|.+.. ....+.|      .|.+  
T Consensus        23 fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreL  102 (529)
T KOG0337|consen   23 FQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTREL  102 (529)
T ss_pred             ccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHH
Confidence            5566677777777777776666677999999999999999999999999933  331111 1111222      1221  


Q ss_pred             ------------------------------------------------HHHhc--cCCCCcCcc------hHHHHHH---
Q psy6094         106 ------------------------------------------------VLNML--KDPELEGVN------NDVIFSL---  126 (455)
Q Consensus       106 ------------------------------------------------ll~~l--~d~~L~~~~------~D~ll~~---  126 (455)
                                                                      ++...  .+-.|..+.      +|.|+.+   
T Consensus       103 a~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemgfq  182 (529)
T KOG0337|consen  103 ALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQ  182 (529)
T ss_pred             HHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhhhH
Confidence                                                            11111  111122221      7777755   


Q ss_pred             --HHHHHHhcCCCCeEEEEccCCC---------CC-ccceEEe------ehhhhhhhhccCCCCChHHHHHHHHc-cCCC
Q psy6094         127 --LQHICTTQRPGAILVYCTYTFM---------GV-SPMKVFF------CKNVLQRLMKGVGANSPKRWVKLLRS-MLVV  187 (455)
Q Consensus       127 --lk~il~~~~~~~k~ilmSAT~~---------g~-~pv~~~~------l~~~~~~~~~~~~~~~~~~l~~~i~~-~~~g  187 (455)
                        |..++.+.+.+.|.++||||+|         |. .|+-+..      -+.....+.......+...|...+.. ..+.
T Consensus       183 eql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~  262 (529)
T KOG0337|consen  183 EQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSILGGRIKDK  262 (529)
T ss_pred             HHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHHHhcccccc
Confidence              7778878888999999999994         55 6665551      11111122233333344445554442 2244


Q ss_pred             CEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeC
Q psy6094         188 PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDC  267 (455)
Q Consensus       188 ~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~  267 (455)
                      +.+||+++...++.+...|...+      +.+--+||+|++..|..-+..|..++..++|.||+|+||+|||..+-|||.
T Consensus       263 ~t~vf~~tk~hve~~~~ll~~~g------~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnviny  336 (529)
T KOG0337|consen  263 QTIVFVATKHHVEYVRGLLRDFG------GEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINY  336 (529)
T ss_pred             ceeEEecccchHHHHHHHHHhcC------CCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccc
Confidence            89999999999999999999875      667779999999999999999999999999999999999999999999996


Q ss_pred             CCC-cccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         268 GKT-KMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       268 g~~-k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      .++ +.+.|                   .||.||+.|.+. |..|.+....
T Consensus       337 d~p~~~klF-------------------vhRVgr~aragrtg~aYs~V~~~  368 (529)
T KOG0337|consen  337 DFPPDDKLF-------------------VHRVGRVARAGRTGRAYSLVAST  368 (529)
T ss_pred             cCCCCCceE-------------------EEEecchhhccccceEEEEEecc
Confidence            663 33333                   388898888886 9999998843

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

Probab=99.82  E-value=1.8e-19  Score=182.67  Aligned_cols=325  Identities=15%  Similarity=0.130  Sum_probs=206.0

Q ss_pred             HHHhcCHHHHHHHHHHccCCCHHHHHHHHHH-HHcCCeEEEEcCCCCCcccc-----hhhhhh-----------------
Q psy6094          38 IRKLQSRRYQEMLEARKKLPSYQMRDAVLDM-VRNNQITVISGETGSGPPLH-----LDFITL-----------------   94 (455)
Q Consensus        38 ~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~-i~~~~~vii~~~TGSGKTtq-----lp~ll~-----------------   94 (455)
                      .+.-..++++.+++.++..-.-++|--.+++ +.+|++.+|++.|+||||..     +|-++.                 
T Consensus       197 deLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQ  276 (830)
T COG1202         197 DELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQ  276 (830)
T ss_pred             cccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHHhhcc
Confidence            3556788999999999888788888887776 78999999999999999922     222221                 


Q ss_pred             ------hh--------cCCCCChH--H---------------------HHHhc--cCCCCcCcc----------------
Q psy6094          95 ------KR--------SETQQYPN--D---------------------VLNML--KDPELEGVN----------------  119 (455)
Q Consensus        95 ------e~--------~~~vg~p~--~---------------------ll~~l--~d~~L~~~~----------------  119 (455)
                            ++        ..+||..|  +                     =+++|  ....+.+++                
T Consensus       277 Ky~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEiHtL~deERG  356 (830)
T COG1202         277 KYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEIHTLEDEERG  356 (830)
T ss_pred             hHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcCCcccccceEEeeeeeeccchhcc
Confidence                  11        11222000  0                     11111  112333333                


Q ss_pred             --hHHHHHHHHHHHHhcCCCCeEEEEccCC--CCC----cc-ceEEeehhh--hhh-hhccCCCCChHHHHHHHHc----
Q psy6094         120 --NDVIFSLLQHICTTQRPGAILVYCTYTF--MGV----SP-MKVFFCKNV--LQR-LMKGVGANSPKRWVKLLRS----  183 (455)
Q Consensus       120 --~D~ll~~lk~il~~~~~~~k~ilmSAT~--~g~----~p-v~~~~l~~~--~~~-~~~~~~~~~~~~l~~~i~~----  183 (455)
                        -|-|++.||    ..-++-|+|.+|||+  |+.    +. --+.|-+.+  ++. .+-+.+....-.+..-+++    
T Consensus       357 ~RLdGLI~RLr----~l~~~AQ~i~LSATVgNp~elA~~l~a~lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~  432 (830)
T COG1202         357 PRLDGLIGRLR----YLFPGAQFIYLSATVGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFS  432 (830)
T ss_pred             cchhhHHHHHH----HhCCCCeEEEEEeecCChHHHHHHhCCeeEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHh
Confidence              344444444    445799999999999  110    00 001111111  111 1111111111112222221    


Q ss_pred             -----cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         184 -----MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       184 -----~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                           .-.|+.+||.++++.+..++..|...+      +.+.|+|++||..+|+.+...|.++...+||+|-.++.|+|.
T Consensus       433 ~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG------~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDF  506 (830)
T COG1202         433 TESSKGYRGQTIVFTYSRRRCHELADALTGKG------LKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDF  506 (830)
T ss_pred             hhhccCcCCceEEEecchhhHHHHHHHhhcCC------cccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCC
Confidence                 457999999999999999999999875      889999999999999999999999999999999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCCh-----hhhcc----------
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYPN-----DVLNM----------  320 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t~-----~~~~~----------  320 (455)
                      |.-.++.++              -.+-..|.|..++.|..|||||.+   .|++|.|.-.     ..|++          
T Consensus       507 PASQVIFEs--------------LaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~~Y~~~m~~TEdevA~kLL  572 (830)
T COG1202         507 PASQVIFES--------------LAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKYHASMEETEDEVAFKLL  572 (830)
T ss_pred             chHHHHHHH--------------HHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCChhhcccccccHHHHHHHHh
Confidence            975444431              112346999999999999999954   4999988661     11111          


Q ss_pred             CCCCcccccC------hHHHHHHHh-----hhcCCC------ChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhh
Q psy6094         321 LKDPELEGVN------NDVIFSLLQ-----HICTTQ------RPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAM  383 (455)
Q Consensus       321 ~~~PEi~r~~------~~~~L~~l~-----~~~~~P------~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~  383 (455)
                      ...||=..+.      .+-+|.-..     ..++.-      ..-..+.++..|.++|.++.+|+.  +.+|+.|+.++.
T Consensus       573 ~s~~e~V~vey~ee~e~e~vLA~~~v~~s~~~i~~v~~~~~g~~~~~~k~l~~Lee~g~i~~~G~~--v~~T~yGrava~  650 (830)
T COG1202         573 ESEPEPVIVEYDEEDEEENVLASAGVTNSLSVIERVNSLMLGAAFDPKKALSKLEEYGMIKKKGNI--VRPTPYGRAVAM  650 (830)
T ss_pred             cCCCCcceeccCcHHHHHHHHHHhhhcCcHHHHhhcChhhccccCCHHHHHHHHHhcCCeeccCCE--eeeccccceeEE
Confidence            1223322222      222331100     001110      012356889999999999988865  567999999988


Q ss_pred             CCCCh
Q psy6094         384 VDNKP  388 (455)
Q Consensus       384 lp~~p  388 (455)
                      -=+.|
T Consensus       651 ~Fl~p  655 (830)
T COG1202         651 SFLGP  655 (830)
T ss_pred             eecCc
Confidence            66777

>KOG0349|consensus

Probab=99.81  E-value=8.3e-20  Score=179.42  Aligned_cols=113  Identities=17%  Similarity=0.217  Sum_probs=99.8

Q ss_pred             HHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCC
Q psy6094         181 LRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDD  260 (455)
Q Consensus       181 i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~  260 (455)
                      +....-...++||.++.+++.|.+++.+.+   +..+.++++||+.-+.+|...++.|+++..|.++|||+|+||+||.+
T Consensus       500 i~~h~mdkaiifcrtk~dcDnLer~~~qkg---g~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g  576 (725)
T KOG0349|consen  500 IRRHAMDKAIIFCRTKQDCDNLERMMNQKG---GKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITG  576 (725)
T ss_pred             hhhhccCceEEEEeccccchHHHHHHHHcC---CccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccC
Confidence            333556789999999999999999999875   35799999999999999999999999999999999999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      +-||||--+                  |-.|.+|.||.||+||... |.++.|..
T Consensus       577 ~p~~invtl------------------pd~k~nyvhrigrvgraermglaislva  613 (725)
T KOG0349|consen  577 LPFMINVTL------------------PDDKTNYVHRIGRVGRAERMGLAISLVA  613 (725)
T ss_pred             CceEEEEec------------------CcccchhhhhhhccchhhhcceeEEEee
Confidence            999999444                  4556678899999999877 99999876

>PRK09401 reverse gyrase; Reviewed

Probab=99.76  E-value=5.2e-18  Score=192.75  Aligned_cols=121  Identities=19%  Similarity=0.249  Sum_probs=88.0

Q ss_pred             CCeEEEEccCCCCC-ccc---------e----EEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHH---H
Q psy6094         137 GAILVYCTYTFMGV-SPM---------K----VFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDT---I  199 (455)
Q Consensus       137 ~~k~ilmSAT~~g~-~pv---------~----~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~e---i  199 (455)
                      +.|++++|||++.+ ...         .    ..++.++.+.|....  .....+..++. ..++.+||||++...   +
T Consensus       268 ~~q~ilfSAT~~~~~~~~~l~~~ll~~~v~~~~~~~rnI~~~yi~~~--~k~~~L~~ll~-~l~~~~LIFv~t~~~~~~a  344 (1176)
T PRK09401        268 KGVLVVSSATGRPRGNRVKLFRELLGFEVGSPVFYLRNIVDSYIVDE--DSVEKLVELVK-RLGDGGLIFVPSDKGKEYA  344 (1176)
T ss_pred             CceEEEEeCCCCccchHHHHhhccceEEecCcccccCCceEEEEEcc--cHHHHHHHHHH-hcCCCEEEEEecccChHHH
Confidence            67899999999532 111         0    011122222222211  22333555554 334679999999777   9


Q ss_pred             HHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEe----CCCCccCCCCCC-eeEEEeCCCCc
Q psy6094         200 NSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA----TNIAETSITIDD-IVYVVDCGKTK  271 (455)
Q Consensus       200 ~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViva----Tniae~gitI~~-V~~VID~g~~k  271 (455)
                      +.+++.|+..+      +.+..+||++     .+.++.|++|+.+|+||    ||+|+||||||+ |+|||++|.|+
T Consensus       345 e~l~~~L~~~g------i~v~~~hg~l-----~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~  410 (1176)
T PRK09401        345 EELAEYLEDLG------INAELAISGF-----ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPK  410 (1176)
T ss_pred             HHHHHHHHHCC------CcEEEEeCcH-----HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCC
Confidence            99999999875      8899999999     23458899999999999    799999999999 89999999998

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.76  E-value=4e-18  Score=194.72  Aligned_cols=106  Identities=20%  Similarity=0.196  Sum_probs=89.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCC---------------------------CCCCeEEEeecCCCChhhHhhhhc
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFF---------------------------NSSRFQIIPLHSMLPTVSQKSIFN  236 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~---------------------------~~~~~~v~~lhs~l~~~~r~~v~~  236 (455)
                      ...+++|||++|+..++.++..|++....                           ....+.+..+||+|++++|..+++
T Consensus       242 ~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~  321 (1490)
T PRK09751        242 LRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQ  321 (1490)
T ss_pred             hcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHH
Confidence            34678999999999999999999764210                           001234778999999999999999


Q ss_pred             CCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCC
Q psy6094         237 TPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR  307 (455)
Q Consensus       237 ~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G  307 (455)
                      .|++|..+|||||+.+|.||||++|++||+.|.                  |.|.+++.||+|||||...|
T Consensus       322 ~fK~G~LrvLVATssLELGIDIg~VDlVIq~gs------------------P~sVas~LQRiGRAGR~~gg  374 (1490)
T PRK09751        322 ALKSGELRCVVATSSLELGIDMGAVDLVIQVAT------------------PLSVASGLQRIGRAGHQVGG  374 (1490)
T ss_pred             HHHhCCceEEEeCcHHHccCCcccCCEEEEeCC------------------CCCHHHHHHHhCCCCCCCCC
Confidence            999999999999999999999999999999553                  67889999999999996433

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.74  E-value=5.1e-17  Score=177.37  Aligned_cols=205  Identities=16%  Similarity=0.135  Sum_probs=138.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcC--C----------CCCCC-------------------eEEEeecCCCChhhHh
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSS--F----------FNSSR-------------------FQIIPLHSMLPTVSQK  232 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~--~----------~~~~~-------------------~~v~~lhs~l~~~~r~  232 (455)
                      ..+|++|||++++.+....++.+....  .          ....+                   .-+.-+|++|+.++|.
T Consensus       251 ~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~  330 (766)
T COG1204         251 AEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQ  330 (766)
T ss_pred             hcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHH
Confidence            678999999999999999999988410  0          00111                   1256678999999999


Q ss_pred             hhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeE
Q psy6094         233 SIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSE  309 (455)
Q Consensus       233 ~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c  309 (455)
                      .+.+.|++|+.|||+||+.++.|++.|.-++||- |   ...||+..|     .+.+++..+.|..|||||.|=   |..
T Consensus       331 ~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk-~---~~~y~~~~g-----~~~i~~~dv~QM~GRAGRPg~d~~G~~  401 (766)
T COG1204         331 LVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIK-D---TRRYDPKGG-----IVDIPVLDVLQMAGRAGRPGYDDYGEA  401 (766)
T ss_pred             HHHHHHhcCCceEEEechHHhhhcCCcceEEEEe-e---eEEEcCCCC-----eEECchhhHhhccCcCCCCCcCCCCcE
Confidence            9999999999999999999999999998777773 2   234776333     368899999999999999652   555


Q ss_pred             EecC-Chhh------hccCCCCcccccC--hHHHH--------------------HHHhhhcCCC-------ChhhHHhH
Q psy6094         310 TQQY-PNDV------LNMLKDPELEGVN--NDVIF--------------------SLLQHICTTQ-------RPGAILVF  353 (455)
Q Consensus       310 ~~L~-t~~~------~~~~~~PEi~r~~--~~~~L--------------------~~l~~~~~~P-------~~~~i~~a  353 (455)
                      +.+- +.+.      ......||.....  .+..+                    .|+....-.|       ....+..+
T Consensus       402 ~i~~~~~~~~~~~~~~~~~~~~e~~~s~l~~~~~~~~~l~~v~~~~~~v~~~~~~~f~~~t~~~~~~~~~~~~~~~i~~~  481 (766)
T COG1204         402 IILATSHDELEYLAELYIQSEPEPIESKLGDELNLRTFLLGVISVGDAVSWLELTDFYERTFYNPQTYGEGMLREEILAS  481 (766)
T ss_pred             EEEecCccchhHHHHHhhccCcchHHHhhcccccchheEEEEEeccchhhHHHHHHHHHHHHhhhhhccccchHHHHHHH
Confidence            5444 3111      1123344441111  11111                    1222222222       34567788


Q ss_pred             Hhhhhhcc-cccCCCCCCcccCChHHHHHhhCCCChhHHHHHHHhhc
Q psy6094         354 LPGWDTIN-SLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLS  399 (455)
Q Consensus       354 l~~L~~lg-ald~~~~l~~~~~T~lG~~l~~lp~~p~~~l~iaa~ls  399 (455)
                      +..|.+.+ .++....  .+.+|++|+.++++.++|+.+..+...+.
T Consensus       482 ~~~L~~~~~~~~~~~~--~~~ate~g~~~s~~yi~~~sa~~~~~~l~  526 (766)
T COG1204         482 LRYLEENGLILDADWE--ALHATELGKLVSRLYIDPESAKIFRDLLA  526 (766)
T ss_pred             HHHHHhccceeecccc--ccchhHHHHHhhhccCCHHHHHHHHHHHH
Confidence            88888876 5554432  35679999999999999965555544443

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

Probab=99.74  E-value=3.1e-17  Score=181.28  Aligned_cols=248  Identities=21%  Similarity=0.206  Sum_probs=158.5

Q ss_pred             HHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc--cchhhhhh------------------------------
Q psy6094          47 QEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP--LHLDFITL------------------------------   94 (455)
Q Consensus        47 ~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT--tqlp~ll~------------------------------   94 (455)
                      .+.+..|.....|.||.+.++.+.+|++|||+.+||||||  +++| |++                              
T Consensus        60 ~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllP-Ild~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~  138 (851)
T COG1205          60 KSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLP-ILDHLLRDPSARALLLYPTNALANDQAERLREL  138 (851)
T ss_pred             HHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHH-HHHHHhhCcCccEEEEechhhhHhhHHHHHHHH
Confidence            4556677888899999999999999999999999999999  4444 222                              


Q ss_pred             --hhcCCCC---C----hHH------------------HHHhc----cC--------------CCCcCcc----hHH--H
Q psy6094          95 --KRSETQQ---Y----PND------------------VLNML----KD--------------PELEGVN----NDV--I  123 (455)
Q Consensus        95 --e~~~~vg---~----p~~------------------ll~~l----~d--------------~~L~~~~----~D~--l  123 (455)
                        ..+..++   |    |..                  +++.+    .+              ..++.|.    +++  |
T Consensus       139 ~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~l  218 (851)
T COG1205         139 ISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALL  218 (851)
T ss_pred             HHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHH
Confidence              1121122   1    110                  22221    00              0222332    443  2


Q ss_pred             HHHHHHHHHhcCCCCeEEEEccCC----------CCC-ccce-----------EEeehhhhhhhhccC-CCCChHHHHHH
Q psy6094         124 FSLLQHICTTQRPGAILVYCTYTF----------MGV-SPMK-----------VFFCKNVLQRLMKGV-GANSPKRWVKL  180 (455)
Q Consensus       124 l~~lk~il~~~~~~~k~ilmSAT~----------~g~-~pv~-----------~~~l~~~~~~~~~~~-~~~~~~~l~~~  180 (455)
                      +-.|++.+.....++|+|.+|||+          .|+ |.+.           .+.+.++........ .......+...
T Consensus       219 lRRL~~~~~~~~~~~q~i~~SAT~~np~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~  298 (851)
T COG1205         219 LRRLLRRLRRYGSPLQIICTSATLANPGEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATL  298 (851)
T ss_pred             HHHHHHHHhccCCCceEEEEeccccChHHHHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhcccchHHHHHHH
Confidence            233555554455789999999999          222 2111           111111100000000 00111111111


Q ss_pred             HHc--cCCCCEEEEcCCHHHHHHHHHH----HHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         181 LRS--MLVVPILVFLPGWDTINSLHRS----MCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       181 i~~--~~~g~iLVFlp~~~ei~~l~~~----L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +..  ..+-..|||+.++..++.+...    +...+  ......+..+||+++.++|.++...++.|..++++|||.+|-
T Consensus       299 ~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~--~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~Alel  376 (851)
T COG1205         299 AALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREG--GKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALEL  376 (851)
T ss_pred             HHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcc--hhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhh
Confidence            111  5677899999999999998633    32222  011245888999999999999999999999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ||||.+++.||.+|+|                 ..|..+++||+|||||.+. +..+-.+.
T Consensus       377 gidiG~ldavi~~g~P-----------------~~s~~~~~Q~~GRaGR~~~~~l~~~v~~  420 (851)
T COG1205         377 GIDIGSLDAVIAYGYP-----------------GVSVLSFRQRAGRAGRRGQESLVLVVLR  420 (851)
T ss_pred             ceeehhhhhHhhcCCC-----------------CchHHHHHHhhhhccCCCCCceEEEEeC
Confidence            9999999999998874                 1277889999999999873 54444444

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.73  E-value=3.7e-17  Score=165.77  Aligned_cols=88  Identities=18%  Similarity=0.193  Sum_probs=72.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++++||||++.+.++.+++.|+..+.    ++.+..+||.+++.+|.++.      +.+|+||||++|+||||+++ +
T Consensus       270 ~~~~k~LIf~nt~~~~~~l~~~L~~~~~----~~~~~~l~g~~~~~~R~~~~------~~~iLVaTdv~~rGiDi~~~-~  338 (357)
T TIGR03158       270 LPGERGAIILDSLDEVNRLSDLLQQQGL----GDDIGRITGFAPKKDRERAM------QFDILLGTSTVDVGVDFKRD-W  338 (357)
T ss_pred             cCCCeEEEEECCHHHHHHHHHHHhhhCC----CceEEeeecCCCHHHHHHhc------cCCEEEEecHHhcccCCCCc-e
Confidence            3567899999999999999999987531    36788999999999997764      46899999999999999987 5


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAG  302 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaG  302 (455)
                      ||-         +           |.+.++|.||+||+|
T Consensus       339 vi~---------~-----------p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       339 LIF---------S-----------ARDAAAFWQRLGRLG  357 (357)
T ss_pred             EEE---------C-----------CCCHHHHhhhcccCC
Confidence            551         1           345678999999998

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.72  E-value=5.4e-17  Score=171.65  Aligned_cols=107  Identities=14%  Similarity=0.050  Sum_probs=90.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC-CCCccCCCCCCee
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT-NIAETSITIDDIV  262 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT-niae~gitI~~V~  262 (455)
                      ..++.+|||+...+.++.+++.|...+      ..+..+||++++++|..+++.+..|...||||| +++.+|+|+|+++
T Consensus       342 ~~~~~~lV~~~~~~h~~~L~~~L~~~g------~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld  415 (501)
T PHA02558        342 KKGENTFVMFKYVEHGKPLYEMLKKVY------DKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLH  415 (501)
T ss_pred             hcCCCEEEEEEEHHHHHHHHHHHHHcC------CCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceecccccccccc
Confidence            456789999999999999999999864      689999999999999999999999999999998 9999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCe-EEecCC
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS-ETQQYP  314 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~-c~~L~t  314 (455)
                      .||.        ++|          +-|+..+.||+||+||.++|. -..+|+
T Consensus       416 ~vIl--------~~p----------~~s~~~~~QriGR~~R~~~~K~~~~i~D  450 (501)
T PHA02558        416 HVIF--------AHP----------SKSKIIVLQSIGRVLRKHGSKSIATVWD  450 (501)
T ss_pred             EEEE--------ecC----------CcchhhhhhhhhccccCCCCCceEEEEE
Confidence            9995        221          235677889999999988753 334443

>TIGR01054 rgy reverse gyrase

Probab=99.70  E-value=1.8e-16  Score=180.41  Aligned_cols=87  Identities=11%  Similarity=0.219  Sum_probs=75.2

Q ss_pred             HHHHHHccCCCCEEEEcCCH---HHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEe----C
Q psy6094         177 WVKLLRSMLVVPILVFLPGW---DTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA----T  249 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~---~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViva----T  249 (455)
                      +..++. ..++.+|||+++.   +.++.+++.|.+.+      +.+..+||++++    .+++.|++|+.+|+||    |
T Consensus       318 L~~ll~-~l~~~~IVFv~t~~~~~~a~~l~~~L~~~g------~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~t  386 (1171)
T TIGR01054       318 LLEIVK-KLGTGGIVYVSIDYGKEKAEEIAEFLENHG------VKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYY  386 (1171)
T ss_pred             HHHHHH-HcCCCEEEEEeccccHHHHHHHHHHHHhCC------ceEEEEeCCCCH----HHHHHHHcCCCCEEEEecccc
Confidence            445554 3356799999999   99999999998864      889999999973    6889999999999999    5


Q ss_pred             CCCccCCCCCC-eeEEEeCCCCcccc
Q psy6094         250 NIAETSITIDD-IVYVVDCGKTKMSN  274 (455)
Q Consensus       250 niae~gitI~~-V~~VID~g~~k~~~  274 (455)
                      |+|+||||||+ |+|||++|.|+.+.
T Consensus       387 dv~aRGIDip~~V~~vI~~~~P~~~~  412 (1171)
T TIGR01054       387 GTLVRGLDLPERVRYAVFLGVPKFKV  412 (1171)
T ss_pred             CcccccCCCCccccEEEEECCCCEEE
Confidence            99999999999 89999999998653

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.69  E-value=2.7e-17  Score=190.91  Aligned_cols=120  Identities=15%  Similarity=0.085  Sum_probs=91.3

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHH---HHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC----
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTI---NSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT----  249 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei---~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT----  249 (455)
                      +..++.. .+..+||||+++..+   +.+++.|...+      +.+.++||+     |..+++.|.+|..+|+|||    
T Consensus       322 L~~ll~~-~g~~gIVF~~t~~~~e~ae~la~~L~~~G------i~a~~~h~~-----R~~~l~~F~~G~~~VLVaT~s~~  389 (1638)
T PRK14701        322 VRELLKK-LGKGGLIFVPIDEGAEKAEEIEKYLLEDG------FKIELVSAK-----NKKGFDLFEEGEIDYLIGVATYY  389 (1638)
T ss_pred             HHHHHHh-CCCCeEEEEeccccchHHHHHHHHHHHCC------CeEEEecch-----HHHHHHHHHcCCCCEEEEecCCC
Confidence            5555553 356899999998765   88999999874      899999995     8889999999999999999    


Q ss_pred             CCCccCCCCCC-eeEEEeCCCCcccc----cccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         250 NIAETSITIDD-IVYVVDCGKTKMSN----FDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       250 niae~gitI~~-V~~VID~g~~k~~~----yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |+|+||||+|+ |+|||+.|+||...    |.+....     .+. ...+.++.|||||.+. +.|+..|.
T Consensus       390 gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~-----~~~-~~~~~~~~~~a~~~g~~~~~~~~~~  454 (1638)
T PRK14701        390 GTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYR-----ILG-LLSEILKIEEELKEGIPIEGVLDVF  454 (1638)
T ss_pred             CeeEecCccCCccCEEEEeCCCCCCcchhhcccchhh-----hhc-chHHHHHhhhhcccCCcchhHHHhH
Confidence            69999999999 99999999998442    3222211     011 2335678899999774 77764444

>KOG0354|consensus

Probab=99.68  E-value=5.9e-16  Score=164.11  Aligned_cols=112  Identities=20%  Similarity=0.245  Sum_probs=89.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC-CCCeEEEeec----CCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFN-SSRFQIIPLH----SMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~-~~~~~v~~lh----s~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                      .+...++||+.+++.+..+.+.|....... .+..-+-.=+    .+|++++|.++++.|++|..+|||||.|||=|+||
T Consensus       411 ~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI  490 (746)
T KOG0354|consen  411 NPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDI  490 (746)
T ss_pred             CCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCc
Confidence            566789999999999999999998422110 0011111111    58999999999999999999999999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      +.++.||=        ||..++.-          ...||+|| ||...|.|+.|++
T Consensus       491 ~ec~lVIc--------Yd~~snpI----------rmIQrrGR-gRa~ns~~vll~t  527 (746)
T KOG0354|consen  491 GECNLVIC--------YDYSSNPI----------RMVQRRGR-GRARNSKCVLLTT  527 (746)
T ss_pred             ccccEEEE--------ecCCccHH----------HHHHHhcc-ccccCCeEEEEEc
Confidence            99999996        76665533          35599999 9999999999999

>PRK13766 Hef nuclease; Provisional

Probab=99.65  E-value=1.3e-15  Score=169.62  Aligned_cols=108  Identities=19%  Similarity=0.234  Sum_probs=94.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCC--------CChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSM--------LPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~--------l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      ..++.+|||+++.+.++.+.+.|...+      +.+..+||.        +++.+|.++++.|+.|..+|+|||++++.|
T Consensus       363 ~~~~kvlIF~~~~~t~~~L~~~L~~~~------~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eG  436 (773)
T PRK13766        363 NPDSRIIVFTQYRDTAEKIVDLLEKEG------IKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEG  436 (773)
T ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHhCC------CceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcC
Confidence            457889999999999999999997654      556677775        999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN  315 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~  315 (455)
                      +|+|++++||+        ||+.          .|...+.||+||+||.++|.+|.|+++
T Consensus       437 ldi~~~~~VI~--------yd~~----------~s~~r~iQR~GR~gR~~~~~v~~l~~~  478 (773)
T PRK13766        437 LDIPSVDLVIF--------YEPV----------PSEIRSIQRKGRTGRQEEGRVVVLIAK  478 (773)
T ss_pred             CCcccCCEEEE--------eCCC----------CCHHHHHHHhcccCcCCCCEEEEEEeC
Confidence            99999999998        6643          345568899999999999999999983

>KOG0352|consensus

Probab=99.64  E-value=2.1e-15  Score=148.58  Aligned_cols=108  Identities=16%  Similarity=0.153  Sum_probs=95.2

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYV  264 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~V  264 (455)
                      ..|..+|+|.|+++++.++-.|...+      +....+|++|-..+|..|.+.+-++..-||+||+-...|+|-|+|++|
T Consensus       254 ~~GCGIVYCRTR~~cEq~AI~l~~~G------i~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFV  327 (641)
T KOG0352|consen  254 FTGCGIVYCRTRNECEQVAIMLEIAG------IPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFV  327 (641)
T ss_pred             cCcceEEEeccHHHHHHHHHHhhhcC------cchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEE
Confidence            46889999999999999999988775      788999999999999999999999999999999999999999999999


Q ss_pred             EeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         265 VDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       265 ID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+        ||+.          .+-+-|.|-.|||||.|. ..|-.-|+++
T Consensus       328 iH--------W~~~----------qn~AgYYQESGRAGRDGk~SyCRLYYsR~  362 (641)
T KOG0352|consen  328 IH--------WSPS----------QNLAGYYQESGRAGRDGKRSYCRLYYSRQ  362 (641)
T ss_pred             Ee--------cCch----------hhhHHHHHhccccccCCCccceeeeeccc
Confidence            98        6544          445678899999999988 6776667743

>PRK09694 helicase Cas3; Provisional

Probab=99.63  E-value=6.9e-15  Score=162.43  Aligned_cols=98  Identities=16%  Similarity=0.209  Sum_probs=79.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHh----hhhcCC-CCCc---eEEEEeCCCCccC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQK----SIFNTP-PEGV---RKIVLATNIAETS  255 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~----~v~~~~-~~g~---~kVivaTniae~g  255 (455)
                      ..++.+|||+||.+.++.+++.|++..   .....+..+||++++.+|.    ++++.| ++|+   .+|+|||+|+|+|
T Consensus       558 ~~g~~vLVf~NTV~~Aq~ly~~L~~~~---~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~G  634 (878)
T PRK09694        558 NAGAQVCLICNLVDDAQKLYQRLKELN---NTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQS  634 (878)
T ss_pred             hcCCEEEEEECCHHHHHHHHHHHHhhC---CCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhhe
Confidence            467889999999999999999998653   1246799999999999994    566667 5565   4799999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL  305 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~  305 (455)
                      +|| |+++||..-                    ....++.||+||+||.+
T Consensus       635 LDI-d~DvlItdl--------------------aPidsLiQRaGR~~R~~  663 (878)
T PRK09694        635 LDL-DFDWLITQL--------------------CPVDLLFQRLGRLHRHH  663 (878)
T ss_pred             eec-CCCeEEECC--------------------CCHHHHHHHHhccCCCC
Confidence            999 578888521                    22468889999999964

>KOG0351|consensus

Probab=99.62  E-value=5.6e-15  Score=162.90  Aligned_cols=109  Identities=17%  Similarity=0.138  Sum_probs=99.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      .+.+.+||+|.++.+++.++..|+..+      .....+|++|+..+|..|...|-.++.+||+||=....|||-|||++
T Consensus       483 ~~~~s~IIYC~sr~~ce~vs~~L~~~~------~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~  556 (941)
T KOG0351|consen  483 HPDQSGIIYCLSRKECEQVSAVLRSLG------KSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRF  556 (941)
T ss_pred             CCCCCeEEEeCCcchHHHHHHHHHHhc------hhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeE
Confidence            678899999999999999999999875      78899999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||+++++|                  |-+.|.|-+|||||-|- ..|..+|+..
T Consensus       557 ViH~~lPk------------------s~E~YYQE~GRAGRDG~~s~C~l~y~~~  592 (941)
T KOG0351|consen  557 VIHYSLPK------------------SFEGYYQEAGRAGRDGLPSSCVLLYGYA  592 (941)
T ss_pred             EEECCCch------------------hHHHHHHhccccCcCCCcceeEEecchh
Confidence            99988865                  33456699999999887 9999999944

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

Probab=99.62  E-value=8.7e-15  Score=141.05  Aligned_cols=106  Identities=20%  Similarity=0.307  Sum_probs=84.0

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +..+|..  ..+.++|||+|+..-.+.++..|+..-    +...+...||.  .+.|.+..+.|++|+.+++++|.|+||
T Consensus       294 l~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~----~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILER  367 (441)
T COG4098         294 LKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKL----PKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILER  367 (441)
T ss_pred             HHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhC----Cccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhc
Confidence            5555554  567899999999999999999996543    24667788876  456777888899999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCC
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT  304 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~  304 (455)
                      |+|+|+|+++|-         +...       .--|+++..|-+||+||.
T Consensus       368 GVTfp~vdV~Vl---------gaeh-------~vfTesaLVQIaGRvGRs  401 (441)
T COG4098         368 GVTFPNVDVFVL---------GAEH-------RVFTESALVQIAGRVGRS  401 (441)
T ss_pred             ccccccceEEEe---------cCCc-------ccccHHHHHHHhhhccCC
Confidence            999999997662         1111       124788999999999994

>KOG0952|consensus

Probab=99.62  E-value=7.8e-15  Score=157.80  Aligned_cols=126  Identities=14%  Similarity=0.120  Sum_probs=96.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCC--------CCC--C-------eEEEeecCCCChhhHhhhhcCCCCCceEEE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFF--------NSS--R-------FQIIPLHSMLPTVSQKSIFNTPPEGVRKIV  246 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--------~~~--~-------~~v~~lhs~l~~~~r~~v~~~~~~g~~kVi  246 (455)
                      ..+.++||||+++.+..+.++.|.+....        .++  +       .-+...|+||.-++|..+.+-|..|..+|+
T Consensus       347 ~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL  426 (1230)
T KOG0952|consen  347 QEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVL  426 (1230)
T ss_pred             HcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEE
Confidence            56889999999999999999999875432        111  1       235567899999999999999999999999


Q ss_pred             EeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCChhh
Q psy6094         247 LATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYPNDV  317 (455)
Q Consensus       247 vaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t~~~  317 (455)
                      +||..++-|+++|+-.++|- |   .+.||+..|.-.    -.+-....|--|||||.+   .|..+-+-+.+.
T Consensus       427 ~cTaTLAwGVNLPA~aViIK-G---T~~ydsskg~f~----dlgilDVlQifGRAGRPqFd~~G~giIiTt~dk  492 (1230)
T KOG0952|consen  427 CCTATLAWGVNLPAYAVIIK-G---TQVYDSSKGSFV----DLGILDVLQIFGRAGRPQFDSSGEGIIITTRDK  492 (1230)
T ss_pred             EecceeeeccCCcceEEEec-C---CcccccccCcee----eehHHHHHHHHhccCCCCCCCCceEEEEecccH
Confidence            99999999999998666663 3   346888776321    234456779999999954   377776666443

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

Probab=99.60  E-value=1.7e-14  Score=145.68  Aligned_cols=111  Identities=20%  Similarity=0.237  Sum_probs=91.7

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeE--EEe-----ecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQ--IIP-----LHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~--v~~-----lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      ..+..++||..-++.++.+.+.|...+.    ...  .+.     --.||+|.+|.++++.|+.|..+|+|||.|+|-|+
T Consensus       364 ~~~~RvIVFT~yRdTae~i~~~L~~~~~----~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGL  439 (542)
T COG1111         364 NGDSRVIVFTEYRDTAEEIVNFLKKIGI----KARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGL  439 (542)
T ss_pred             CCCceEEEEehhHhHHHHHHHHHHhcCC----cceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccccccC
Confidence            3456899999999999999999998753    121  111     12579999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~  316 (455)
                      |||++++||=        |+|-.          |-=-+.||.||+||..+|..|-|+++.
T Consensus       440 DIp~vDlVif--------YEpvp----------SeIR~IQR~GRTGR~r~Grv~vLvt~g  481 (542)
T COG1111         440 DIPEVDLVIF--------YEPVP----------SEIRSIQRKGRTGRKRKGRVVVLVTEG  481 (542)
T ss_pred             CCCcccEEEE--------ecCCc----------HHHHHHHhhCccccCCCCeEEEEEecC
Confidence            9999999994        65432          223467999999999999999999955

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

Probab=99.56  E-value=1e-14  Score=152.87  Aligned_cols=154  Identities=16%  Similarity=0.149  Sum_probs=114.8

Q ss_pred             HHHhcCC-CCeEEEEccCC----------------------CCCccceEEeehhhhhhhhccCCCCChHHHHHHHHc--c
Q psy6094         130 ICTTQRP-GAILVYCTYTF----------------------MGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRS--M  184 (455)
Q Consensus       130 il~~~~~-~~k~ilmSAT~----------------------~g~~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~--~  184 (455)
                      .+..+.. .+.+++||||+                      +||.|+..+.+.+--           ...+...+..  .
T Consensus       403 ~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~-----------~~~v~e~i~~ei~  471 (677)
T COG1200         403 ALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHER-----------RPEVYERIREEIA  471 (677)
T ss_pred             HHHHhCCCCCcEEEEeCCCchHHHHHHHhccccchhhccCCCCCCceEEEEecccc-----------HHHHHHHHHHHHH
Confidence            3435556 68999999999                      677888877765311           1122333332  4


Q ss_pred             CCCCEEEEcCCHHHH--------HHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         185 LVVPILVFLPGWDTI--------NSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei--------~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      .+.++-+-||=.+|-        +.+++.|...    .+++.+..+||.|+.++.++|++.|++|..+|+|||.|.|-||
T Consensus       472 ~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~----~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGV  547 (677)
T COG1200         472 KGRQAYVVCPLIEESEKLELQAAEELYEELKSF----LPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGV  547 (677)
T ss_pred             cCCEEEEEeccccccccchhhhHHHHHHHHHHH----cccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecc
Confidence            567788888865544        4455566532    2468899999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCccccccc-CCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDV-KDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~-~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+||.++.|-        +|+ +-|+          |+..|-+||+||... +.|+-+|...
T Consensus       548 dVPnATvMVI--------e~AERFGL----------aQLHQLRGRVGRG~~qSyC~Ll~~~~  591 (677)
T COG1200         548 DVPNATVMVI--------ENAERFGL----------AQLHQLRGRVGRGDLQSYCVLLYKPP  591 (677)
T ss_pred             cCCCCeEEEE--------echhhhhH----------HHHHHhccccCCCCcceEEEEEeCCC
Confidence            9999998774        442 3454          456699999999776 9999999843

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.53  E-value=7.7e-14  Score=152.26  Aligned_cols=102  Identities=14%  Similarity=0.137  Sum_probs=73.4

Q ss_pred             HHHHHHHHHHhcCCCCCCCeEEEeecCCCCh--hhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE--eCCCCccc
Q psy6094         198 TINSLHRSMCQSSFFNSSRFQIIPLHSMLPT--VSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV--DCGKTKMS  273 (455)
Q Consensus       198 ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~--~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI--D~g~~k~~  273 (455)
                      .++++++.|.+..    ++..+..+|+++.+  .+++++++.|++|+..|+|+|+++++|+|+|+|+.|+  |.+.    
T Consensus       438 G~e~~~e~l~~~f----p~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~----  509 (679)
T PRK05580        438 GTERLEEELAELF----PEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADL----  509 (679)
T ss_pred             cHHHHHHHHHHhC----CCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCch----
Confidence            4555556665542    24678999999975  5688999999999999999999999999999999885  5322    


Q ss_pred             ccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEe
Q psy6094         274 NFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQ  311 (455)
Q Consensus       274 ~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~  311 (455)
                          ..+...+...--.-+.+.|++|||||.+. |.|+-
T Consensus       510 ----~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~vii  544 (679)
T PRK05580        510 ----GLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLI  544 (679)
T ss_pred             ----hccCCccchHHHHHHHHHHHHhhccCCCCCCEEEE
Confidence                22222222112223567899999999665 88883

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.53  E-value=4.2e-14  Score=152.48  Aligned_cols=103  Identities=14%  Similarity=0.107  Sum_probs=86.7

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ceEEEEeCCCCccCCCCCCeeE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~kVivaTniae~gitI~~V~~  263 (455)
                      .+..+|||+.....++.+++.|.           +..+||++++.+|.++++.|+.| ..++||+|+++.+|||+|++++
T Consensus       495 ~g~kiLVF~~~~~~l~~~a~~L~-----------~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~v  563 (732)
T TIGR00603       495 RGDKIIVFSDNVFALKEYAIKLG-----------KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANV  563 (732)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHcC-----------CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCE
Confidence            56799999999998888887763           23489999999999999999865 7799999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeE-------EecCCh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSE-------TQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c-------~~L~t~  315 (455)
                      ||.        ++..         +-|+.++.||.||++|.++ |.+       |.|.+.
T Consensus       564 vI~--------~s~~---------~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~  606 (732)
T TIGR00603       564 LIQ--------ISSH---------YGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSK  606 (732)
T ss_pred             EEE--------eCCC---------CCCHHHHHHHhcccccCCCCCccccccceEEEEecC
Confidence            997        3322         2478899999999999887 555       888883

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=99.52  E-value=2.4e-14  Score=152.63  Aligned_cols=114  Identities=18%  Similarity=0.127  Sum_probs=91.3

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+.++|||+++.++++.+++.|...+      +.+..|||...+.++..+...+.+  .+|+||||+|.|
T Consensus       462 L~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~g------i~~~~Lhg~~~~rE~~ii~~ag~~--g~VlVATdmAgR  533 (656)
T PRK12898        462 VAARVRELHAQGRPVLVGTRSVAASERLSALLREAG------LPHQVLNAKQDAEEAAIVARAGQR--GRITVATNMAGR  533 (656)
T ss_pred             HHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC------CCEEEeeCCcHHHHHHHHHHcCCC--CcEEEEccchhc
Confidence            4444433  236789999999999999999999874      889999999776666555554444  469999999999


Q ss_pred             CCCCC---Cee-----EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         255 SITID---DIV-----YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       255 gitI~---~V~-----~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+||+   +|.     +||++.++                  -|...+.||+||+||.|. |.|+.+++.+
T Consensus       534 GtDI~l~~~V~~~GGLhVI~~d~P------------------~s~r~y~hr~GRTGRqG~~G~s~~~is~e  586 (656)
T PRK12898        534 GTDIKLEPGVAARGGLHVILTERH------------------DSARIDRQLAGRCGRQGDPGSYEAILSLE  586 (656)
T ss_pred             ccCcCCccchhhcCCCEEEEcCCC------------------CCHHHHHHhcccccCCCCCeEEEEEechh
Confidence            99999   776     99996553                  455567799999999986 9999999943

>KOG0921|consensus

Probab=99.48  E-value=1.9e-15  Score=159.67  Aligned_cols=302  Identities=8%  Similarity=-0.152  Sum_probs=219.5

Q ss_pred             HHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-h------------hhh-----------------
Q psy6094          45 RYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-F------------ITL-----------------   94 (455)
Q Consensus        45 ~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~------------ll~-----------------   94 (455)
                      ....+...+.-+|+.++...|++++..+.+.++-+.|||||+++.| +            +.+                 
T Consensus       394 ~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tvgy~vRf~Sa~prpyg  473 (1282)
T KOG0921|consen  394 RVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETCGYNVRFDSATPRPYG  473 (1282)
T ss_pred             ceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccccccccccccccccccc
Confidence            3334446677899999999999999999999999999999999866 1            222                 


Q ss_pred             ---hhcCCCC----C--------hH-----------H----HHHhc--cCCCCc------CcchHHHHHHHHHHHHhcCC
Q psy6094          95 ---KRSETQQ----Y--------PN-----------D----VLNML--KDPELE------GVNNDVIFSLLQHICTTQRP  136 (455)
Q Consensus        95 ---e~~~~vg----~--------p~-----------~----ll~~l--~d~~L~------~~~~D~ll~~lk~il~~~~~  136 (455)
                         +.+..++    +        |+           +    +++.|  ..+.|.      .++||+++.+++.+.     
T Consensus       474 ~i~fctvgvllr~~e~glrg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~lmsatIdTd~f~~~f~~~p-----  548 (1282)
T KOG0921|consen  474 SIMFCTVGVLLRMMENGLRGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLMSATIDTDLFTNFFSSIP-----  548 (1282)
T ss_pred             ceeeeccchhhhhhhhcccccccccchhhhhhccchHHHHHHHHhhhccchhhhhhhhhcccchhhhhhhhcccc-----
Confidence               1111111    0        11           1    44444  222222      122888887776654     


Q ss_pred             CCeEEEEccCC-----------------CCC-ccceEEeehhhhhhhhc-------------------------cCC--C
Q psy6094         137 GAILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLMK-------------------------GVG--A  171 (455)
Q Consensus       137 ~~k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~~-------------------------~~~--~  171 (455)
                        +++++++|+                 +++ ++++.++.++-.+....                         ...  +
T Consensus       549 --~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~dd~~~~~~~~am~~~se~d~~  626 (1282)
T KOG0921|consen  549 --DVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCDPSYNESTRTAMSRLSEKDIP  626 (1282)
T ss_pred             --ceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhcccccccccChhhcchhhhhhhcchhhcch
Confidence              669999999                 566 77666654332110000                         000  0


Q ss_pred             ----C--ChHH----HHHHH-HccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCC
Q psy6094         172 ----N--SPKR----WVKLL-RSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPE  240 (455)
Q Consensus       172 ----~--~~~~----l~~~i-~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~  240 (455)
                          .  ...+    +..+| .-.+++..|+||+++.-+......+.....+......+.+.|..+...++..+++..+.
T Consensus       627 f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~s  706 (1282)
T KOG0921|consen  627 FGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILS  706 (1282)
T ss_pred             hHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccc
Confidence                0  0111    11122 22678999999999999988888888877777778899999999999999999999999


Q ss_pred             CceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh---hh
Q psy6094         241 GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN---DV  317 (455)
Q Consensus       241 g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~---~~  317 (455)
                      +..+++..|+.+++.+++..+.+|++++..+.+.+-....++...+.|-++-.-.||.|+++|...+.||.+.+.   ..
T Consensus       707 tniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grvR~G~~f~lcs~arF~~l~~~~t~e  786 (1282)
T KOG0921|consen  707 TNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRARFEALEDHGTAE  786 (1282)
T ss_pred             cceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCceecccccccccHHHHHHHHHhcCcHh
Confidence            999999999999999999999999999999999888888999999999999999999999999999999999994   45


Q ss_pred             hccCCCCcccccC--------hHHHH----HHHhhhcCCCChhhHHhH
Q psy6094         318 LNMLKDPELEGVN--------NDVIF----SLLQHICTTQRPGAILVF  353 (455)
Q Consensus       318 ~~~~~~PEi~r~~--------~~~~L----~~l~~~~~~P~~~~i~~a  353 (455)
                      |..++.|||.++.        ..+.+    .+..+++.+|+......+
T Consensus       787 m~r~plhemalTikll~l~SI~~fl~kal~~~p~dav~e~e~~l~~m~  834 (1282)
T KOG0921|consen  787 MFRTPLHEIALTIKLLRLGSIGEFLGKALQPPPYDAVIEAEAVLREMG  834 (1282)
T ss_pred             hhcCccHHHHhhHHHHHhhhHHHHHhhccCCCchhhccCchHHHHHhh
Confidence            6777888887654        33444    334466666655554433

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

Probab=99.47  E-value=1.2e-13  Score=152.27  Aligned_cols=154  Identities=17%  Similarity=0.125  Sum_probs=122.9

Q ss_pred             HHHHHhcCCCCeEEEEccCC---------------------C-CCccceEEeehhhhhhhhccCCCCChHHHHHHHHc--
Q psy6094         128 QHICTTQRPGAILVYCTYTF---------------------M-GVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRS--  183 (455)
Q Consensus       128 k~il~~~~~~~k~ilmSAT~---------------------~-g~~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~--  183 (455)
                      |+-++..+.+..++-||||+                     | +|+||..+..+.-            +..+...|..  
T Consensus       733 KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d------------~~~ireAI~REl  800 (1139)
T COG1197         733 KEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYD------------DLLIREAILREL  800 (1139)
T ss_pred             HHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCC------------hHHHHHHHHHHH
Confidence            55555778899999999999                     3 3488887765421            1112222221  


Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+|++-.-.|..++|+.+++.|+...    +..++...||+|+..+-..+|..|-+|...|+|||.|.|+|||||++.-
T Consensus       801 ~RgGQvfYv~NrV~~Ie~~~~~L~~LV----PEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANT  876 (1139)
T COG1197         801 LRGGQVFYVHNRVESIEKKAERLRELV----PEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANT  876 (1139)
T ss_pred             hcCCEEEEEecchhhHHHHHHHHHHhC----CceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCce
Confidence            568999999999999999999999875    4789999999999999999999999999999999999999999999987


Q ss_pred             EEeCCCCcccccc-cCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         264 VVDCGKTKMSNFD-VKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd-~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      .|-        .+ ..-|+          |+..|-+||+||... |.||-||+.
T Consensus       877 iII--------e~AD~fGL----------sQLyQLRGRVGRS~~~AYAYfl~p~  912 (1139)
T COG1197         877 III--------ERADKFGL----------AQLYQLRGRVGRSNKQAYAYFLYPP  912 (1139)
T ss_pred             EEE--------eccccccH----------HHHHHhccccCCccceEEEEEeecC
Confidence            762        11 12343          456699999999877 999999993

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.46  E-value=2e-13  Score=148.60  Aligned_cols=112  Identities=17%  Similarity=0.174  Sum_probs=95.6

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+.++||||.+.++++.+++.|...+      +.+..|||.+.++++..+...+.+|  +|+||||+|.|
T Consensus       417 l~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~g------i~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgR  488 (790)
T PRK09200        417 VIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAG------IPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGR  488 (790)
T ss_pred             HHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC------CCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhc
Confidence            4444433  467889999999999999999999874      7899999999999988888877766  79999999999


Q ss_pred             CCCC---CCee-----EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         255 SITI---DDIV-----YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       255 gitI---~~V~-----~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |+||   ++|.     +||++.+                  |-|...+.||+|||||.|. |.|+.+++
T Consensus       489 G~DI~l~~~V~~~GGL~VI~~d~------------------p~s~r~y~qr~GRtGR~G~~G~s~~~is  539 (790)
T PRK09200        489 GTDIKLGEGVHELGGLAVIGTER------------------MESRRVDLQLRGRSGRQGDPGSSQFFIS  539 (790)
T ss_pred             CcCCCcccccccccCcEEEeccC------------------CCCHHHHHHhhccccCCCCCeeEEEEEc
Confidence            9999   7999     9999554                  3455667899999999986 99999998

>KOG0950|consensus

Probab=99.46  E-value=3.6e-13  Score=144.47  Aligned_cols=117  Identities=17%  Similarity=0.161  Sum_probs=92.3

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCC-----------------------C---------CCCeEEEeecCCCChhhHh
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFF-----------------------N---------SSRFQIIPLHSMLPTVSQK  232 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~-----------------------~---------~~~~~v~~lhs~l~~~~r~  232 (455)
                      .+.++|||||++..++.++..+......                       .         .-.+-+..+|++++.++|+
T Consensus       459 e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~  538 (1008)
T KOG0950|consen  459 EGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEERE  538 (1008)
T ss_pred             cCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHH
Confidence            3445999999999999988666542100                       0         0123467789999999999


Q ss_pred             hhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeE
Q psy6094         233 SIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSE  309 (455)
Q Consensus       233 ~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c  309 (455)
                      .|...|++|..+|++||+.++.|++.|..+++|-.-+              ......++.+|.|+.|||||+|-   |.+
T Consensus       539 ~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~--------------~g~~~l~~~~YkQM~GRAGR~gidT~Gds  604 (1008)
T KOG0950|consen  539 IIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPY--------------VGREFLTRLEYKQMVGRAGRTGIDTLGDS  604 (1008)
T ss_pred             HHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCc--------------cccchhhhhhHHhhhhhhhhcccccCcce
Confidence            9999999999999999999999999999999995332              12345678899999999999864   889


Q ss_pred             EecCCh
Q psy6094         310 TQQYPN  315 (455)
Q Consensus       310 ~~L~t~  315 (455)
                      +-.+.+
T Consensus       605 iLI~k~  610 (1008)
T KOG0950|consen  605 ILIIKS  610 (1008)
T ss_pred             EEEeec
Confidence            988883

>KOG0329|consensus

Probab=99.45  E-value=2.9e-13  Score=125.73  Aligned_cols=221  Identities=12%  Similarity=0.163  Sum_probs=141.2

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      -|.+..+.|+....+-.-+.--....|.+.|+...-|-+++.+|..|-|||..+. ..+.                    
T Consensus        43 gfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrel  122 (387)
T KOG0329|consen   43 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTREL  122 (387)
T ss_pred             chhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHH
Confidence            3566777888877777777766666777666655556679999999999994432 1111                    


Q ss_pred             ---------------------------------h-----hcCCCCChHHHHHhc--cCCCCcCcc------hHHHHHH--
Q psy6094          95 ---------------------------------K-----RSETQQYPNDVLNML--KDPELEGVN------NDVIFSL--  126 (455)
Q Consensus        95 ---------------------------------e-----~~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~~--  126 (455)
                                                       |     -...||+|++++...  ..-.|.++.      .|-+|..  
T Consensus       123 afqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lD  202 (387)
T KOG0329|consen  123 AFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLD  202 (387)
T ss_pred             HHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHH
Confidence                                             1     122356788877655  444555555      5656543  


Q ss_pred             ----HHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhhhhhhccCCC----------------CChHHHHHHHHccC
Q psy6094         127 ----LQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVLQRLMKGVGA----------------NSPKRWVKLLRSML  185 (455)
Q Consensus       127 ----lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~~~~~~~~~~----------------~~~~~l~~~i~~~~  185 (455)
                          +..+.+..+.+.|+..||||++.. -||-..|+.++.+.|+.....                .+...+.+++....
T Consensus       203 MrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~Le  282 (387)
T KOG0329|consen  203 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLE  282 (387)
T ss_pred             HHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhh
Confidence                234443456788999999999777 788777877776665532211                11111112222122


Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV  265 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI  265 (455)
                      -.+++||+.+...                                  ..|      .++ +||||+..||+||..|..|+
T Consensus       283 FNQVvIFvKsv~R----------------------------------l~f------~kr-~vat~lfgrgmdiervNi~~  321 (387)
T KOG0329|consen  283 FNQVVIFVKSVQR----------------------------------LSF------QKR-LVATDLFGRGMDIERVNIVF  321 (387)
T ss_pred             hcceeEeeehhhh----------------------------------hhh------hhh-hHHhhhhccccCcccceeee
Confidence            3344444443221                                  112      123 99999999999999999999


Q ss_pred             eCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         266 DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       266 D~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      |        ||.+.+          -.+|.||.|||||.|. |.++.+.+.
T Consensus       322 N--------Ydmp~~----------~DtYlHrv~rAgrfGtkglaitfvs~  354 (387)
T KOG0329|consen  322 N--------YDMPED----------SDTYLHRVARAGRFGTKGLAITFVSD  354 (387)
T ss_pred             c--------cCCCCC----------chHHHHHhhhhhccccccceeehhcc
Confidence            9        543333          3457799999999988 999998883

>KOG0951|consensus

Probab=99.44  E-value=7.6e-12  Score=136.79  Aligned_cols=197  Identities=12%  Similarity=0.097  Sum_probs=133.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCC------------------C-------CC------CCeEEEeecCCCChhhHh
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSF------------------F-------NS------SRFQIIPLHSMLPTVSQK  232 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~------------------~-------~~------~~~~v~~lhs~l~~~~r~  232 (455)
                      ...+++|||+.+++|..+.++.+++...                  +       ..      -.+-+...|+||...+|.
T Consensus       544 agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~  623 (1674)
T KOG0951|consen  544 AGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRE  623 (1674)
T ss_pred             CCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHH
Confidence            4558999999999999999998884210                  0       00      124577789999999999


Q ss_pred             hhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC-----CC
Q psy6094         233 SIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL-----KR  307 (455)
Q Consensus       233 ~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~-----~G  307 (455)
                      .+..-|..|.++|+++|-..+.|++.|.-+++|- |   ..+|||..|..    ...|.-...||.|||||.+     .|
T Consensus       624 ~~EdLf~~g~iqvlvstatlawgvnlpahtViik-g---tqvy~pekg~w----~elsp~dv~qmlgragrp~~D~~geg  695 (1674)
T KOG0951|consen  624 LVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIK-G---TQVYDPEKGRW----TELSPLDVMQMLGRAGRPQYDTCGEG  695 (1674)
T ss_pred             HHHHHHhcCceeEEEeehhhhhhcCCCcceEEec-C---ccccCcccCcc----ccCCHHHHHHHHhhcCCCccCcCCce
Confidence            9999999999999999999999999999777773 2   35799999854    3567788999999999954     34


Q ss_pred             eEEecCCh-----hhhccCCCCcccccC-------hHHHHH---------HHh------hhcCCCC--------------
Q psy6094         308 SETQQYPN-----DVLNMLKDPELEGVN-------NDVIFS---------LLQ------HICTTQR--------------  346 (455)
Q Consensus       308 ~c~~L~t~-----~~~~~~~~PEi~r~~-------~~~~L~---------~l~------~~~~~P~--------------  346 (455)
                      +...=+++     ..|++.-+-|-+..+       .++++-         .+.      ..+.-|.              
T Consensus       696 iiit~~se~qyyls~mn~qLpiesq~~~rl~d~lnaeiv~Gv~~~~d~~~wl~yTylyvRm~~~p~ly~~~~~~~d~~le  775 (1674)
T KOG0951|consen  696 IIITDHSELQYYLSLMNQQLPIESQFVSRLADCLNAEIVLGVRSARDAVDWLGYTYLYVRMVRNPTLYGVSPEASDRLLE  775 (1674)
T ss_pred             eeccCchHhhhhHHhhhhcCCChHHHHHHhhhhhhhhhhcchhhHHHHHhhhcceeeEEeeccCchhccCCcccchHHHH
Confidence            44433332     122222222222211       333331         110      0111111              


Q ss_pred             ---hhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh
Q psy6094         347 ---PGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP  388 (455)
Q Consensus       347 ---~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p  388 (455)
                         .+-+..|...|+..|.+-.+..-.-+.+|.+|+.-+...+.-
T Consensus       776 ~~r~~lvhsa~~ll~~~~li~yd~~s~~~~~telg~ias~yyi~~  820 (1674)
T KOG0951|consen  776 QRRADLVHSAATLLDKAGLIKYDRKSGAIQATELGRIASSYYITH  820 (1674)
T ss_pred             HHHhhhHHHHHhhHhhcCccccccccCcccchhhccccceeeeec
Confidence               144677888888888886554333356799999999988876

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.43  E-value=4.4e-13  Score=145.01  Aligned_cols=120  Identities=15%  Similarity=0.121  Sum_probs=101.8

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+..+|||++++..++.+++.|...+      +.+..+||++++.+|.+++..|++|...|+||||++++
T Consensus       431 Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~g------i~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~r  504 (655)
T TIGR00631       431 LLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELG------IKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE  504 (655)
T ss_pred             HHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhc------cceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcC
Confidence            4444443  567789999999999999999999864      78899999999999999999999999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN  315 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~  315 (455)
                      |+|+|++++||.++-        ..     ...|-|..++.||+|||||...|.|+.+++.
T Consensus       505 GfDiP~v~lVvi~Da--------di-----fG~p~~~~~~iqriGRagR~~~G~vi~~~~~  552 (655)
T TIGR00631       505 GLDLPEVSLVAILDA--------DK-----EGFLRSERSLIQTIGRAARNVNGKVIMYADK  552 (655)
T ss_pred             CeeeCCCcEEEEeCc--------cc-----ccCCCCHHHHHHHhcCCCCCCCCEEEEEEcC
Confidence            999999999997432        11     0134567789999999999988999988873

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

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.42  E-value=6.9e-13  Score=143.31  Aligned_cols=104  Identities=15%  Similarity=0.153  Sum_probs=90.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC----
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID----  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~----  259 (455)
                      ..+.++||||++...++.+.+.|...+      +.+..|||.+.+.++..+...+.+|  +|+||||+|.||+||+    
T Consensus       422 ~~~~pvLIft~s~~~se~ls~~L~~~g------i~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~  493 (762)
T TIGR03714       422 ETGQPVLLITGSVEMSEIYSELLLREG------IPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKG  493 (762)
T ss_pred             hCCCCEEEEECcHHHHHHHHHHHHHCC------CCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCcc
Confidence            567889999999999999999999875      7788999999999998888888777  7999999999999999    


Q ss_pred             -----CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         260 -----DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       260 -----~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                           ++.+||+        |++++.          +. ..||+|||||.|. |.|+.+++
T Consensus       494 v~~~GGL~vIit--------~~~ps~----------ri-d~qr~GRtGRqG~~G~s~~~is  535 (762)
T TIGR03714       494 VAELGGLAVIGT--------ERMENS----------RV-DLQLRGRSGRQGDPGSSQFFVS  535 (762)
T ss_pred             ccccCCeEEEEe--------cCCCCc----------HH-HHHhhhcccCCCCceeEEEEEc
Confidence                 9999998        544432          22 2699999999986 99999998

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.

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

Probab=99.42  E-value=5.4e-13  Score=114.56  Aligned_cols=111  Identities=20%  Similarity=0.286  Sum_probs=95.3

Q ss_pred             HHHHHHcc--CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRSM--LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~~--~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+...  .++++|||+++...++.+++.|...      ...+..+||+++..++..+++.|.+|..+|+++|+.++.
T Consensus        17 i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~------~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~   90 (131)
T cd00079          17 LLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKP------GIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIAR   90 (131)
T ss_pred             HHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhc------CCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhc
Confidence            44444432  5789999999999999999999874      367999999999999999999999999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEe
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQ  311 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~  311 (455)
                      |+|+|++++||-.+.                  |.+...+.|+.||+||.+. |.|+.
T Consensus        91 G~d~~~~~~vi~~~~------------------~~~~~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079          91 GIDLPNVSVVINYDL------------------PWSPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             CcChhhCCEEEEeCC------------------CCCHHHheecccccccCCCCceEEe
Confidence            999999999996443                  5667788899999999985 88775

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.42  E-value=6.2e-13  Score=144.56  Aligned_cols=119  Identities=17%  Similarity=0.129  Sum_probs=101.9

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+..+|||+++...++.+++.|...+      +.+..+||++++.+|..++..|++|...|+|||+++++
T Consensus       435 L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~g------i~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~r  508 (652)
T PRK05298        435 LLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELG------IKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE  508 (652)
T ss_pred             HHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcc------eeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhC
Confidence            4444443  457789999999999999999999864      88999999999999999999999999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      |+++|++++||.++...       .|      .|.+..++.||+||+||...|.|+.+.+
T Consensus       509 Gfdlp~v~lVii~d~ei-------fG------~~~~~~~yiqr~GR~gR~~~G~~i~~~~  555 (652)
T PRK05298        509 GLDIPEVSLVAILDADK-------EG------FLRSERSLIQTIGRAARNVNGKVILYAD  555 (652)
T ss_pred             CccccCCcEEEEeCCcc-------cc------cCCCHHHHHHHhccccCCCCCEEEEEec
Confidence            99999999999844321       11      2457788999999999987899999988

>TIGR00595 priA primosomal protein N'

Probab=99.41  E-value=9.4e-13  Score=139.01  Aligned_cols=100  Identities=15%  Similarity=0.175  Sum_probs=74.6

Q ss_pred             HHHHHHHHHhcCCCCCCCeEEEeecCCCChhhH--hhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE--eCCCCcccc
Q psy6094         199 INSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQ--KSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV--DCGKTKMSN  274 (455)
Q Consensus       199 i~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r--~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI--D~g~~k~~~  274 (455)
                      ++++.+.|.+..    ++..+..+|++++..++  .++++.|++|+.+|+|+|+++++|+|+|+|+.|+  |        
T Consensus       271 te~~~e~l~~~f----p~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~--------  338 (505)
T TIGR00595       271 TEQVEEELAKLF----PGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLD--------  338 (505)
T ss_pred             HHHHHHHHHhhC----CCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEc--------
Confidence            566667776642    24789999999988766  7899999999999999999999999999999885  5        


Q ss_pred             cccCCCcccccccccchhhHHhhhcccCCCCC-CeEE
Q psy6094         275 FDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSET  310 (455)
Q Consensus       275 yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~  310 (455)
                      +|...+...+...--.-..+.|++|||||.+. |.++
T Consensus       339 aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~vi  375 (505)
T TIGR00595       339 ADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVI  375 (505)
T ss_pred             CcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEE
Confidence            33322222222222233567899999999665 8887

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).

>KOG0353|consensus

Probab=99.40  E-value=2.1e-12  Score=125.79  Aligned_cols=91  Identities=12%  Similarity=0.135  Sum_probs=79.3

Q ss_pred             HHHHHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         177 WVKLLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       177 l~~~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      +...|.. -.+...+|+|-++.+++.++..|+.++      +..-.+|+.|.++++..+-+.+-.|...|||||-....|
T Consensus       307 i~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~g------i~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmg  380 (695)
T KOG0353|consen  307 IAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHG------IHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMG  380 (695)
T ss_pred             HHHHhccccCCCcceEEEeccccHHHHHHHHHhcC------ccccccccccCccccccccccccccceEEEEEEeeeccc
Confidence            3344433 345568999999999999999999886      788899999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCccc
Q psy6094         256 ITIDDIVYVVDCGKTKMS  273 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~  273 (455)
                      ||-|||++||+-.++|..
T Consensus       381 idkpdvrfvihhsl~ksi  398 (695)
T KOG0353|consen  381 IDKPDVRFVIHHSLPKSI  398 (695)
T ss_pred             CCCCCeeEEEecccchhH
Confidence            999999999998887743

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.37  E-value=4.8e-13  Score=105.11  Aligned_cols=72  Identities=24%  Similarity=0.276  Sum_probs=66.2

Q ss_pred             CeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHH
Q psy6094         216 RFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAK  295 (455)
Q Consensus       216 ~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~  295 (455)
                      ++.+..+||++++++|..+++.|..|..+||+||++++.|||+|++++||.++.                  +-|..++.
T Consensus         7 ~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~------------------~~~~~~~~   68 (78)
T PF00271_consen    7 GIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDP------------------PWSPEEYI   68 (78)
T ss_dssp             TSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSS------------------ESSHHHHH
T ss_pred             CCcEEEEECCCCHHHHHHHHHHhhccCceEEEeecccccccccccccccccccc------------------CCCHHHHH
Confidence            488999999999999999999999999999999999999999999999998554                  56778899


Q ss_pred             hhhcccCCCC
Q psy6094         296 QRRGRAGRTL  305 (455)
Q Consensus       296 QR~GRaGR~~  305 (455)
                      ||.||+||.|
T Consensus        69 Q~~GR~~R~g   78 (78)
T PF00271_consen   69 QRIGRAGRIG   78 (78)
T ss_dssp             HHHTTSSTTT
T ss_pred             HHhhcCCCCC
Confidence            9999999974

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.32  E-value=1.3e-11  Score=136.12  Aligned_cols=104  Identities=19%  Similarity=0.181  Sum_probs=85.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCC----CCCceEEEEeCCCCccCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTP----PEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~----~~g~~kVivaTniae~gitI~  259 (455)
                      ..++.+||-++|.+.+.++++.|+..+     . .++.+||.+...+|.+..+..    ..+.-.|+|||-|.|.|+||+
T Consensus       438 ~~~~kvlvI~NTV~~Aie~Y~~Lk~~~-----~-~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid  511 (733)
T COG1203         438 KEGKKVLVIVNTVDRAIELYEKLKEKG-----P-KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID  511 (733)
T ss_pred             ccCCcEEEEEecHHHHHHHHHHHHhcC-----C-CEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc
Confidence            678899999999999999999999875     2 799999999999999876632    345678999999999999987


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC--C-CeEEecCC
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL--K-RSETQQYP  314 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~--~-G~c~~L~t  314 (455)
                       .+.+|                    +...+-.+..||+||.+|.|  . |..|..-.
T Consensus       512 -fd~mI--------------------Te~aPidSLIQR~GRv~R~g~~~~~~~~v~~~  548 (733)
T COG1203         512 -FDVLI--------------------TELAPIDSLIQRAGRVNRHGKKENGKIYVYND  548 (733)
T ss_pred             -cCeee--------------------ecCCCHHHHHHHHHHHhhcccccCCceeEeec
Confidence             56666                    34566678889999999988  3 66665544

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.30  E-value=9.6e-12  Score=133.82  Aligned_cols=105  Identities=19%  Similarity=0.146  Sum_probs=92.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCC---
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDD---  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~---  260 (455)
                      ..+.++||||++..+.+.+.+.|...+      +....||+.  +.+|...+..+..+.-.|+||||+|.||+||+.   
T Consensus       403 ~~grpvLV~t~si~~se~ls~~L~~~g------i~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V  474 (745)
T TIGR00963       403 AKGQPVLVGTTSVEKSELLSNLLKERG------IPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEV  474 (745)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHcC------CCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccch
Confidence            678899999999999999999999875      677889998  778888888898899999999999999999998   


Q ss_pred             ----eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         261 ----IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       261 ----V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                          ..|||++.+                  |-|+..+.||+||+||.|. |.+..+.+
T Consensus       475 ~~~GGl~VI~t~~------------------p~s~ri~~q~~GRtGRqG~~G~s~~~ls  515 (745)
T TIGR00963       475 KELGGLYVIGTER------------------HESRRIDNQLRGRSGRQGDPGSSRFFLS  515 (745)
T ss_pred             hhcCCcEEEecCC------------------CCcHHHHHHHhccccCCCCCcceEEEEe
Confidence                449998554                  4566678899999999987 99988888

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.29  E-value=1e-11  Score=134.72  Aligned_cols=105  Identities=21%  Similarity=0.206  Sum_probs=92.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCC---CC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITI---DD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI---~~  260 (455)
                      ..+.++||||.+....+.+++.|.+.+      +....||+...+.++..+.....+|.  |+||||+|.||+||   ++
T Consensus       438 ~~g~pvLI~t~si~~se~ls~~L~~~g------i~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~  509 (796)
T PRK12906        438 AKGQPVLVGTVAIESSERLSHLLDEAG------IPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPG  509 (796)
T ss_pred             hCCCCEEEEeCcHHHHHHHHHHHHHCC------CCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcc
Confidence            578899999999999999999999875      67889999999988888888888776  99999999999999   59


Q ss_pred             ee-----EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         261 IV-----YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       261 V~-----~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |.     +||++.+                  |-|+-.+.||.|||||.|. |.+..+++
T Consensus       510 V~~~GGLhVI~te~------------------pes~ri~~Ql~GRtGRqG~~G~s~~~~s  551 (796)
T PRK12906        510 VKELGGLAVIGTER------------------HESRRIDNQLRGRSGRQGDPGSSRFYLS  551 (796)
T ss_pred             hhhhCCcEEEeeec------------------CCcHHHHHHHhhhhccCCCCcceEEEEe
Confidence            99     9998655                  4556667899999999987 99988888

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.25  E-value=8.5e-12  Score=97.93  Aligned_cols=80  Identities=26%  Similarity=0.302  Sum_probs=70.1

Q ss_pred             HHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCc
Q psy6094         202 LHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNI  281 (455)
Q Consensus       202 l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~  281 (455)
                      +++.|+..      ++.+..+||++++++|..+++.|.+|..+|+++|++++.|+|++++++||..+.            
T Consensus         3 l~~~l~~~------~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~------------   64 (82)
T smart00490        3 LAELLKEL------GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL------------   64 (82)
T ss_pred             HHHHHHHC------CCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCC------------
Confidence            45556554      378999999999999999999999999999999999999999999999998554            


Q ss_pred             ccccccccchhhHHhhhcccCCCC
Q psy6094         282 ATLKPEWISLANAKQRRGRAGRTL  305 (455)
Q Consensus       282 ~~l~~~~iSka~~~QR~GRaGR~~  305 (455)
                            |.+.+.+.|+.||+||.+
T Consensus        65 ------~~~~~~~~Q~~gR~~R~g   82 (82)
T smart00490       65 ------PWSPASYIQRIGRAGRAG   82 (82)
T ss_pred             ------CCCHHHHHHhhcccccCC
Confidence                  567888999999999964

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.23  E-value=3e-11  Score=134.70  Aligned_cols=113  Identities=14%  Similarity=0.123  Sum_probs=92.9

Q ss_pred             HHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCC--CceEEEEeCCCCccCC
Q psy6094         179 KLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPE--GVRKIVLATNIAETSI  256 (455)
Q Consensus       179 ~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~--g~~kVivaTniae~gi  256 (455)
                      .++....+.++||||.++..+..+.+.|+...     ++.+..+||++++.+|.++++.|..  |..+|+|||+++++|+
T Consensus       486 ~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~-----Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGl  560 (956)
T PRK04914        486 DFLKSHRSEKVLVICAKAATALQLEQALRERE-----GIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGR  560 (956)
T ss_pred             HHHHhcCCCeEEEEeCcHHHHHHHHHHHhhcc-----CeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCC
Confidence            33333457799999999999999999996432     3889999999999999999999986  4689999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-C--eEEecCC
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-R--SETQQYP  314 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G--~c~~L~t  314 (455)
                      |++.+++||+++++                  -+-..+.||.||+||.|. |  ..|.++.
T Consensus       561 Nlq~a~~VInfDlP------------------~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~  603 (956)
T PRK04914        561 NFQFASHLVLFDLP------------------FNPDLLEQRIGRLDRIGQKHDIQIHVPYL  603 (956)
T ss_pred             CcccccEEEEecCC------------------CCHHHHHHHhcccccCCCCceEEEEEccC
Confidence            99999999994443                  344567899999999776 4  4556665

>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length

Probab=99.22  E-value=2.4e-11  Score=100.90  Aligned_cols=71  Identities=13%  Similarity=0.076  Sum_probs=51.0

Q ss_pred             hHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhc----CcCCcChHHHHH-
Q psy6094         352 VFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLS----FECKPSTAKIIK-  411 (455)
Q Consensus       352 ~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~ls----f~~p~~~~~~~~-  411 (455)
                      +|++.|..+||||.++++     |++|+.|+.||++|               +++++|||+||    |..|..+++..+ 
T Consensus         1 ~A~~~L~~Lgald~~~~l-----T~lG~~~~~lPl~p~~a~~Ll~~~~~~~~~~~~~iaa~ls~~~~f~~~~~~~~~~~~   75 (102)
T PF04408_consen    1 KALELLKSLGALDENGNL-----TPLGRKMSQLPLDPRLAKMLLYGIQFGCLDEALIIAAILSVRSPFINPDDKEENAEQ   75 (102)
T ss_dssp             -HHHHHHHTTSB-TTS-B------HHHHHHTTSSS-HHHHHHHHHHHHCT-HHHHHHHHHHHTSS--B---CCGHHHHHH
T ss_pred             CHHHHHHHCCCCCCCCCc-----CHHHHHHHHCCCchHhHhHhhhccccccHHHHHHHHHHHcCCCcccCccHHHHHHHH
Confidence            478999999999999999     99999999999999               89999999999    666655444332 


Q ss_pred             -HHHhhh---------C-CCCcHHHHH
Q psy6094         412 -ELRARL---------D-MLLAHKLSH  427 (455)
Q Consensus       412 -~~~~~~---------~-~~sD~~~~~  427 (455)
                       ..+.+|         . ..|||++++
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~sDhltlL  102 (102)
T PF04408_consen   76 DNAKKKFRIKQARKKFSDDESDHLTLL  102 (102)
T ss_dssp             --HHHTT----------BTTBHHHHHH
T ss_pred             HHHHHHhhhhhcccccCCCCCCHHhcC
Confidence             244444         5 889999986

It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.

>KOG0948|consensus

Probab=99.21  E-value=1.9e-11  Score=127.97  Aligned_cols=129  Identities=24%  Similarity=0.227  Sum_probs=96.1

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCC-------------------C-----CC---------CeEEEeec
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFF-------------------N-----SS---------RFQIIPLH  223 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~-------------------~-----~~---------~~~v~~lh  223 (455)
                      ++..+....-.+++||.=+++||+.++-.+.+.-..                   +     .+         .--+...|
T Consensus       374 iVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHH  453 (1041)
T KOG0948|consen  374 IVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHH  453 (1041)
T ss_pred             HHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhcccccc
Confidence            334444466778999999999999999777654211                   0     00         01255678


Q ss_pred             CCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCC
Q psy6094         224 SMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR  303 (455)
Q Consensus       224 s~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR  303 (455)
                      |||-+--...|.=-|.+|-.||++||-..+.|++.|.-++|.-    ..+.||-..      -.|||-.+|+|.+|||||
T Consensus       454 sGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT----~~rKfDG~~------fRwissGEYIQMSGRAGR  523 (1041)
T KOG0948|consen  454 SGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFT----AVRKFDGKK------FRWISSGEYIQMSGRAGR  523 (1041)
T ss_pred             ccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEe----eccccCCcc------eeeecccceEEecccccc
Confidence            9998866655544578999999999999999999998777763    233455433      379999999999999999


Q ss_pred             CCC---CeEEecCCh
Q psy6094         304 TLK---RSETQQYPN  315 (455)
Q Consensus       304 ~~~---G~c~~L~t~  315 (455)
                      .|-   |+|+.+.++
T Consensus       524 RG~DdrGivIlmiDe  538 (1041)
T KOG0948|consen  524 RGIDDRGIVILMIDE  538 (1041)
T ss_pred             cCCCCCceEEEEecC
Confidence            774   999999984

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

Probab=99.16  E-value=5.8e-10  Score=123.33  Aligned_cols=128  Identities=22%  Similarity=0.226  Sum_probs=95.2

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCC--------------------C-CC-Ce-------------EEEe
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFF--------------------N-SS-RF-------------QIIP  221 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--------------------~-~~-~~-------------~v~~  221 (455)
                      ++.++.....-++++|+=++.+|+..+..+......                    . .+ .+             -+..
T Consensus       370 iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiav  449 (1041)
T COG4581         370 IVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAV  449 (1041)
T ss_pred             HHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhh
Confidence            444555466678999999999999988777632100                    0 00 01             1336


Q ss_pred             ecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhccc
Q psy6094         222 LHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRA  301 (455)
Q Consensus       222 lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRa  301 (455)
                      .|++|-+..+..+..-|..|-.||++||.+.+-|++.|.-++|+ +++.|   +|-      -.-.|.+-.+|.|.+|||
T Consensus       450 HH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~-~~l~K---~dG------~~~r~L~~gEy~QmsGRA  519 (1041)
T COG4581         450 HHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVF-TSLSK---FDG------NGHRWLSPGEYTQMSGRA  519 (1041)
T ss_pred             hccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceee-eeeEE---ecC------CceeecChhHHHHhhhhh
Confidence            78999999999998889999999999999999999999766665 44443   331      123699999999999999


Q ss_pred             CCCCC---CeEEecCC
Q psy6094         302 GRTLK---RSETQQYP  314 (455)
Q Consensus       302 GR~~~---G~c~~L~t  314 (455)
                      ||.|-   |..+..-+
T Consensus       520 GRRGlD~~G~vI~~~~  535 (1041)
T COG4581         520 GRRGLDVLGTVIVIEP  535 (1041)
T ss_pred             ccccccccceEEEecC
Confidence            99763   88888744

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.15  E-value=9.1e-11  Score=128.43  Aligned_cols=112  Identities=18%  Similarity=0.151  Sum_probs=91.5

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+.++|||+++....+.+.+.|...+      +....||+  .+.+|...+..+..+.-.|+||||+|.|
T Consensus       587 li~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~g------I~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGR  658 (1025)
T PRK12900        587 IVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKR------IAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGR  658 (1025)
T ss_pred             HHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcC------CCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCC
Confidence            4445532  568899999999999999999999875      66778886  5778888888888889999999999999


Q ss_pred             CCCCC---CeeE-----EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         255 SITID---DIVY-----VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       255 gitI~---~V~~-----VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |+||+   +|..     ||++.+                  +-|+-.+.||+|||||.|. |.+..+++
T Consensus       659 GtDIkl~~~V~~vGGL~VIgter------------------hes~Rid~Ql~GRtGRqGdpGsS~ffvS  709 (1025)
T PRK12900        659 GTDIKLGEGVRELGGLFILGSER------------------HESRRIDRQLRGRAGRQGDPGESVFYVS  709 (1025)
T ss_pred             CCCcCCccchhhhCCceeeCCCC------------------CchHHHHHHHhhhhhcCCCCcceEEEec
Confidence            99999   5543     355333                  4455667899999999987 99999999

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

Probab=99.13  E-value=6.9e-10  Score=115.72  Aligned_cols=96  Identities=15%  Similarity=0.138  Sum_probs=83.6

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYV  264 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~V  264 (455)
                      .+..++||+........++..+...+      . +..+.|..+..+|..+++.|+.|..++|+++.|+.-|+|+|++..+
T Consensus       282 ~~~~~lif~~~~~~a~~i~~~~~~~~------~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~  354 (442)
T COG1061         282 RGDKTLIFASDVEHAYEIAKLFLAPG------I-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVL  354 (442)
T ss_pred             CCCcEEEEeccHHHHHHHHHHhcCCC------c-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEE
Confidence            46799999999999999999888754      3 7788999999999999999999999999999999999999999999


Q ss_pred             EeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC
Q psy6094         265 VDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL  305 (455)
Q Consensus       265 ID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~  305 (455)
                      |-                  ....-|+..+.||.||.=|..
T Consensus       355 i~------------------~~~t~S~~~~~Q~lGR~LR~~  377 (442)
T COG1061         355 II------------------LRPTGSRRLFIQRLGRGLRPA  377 (442)
T ss_pred             EE------------------eCCCCcHHHHHHHhhhhccCC
Confidence            93                  112357788999999998843

>KOG0947|consensus

Probab=99.08  E-value=9.6e-10  Score=118.05  Aligned_cols=128  Identities=16%  Similarity=0.160  Sum_probs=94.1

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCC--------------------CCC-------------eEEEeec
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFN--------------------SSR-------------FQIIPLH  223 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~--------------------~~~-------------~~v~~lh  223 (455)
                      ++.|+....--+++||+=+++.|++.++.|......+                    .++             --+..+|
T Consensus       558 lin~L~k~~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH  637 (1248)
T KOG0947|consen  558 LINHLRKKNLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHH  637 (1248)
T ss_pred             HHHHHhhcccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhc
Confidence            4455555667789999999999999999997643110                    011             1266789


Q ss_pred             CCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCC
Q psy6094         224 SMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR  303 (455)
Q Consensus       224 s~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR  303 (455)
                      |++-+--..-|..-|..|-.||++||-..+.||+.|.-++|+|+=..    .|-..      -.-..-.+|.|.+|||||
T Consensus       638 ~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~Sl~K----hDG~e------fR~L~PGEytQMAGRAGR  707 (1248)
T KOG0947|consen  638 GGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRK----HDGNE------FRELLPGEYTQMAGRAGR  707 (1248)
T ss_pred             ccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEeeehhh----ccCcc------eeecCChhHHhhhccccc
Confidence            99988777777667889999999999999999999998888874332    22111      123455789999999999


Q ss_pred             CCC---CeEEecCC
Q psy6094         304 TLK---RSETQQYP  314 (455)
Q Consensus       304 ~~~---G~c~~L~t  314 (455)
                      .|-   |.++-+-.
T Consensus       708 RGlD~tGTVii~~~  721 (1248)
T KOG0947|consen  708 RGLDETGTVIIMCK  721 (1248)
T ss_pred             cccCcCceEEEEec
Confidence            763   87776654

>KOG4150|consensus

Probab=99.02  E-value=7.7e-09  Score=105.80  Aligned_cols=105  Identities=22%  Similarity=0.111  Sum_probs=83.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCC--eEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSR--FQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~--~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V  261 (455)
                      ..+-..+.|||.++-++-+....+.-..-.+..  -.+..+.|+...++|+++.+..--|+.+-|+|||.+|.||||.++
T Consensus       523 ~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~L  602 (1034)
T KOG4150|consen  523 QHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHL  602 (1034)
T ss_pred             HcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccc
Confidence            457789999999988877654443311000111  135668899999999999998888999999999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK  306 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~  306 (455)
                      +.|+.+|+                  |.|-++..|..|||||...
T Consensus       603 DAVl~~GF------------------P~S~aNl~QQ~GRAGRRNk  629 (1034)
T KOG4150|consen  603 DAVLHLGF------------------PGSIANLWQQAGRAGRRNK  629 (1034)
T ss_pred             eeEEEccC------------------chhHHHHHHHhccccccCC
Confidence            99999997                  5788999999999998654

>smart00847 HA2 Helicase associated domain (HA2) Add an annotation

Probab=98.99  E-value=9.9e-10  Score=89.23  Aligned_cols=70  Identities=20%  Similarity=0.100  Sum_probs=57.7

Q ss_pred             hHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh----------------hHHHHHHHhhc----CcCCcChHHHHH
Q psy6094         352 VFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP----------------KEIITVRDCLS----FECKPSTAKIIK  411 (455)
Q Consensus       352 ~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p----------------~~~l~iaa~ls----f~~p~~~~~~~~  411 (455)
                      +|++.|..+||||.++++     |++|+.|+.||++|                +++++|+|+++    |..| ....++.
T Consensus         1 ~A~~~L~~LgAld~~~~l-----T~lG~~m~~lPl~Prla~~Ll~a~~~~~c~~~~~~i~a~ls~~~~~~~~-~~~~~~~   74 (92)
T smart00847        1 AALELLYELGALDDDGRL-----TPLGRKMAELPLDPRLAKMLLAAAELFGCLDEILTIAAMLSVGDPFPRP-EKRAEAD   74 (92)
T ss_pred             CHHHHHHHCCCcCCCCCc-----CHHHHHHHHCCCChHHHHHHHHHHhhcCcHHHHHHHHHHhcCCCCcCCc-hHHHHHH
Confidence            478899999999999999     99999999999999                56778888888    3333 4556677


Q ss_pred             HHHhhhC-C-CCcHHHHH
Q psy6094         412 ELRARLD-M-LLAHKLSH  427 (455)
Q Consensus       412 ~~~~~~~-~-~sD~~~~~  427 (455)
                      ..+..|. . .|||++++
T Consensus        75 ~~~~~~~~~~~~D~~~~l   92 (92)
T smart00847       75 AARRRFASGRESDHLTLL   92 (92)
T ss_pred             HHHHHccCCCCCChhhhC
Confidence            7788888 6 89999863

This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.82  E-value=1.8e-08  Score=110.44  Aligned_cols=68  Identities=18%  Similarity=0.181  Sum_probs=63.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      ..+.++|||+.+.+..+.+++.|...+      +....||+.+.+.++..+.+.+.+|.  |.||||+|.||+||.
T Consensus       442 ~~g~PVLVgt~Sie~sE~ls~~L~~~g------i~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGRGtDI~  509 (896)
T PRK13104        442 VRKQPVLVGTVSIEASEFLSQLLKKEN------IKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGRGTDIV  509 (896)
T ss_pred             hCCCCEEEEeCcHHHHHHHHHHHHHcC------CCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccCCccee
Confidence            678899999999999999999999875      78899999999999999999999994  999999999999985

>KOG0953|consensus

Probab=98.82  E-value=1.2e-07  Score=97.32  Aligned_cols=147  Identities=17%  Similarity=0.234  Sum_probs=101.5

Q ss_pred             HHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHh---hhhcCCCCCceEEEEeCCCCccCCC
Q psy6094         181 LRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQK---SIFNTPPEGVRKIVLATNIAETSIT  257 (455)
Q Consensus       181 i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~---~v~~~~~~g~~kVivaTniae~git  257 (455)
                      +..-.+|+.+|-+ ++++|-.+...+.+.+     +..+..+||+||++.|.   ..|. -+++..+|+||||....|++
T Consensus       352 l~nlk~GDCvV~F-Skk~I~~~k~kIE~~g-----~~k~aVIYGsLPPeTr~aQA~~FN-d~~~e~dvlVAsDAIGMGLN  424 (700)
T KOG0953|consen  352 LSNLKPGDCVVAF-SKKDIFTVKKKIEKAG-----NHKCAVIYGSLPPETRLAQAALFN-DPSNECDVLVASDAIGMGLN  424 (700)
T ss_pred             hccCCCCCeEEEe-ehhhHHHHHHHHHHhc-----CcceEEEecCCCCchhHHHHHHhC-CCCCccceEEeecccccccc
Confidence            3335678777755 4788999999999876     46688899999998544   4444 34588999999999999999


Q ss_pred             CCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC----CeEEecCChhh--hc---cCCCCcccc
Q psy6094         258 IDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK----RSETQQYPNDV--LN---MLKDPELEG  328 (455)
Q Consensus       258 I~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~----G~c~~L~t~~~--~~---~~~~PEi~r  328 (455)
                      +. |+-||=+.+.|   |+      .-.+.+++.+++.|=+|||||.+.    |..-.|+.++-  +.   ..++-.|..
T Consensus       425 L~-IrRiiF~sl~K---ys------g~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~eDL~~L~~~l~~p~epi~~  494 (700)
T KOG0953|consen  425 LN-IRRIIFYSLIK---YS------GRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSEDLKLLKRILKRPVEPIKN  494 (700)
T ss_pred             cc-eeEEEEeeccc---CC------cccceeccHHHHHHHhhcccccccCCcCceEEEeeHhhHHHHHHHHhCCchHHHh
Confidence            74 66666433332   32      235678999999999999999663    88888887541  11   223333433


Q ss_pred             cC----hHHHHHHHhhhcCC
Q psy6094         329 VN----NDVIFSLLQHICTT  344 (455)
Q Consensus       329 ~~----~~~~L~~l~~~~~~  344 (455)
                      ..    .+.|-.|..++++.
T Consensus       495 agl~pt~eqie~fa~~~Pd~  514 (700)
T KOG0953|consen  495 AGLWPTDEQIELFAYHLPDA  514 (700)
T ss_pred             ccCCccHHHHHHHHHhCCCc
Confidence            33    55555666666543

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.76  E-value=3.5e-08  Score=107.95  Aligned_cols=68  Identities=19%  Similarity=0.168  Sum_probs=63.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~  259 (455)
                      ..+.++|||+.+....+.+++.|...+      +....||+..++.++..+.+.+.+|.  |+||||+|.||+||.
T Consensus       447 ~~GrpVLV~t~sv~~se~ls~~L~~~g------i~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIk  514 (908)
T PRK13107        447 ERGQPVLVGTVSIEQSELLARLMVKEK------IPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIV  514 (908)
T ss_pred             HcCCCEEEEeCcHHHHHHHHHHHHHCC------CCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCccee
Confidence            568899999999999999999999875      77888999999999999999999998  999999999999985

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.73  E-value=3.6e-07  Score=101.22  Aligned_cols=98  Identities=19%  Similarity=0.148  Sum_probs=70.1

Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcC--------------------------CCCCc
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNT--------------------------PPEGV  242 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~--------------------------~~~g~  242 (455)
                      .||=+.+.+.+-.+++.|..........+.++.+||.-+...|..+.+.                          ...+.
T Consensus       759 GliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~  838 (1110)
T TIGR02562       759 GLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNH  838 (1110)
T ss_pred             EEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCC
Confidence            5677788888888888777654333446789999999988776654322                          11246


Q ss_pred             eEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCC
Q psy6094         243 RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR  307 (455)
Q Consensus       243 ~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G  307 (455)
                      ..|||||.|.|.|+||+ .+.+|                    +.+.+-.+..||+||..|.+..
T Consensus       839 ~~i~v~Tqv~E~g~D~d-fd~~~--------------------~~~~~~~sliQ~aGR~~R~~~~  882 (1110)
T TIGR02562       839 LFIVLATPVEEVGRDHD-YDWAI--------------------ADPSSMRSIIQLAGRVNRHRLE  882 (1110)
T ss_pred             CeEEEEeeeEEEEeccc-CCeee--------------------eccCcHHHHHHHhhcccccccC
Confidence            78999999999999986 33333                    2345666788999999997764

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.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.73  E-value=3.4e-08  Score=108.02  Aligned_cols=75  Identities=15%  Similarity=0.120  Sum_probs=64.7

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+.++||||.+..+.+.+++.|...+      +....|||.  +.+|...+..+..+.-.|+||||+|.|
T Consensus       419 I~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~g------i~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGR  490 (830)
T PRK12904        419 VVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAG------IPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGR  490 (830)
T ss_pred             HHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCC------CceEeccCc--hHHHHHHHHHhcCCCceEEEecccccC
Confidence            4444433  567799999999999999999999875      778889995  778888888899999999999999999


Q ss_pred             CCCCC
Q psy6094         255 SITID  259 (455)
Q Consensus       255 gitI~  259 (455)
                      |+||+
T Consensus       491 GtDI~  495 (830)
T PRK12904        491 GTDIK  495 (830)
T ss_pred             CcCcc
Confidence            99986

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

Probab=98.49  E-value=4.7e-06  Score=91.23  Aligned_cols=123  Identities=17%  Similarity=0.171  Sum_probs=88.8

Q ss_pred             CCCeEEEEccCCCCC------------ccc--eEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCC---HHH
Q psy6094         136 PGAILVYCTYTFMGV------------SPM--KVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPG---WDT  198 (455)
Q Consensus       136 ~~~k~ilmSAT~~g~------------~pv--~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~---~~e  198 (455)
                      +.-.+|++|||..-+            |.|  ...++.++.+.|...   ........++. .-+...|||+|.   .+.
T Consensus       275 k~g~LvvsSATg~~rg~R~~LfReLlgFevG~~~~~LRNIvD~y~~~---~~~e~~~elvk-~lG~GgLIfV~~d~G~e~  350 (1187)
T COG1110         275 KLGILVVSSATGKPRGSRLKLFRELLGFEVGSGGEGLRNIVDIYVES---ESLEKVVELVK-KLGDGGLIFVPIDYGREK  350 (1187)
T ss_pred             CCceEEEeeccCCCCCchHHHHHHHhCCccCccchhhhheeeeeccC---ccHHHHHHHHH-HhCCCeEEEEEcHHhHHH
Confidence            456799999998111            111  223455555555443   22223444554 345578999999   889


Q ss_pred             HHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEe----CCCCccCCCCC-CeeEEEeCCCCccc
Q psy6094         199 INSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA----TNIAETSITID-DIVYVVDCGKTKMS  273 (455)
Q Consensus       199 i~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViva----Tniae~gitI~-~V~~VID~g~~k~~  273 (455)
                      ++++++.|+.++      +.+...|+.     ..+.++.|..|...|+|.    .+++-||||.| -|+|+|=.|.||.+
T Consensus       351 aeel~e~Lr~~G------i~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk~r  419 (1187)
T COG1110         351 AEELAEYLRSHG------INAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPKFR  419 (1187)
T ss_pred             HHHHHHHHHhcC------ceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCcee
Confidence            999999999875      888888873     257888899999999986    57899999998 57899999999754

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

Probab=98.39  E-value=2.3e-06  Score=97.96  Aligned_cols=111  Identities=14%  Similarity=0.083  Sum_probs=85.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCC---CCCCeEEEeecCCCChhhHhhhhcCCCCCce-EEEEeCCCCccCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFF---NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVR-KIVLATNIAETSITID  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~---~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~-kVivaTniae~gitI~  259 (455)
                      ..++.+||||.+.+.++.+++.|......   ......+..+||+.+.  +..+++.|+++.. +|+|+++++.||+|+|
T Consensus       696 ~~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~~--~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP  773 (1123)
T PRK11448        696 TGEGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSIDK--PDQLIRRFKNERLPNIVVTVDLLTTGIDVP  773 (1123)
T ss_pred             cCCCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCccc--hHHHHHHHhCCCCCeEEEEecccccCCCcc
Confidence            34589999999999999999888764210   0112345668888754  5678888988775 7999999999999999


Q ss_pred             CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC--C-eEEecCC
Q psy6094         260 DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK--R-SETQQYP  314 (455)
Q Consensus       260 ~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~--G-~c~~L~t  314 (455)
                      +|..||-        ++          ..-|+..+.|+.||+.|..+  | .+|.+|.
T Consensus       774 ~v~~vVf--------~r----------pvkS~~lf~QmIGRgtR~~~~~~K~~f~I~D  813 (1123)
T PRK11448        774 SICNLVF--------LR----------RVRSRILYEQMLGRATRLCPEIGKTHFRIFD  813 (1123)
T ss_pred             cccEEEE--------ec----------CCCCHHHHHHHHhhhccCCccCCCceEEEEe
Confidence            9999995        21          23577788999999999877  3 5667777

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

Probab=98.37  E-value=2.9e-06  Score=87.17  Aligned_cols=120  Identities=16%  Similarity=0.118  Sum_probs=99.3

Q ss_pred             HHHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCc
Q psy6094         176 RWVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAE  253 (455)
Q Consensus       176 ~l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae  253 (455)
                      ++..-|..  ..+..+||-.-|++-.+.|.+.|...+      +++-.+||++..-+|.++++..+.|...|+|--|.+-
T Consensus       434 DL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~Yl~e~g------ikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLR  507 (663)
T COG0556         434 DLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELG------IKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLR  507 (663)
T ss_pred             HHHHHHHHHHhcCCeEEEEeehHHHHHHHHHHHHhcC------ceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhh
Confidence            35554443  567899999999999999999999885      8999999999999999999999999999999999999


Q ss_pred             cCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         254 TSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       254 ~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      -|+|||.|..|.-.+--|+       |      ..-|-.+..|=.|||.|.-.|.++.-..
T Consensus       508 EGLDiPEVsLVAIlDADKe-------G------FLRse~SLIQtIGRAARN~~GkvIlYAD  555 (663)
T COG0556         508 EGLDLPEVSLVAILDADKE-------G------FLRSERSLIQTIGRAARNVNGKVILYAD  555 (663)
T ss_pred             ccCCCcceeEEEEeecCcc-------c------cccccchHHHHHHHHhhccCCeEEEEch
Confidence            9999999999874222222       1      2235567889999999999998765433

>cd00268 DEADc DEAD-box helicases

Probab=98.32  E-value=9.4e-06  Score=75.33  Aligned_cols=141  Identities=11%  Similarity=0.071  Sum_probs=95.5

Q ss_pred             HHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHhccCCCCcC
Q psy6094          38 IRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEG  117 (455)
Q Consensus        38 ~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~l~d~~L~~  117 (455)
                      ++...++...+.+...+....+.+|.++++.+.+++++++.++||+|||..                             
T Consensus         2 ~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~-----------------------------   52 (203)
T cd00268           2 EELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAA-----------------------------   52 (203)
T ss_pred             CcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHH-----------------------------
Confidence            344566666766766667778999999999999999999999999999921                             


Q ss_pred             cchHHHHHHHHHHHHhcCCCCeEEEEccCCCCCccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHH
Q psy6094         118 VNNDVIFSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWD  197 (455)
Q Consensus       118 ~~~D~ll~~lk~il~~~~~~~k~ilmSAT~~g~~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~  197 (455)
                          .++.++..+. ..+                                               ...++.+||.+|+.+
T Consensus        53 ----~~~~~l~~~~-~~~-----------------------------------------------~~~~~~viii~p~~~   80 (203)
T cd00268          53 ----FLIPILEKLD-PSP-----------------------------------------------KKDGPQALILAPTRE   80 (203)
T ss_pred             ----HHHHHHHHHH-hhc-----------------------------------------------ccCCceEEEEcCCHH
Confidence                1122232222 000                                               012456888888888


Q ss_pred             HHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC-----C-ccCCCCCCeeEEE
Q psy6094         198 TINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI-----A-ETSITIDDIVYVV  265 (455)
Q Consensus       198 ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni-----a-e~gitI~~V~~VI  265 (455)
                      -+....+.+.....  ..+..+..+||+.+..+....++    +...|+|+|+-     . ..-..++++.++|
T Consensus        81 L~~q~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lI  148 (203)
T cd00268          81 LALQIAEVARKLGK--HTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATPGRLLDLLERGKLDLSKVKYLV  148 (203)
T ss_pred             HHHHHHHHHHHHhc--cCCceEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHHHHHHcCCCChhhCCEEE
Confidence            88877776665432  13577888999998877666554    44679999952     1 2225667788766

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.

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

Probab=98.21  E-value=1.8e-05  Score=86.25  Aligned_cols=85  Identities=19%  Similarity=0.220  Sum_probs=56.1

Q ss_pred             CeEEEeecCCCChhh--HhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE----eCCCCcccccccCCCccccccccc
Q psy6094         216 RFQIIPLHSMLPTVS--QKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV----DCGKTKMSNFDVKDNIATLKPEWI  289 (455)
Q Consensus       216 ~~~v~~lhs~l~~~~--r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI----D~g~~k~~~yd~~~~~~~l~~~~i  289 (455)
                      +..++.+-++.....  -+..+..|.+|+..|+|-|-+.+-|.+.|+|+.|.    |+++-   .-|.+..       --
T Consensus       506 ~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~---~~DfRA~-------Er  575 (730)
T COG1198         506 GARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLG---SPDFRAS-------ER  575 (730)
T ss_pred             CCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhc---CCCcchH-------HH
Confidence            355666666554432  23567788899999999999999999999999875    44431   1122211       11


Q ss_pred             chhhHHhhhcccCCC-CCCeEE
Q psy6094         290 SLANAKQRRGRAGRT-LKRSET  310 (455)
Q Consensus       290 Ska~~~QR~GRaGR~-~~G~c~  310 (455)
                      .-.-+.|=+|||||. .+|..+
T Consensus       576 ~fqll~QvaGRAgR~~~~G~Vv  597 (730)
T COG1198         576 TFQLLMQVAGRAGRAGKPGEVV  597 (730)
T ss_pred             HHHHHHHHHhhhccCCCCCeEE
Confidence            223366899999997 557554

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

Probab=98.17  E-value=6.2e-06  Score=73.88  Aligned_cols=31  Identities=23%  Similarity=0.382  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.|.++++.+.+++++++.|+||||||+.+.
T Consensus         2 ~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~   32 (169)
T PF00270_consen    2 PLQQEAIEAIISGKNVLISAPTGSGKTLAYI   32 (169)
T ss_dssp             HHHHHHHHHHHTTSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCCEEEECCCCCccHHHHH
Confidence            5799999999999999999999999997655

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 ....

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.75  E-value=0.00017  Score=79.10  Aligned_cols=104  Identities=22%  Similarity=0.232  Sum_probs=71.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ceEEEEeCCCCccCCCCCCee
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~kVivaTniae~gitI~~V~  262 (455)
                      ..+.+|||.+.+.+..+.+.+.|.+.+      +..-.|++.-...+- .+...  .| .-.|.||||.|.||.||.==.
T Consensus       424 ~~gqPVLVgT~SIe~SE~ls~~L~~~g------i~h~vLNAk~~e~EA-~IIa~--AG~~GaVTIATNMAGRGTDI~Lg~  494 (925)
T PRK12903        424 KKGQPILIGTAQVEDSETLHELLLEAN------IPHTVLNAKQNAREA-EIIAK--AGQKGAITIATNMAGRGTDIKLSK  494 (925)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHCC------CCceeecccchhhHH-HHHHh--CCCCCeEEEecccccCCcCccCch
Confidence            568899999999999999999999875      333345544222232 33332  23 347999999999999986222


Q ss_pred             --------EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         263 --------YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       263 --------~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                              |||-+.++....                  -=.|-+|||||.|. |.+-.+.|
T Consensus       495 ~V~~~GGLhVIgTerheSrR------------------IDnQLrGRaGRQGDpGss~f~lS  537 (925)
T PRK12903        495 EVLELGGLYVLGTDKAESRR------------------IDNQLRGRSGRQGDVGESRFFIS  537 (925)
T ss_pred             hHHHcCCcEEEecccCchHH------------------HHHHHhcccccCCCCCcceEEEe
Confidence                    777655432222                  23499999999886 86655555

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.65  E-value=0.00018  Score=81.58  Aligned_cols=108  Identities=12%  Similarity=0.046  Sum_probs=84.8

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCC---CceEEEEeCCCCccCCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPE---GVRKIVLATNIAETSITIDD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~---g~~kVivaTniae~gitI~~  260 (455)
                      ..+..+|||..-...++.+.+.|...+      +.++.+||+++..+|..+++.|..   +..-+|+||.++..||++..
T Consensus       485 ~~g~KVLIFSQft~~LdiLed~L~~~g------~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~  558 (1033)
T PLN03142        485 ERDSRVLIFSQMTRLLDILEDYLMYRG------YQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLAT  558 (1033)
T ss_pred             hcCCeEEeehhHHHHHHHHHHHHHHcC------CcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhh
Confidence            456789999988888888888887653      778899999999999999999853   34567899999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEEecCCh
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSETQQYPN  315 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~~L~t~  315 (455)
                      .++||.        ||+.=          +-+...|+.||+-|.|.   =.+|+|++.
T Consensus       559 Ad~VIi--------yD~dW----------NP~~d~QAidRaHRIGQkk~V~VyRLIt~  598 (1033)
T PLN03142        559 ADIVIL--------YDSDW----------NPQVDLQAQDRAHRIGQKKEVQVFRFCTE  598 (1033)
T ss_pred             CCEEEE--------eCCCC----------ChHHHHHHHHHhhhcCCCceEEEEEEEeC
Confidence            999998        44332          22344588888877655   378899984

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

Probab=97.61  E-value=0.0002  Score=80.92  Aligned_cols=124  Identities=13%  Similarity=0.082  Sum_probs=83.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCee-
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIV-  262 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~-  262 (455)
                      ..+|.+|||+++.+.++.+++.|......  .++.++.  .+.. .+|.++++.|++|...|+++|+....|||+++.. 
T Consensus       672 ~~~g~~LVlftS~~~l~~v~~~L~~~~~~--~~~~~l~--q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l  746 (850)
T TIGR01407       672 ITSPKILVLFTSYEMLHMVYDMLNELPEF--EGYEVLA--QGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGL  746 (850)
T ss_pred             hcCCCEEEEeCCHHHHHHHHHHHhhhccc--cCceEEe--cCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCce
Confidence            56799999999999999999999763211  1233322  2222 4678888999999999999999999999998765 


Q ss_pred             -EEEeCCCCcccccccC----------CCcccccc--cccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         263 -YVVDCGKTKMSNFDVK----------DNIATLKP--EWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       263 -~VID~g~~k~~~yd~~----------~~~~~l~~--~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                       .||-.|+|-..--||.          .|-..+..  .|-.--...|-.||.=|...  |..+-|
T Consensus       747 ~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~il  811 (850)
T TIGR01407       747 VCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVIL  811 (850)
T ss_pred             EEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEE
Confidence             6677888743222211          11111111  13233457888999988664  765544

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.

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

Probab=97.60  E-value=0.0023  Score=70.47  Aligned_cols=102  Identities=9%  Similarity=-0.047  Sum_probs=68.9

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChh---------------------hHhhhhcCCCC-Cce
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTV---------------------SQKSIFNTPPE-GVR  243 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~---------------------~r~~v~~~~~~-g~~  243 (455)
                      ++..+|||.++..+..+.+.|.+..... .....+.++++-..+                     ....+.+.|.+ +..
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~-~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~  592 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEK-FEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENP  592 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccc-cCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCc
Confidence            5899999999999999998887643110 012344444443222                     11245566654 577


Q ss_pred             EEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCC-CCC
Q psy6094         244 KIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT-LKR  307 (455)
Q Consensus       244 kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~-~~G  307 (455)
                      +|+|.+|..-||+|.|.+..++         .|          .|..-..+.|-.||+-|. .+|
T Consensus       593 ~ilIVvdmllTGFDaP~l~tLy---------ld----------Kplk~h~LlQai~R~nR~~~~~  638 (667)
T TIGR00348       593 KLLIVVDMLLTGFDAPILNTLY---------LD----------KPLKYHGLLQAIARTNRIDGKD  638 (667)
T ss_pred             eEEEEEcccccccCCCccceEE---------Ee----------ccccccHHHHHHHHhccccCCC
Confidence            9999999999999999998766         22          233334577999999994 444

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

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.55  E-value=0.00051  Score=74.39  Aligned_cols=105  Identities=19%  Similarity=0.179  Sum_probs=72.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC----
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID----  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~----  259 (455)
                      ..+.+|||.+.+.++.+.+.+.|.+.+      +....|++.-...| ..+...... .-.|.||||.|.||.||.    
T Consensus       425 ~~GrPVLVgt~sI~~SE~ls~~L~~~g------I~h~vLNAk~~~~E-A~IIa~AG~-~gaVTIATNMAGRGTDIkLg~~  496 (764)
T PRK12326        425 ETGQPVLVGTHDVAESEELAERLRAAG------VPAVVLNAKNDAEE-ARIIAEAGK-YGAVTVSTQMAGRGTDIRLGGS  496 (764)
T ss_pred             HcCCCEEEEeCCHHHHHHHHHHHHhCC------CcceeeccCchHhH-HHHHHhcCC-CCcEEEEecCCCCccCeecCCC
Confidence            678899999999999999999999875      44444555533333 344433211 246999999999999985    


Q ss_pred             ------Ce-----eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         260 ------DI-----VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       260 ------~V-----~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                            +|     -|||=+.++                  -|+--=.|-+|||||.|. |.+-.+.|
T Consensus       497 ~~~~~~~V~~~GGLhVIgTerh------------------eSrRID~QLrGRaGRQGDpGss~f~lS  545 (764)
T PRK12326        497 DEADRDRVAELGGLHVIGTGRH------------------RSERLDNQLRGRAGRQGDPGSSVFFVS  545 (764)
T ss_pred             cccchHHHHHcCCcEEEeccCC------------------chHHHHHHHhcccccCCCCCceeEEEE
Confidence                  11     255544433                  333334599999999886 87776666

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.01  E-value=0.0024  Score=70.86  Aligned_cols=67  Identities=19%  Similarity=0.197  Sum_probs=47.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ceEEEEeCCCCccCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VRKIVLATNIAETSITID  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~kVivaTniae~gitI~  259 (455)
                      ..+.+|||-+.+.+.-+.+.++|...+.      ..-.|.+.-...|- .+....  | .-.|.||||.|.||-||.
T Consensus       447 ~~GrPVLVGT~SVe~SE~ls~~L~~~gi------~h~VLNAk~~~~EA-~IIa~A--G~~GaVTIATNMAGRGTDIk  514 (913)
T PRK13103        447 ALGRPVLVGTATIETSEHMSNLLKKEGI------EHKVLNAKYHEKEA-EIIAQA--GRPGALTIATNMAGRGTDIL  514 (913)
T ss_pred             hCCCCEEEEeCCHHHHHHHHHHHHHcCC------cHHHhccccchhHH-HHHHcC--CCCCcEEEeccCCCCCCCEe
Confidence            6788999999999999999999998752      22223343223333 343322  3 246999999999999983

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=96.83  E-value=0.0052  Score=68.45  Aligned_cols=105  Identities=20%  Similarity=0.213  Sum_probs=71.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC---C
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID---D  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~---~  260 (455)
                      ..+.+|||-+.+...-+.++..|...+      +....|++.-...|- .+...... .-.|.||||.|.||-||.   +
T Consensus       566 ~~grPvLigt~si~~se~ls~~L~~~g------i~h~vLNak~~~~Ea-~iia~AG~-~g~VTIATNmAGRGTDIkl~~~  637 (970)
T PRK12899        566 RKGNPILIGTESVEVSEKLSRILRQNR------IEHTVLNAKNHAQEA-EIIAGAGK-LGAVTVATNMAGRGTDIKLDEE  637 (970)
T ss_pred             hCCCCEEEEeCcHHHHHHHHHHHHHcC------CcceecccchhhhHH-HHHHhcCC-CCcEEEeeccccCCcccccCch
Confidence            567789999999999999999999875      333444444222232 33332211 247999999999999984   1


Q ss_pred             e-----eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         261 I-----VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       261 V-----~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |     -+||-+.++                  -|+--=.|-.|||||.|. |.+-.+.|
T Consensus       638 v~~~GGLhVIgTer~------------------es~Rid~Ql~GRagRQGdpGss~f~lS  679 (970)
T PRK12899        638 AVAVGGLYVIGTSRH------------------QSRRIDRQLRGRCARLGDPGAAKFFLS  679 (970)
T ss_pred             HHhcCCcEEEeeccC------------------chHHHHHHHhcccccCCCCCceeEEEE
Confidence            2     255544433                  233344599999999987 98776666

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

Probab=96.77  E-value=0.0024  Score=59.62  Aligned_cols=34  Identities=24%  Similarity=0.477  Sum_probs=25.1

Q ss_pred             cCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          55 KLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      .-|....|...++++.+++.+++.|+.|||||+.
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~L   35 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFL   35 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHH
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHH
Confidence            3477788999999999999999999999999954

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

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=96.75  E-value=0.0034  Score=70.26  Aligned_cols=105  Identities=21%  Similarity=0.184  Sum_probs=71.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC----
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID----  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~----  259 (455)
                      ..+.+|||-+.+.+.-+.+.++|...+      +..-.|.+.....|-.-|-+.-.+|  .|-||||.|.||-||.    
T Consensus       626 ~~GrPVLVGT~SVe~SE~lS~~L~~~g------I~H~VLNAK~h~~EAeIVA~AG~~G--aVTIATNMAGRGTDIkLg~~  697 (1112)
T PRK12901        626 EAGRPVLVGTTSVEISELLSRMLKMRK------IPHNVLNAKLHQKEAEIVAEAGQPG--TVTIATNMAGRGTDIKLSPE  697 (1112)
T ss_pred             HCCCCEEEEeCcHHHHHHHHHHHHHcC------CcHHHhhccchhhHHHHHHhcCCCC--cEEEeccCcCCCcCcccchh
Confidence            578899999999999999999999875      2222334433333433333333333  6999999999999985    


Q ss_pred             ----CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         260 ----DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       260 ----~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                          +=-|||-+.++                  -|+--=.|-+|||||.|. |.+-.+.|
T Consensus       698 V~e~GGL~VIgTerh------------------eSrRID~QLrGRaGRQGDPGsS~f~lS  739 (1112)
T PRK12901        698 VKAAGGLAIIGTERH------------------ESRRVDRQLRGRAGRQGDPGSSQFYVS  739 (1112)
T ss_pred             hHHcCCCEEEEccCC------------------CcHHHHHHHhcccccCCCCCcceEEEE
Confidence                22366654443                  233334599999999886 87665555

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.66  E-value=0.0093  Score=66.03  Aligned_cols=67  Identities=18%  Similarity=0.141  Sum_probs=47.7

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCC-ChhhHhhhhcCC-CCCceEEEEeCCCCccCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSML-PTVSQKSIFNTP-PEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l-~~~~r~~v~~~~-~~g~~kVivaTniae~gitI  258 (455)
                      ..+.+|||-+.+.+.-+.+.+.|...+      +..-.|++.- ..++-..+.... .+  -.|.||||.|.||.||
T Consensus       422 ~~grPVLIgT~SIe~SE~ls~~L~~~g------i~h~vLNAk~~~~~~EA~IIA~AG~~--G~VTIATNMAGRGTDI  490 (870)
T CHL00122        422 QTGRPILIGTTTIEKSELLSQLLKEYR------LPHQLLNAKPENVRRESEIVAQAGRK--GSITIATNMAGRGTDI  490 (870)
T ss_pred             hcCCCEEEeeCCHHHHHHHHHHHHHcC------CccceeeCCCccchhHHHHHHhcCCC--CcEEEeccccCCCcCe
Confidence            678899999999999999999999875      3334455431 112223344332 23  3699999999999987

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

Probab=96.58  E-value=0.048  Score=59.96  Aligned_cols=107  Identities=12%  Similarity=0.060  Sum_probs=68.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+.+|-||..|..-.+.+++..+...      -.|+.+.|.-+..+   + +.+  +..+|++=|.+...|+++++..+
T Consensus       280 ~~gknIcvfsSt~~~~~~v~~~~~~~~------~~Vl~l~s~~~~~d---v-~~W--~~~~VviYT~~itvG~Sf~~~HF  347 (824)
T PF02399_consen  280 NAGKNICVFSSTVSFAEIVARFCARFT------KKVLVLNSTDKLED---V-ESW--KKYDVVIYTPVITVGLSFEEKHF  347 (824)
T ss_pred             hCCCcEEEEeChHHHHHHHHHHHHhcC------CeEEEEcCCCCccc---c-ccc--cceeEEEEeceEEEEeccchhhc
Confidence            457788899999888888887777653      56777777655542   2 222  46799999999999999875433


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      =-=+++.|...+    |        .+..+..|..||+-.......|.-+.
T Consensus       348 ~~~f~yvk~~~~----g--------pd~~s~~Q~lgRvR~l~~~ei~v~~d  386 (824)
T PF02399_consen  348 DSMFAYVKPMSY----G--------PDMVSVYQMLGRVRSLLDNEIYVYID  386 (824)
T ss_pred             eEEEEEecCCCC----C--------CcHHHHHHHHHHHHhhccCeEEEEEe
Confidence            111122111111    1        23345779999997666666655555

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

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

Probab=96.42  E-value=0.016  Score=66.34  Aligned_cols=125  Identities=12%  Similarity=0.034  Sum_probs=82.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCC--e
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDD--I  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~--V  261 (455)
                      ..+|.+|||+++.+.++.+++.|.....  ..++.++. . ++....+.++.+.|+.+...|+++|+-..-|||+|+  +
T Consensus       750 ~~~g~~LVLFtSy~~l~~v~~~l~~~~~--~~~~~ll~-Q-g~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l  825 (928)
T PRK08074        750 ATKGRMLVLFTSYEMLKKTYYNLKNEEE--LEGYVLLA-Q-GVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDEL  825 (928)
T ss_pred             hCCCCEEEEECCHHHHHHHHHHHhhccc--ccCceEEe-c-CCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCce
Confidence            5789999999999999999999986431  11122222 2 333345677788888888899999999999999986  5


Q ss_pred             eEEEeCCCCccccccc----------CCCccccc--ccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         262 VYVVDCGKTKMSNFDV----------KDNIATLK--PEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~----------~~~~~~l~--~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                      ..||-.++|-..--||          ..|-..+.  ..|...-...|=.||.=|...  |..+.|
T Consensus       826 ~~viI~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~il  890 (928)
T PRK08074        826 SCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVL  890 (928)
T ss_pred             EEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEe
Confidence            7888888874211111          11111121  123334456788888877654  766533

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=96.42  E-value=0.0043  Score=56.03  Aligned_cols=123  Identities=15%  Similarity=0.055  Sum_probs=74.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCC--CCccCCCCCC-
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATN--IAETSITIDD-  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTn--iae~gitI~~-  260 (455)
                      ..+|.+|||+|+.+..+.+.+.+......  .++.++.=    ...+...+++.|..+..-|++++.  -..-|||++| 
T Consensus         7 ~~~g~~lv~f~Sy~~l~~~~~~~~~~~~~--~~~~v~~q----~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~   80 (167)
T PF13307_consen    7 AVPGGVLVFFPSYRRLEKVYERLKERLEE--KGIPVFVQ----GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGD   80 (167)
T ss_dssp             CCSSEEEEEESSHHHHHHHHTT-TSS-E---ETSCEEES----TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECE
T ss_pred             cCCCCEEEEeCCHHHHHHHHHHHHhhccc--ccceeeec----CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCc
Confidence            56799999999999999999988865310  11222221    355667788888888899999998  7888999986 


Q ss_pred             -eeEEEeCCCCcccccccCCCc------------ccccccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         261 -IVYVVDCGKTKMSNFDVKDNI------------ATLKPEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       261 -V~~VID~g~~k~~~yd~~~~~------------~~l~~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                       .+.||-.|+|-....|+....            ......+..--...|=.||+=|...  |..+-|
T Consensus        81 ~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~ll  147 (167)
T PF13307_consen   81 LLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILL  147 (167)
T ss_dssp             SEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEE
T ss_pred             hhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEE
Confidence             778999999865444332110            0111122333357788999988766  555543

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

Probab=96.31  E-value=0.0067  Score=53.08  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=17.4

Q ss_pred             HcCCeEEEEcCCCCCcccc-hh-hhhh
Q psy6094          70 RNNQITVISGETGSGPPLH-LD-FITL   94 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtq-lp-~ll~   94 (455)
                      ..++..+|.-.+|+|||+. +| .+-+
T Consensus         2 ~kg~~~~~d~hpGaGKTr~vlp~~~~~   28 (148)
T PF07652_consen    2 RKGELTVLDLHPGAGKTRRVLPEIVRE   28 (148)
T ss_dssp             STTEEEEEE--TTSSTTTTHHHHHHHH
T ss_pred             CCCceeEEecCCCCCCcccccHHHHHH
Confidence            3577889999999999997 55 4443

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 ....

>KOG0949|consensus

Probab=96.30  E-value=0.0038  Score=68.77  Aligned_cols=95  Identities=22%  Similarity=0.143  Sum_probs=66.5

Q ss_pred             EEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhh
Q psy6094         219 IIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRR  298 (455)
Q Consensus       219 v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~  298 (455)
                      +-..|++|...+|..|.--|+.|...|++||..++-||+.|=-++|.-              .++|+.   .--+|.|.+
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~--------------gDsLQL---~plny~Qma 1027 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFA--------------GDSLQL---DPLNYKQMA 1027 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEe--------------cccccc---CchhHHhhh
Confidence            566799999999999988899999999999999999999996555542              122332   335788999


Q ss_pred             cccCCCCC---CeEEec-CChhh---hccCCCCcccccC
Q psy6094         299 GRAGRTLK---RSETQQ-YPNDV---LNMLKDPELEGVN  330 (455)
Q Consensus       299 GRaGR~~~---G~c~~L-~t~~~---~~~~~~PEi~r~~  330 (455)
                      |||||.|=   |.+.-+ ++...   +--...|.|+-..
T Consensus      1028 GRAGRRGFD~lGnV~FmgiP~~kv~rLlts~L~diqG~~ 1066 (1330)
T KOG0949|consen 1028 GRAGRRGFDTLGNVVFMGIPRQKVQRLLTSLLPDIQGAY 1066 (1330)
T ss_pred             ccccccccccccceEEEeCcHHHHHHHHHHhhhcccCCC
Confidence            99999762   655433 33211   2223355565555

>KOG0391|consensus

Probab=96.14  E-value=0.03  Score=63.02  Aligned_cols=114  Identities=16%  Similarity=0.130  Sum_probs=93.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCce--EEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVR--KIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~--kVivaTniae~gitI~~V  261 (455)
                      ..+..+|||.--..-.+-|...|..++      +..+.|-|.-..++|+..+++|....|  ..|++|--...||++-+.
T Consensus      1274 ~eghRvLIfTQMtkmLDVLeqFLnyHg------ylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgA 1347 (1958)
T KOG0391|consen 1274 SEGHRVLIFTQMTKMLDVLEQFLNYHG------YLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGA 1347 (1958)
T ss_pred             hcCceEEehhHHHHHHHHHHHHHhhcc------eEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccccccccC
Confidence            678899999988888888888888775      889999999999999999999976543  568999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhhh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVL  318 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~~  318 (455)
                      +.||=        ||..-+       |.=-++|.-|.-|.|+++.=+.|||+++...
T Consensus      1348 DTVvF--------YDsDwN-------PtMDaQAQDrChRIGqtRDVHIYRLISe~TI 1389 (1958)
T KOG0391|consen 1348 DTVVF--------YDSDWN-------PTMDAQAQDRCHRIGQTRDVHIYRLISERTI 1389 (1958)
T ss_pred             ceEEE--------ecCCCC-------chhhhHHHHHHHhhcCccceEEEEeeccchH
Confidence            99994        554433       2223677789999999999999999995443

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=96.09  E-value=0.038  Score=61.82  Aligned_cols=29  Identities=14%  Similarity=0.149  Sum_probs=28.1

Q ss_pred             CHHHHHHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          58 SYQMRDAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        58 ~~~~q~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      +.++|.+++..+..++++|+.++||||||
T Consensus        93 ~tp~qvQ~I~~i~l~~gvIAeaqTGeGKT  121 (970)
T PRK12899         93 MVPYDVQILGAIAMHKGFITEMQTGEGKT  121 (970)
T ss_pred             CChHHHHHhhhhhcCCCeEEEeCCCCChH
Confidence            78899999999999999999999999999

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

Probab=95.91  E-value=0.057  Score=59.51  Aligned_cols=123  Identities=10%  Similarity=-0.061  Sum_probs=81.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCce-EEEEeCCCCccCCCCCCe-
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVR-KIVLATNIAETSITIDDI-  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~-kVivaTniae~gitI~~V-  261 (455)
                      ..+|.+|||+|+.+..+.+.+.+.....     ...+..+|.-+..+   .+++|.++.- -++|+|.-..-|||+++= 
T Consensus       477 ~~~~~~lvlF~Sy~~l~~~~~~~~~~~~-----~~~v~~q~~~~~~~---~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~  548 (654)
T COG1199         477 ASPGGVLVLFPSYEYLKRVAERLKDERS-----TLPVLTQGEDEREE---LLEKFKASGEGLILVGGGSFWEGVDFPGDA  548 (654)
T ss_pred             hcCCCEEEEeccHHHHHHHHHHHhhcCc-----cceeeecCCCcHHH---HHHHHHHhcCCeEEEeeccccCcccCCCCC
Confidence            6778999999999999999999987542     13455666666554   4444444433 899999999999999864 


Q ss_pred             -eEEEeCCCCcccccc----------cCCCc--ccccccccchhhHHhhhcccCCCCC--CeEEecCC
Q psy6094         262 -VYVVDCGKTKMSNFD----------VKDNI--ATLKPEWISLANAKQRRGRAGRTLK--RSETQQYP  314 (455)
Q Consensus       262 -~~VID~g~~k~~~yd----------~~~~~--~~l~~~~iSka~~~QR~GRaGR~~~--G~c~~L~t  314 (455)
                       +.||-.|+|-...-|          ...|-  ......+..--...|=.||+=|...  |.++-|=.
T Consensus       549 l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~  616 (654)
T COG1199         549 LRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDK  616 (654)
T ss_pred             eeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecc
Confidence             667777877543222          22221  1223334445567788888877544  77776533

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=95.89  E-value=0.0067  Score=54.67  Aligned_cols=36  Identities=17%  Similarity=0.234  Sum_probs=31.0

Q ss_pred             cCCCHHHHHHHHHHHHcC-CeEEEEcCCCCCcccchh
Q psy6094          55 KLPSYQMRDAVLDMVRNN-QITVISGETGSGPPLHLD   90 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~~~-~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..++|.++++.+.+. +++++.|+||||||+.+.
T Consensus         6 ~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~   42 (201)
T smart00487        6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAAL   42 (201)
T ss_pred             CCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHH
Confidence            456678899999999988 999999999999996544

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

Probab=95.81  E-value=0.027  Score=61.62  Aligned_cols=109  Identities=17%  Similarity=0.228  Sum_probs=74.7

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhH-hhhhcCCCCCceEEEEeCCCCccCCCCCCeeEE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQ-KSIFNTPPEGVRKIVLATNIAETSITIDDIVYV  264 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r-~~v~~~~~~g~~kVivaTniae~gitI~~V~~V  264 (455)
                      .|..||||.+...++.+.+.+........+++ +..+-|.-.+.++ ...|.. .+.--+|.++-+.+.||||+|.|..+
T Consensus       426 ~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~-a~~IT~d~~~~q~~Id~f~~-ke~~P~IaitvdlL~TGiDvpev~nl  503 (875)
T COG4096         426 IGKTIVFAKNHDHAERIREALVNEYPEYNGRY-AMKITGDAEQAQALIDNFID-KEKYPRIAITVDLLTTGVDVPEVVNL  503 (875)
T ss_pred             cCceEEEeeCcHHHHHHHHHHHHhCccccCce-EEEEeccchhhHHHHHHHHh-cCCCCceEEehhhhhcCCCchheeee
Confidence            56899999999999999999987643222233 3334444333222 122332 33445899999999999999999988


Q ss_pred             EeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC--C------eEEecCC
Q psy6094         265 VDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK--R------SETQQYP  314 (455)
Q Consensus       265 ID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~--G------~c~~L~t  314 (455)
                      |         |+-.         --||.-++|..||+=|..+  |      ..|.++.
T Consensus       504 V---------F~r~---------VrSktkF~QMvGRGTRl~~~~~~~~~dK~~F~ifD  543 (875)
T COG4096         504 V---------FDRK---------VRSKTKFKQMVGRGTRLCPDLGGPEQDKEFFTIFD  543 (875)
T ss_pred             e---------ehhh---------hhhHHHHHHHhcCccccCccccCccccceeEEEEE
Confidence            8         3322         2388889999999988655  3      4456666

>KOG0392|consensus

Probab=95.81  E-value=0.031  Score=63.21  Aligned_cols=115  Identities=14%  Similarity=0.192  Sum_probs=88.0

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ceEE-EEeCCCCccCCCCCCeeE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VRKI-VLATNIAETSITIDDIVY  263 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~kV-ivaTniae~gitI~~V~~  263 (455)
                      +..+||||.=+..++-+.+.|.+...   +.+....|-|++++.+|.++.++|.++ ...| +++|-|..-|++.-+.+-
T Consensus      1340 qHRiLIFcQlK~mlDlVekDL~k~~m---psVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADT 1416 (1549)
T KOG0392|consen 1340 QHRILIFCQLKSMLDLVEKDLFKKYM---PSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADT 1416 (1549)
T ss_pred             cceeEEeeeHHHHHHHHHHHHhhhhc---CceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCce
Confidence            45799999998888888877776542   356777899999999999999999887 4454 678999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhhh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVL  318 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~~  318 (455)
                      ||=.    +-.|||-..           -+|.-|+-|-|..+-=.+|||+++..+
T Consensus      1417 VVFv----EHDWNPMrD-----------LQAMDRAHRIGQKrvVNVyRlItrGTL 1456 (1549)
T KOG0392|consen 1417 VVFV----EHDWNPMRD-----------LQAMDRAHRIGQKRVVNVYRLITRGTL 1456 (1549)
T ss_pred             EEEE----ecCCCchhh-----------HHHHHHHHhhcCceeeeeeeehhcccH
Confidence            9820    011444444           246668888887666789999995443

>KOG0385|consensus

Probab=95.79  E-value=0.17  Score=55.03  Aligned_cols=112  Identities=12%  Similarity=0.076  Sum_probs=82.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC---ceEEEEeCCCCccCCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG---VRKIVLATNIAETSITIDD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g---~~kVivaTniae~gitI~~  260 (455)
                      ..+..||+|-.-..-.+-+.+...-+      +|..+.+-|+.+.++|...++.|...   +.-.+++|-.+.-||++-.
T Consensus       485 ~~GhRVLIFSQmt~mLDILeDyc~~R------~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~a  558 (971)
T KOG0385|consen  485 EQGHRVLIFSQMTRMLDILEDYCMLR------GYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTA  558 (971)
T ss_pred             hCCCeEEEeHHHHHHHHHHHHHHHhc------CceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecccccccccccc
Confidence            56788999954333333333333322      48899999999999999988877543   3456789999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND  316 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~  316 (455)
                      .+.||=++    ..|||...           -+|.+|+-|.|...+=.+|||.|++
T Consensus       559 ADtVIlyD----SDWNPQ~D-----------LQAmDRaHRIGQ~K~V~V~RLiten  599 (971)
T KOG0385|consen  559 ADTVILYD----SDWNPQVD-----------LQAMDRAHRIGQKKPVVVYRLITEN  599 (971)
T ss_pred             ccEEEEec----CCCCchhh-----------hHHHHHHHhhCCcCceEEEEEeccc
Confidence            99888411    11444444           4688999999999999999999944

>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=95.61  E-value=0.0084  Score=53.92  Aligned_cols=30  Identities=17%  Similarity=0.288  Sum_probs=25.2

Q ss_pred             CCHHHHHHHHHHHHc-------CCeEEEEcCCCCCcc
Q psy6094          57 PSYQMRDAVLDMVRN-------NQITVISGETGSGPP   86 (455)
Q Consensus        57 P~~~~q~~il~~i~~-------~~~vii~~~TGSGKT   86 (455)
                      .++++|.+++..+.+       +..+++.++||||||
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT   39 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKT   39 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcC
Confidence            457789998888873       688999999999999

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 ....

>PF13245 AAA_19: Part of AAA domain

Probab=95.57  E-value=0.0075  Score=47.03  Aligned_cols=25  Identities=20%  Similarity=0.386  Sum_probs=19.2

Q ss_pred             HHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          66 LDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        66 l~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..++.++..++|.|++|||||+.+.
T Consensus         4 ~~al~~~~~~vv~g~pGtGKT~~~~   28 (76)
T PF13245_consen    4 RRALAGSPLFVVQGPPGTGKTTTLA   28 (76)
T ss_pred             HHHHhhCCeEEEECCCCCCHHHHHH
Confidence            3356667888889999999995543

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

Probab=95.39  E-value=0.012  Score=54.78  Aligned_cols=18  Identities=22%  Similarity=0.503  Sum_probs=16.3

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      +++++.|+||+||||.++
T Consensus         2 ~vi~lvGptGvGKTTt~a   19 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIA   19 (196)
T ss_dssp             EEEEEEESTTSSHHHHHH
T ss_pred             EEEEEECCCCCchHhHHH
Confidence            478899999999999988

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

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=95.33  E-value=0.094  Score=58.15  Aligned_cols=119  Identities=9%  Similarity=0.009  Sum_probs=75.2

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhc----CCCCCceEEEEeCCCCccCCCCCC
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFN----TPPEGVRKIVLATNIAETSITIDD  260 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~----~~~~g~~kVivaTniae~gitI~~  260 (455)
                      .+|.+|||+++.+..+.+++.|....     ...+ ..+|..   .+.++++    .|..|...|+++|.-..-|||+|+
T Consensus       533 ~~gg~LVlFtSy~~l~~v~~~l~~~~-----~~~l-l~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pG  603 (697)
T PRK11747        533 KHKGSLVLFASRRQMQKVADLLPRDL-----RLML-LVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPG  603 (697)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHhc-----CCcE-EEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCC
Confidence            56669999999999999999987532     1222 235543   3444553    344567789999999999999986


Q ss_pred             --eeEEEeCCCCcccccccC----------CCccccc--ccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         261 --IVYVVDCGKTKMSNFDVK----------DNIATLK--PEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       261 --V~~VID~g~~k~~~yd~~----------~~~~~l~--~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                        .+.||-.++|-..--||-          .|-+.+.  ..|-.--...|=.||.=|...  |..+-|
T Consensus       604 d~l~~vII~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~il  671 (697)
T PRK11747        604 DYLTQVIITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTIL  671 (697)
T ss_pred             CceEEEEEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEE
Confidence              788998888743222221          1111111  112222346788888877543  766644

>KOG0951|consensus

Probab=95.30  E-value=0.1  Score=59.49  Aligned_cols=120  Identities=17%  Similarity=0.087  Sum_probs=76.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC----------------CCCeEEEeecCCCChhhHhhhhcCCCCCceEEEE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFN----------------SSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL  247 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~----------------~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViv  247 (455)
                      ..+.+.+||+|+++.+..++..+-......                ...+....=|-+++..++..+-.-|..|..+|+|
T Consensus      1357 ~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v 1436 (1674)
T KOG0951|consen 1357 GNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCV 1436 (1674)
T ss_pred             cCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEE
Confidence            567889999999999988876554321100                0111111118899999999888888899998887


Q ss_pred             eCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         248 ATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       248 aTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      ..-= -.|+.... ..||--|   ...||-+.+.    ....+-+...|..|+|.|  .|.|+-+..
T Consensus      1437 ~s~~-~~~~~~~~-~lVvvmg---t~~ydg~e~~----~~~y~i~~ll~m~G~a~~--~~k~vi~~~ 1492 (1674)
T KOG0951|consen 1437 MSRD-CYGTKLKA-HLVVVMG---TQYYDGKEHS----YEDYPIAELLQMVGLASG--AGKCVIMCH 1492 (1674)
T ss_pred             EEcc-cccccccc-eEEEEec---ceeecccccc----cccCchhHHHHHhhhhcC--CccEEEEec
Confidence            6432 33333221 2233223   2346655442    234567889999999988  578887766

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

Probab=95.27  E-value=0.0097  Score=57.95  Aligned_cols=24  Identities=42%  Similarity=0.538  Sum_probs=20.2

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+++.+.+++|+|+|||||||.+-
T Consensus       122 ~~v~~~~~ili~G~tGSGKTT~l~  145 (270)
T PF00437_consen  122 SAVRGRGNILISGPTGSGKTTLLN  145 (270)
T ss_dssp             HCHHTTEEEEEEESTTSSHHHHHH
T ss_pred             hccccceEEEEECCCccccchHHH
Confidence            345778999999999999997765

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

>KOG1123|consensus

Probab=95.24  E-value=0.055  Score=55.96  Aligned_cols=105  Identities=15%  Similarity=0.091  Sum_probs=76.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ceEEEEeCCCCccCCCCCCee
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~kVivaTniae~gitI~~V~  262 (455)
                      ..+..|+||--..-.....+-.|.+-           .+||.-++.+|.+|++.|.-. ...-|+-.-|+.+|||+|...
T Consensus       541 ~RgDKiIVFsDnvfALk~YAikl~Kp-----------fIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAn  609 (776)
T KOG1123|consen  541 RRGDKIIVFSDNVFALKEYAIKLGKP-----------FIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEAN  609 (776)
T ss_pred             hcCCeEEEEeccHHHHHHHHHHcCCc-----------eEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCccc
Confidence            56778999988777666666555442           278999999999999998643 456677778999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCC-------eEEecCChh
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR-------SETQQYPND  316 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G-------~c~~L~t~~  316 (455)
                      +.|.-.        .         -..|+-+-.||.||.=|+..+       .-|.|.+.+
T Consensus       610 vLIQIS--------S---------H~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~D  653 (776)
T KOG1123|consen  610 VLIQIS--------S---------HGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKD  653 (776)
T ss_pred             EEEEEc--------c---------cccchHHHHHHHHHHHHHhhcCccccceeeeeeeecc
Confidence            998511        1         124666677999988775432       455666643

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=95.24  E-value=0.016  Score=57.25  Aligned_cols=28  Identities=18%  Similarity=0.466  Sum_probs=24.1

Q ss_pred             HHHHHH----HHHHHHcCCeEEEEcCCCCCcc
Q psy6094          59 YQMRDA----VLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        59 ~~~q~~----il~~i~~~~~vii~~~TGSGKT   86 (455)
                      ++.|.+    +..++.+++.+++.+|||+|||
T Consensus        10 r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKT   41 (289)
T smart00488       10 YPIQYEFMEELKRVLDRGKIGILESPTGTGKT   41 (289)
T ss_pred             CHHHHHHHHHHHHHHHcCCcEEEECCCCcchh
Confidence            677777    6666778999999999999999

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=95.24  E-value=0.016  Score=57.25  Aligned_cols=28  Identities=18%  Similarity=0.466  Sum_probs=24.1

Q ss_pred             HHHHHH----HHHHHHcCCeEEEEcCCCCCcc
Q psy6094          59 YQMRDA----VLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        59 ~~~q~~----il~~i~~~~~vii~~~TGSGKT   86 (455)
                      ++.|.+    +..++.+++.+++.+|||+|||
T Consensus        10 r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKT   41 (289)
T smart00489       10 YPIQYEFMEELKRVLDRGKIGILESPTGTGKT   41 (289)
T ss_pred             CHHHHHHHHHHHHHHHcCCcEEEECCCCcchh
Confidence            677777    6666778999999999999999

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

Probab=95.18  E-value=0.013  Score=54.77  Aligned_cols=31  Identities=19%  Similarity=0.333  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHcCCe-EEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQI-TVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~-vii~~~TGSGKTtqlp   90 (455)
                      ..|.+.+..+.++.. .+|.||+||||||.+.
T Consensus         4 ~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~   35 (236)
T PF13086_consen    4 ESQREAIQSALSSNGITLIQGPPGTGKTTTLA   35 (236)
T ss_dssp             HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCEEEECCCCCChHHHHH
Confidence            468888888888886 9999999999997776

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

Probab=95.11  E-value=0.16  Score=57.34  Aligned_cols=120  Identities=15%  Similarity=0.037  Sum_probs=77.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC--Ce
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID--DI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~--~V  261 (455)
                      ..+|.+||++++.+.++.+++.|....      ..++ ..|.-.  .+.++.+.|..+...|+++|+-.--|||+|  +.
T Consensus       645 ~~~g~~LVLFtS~~~l~~v~~~l~~~~------~~~l-~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~  715 (820)
T PRK07246        645 QLQQPILVLFNSKKHLLAVSDLLDQWQ------VSHL-AQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADR  715 (820)
T ss_pred             hcCCCEEEEECcHHHHHHHHHHHhhcC------CcEE-EeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCe
Confidence            568999999999999999999987531      2222 223111  234567777778889999999999999996  45


Q ss_pred             eEEEeCCCCcccccccC----------CCcccccc--cccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         262 VYVVDCGKTKMSNFDVK----------DNIATLKP--EWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~----------~~~~~l~~--~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                      ..||-.++|-..-.||-          .|-+.+..  .|-.--...|=.||.=|...  |..+.|
T Consensus       716 ~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~il  780 (820)
T PRK07246        716 MIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLIL  780 (820)
T ss_pred             EEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEE
Confidence            66666787744332321          12122222  23333457788888888664  765543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=95.11  E-value=0.096  Score=58.25  Aligned_cols=124  Identities=13%  Similarity=0.110  Sum_probs=76.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC----CCCeEEEeecCCCChhhHhhhhcCCCC----CceEEEEeC--CCCc
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFN----SSRFQIIPLHSMLPTVSQKSIFNTPPE----GVRKIVLAT--NIAE  253 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~----~~~~~v~~lhs~l~~~~r~~v~~~~~~----g~~kVivaT--niae  253 (455)
                      ..+|.+|||+|+..-.+.+.+.+...+...    ...+.+-+ .+   ..++..+++.|..    |.--|++|+  .-..
T Consensus       520 ~~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~-~~---~~~~~~~l~~f~~~~~~~~gavL~av~gGk~s  595 (705)
T TIGR00604       520 IIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVET-KD---AQETSDALERYKQAVSEGRGAVLLSVAGGKVS  595 (705)
T ss_pred             cCCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeC-CC---cchHHHHHHHHHHHHhcCCceEEEEecCCccc
Confidence            568999999999999999998887543110    01122222 11   1355667776643    445699999  7788


Q ss_pred             cCCCCCC--eeEEEeCCCCcccccccCCC-------------cc-cccccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         254 TSITIDD--IVYVVDCGKTKMSNFDVKDN-------------IA-TLKPEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       254 ~gitI~~--V~~VID~g~~k~~~yd~~~~-------------~~-~l~~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                      =|||++|  .+.||-.|+|-....|+...             -. .+. ....--...|=+||+=|...  |..+-+
T Consensus       596 EGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y-~~~a~~~v~QaiGR~IR~~~D~G~iill  671 (705)
T TIGR00604       596 EGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFY-EFDAMRAVNQAIGRVIRHKDDYGSIVLL  671 (705)
T ss_pred             CccccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHH-HHHHHHHHHHHhCccccCcCceEEEEEE
Confidence            8999986  68888899986433222211             00 111 11112346788888888765  655443

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).

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.04  E-value=0.017  Score=57.76  Aligned_cols=26  Identities=31%  Similarity=0.390  Sum_probs=21.6

Q ss_pred             HHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++..+.+++|+|+|||||||.+-
T Consensus       137 L~~~v~~~~nilI~G~tGSGKTTll~  162 (323)
T PRK13833        137 IRSAIDSRLNIVISGGTGSGKTTLAN  162 (323)
T ss_pred             HHHHHHcCCeEEEECCCCCCHHHHHH
Confidence            45567788899999999999997664

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=94.98  E-value=0.012  Score=43.93  Aligned_cols=20  Identities=40%  Similarity=0.697  Sum_probs=17.2

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+.+++|.|++||||||.+-
T Consensus        22 ~g~~tli~G~nGsGKSTllD   41 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLLD   41 (62)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            34589999999999998875

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.95  E-value=0.021  Score=56.70  Aligned_cols=28  Identities=25%  Similarity=0.366  Sum_probs=22.5

Q ss_pred             HHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          63 DAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        63 ~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +-+..++..+.+++|+|+|||||||.+-
T Consensus       123 ~~L~~~v~~~~~ilI~G~tGSGKTTll~  150 (299)
T TIGR02782       123 DVLREAVLARKNILVVGGTGSGKTTLAN  150 (299)
T ss_pred             HHHHHHHHcCCeEEEECCCCCCHHHHHH
Confidence            3345567788899999999999997764

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

>PRK10536 hypothetical protein; Provisional

Probab=94.94  E-value=0.02  Score=55.19  Aligned_cols=35  Identities=20%  Similarity=0.341  Sum_probs=30.9

Q ss_pred             ccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          54 KKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        54 ~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      ..-|....|...+.++.++.++++.|++|||||+.
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~L   90 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWI   90 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            34677888999999999999999999999999944

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=94.91  E-value=0.18  Score=56.24  Aligned_cols=68  Identities=16%  Similarity=0.105  Sum_probs=46.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCC-CChhhHhhhhcCCCCCceEEEEeCCCCccCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSM-LPTVSQKSIFNTPPEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~-l~~~~r~~v~~~~~~g~~kVivaTniae~gitI  258 (455)
                      ..+.+|||-+.+.+.-+.+.+.|...+      +..-.|++. ...+.-..+...... .-.|-||||.|.||-||
T Consensus       437 ~~GrPVLIgT~SVe~SE~ls~~L~~~g------i~h~vLNAk~~~~~~EA~IIa~AG~-~GaVTIATNMAGRGTDI  505 (939)
T PRK12902        437 KQGRPVLVGTTSVEKSELLSALLQEQG------IPHNLLNAKPENVEREAEIVAQAGR-KGAVTIATNMAGRGTDI  505 (939)
T ss_pred             hCCCCEEEeeCCHHHHHHHHHHHHHcC------CchheeeCCCcchHhHHHHHHhcCC-CCcEEEeccCCCCCcCE
Confidence            578899999999999999999999875      222334443 121222334443211 23699999999999887

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=94.84  E-value=0.029  Score=53.66  Aligned_cols=22  Identities=27%  Similarity=0.546  Sum_probs=19.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+++.|+.||||||.+-
T Consensus        24 I~~gef~vliGpSGsGKTTtLk   45 (309)
T COG1125          24 IEEGEFLVLIGPSGSGKTTTLK   45 (309)
T ss_pred             ecCCeEEEEECCCCCcHHHHHH
Confidence            5678899999999999999876

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

Probab=94.74  E-value=0.025  Score=51.92  Aligned_cols=24  Identities=38%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++..+.+++|.|+|||||||.+-
T Consensus        20 ~~v~~g~~i~I~G~tGSGKTTll~   43 (186)
T cd01130          20 LAVEARKNILISGGTGSGKTTLLN   43 (186)
T ss_pred             HHHhCCCEEEEECCCCCCHHHHHH
Confidence            346789999999999999997654

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

>KOG0384|consensus

Probab=94.64  E-value=0.084  Score=59.92  Aligned_cols=114  Identities=11%  Similarity=0.127  Sum_probs=90.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCC---CceEEEEeCCCCccCCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPE---GVRKIVLATNIAETSITIDD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~---g~~kVivaTniae~gitI~~  260 (455)
                      ..+..||||-.-.+-.+-|++.|..++      |..-.|-|++..+-|+.++..|..   ...-.++||-...-||++-.
T Consensus       697 ~~GHrVLIFSQMVRmLDIL~eYL~~r~------ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLat  770 (1373)
T KOG0384|consen  697 EGGHRVLIFSQMVRMLDILAEYLSLRG------YPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLAT  770 (1373)
T ss_pred             cCCceEEEhHHHHHHHHHHHHHHHHcC------CcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccc
Confidence            456789999888888888899988774      778889999999999999887743   34677899999999999988


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhhh
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVL  318 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~~  318 (455)
                      .+-||-++    ..+||.+.+           +|.-|+-|.|....=..|||.|.+..
T Consensus       771 ADTVIIFD----SDWNPQNDL-----------QAqARaHRIGQkk~VnVYRLVTk~Tv  813 (1373)
T KOG0384|consen  771 ADTVIIFD----SDWNPQNDL-----------QAQARAHRIGQKKHVNVYRLVTKNTV  813 (1373)
T ss_pred             cceEEEeC----CCCCcchHH-----------HHHHHHHhhcccceEEEEEEecCCch
Confidence            88888433    237777774           35558888887766789999995433

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=94.60  E-value=0.072  Score=59.25  Aligned_cols=30  Identities=10%  Similarity=0.272  Sum_probs=24.4

Q ss_pred             CCHHHHHHHHH----HHHcCCeEEEEcCCCCCcc
Q psy6094          57 PSYQMRDAVLD----MVRNNQITVISGETGSGPP   86 (455)
Q Consensus        57 P~~~~q~~il~----~i~~~~~vii~~~TGSGKT   86 (455)
                      |+|+.|.++++    ++.+++..++.+|||+|||
T Consensus        10 ~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKT   43 (705)
T TIGR00604        10 KIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKT   43 (705)
T ss_pred             CCCHHHHHHHHHHHHHhccCCceEEeCCCCCCcc
Confidence            45777777554    5668999999999999999

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).

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.60  E-value=0.02  Score=57.59  Aligned_cols=27  Identities=22%  Similarity=0.263  Sum_probs=21.9

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchhhhh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .++..+.+++|+|+|||||||.+-.++
T Consensus       155 ~~v~~~~nili~G~tgSGKTTll~aL~  181 (332)
T PRK13900        155 HAVISKKNIIISGGTSTGKTTFTNAAL  181 (332)
T ss_pred             HHHHcCCcEEEECCCCCCHHHHHHHHH
Confidence            456788999999999999997775333

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.60  E-value=0.026  Score=57.06  Aligned_cols=24  Identities=25%  Similarity=0.308  Sum_probs=20.5

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++..+.+++|+|+|||||||.+-
T Consensus       157 ~~v~~~~nilI~G~tGSGKTTll~  180 (344)
T PRK13851        157 ACVVGRLTMLLCGPTGSGKTTMSK  180 (344)
T ss_pred             HHHHcCCeEEEECCCCccHHHHHH
Confidence            456788999999999999997765

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=94.46  E-value=0.03  Score=56.05  Aligned_cols=26  Identities=27%  Similarity=0.502  Sum_probs=21.3

Q ss_pred             HHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++..+.+++|+|+|||||||.+-
T Consensus       141 L~~~v~~~~~ilI~G~tGSGKTTll~  166 (319)
T PRK13894        141 IIAAVRAHRNILVIGGTGSGKTTLVN  166 (319)
T ss_pred             HHHHHHcCCeEEEECCCCCCHHHHHH
Confidence            34467889999999999999996653

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

Probab=94.39  E-value=0.034  Score=47.30  Aligned_cols=27  Identities=15%  Similarity=0.262  Sum_probs=20.1

Q ss_pred             HHHHHHHHc--CCeEEEEcCCCCCcccch
Q psy6094          63 DAVLDMVRN--NQITVISGETGSGPPLHL   89 (455)
Q Consensus        63 ~~il~~i~~--~~~vii~~~TGSGKTtql   89 (455)
                      .++...+..  +..++|.|++|||||+.+
T Consensus         8 ~~i~~~~~~~~~~~v~i~G~~G~GKT~l~   36 (151)
T cd00009           8 EALREALELPPPKNLLLYGPPGTGKTTLA   36 (151)
T ss_pred             HHHHHHHhCCCCCeEEEECCCCCCHHHHH
Confidence            344555555  788999999999999443

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

>KOG1802|consensus

Probab=94.16  E-value=0.14  Score=54.84  Aligned_cols=28  Identities=18%  Similarity=0.388  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          59 YQMRDAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        59 ~~~q~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      -..|...+.+++++...+|+||+|+|||
T Consensus       412 N~SQ~~AV~~VL~rplsLIQGPPGTGKT  439 (935)
T KOG1802|consen  412 NASQSNAVKHVLQRPLSLIQGPPGTGKT  439 (935)
T ss_pred             chHHHHHHHHHHcCCceeeecCCCCCce
Confidence            4568999999999999999999999999

>KOG0389|consensus

Probab=94.00  E-value=0.31  Score=53.16  Aligned_cols=114  Identities=13%  Similarity=0.119  Sum_probs=85.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCc--eEEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV--RKIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~--~kVivaTniae~gitI~~V  261 (455)
                      ..+..||+|--=..-.+-|...|...      ++..+.|-|+-+-.+|+.++..|-..+  .-.++||-...-||++-..
T Consensus       775 ~~G~RVLiFSQFTqmLDILE~~L~~l------~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~A  848 (941)
T KOG0389|consen  775 KKGDRVLIFSQFTQMLDILEVVLDTL------GYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCA  848 (941)
T ss_pred             hcCCEEEEeeHHHHHHHHHHHHHHhc------CceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceeccccc
Confidence            45678999954333333344445544      488999999999999999999986543  4568899999999999988


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhhh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVL  318 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~~  318 (455)
                      ..||-.+..    |||-..           -+|.-|+-|.|.+.|=..|||+|+...
T Consensus       849 n~VIihD~d----FNP~dD-----------~QAEDRcHRvGQtkpVtV~rLItk~TI  890 (941)
T KOG0389|consen  849 NTVIIHDID----FNPYDD-----------KQAEDRCHRVGQTKPVTVYRLITKSTI  890 (941)
T ss_pred             ceEEEeecC----CCCccc-----------chhHHHHHhhCCcceeEEEEEEecCcH
Confidence            888853332    554444           457789999999999999999996644

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=93.92  E-value=0.022  Score=53.09  Aligned_cols=22  Identities=36%  Similarity=0.587  Sum_probs=19.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.+++|+||.||||||.+-
T Consensus        25 v~~Gevv~iiGpSGSGKSTlLR   46 (240)
T COG1126          25 VEKGEVVVIIGPSGSGKSTLLR   46 (240)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5689999999999999998876

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.91  E-value=0.037  Score=56.29  Aligned_cols=28  Identities=18%  Similarity=0.122  Sum_probs=20.7

Q ss_pred             CeEEEeecCCCChhhHhhhhcCCCCCce
Q psy6094         216 RFQIIPLHSMLPTVSQKSIFNTPPEGVR  243 (455)
Q Consensus       216 ~~~v~~lhs~l~~~~r~~v~~~~~~g~~  243 (455)
                      ...+..+|+.=...--.+.+..++.+.+
T Consensus       238 h~v~tTlHa~~~~~~i~Rl~~~~~~~~~  265 (358)
T TIGR02524       238 HPVYTTLHSSGVAETIRRLVGSFPAEER  265 (358)
T ss_pred             CcEEEeeccCCHHHHHHHHHHhCCccch
Confidence            4678889988777777777777776654

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

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=93.81  E-value=0.95  Score=49.51  Aligned_cols=29  Identities=10%  Similarity=0.077  Sum_probs=26.0

Q ss_pred             CCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          56 LPSYQMRDAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        56 lP~~~~q~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      +-.|+.|...+..+..|+  |+.+.||+|||
T Consensus       102 ~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKT  130 (656)
T PRK12898        102 QRHFDVQLMGGLALLSGR--LAEMQTGEGKT  130 (656)
T ss_pred             CCCChHHHHHHHHHhCCC--eeeeeCCCCcH
Confidence            566788999999999998  89999999999

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=93.78  E-value=0.19  Score=51.37  Aligned_cols=19  Identities=26%  Similarity=0.511  Sum_probs=17.8

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++++.+.||||-||||-++
T Consensus       203 ~~vi~LVGPTGVGKTTTlA  221 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLA  221 (407)
T ss_pred             CcEEEEECCCCCcHHHHHH
Confidence            7899999999999999877

>KOG0387|consensus

Probab=93.65  E-value=0.45  Score=52.02  Aligned_cols=112  Identities=11%  Similarity=0.178  Sum_probs=90.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCc--eEEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV--RKIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~--~kVivaTniae~gitI~~V  261 (455)
                      ..+..+|+|-.++.-++-+...|....     ++..+.+-|.-+...|.....+|.++.  .-.+++|-|..-|+++-+.
T Consensus       544 kqg~rvllFsqs~~mLdilE~fL~~~~-----~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgA  618 (923)
T KOG0387|consen  544 KQGDRVLLFSQSRQMLDILESFLRRAK-----GYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGA  618 (923)
T ss_pred             hCCCEEEEehhHHHHHHHHHHHHHhcC-----CceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecccccccccccC
Confidence            566789999999999998888888532     589999999999999999999998764  3457789999999999888


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN  315 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~  315 (455)
                      .-||-++    +.+||.+.           .+|.-|+-|-|....=..|||.+.
T Consensus       619 nRVIIfD----PdWNPStD-----------~QAreRawRiGQkkdV~VYRL~t~  657 (923)
T KOG0387|consen  619 NRVIIFD----PDWNPSTD-----------NQARERAWRIGQKKDVVVYRLMTA  657 (923)
T ss_pred             ceEEEEC----CCCCCccc-----------hHHHHHHHhhcCccceEEEEEecC
Confidence            8777421    22444444           567789999999887899999993

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=93.58  E-value=0.027  Score=53.27  Aligned_cols=22  Identities=27%  Similarity=0.534  Sum_probs=19.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.||+||||||.+-
T Consensus        28 i~~Ge~vaI~GpSGSGKSTLLn   49 (226)
T COG1136          28 IEAGEFVAIVGPSGSGKSTLLN   49 (226)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998876

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

Probab=93.55  E-value=0.059  Score=52.46  Aligned_cols=25  Identities=28%  Similarity=0.474  Sum_probs=18.7

Q ss_pred             HHHHH-cCCeEEEEcCCCCCcccchh
Q psy6094          66 LDMVR-NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        66 l~~i~-~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..++. .+..++|+|+|||||||.+-
T Consensus        73 ~~~~~~~~GlilisG~tGSGKTT~l~   98 (264)
T cd01129          73 RKLLEKPHGIILVTGPTGSGKTTTLY   98 (264)
T ss_pred             HHHHhcCCCEEEEECCCCCcHHHHHH
Confidence            34444 34579999999999997664

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

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=93.50  E-value=0.035  Score=46.71  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=15.9

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++.+++.|++||||||.+-
T Consensus         2 ~~~~~l~G~~G~GKTtl~~   20 (148)
T smart00382        2 GEVILIVGPPGSGKTTLAR   20 (148)
T ss_pred             CCEEEEECCCCCcHHHHHH
Confidence            5679999999999996553

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

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

Probab=93.48  E-value=0.059  Score=56.26  Aligned_cols=28  Identities=25%  Similarity=0.491  Sum_probs=19.4

Q ss_pred             HHHHHHHHc-CCeEEEEcCCCCCcccchh
Q psy6094          63 DAVLDMVRN-NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        63 ~~il~~i~~-~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..++.. +-.++++|||||||||-+=
T Consensus       248 ~~~~~~~~~p~GliLvTGPTGSGKTTTLY  276 (500)
T COG2804         248 ARLLRLLNRPQGLILVTGPTGSGKTTTLY  276 (500)
T ss_pred             HHHHHHHhCCCeEEEEeCCCCCCHHHHHH
Confidence            344444443 4478899999999996654

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

Probab=93.46  E-value=0.033  Score=54.43  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=18.3

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .--++|+|||||||||-++.+++
T Consensus       125 ~GLILVTGpTGSGKSTTlAamId  147 (353)
T COG2805         125 RGLILVTGPTGSGKSTTLAAMID  147 (353)
T ss_pred             CceEEEeCCCCCcHHHHHHHHHH
Confidence            34688999999999988874444

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

Probab=92.98  E-value=0.067  Score=53.33  Aligned_cols=23  Identities=39%  Similarity=0.401  Sum_probs=19.2

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ++....+++|+|.|||||||.+-
T Consensus       169 av~~r~NILisGGTGSGKTTlLN  191 (355)
T COG4962         169 AVGIRCNILISGGTGSGKTTLLN  191 (355)
T ss_pred             HHhhceeEEEeCCCCCCHHHHHH
Confidence            34555699999999999998876

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.98  E-value=0.05  Score=54.22  Aligned_cols=23  Identities=35%  Similarity=0.533  Sum_probs=19.9

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ++..+.+++|+|+|||||||.+-
T Consensus       140 ~v~~~~~ili~G~tGsGKTTll~  162 (308)
T TIGR02788       140 AIASRKNIIISGGTGSGKTTFLK  162 (308)
T ss_pred             HhhCCCEEEEECCCCCCHHHHHH
Confidence            46688999999999999997664

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=92.78  E-value=0.051  Score=45.73  Aligned_cols=17  Identities=29%  Similarity=0.341  Sum_probs=14.5

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      ++++.|+||||||+.+.
T Consensus         2 ~~~i~~~~G~GKT~~~~   18 (144)
T cd00046           2 DVLLAAPTGSGKTLAAL   18 (144)
T ss_pred             CEEEECCCCCchhHHHH
Confidence            58999999999996654

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.75  E-value=0.2  Score=51.39  Aligned_cols=18  Identities=33%  Similarity=0.464  Sum_probs=16.3

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      +++.+.|+||+||||.+.
T Consensus       242 ~vI~LVGptGvGKTTTia  259 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLA  259 (436)
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            578899999999998877

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=92.68  E-value=0.37  Score=54.56  Aligned_cols=110  Identities=13%  Similarity=0.116  Sum_probs=89.2

Q ss_pred             CEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC--ceEEEEeCCCCccCCCCCCeeEEE
Q psy6094         188 PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG--VRKIVLATNIAETSITIDDIVYVV  265 (455)
Q Consensus       188 ~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g--~~kVivaTniae~gitI~~V~~VI  265 (455)
                      .+|+|.+-..-.+-+...+...+      +..+.++|+++.++|...+..|.++  ..-.+++|-.+..|++.-.-+.||
T Consensus       713 kvlifsq~t~~l~il~~~l~~~~------~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi  786 (866)
T COG0553         713 KVLIFSQFTPVLDLLEDYLKALG------IKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVI  786 (866)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcC------CcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEE
Confidence            79999999998888888888763      6789999999999999999999875  567788888999999999999999


Q ss_pred             eCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhhh
Q psy6094         266 DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDVL  318 (455)
Q Consensus       266 D~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~~  318 (455)
                      -        ||+.-+       |.-..+|..|+-|.|+..+=..|++.+++..
T Consensus       787 ~--------~d~~wn-------p~~~~Qa~dRa~RigQ~~~v~v~r~i~~~ti  824 (866)
T COG0553         787 L--------FDPWWN-------PAVELQAIDRAHRIGQKRPVKVYRLITRGTI  824 (866)
T ss_pred             E--------eccccC-------hHHHHHHHHHHHHhcCcceeEEEEeecCCcH
Confidence            6        554333       2333567778888888888889999886644

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

Probab=92.53  E-value=0.046  Score=46.46  Aligned_cols=21  Identities=38%  Similarity=0.605  Sum_probs=13.8

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ++++.++|.|++|||||+.+-
T Consensus         2 ~~~~~~~i~G~~G~GKT~~~~   22 (131)
T PF13401_consen    2 QSQRILVISGPPGSGKTTLIK   22 (131)
T ss_dssp             -----EEEEE-TTSSHHHHHH
T ss_pred             CCCcccEEEcCCCCCHHHHHH
Confidence            356789999999999997776

>KOG0390|consensus

Probab=92.51  E-value=0.58  Score=51.71  Aligned_cols=106  Identities=12%  Similarity=0.148  Sum_probs=76.8

Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCC--Cc-eEEEEeCCCCccCCCCCCeeEEE
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPE--GV-RKIVLATNIAETSITIDDIVYVV  265 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~--g~-~kVivaTniae~gitI~~V~~VI  265 (455)
                      -.|.+.....+.++.+.+..-.     ++.++.|||.++..+|+.+++.|-+  +. .-.++||-...-||.+=+..-||
T Consensus       597 ~~v~Isny~~tldl~e~~~~~~-----g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRli  671 (776)
T KOG0390|consen  597 KSVLISNYTQTLDLFEQLCRWR-----GYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLI  671 (776)
T ss_pred             EEEEeccHHHHHHHHHHHHhhc-----CceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEE
Confidence            3444556666666666665543     5899999999999999999888743  33 34456788888999987777777


Q ss_pred             eCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         266 DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       266 D~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      =        ||+.=+       |.--.+|.-|+-|-|...+=..|||.+
T Consensus       672 l--------~D~dWN-------Pa~d~QAmaR~~RdGQKk~v~iYrLla  705 (776)
T KOG0390|consen  672 L--------FDPDWN-------PAVDQQAMARAWRDGQKKPVYIYRLLA  705 (776)
T ss_pred             E--------eCCCCC-------chhHHHHHHHhccCCCcceEEEEEeec
Confidence            4        444333       333356777999999888889999999

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.50  E-value=0.052  Score=50.37  Aligned_cols=17  Identities=35%  Similarity=0.688  Sum_probs=14.8

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .++|+|+|||||||.+-
T Consensus         3 lilI~GptGSGKTTll~   19 (198)
T cd01131           3 LVLVTGPTGSGKSTTLA   19 (198)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58899999999997764

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

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

Probab=92.43  E-value=0.11  Score=48.12  Aligned_cols=31  Identities=16%  Similarity=0.413  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHc-C-CeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRN-N-QITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~-~-~~vii~~~TGSGKTtqlp   90 (455)
                      .-|.+++..+.. + ++++|+|+.||||||.+-
T Consensus         4 ~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~   36 (196)
T PF13604_consen    4 EEQREAVRAILTSGDRVSVLQGPAGTGKTTLLK   36 (196)
T ss_dssp             HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHH
T ss_pred             HHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHH
Confidence            457777887753 3 589999999999996554

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=92.41  E-value=0.16  Score=56.26  Aligned_cols=105  Identities=20%  Similarity=0.186  Sum_probs=65.8

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC---C
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID---D  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~---~  260 (455)
                      ..++++||-..+.+.-+.+.+.|.+.+.      .-..|...-..++-..+-+.-..|  -|=+|||.|.||-||.   +
T Consensus       427 ~~gqPvLvgT~sie~SE~ls~~L~~~~i------~h~VLNAk~h~~EA~Iia~AG~~g--aVTiATNMAGRGTDIkLg~~  498 (822)
T COG0653         427 EKGQPVLVGTVSIEKSELLSKLLRKAGI------PHNVLNAKNHAREAEIIAQAGQPG--AVTIATNMAGRGTDIKLGGN  498 (822)
T ss_pred             hcCCCEEEcCcceecchhHHHHHHhcCC------CceeeccccHHHHHHHHhhcCCCC--ccccccccccCCcccccCCC
Confidence            6789999999999999999999997652      112222222233333333322222  5789999999999983   3


Q ss_pred             ee--------EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         261 IV--------YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       261 V~--------~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ..        +||=+........                  =.|-+||+||.|. |..--+.|
T Consensus       499 ~~~V~~lGGL~VIgTERhESRRI------------------DnQLRGRsGRQGDpG~S~F~lS  543 (822)
T COG0653         499 PEFVMELGGLHVIGTERHESRRI------------------DNQLRGRAGRQGDPGSSRFYLS  543 (822)
T ss_pred             HHHHHHhCCcEEEecccchhhHH------------------HHHhhcccccCCCcchhhhhhh
Confidence            22        4554443322222                  2488999999886 75444444

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

Probab=92.37  E-value=0.059  Score=45.26  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=17.0

Q ss_pred             eEEEEcCCCCCcccchhhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      +++|.|++||||||..-.|.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999766555443

...

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=92.35  E-value=0.5  Score=40.89  Aligned_cols=86  Identities=17%  Similarity=0.271  Sum_probs=45.0

Q ss_pred             HHHHHHHHHcCCeEEEEcCCCCCcccchhhhhhhhcCCCC---------ChHHHHHhccC--CCCcCcc---hHHHHHHH
Q psy6094          62 RDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQ---------YPNDVLNMLKD--PELEGVN---NDVIFSLL  127 (455)
Q Consensus        62 q~~il~~i~~~~~vii~~~TGSGKTtqlp~ll~e~~~~vg---------~p~~ll~~l~d--~~L~~~~---~D~ll~~l  127 (455)
                      ++++-.+...+..|+|.|++||||++..-+|....+...+         .+.++++...+  -.+.++.   .+....++
T Consensus        11 ~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~~~~l~~a~~gtL~l~~i~~L~~~~Q~~L~   90 (138)
T PF14532_consen   11 RRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLPAELLEQAKGGTLYLKNIDRLSPEAQRRLL   90 (138)
T ss_dssp             HHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTCHHHHHHCTTSEEEEECGCCS-HHHHHHHH
T ss_pred             HHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCcHHHHHHcCCCEEEECChHHCCHHHHHHHH
Confidence            4455556677888999999999999644466553322222         24445555411  1222222   22222333


Q ss_pred             HHHHHhcCCCCeEEEEccCC
Q psy6094         128 QHICTTQRPGAILVYCTYTF  147 (455)
Q Consensus       128 k~il~~~~~~~k~ilmSAT~  147 (455)
                      ..+-...+.+.|+|..|.+-
T Consensus        91 ~~l~~~~~~~~RlI~ss~~~  110 (138)
T PF14532_consen   91 DLLKRQERSNVRLIASSSQD  110 (138)
T ss_dssp             HHHHHCTTTTSEEEEEECC-
T ss_pred             HHHHhcCCCCeEEEEEeCCC
Confidence            32221235678887766653

>PRK05580 primosome assembly protein PriA; Validated

Probab=92.30  E-value=0.22  Score=55.13  Aligned_cols=74  Identities=15%  Similarity=0.172  Sum_probs=61.1

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV  265 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI  265 (455)
                      ++.+||.+|+.+-+..+.+.+++..     +..+..+||+++..+|.+++.....|..+|||+|.-+-. +.+.++.+||
T Consensus       190 g~~vLvLvPt~~L~~Q~~~~l~~~f-----g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-~p~~~l~liV  263 (679)
T PRK05580        190 GKQALVLVPEIALTPQMLARFRARF-----GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-LPFKNLGLII  263 (679)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHHh-----CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-ccccCCCEEE
Confidence            5679999999999999999998743     256889999999999999998888898999999974432 4567887666

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=92.20  E-value=0.054  Score=54.29  Aligned_cols=22  Identities=23%  Similarity=0.517  Sum_probs=19.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+++.||+||||||.+-
T Consensus        26 i~~Gef~vllGPSGcGKSTlLr   47 (338)
T COG3839          26 IEDGEFVVLLGPSGCGKSTLLR   47 (338)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5678899999999999999876

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=92.16  E-value=0.079  Score=54.09  Aligned_cols=20  Identities=35%  Similarity=0.488  Sum_probs=16.9

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..++|+|+|||||||.+-
T Consensus       148 ~~GlilI~G~TGSGKTT~l~  167 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLAA  167 (372)
T ss_pred             cCCEEEEECCCCCCHHHHHH
Confidence            55678999999999997765

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

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

Probab=92.14  E-value=0.084  Score=52.66  Aligned_cols=26  Identities=23%  Similarity=0.339  Sum_probs=23.2

Q ss_pred             HHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+++++++++++|+|||||||.+-
T Consensus       136 L~~~ie~~~siii~G~t~sGKTt~ln  161 (312)
T COG0630         136 LWLAIEARKSIIICGGTASGKTTLLN  161 (312)
T ss_pred             HHHHHHcCCcEEEECCCCCCHHHHHH
Confidence            67788999999999999999997764

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=92.05  E-value=0.12  Score=50.15  Aligned_cols=31  Identities=13%  Similarity=0.237  Sum_probs=25.0

Q ss_pred             HHHHHHHHHcCCeEEEEcCCCCCcccchhhh
Q psy6094          62 RDAVLDMVRNNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        62 q~~il~~i~~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      .+.++..+..+..+++.|++|||||+.+-.+
T Consensus        11 ~~~~l~~l~~g~~vLL~G~~GtGKT~lA~~l   41 (262)
T TIGR02640        11 TSRALRYLKSGYPVHLRGPAGTGKTTLAMHV   41 (262)
T ss_pred             HHHHHHHHhcCCeEEEEcCCCCCHHHHHHHH
Confidence            4567788889999999999999999655433

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

>KOG2373|consensus

Probab=91.94  E-value=0.094  Score=52.09  Aligned_cols=32  Identities=31%  Similarity=0.451  Sum_probs=24.7

Q ss_pred             HHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh
Q psy6094          63 DAVLDMVRNNQITVISGETGSGPPLHLD-FITL   94 (455)
Q Consensus        63 ~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~   94 (455)
                      .+++.-.+.|..+|++|+|||||||.+. |-++
T Consensus       264 Nk~LkGhR~GElTvlTGpTGsGKTTFlsEYsLD  296 (514)
T KOG2373|consen  264 NKYLKGHRPGELTVLTGPTGSGKTTFLSEYSLD  296 (514)
T ss_pred             HHHhccCCCCceEEEecCCCCCceeEehHhhHH
Confidence            3344444566789999999999999988 7776

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=91.88  E-value=0.061  Score=51.28  Aligned_cols=22  Identities=27%  Similarity=0.469  Sum_probs=19.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+-|.|++||||||.+-
T Consensus        26 v~~GEfvsilGpSGcGKSTLLr   47 (248)
T COG1116          26 VEKGEFVAILGPSGCGKSTLLR   47 (248)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999999876

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

Probab=91.86  E-value=0.07  Score=46.14  Aligned_cols=20  Identities=20%  Similarity=0.433  Sum_probs=16.3

Q ss_pred             eEEEEcCCCCCcccchhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll   93 (455)
                      ++++.|++||||||.+-.+.
T Consensus         1 lii~~G~pgsGKSt~a~~l~   20 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLA   20 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHH
Confidence            58999999999998765443

...

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=91.76  E-value=0.083  Score=53.45  Aligned_cols=20  Identities=30%  Similarity=0.549  Sum_probs=17.3

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..++|+|+|||||||.+-
T Consensus       121 ~~g~ili~G~tGSGKTT~l~  140 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLA  140 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHH
Confidence            46789999999999997765

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>TIGR03263 guanyl_kin guanylate kinase

Probab=91.57  E-value=0.085  Score=47.75  Aligned_cols=21  Identities=29%  Similarity=0.474  Sum_probs=17.3

Q ss_pred             CCeEEEEcCCCCCcccchhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~l   92 (455)
                      |+.+++.|++||||||++-.|
T Consensus         1 g~ii~l~G~~GsGKsTl~~~L   21 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTLVKAL   21 (180)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            567999999999999876533

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>KOG1000|consensus

Probab=91.48  E-value=2.1  Score=44.69  Aligned_cols=106  Identities=17%  Similarity=0.166  Sum_probs=75.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC--ceEEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG--VRKIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g--~~kVivaTniae~gitI~~V  261 (455)
                      .++...|||+.-..-.+.+...+++++      +-.+.+-|..+..+|...-+.|...  .+--|++-..|..|+|....
T Consensus       490 ~~~~KflVFaHH~~vLd~Iq~~~~~r~------vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa  563 (689)
T KOG1000|consen  490 APPRKFLVFAHHQIVLDTIQVEVNKRK------VGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAA  563 (689)
T ss_pred             CCCceEEEEehhHHHHHHHHHHHHHcC------CCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeecc
Confidence            456679999998888888888887764      6677888999999998887776543  45557788889999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEE
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSET  310 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~  310 (455)
                      +.||=.-+.    ++|..    |       -+|.-|+-|.|.... ++.|
T Consensus       564 ~~VVFaEL~----wnPgv----L-------lQAEDRaHRiGQkssV~v~y  598 (689)
T KOG1000|consen  564 SVVVFAELH----WNPGV----L-------LQAEDRAHRIGQKSSVFVQY  598 (689)
T ss_pred             ceEEEEEec----CCCce----E-------EechhhhhhccccceeeEEE
Confidence            999954443    22221    1       134567777777666 4444

>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=91.44  E-value=0.082  Score=48.69  Aligned_cols=22  Identities=23%  Similarity=0.548  Sum_probs=19.5

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |.+++.+++.|+.||||||.+-
T Consensus        28 ia~ge~vv~lGpSGcGKTTLLn   49 (259)
T COG4525          28 IASGELVVVLGPSGCGKTTLLN   49 (259)
T ss_pred             ecCCCEEEEEcCCCccHHHHHH
Confidence            5689999999999999998764

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.38  E-value=0.24  Score=50.49  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=18.2

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..++++++.|+||+||||.+.
T Consensus       204 ~~~~ii~lvGptGvGKTTt~a  224 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLV  224 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHH
Confidence            357789999999999998877

>PRK10436 hypothetical protein; Provisional

Probab=91.31  E-value=0.17  Score=53.28  Aligned_cols=20  Identities=30%  Similarity=0.561  Sum_probs=16.6

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+-.++|+|+|||||||.+-
T Consensus       217 ~~GliLvtGpTGSGKTTtL~  236 (462)
T PRK10436        217 PQGLILVTGPTGSGKTVTLY  236 (462)
T ss_pred             cCCeEEEECCCCCChHHHHH
Confidence            55579999999999997654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=91.29  E-value=2.4  Score=46.91  Aligned_cols=55  Identities=15%  Similarity=0.014  Sum_probs=34.9

Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      ++|-.|+..=+.+-++.+.....+  -++.+..+.|+++.++|.....      ..|+++|+-
T Consensus       100 V~VvTpt~~LA~qdae~~~~l~~~--LGLsv~~i~g~~~~~~r~~~y~------~dIvyGT~~  154 (745)
T TIGR00963       100 VHVVTVNDYLAQRDAEWMGQVYRF--LGLSVGLILSGMSPEERREAYA------CDITYGTNN  154 (745)
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhcc--CCCeEEEEeCCCCHHHHHHhcC------CCEEEECCC
Confidence            444445544444444433332211  1378899999999988887775      479999986

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.

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=91.28  E-value=0.063  Score=46.17  Aligned_cols=23  Identities=30%  Similarity=0.502  Sum_probs=19.2

Q ss_pred             HcCCeEEEEcCCCCCcccchhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      ..|+.+.|.|+.||||||.+-.+
T Consensus         9 ~~g~~~~i~G~nGsGKStLl~~l   31 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKSTLLKAL   31 (137)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHH
T ss_pred             cCCCEEEEEccCCCccccceeee
Confidence            46889999999999999877633

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=91.23  E-value=0.076  Score=44.22  Aligned_cols=23  Identities=22%  Similarity=0.176  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDF   91 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~   91 (455)
                      +..++.+.+.|++||||||.+..
T Consensus        12 i~~ge~v~I~GpSGsGKSTLl~~   34 (107)
T cd00820          12 VYGKVGVLITGDSGIGKTELALE   34 (107)
T ss_pred             EcCCEEEEEEcCCCCCHHHHHHH
Confidence            34678899999999999987753

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.20  E-value=0.16  Score=53.75  Aligned_cols=19  Identities=37%  Similarity=0.581  Sum_probs=16.0

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++|+|+|||||||.+-
T Consensus       242 ~GlilitGptGSGKTTtL~  260 (486)
T TIGR02533       242 HGIILVTGPTGSGKTTTLY  260 (486)
T ss_pred             CCEEEEEcCCCCCHHHHHH
Confidence            3478999999999997765

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

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=91.17  E-value=0.17  Score=54.83  Aligned_cols=26  Identities=27%  Similarity=0.562  Sum_probs=19.2

Q ss_pred             HHHHHH-cCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVR-NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~-~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+++. .+-.++|+|+|||||||.+-
T Consensus       308 l~~~~~~~~Glilv~G~tGSGKTTtl~  334 (564)
T TIGR02538       308 FLEAIHKPQGMVLVTGPTGSGKTVSLY  334 (564)
T ss_pred             HHHHHHhcCCeEEEECCCCCCHHHHHH
Confidence            344444 45578899999999997764

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

>TIGR00595 priA primosomal protein N'

Probab=91.13  E-value=0.31  Score=51.94  Aligned_cols=75  Identities=17%  Similarity=0.204  Sum_probs=60.8

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYV  264 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~V  264 (455)
                      .++.+||-+|+..-+....+.+++..     ...+..+||+++..+|.+++.....|..+|||+|..+-. ..+.++..|
T Consensus        24 ~g~~vLvlvP~i~L~~Q~~~~l~~~f-----~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lI   97 (505)
T TIGR00595        24 LGKSVLVLVPEIALTPQMIQRFKYRF-----GSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLI   97 (505)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHh-----CCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEE
Confidence            35689999999999999999998753     245778999999999999998888899999999975432 456777766


Q ss_pred             E
Q psy6094         265 V  265 (455)
Q Consensus       265 I  265 (455)
                      |
T Consensus        98 I   98 (505)
T TIGR00595        98 I   98 (505)
T ss_pred             E
Confidence            6

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).

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=91.12  E-value=0.48  Score=46.55  Aligned_cols=19  Identities=26%  Similarity=0.461  Sum_probs=16.3

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++++++.|+||+||||.+.
T Consensus       194 ~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4588899999999997765

>PF05729 NACHT: NACHT domain

Probab=91.11  E-value=0.11  Score=45.84  Aligned_cols=18  Identities=44%  Similarity=0.610  Sum_probs=15.7

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ++++|.|++|+||||.+.
T Consensus         1 r~l~I~G~~G~GKStll~   18 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLR   18 (166)
T ss_pred             CEEEEECCCCCChHHHHH
Confidence            478999999999997765

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=91.06  E-value=0.093  Score=48.98  Aligned_cols=22  Identities=27%  Similarity=0.549  Sum_probs=19.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..++++-+.||+||||||.+-
T Consensus        30 i~~~~VTAlIGPSGcGKST~LR   51 (253)
T COG1117          30 IPKNKVTALIGPSGCGKSTLLR   51 (253)
T ss_pred             ccCCceEEEECCCCcCHHHHHH
Confidence            4589999999999999998875

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

Probab=90.98  E-value=0.25  Score=56.21  Aligned_cols=29  Identities=24%  Similarity=0.344  Sum_probs=23.1

Q ss_pred             CHHHHHH----HHHHHHcCCeEEEEcCCCCCcc
Q psy6094          58 SYQMRDA----VLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        58 ~~~~q~~----il~~i~~~~~vii~~~TGSGKT   86 (455)
                      ..+.|.+    +.+++.+++++++.|+||+|||
T Consensus       246 ~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT  278 (850)
T TIGR01407       246 YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKT  278 (850)
T ss_pred             cCHHHHHHHHHHHHHhccCCcEEEECCCCCchh
Confidence            3355665    4447778999999999999999

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.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=90.93  E-value=0.09  Score=47.93  Aligned_cols=22  Identities=27%  Similarity=0.524  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        18 i~~G~~~~l~G~nG~GKSTLl~   39 (176)
T cd03238          18 IPLNVLVVVTGVSGSGKSTLVN   39 (176)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998875

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK14974 cell division protein FtsY; Provisional

Probab=90.68  E-value=0.46  Score=47.90  Aligned_cols=18  Identities=22%  Similarity=0.458  Sum_probs=16.1

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      .++++.|++|+||||.+.
T Consensus       141 ~vi~~~G~~GvGKTTtia  158 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIA  158 (336)
T ss_pred             eEEEEEcCCCCCHHHHHH
Confidence            578899999999999877

>PRK14873 primosome assembly protein PriA; Provisional

Probab=90.68  E-value=0.49  Score=52.04  Aligned_cols=77  Identities=16%  Similarity=0.119  Sum_probs=61.7

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++++||-+|....+..+.+.++....    .-.+..+||++++.+|.+.+.....|..+|||-|--|-- .-++|...
T Consensus       186 ~~Gk~vLvLvPEi~lt~q~~~rl~~~f~----~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAvF-aP~~~LgL  260 (665)
T PRK14873        186 RAGRGALVVVPDQRDVDRLEAALRALLG----AGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVF-APVEDLGL  260 (665)
T ss_pred             HcCCeEEEEecchhhHHHHHHHHHHHcC----CCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeEE-eccCCCCE
Confidence            4577899999999999999999987641    135888999999999999999999999999999854321 23456665


Q ss_pred             EE
Q psy6094         264 VV  265 (455)
Q Consensus       264 VI  265 (455)
                      ||
T Consensus       261 II  262 (665)
T PRK14873        261 VA  262 (665)
T ss_pred             EE
Confidence            54

>PRK00300 gmk guanylate kinase; Provisional

Probab=90.64  E-value=0.12  Score=47.82  Aligned_cols=23  Identities=26%  Similarity=0.518  Sum_probs=18.6

Q ss_pred             HcCCeEEEEcCCCCCcccchhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      ..++.+++.|++||||||.+-.+
T Consensus         3 ~~g~~i~i~G~sGsGKstl~~~l   25 (205)
T PRK00300          3 RRGLLIVLSGPSGAGKSTLVKAL   25 (205)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
Confidence            36789999999999999765433

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=90.62  E-value=0.51  Score=52.24  Aligned_cols=92  Identities=21%  Similarity=0.307  Sum_probs=58.5

Q ss_pred             CHHHHHHHHHHHHcC---CeEEEEcCCCCCcccchh-hh-hhhhcCCCC---------ChHH------------------
Q psy6094          58 SYQMRDAVLDMVRNN---QITVISGETGSGPPLHLD-FI-TLKRSETQQ---------YPND------------------  105 (455)
Q Consensus        58 ~~~~q~~il~~i~~~---~~vii~~~TGSGKTtqlp-~l-l~e~~~~vg---------~p~~------------------  105 (455)
                      -|..+..+++.+.++   +.++|++|.|+||||.+. +. ...-+..|+         .|.+                  
T Consensus        20 ~~v~R~rL~~~L~~~~~~RL~li~APAGfGKttl~aq~~~~~~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~   99 (894)
T COG2909          20 NYVVRPRLLDRLRRANDYRLILISAPAGFGKTTLLAQWRELAADGAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGD   99 (894)
T ss_pred             cccccHHHHHHHhcCCCceEEEEeCCCCCcHHHHHHHHHHhcCcccceeEeecCCccCCHHHHHHHHHHHHHHhCccccH
Confidence            345566777777654   789999999999999998 53 122222233         1221                  


Q ss_pred             --------------------HHHhc---cCC---CCcCcc---hHHHHHHHHHHHHhcCCCCeEEEEccCCCC
Q psy6094         106 --------------------VLNML---KDP---ELEGVN---NDVIFSLLQHICTTQRPGAILVYCTYTFMG  149 (455)
Q Consensus       106 --------------------ll~~l---~d~---~L~~~~---~D~ll~~lk~il~~~~~~~k~ilmSAT~~g  149 (455)
                                          |+.+|   .+|   .+++|.   ...+-.-++.+++..++++.+|+.|=+-|+
T Consensus       100 ~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         100 EAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence                                44444   234   234444   444556677888788899999998877643

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=90.57  E-value=1.7  Score=48.39  Aligned_cols=19  Identities=21%  Similarity=0.356  Sum_probs=17.2

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++++.+.|+||+||||.+.
T Consensus       185 g~Vi~lVGpnGvGKTTTia  203 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTA  203 (767)
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            5688999999999999877

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

Probab=90.43  E-value=0.23  Score=54.10  Aligned_cols=24  Identities=25%  Similarity=0.421  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          63 DAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        63 ~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      +.+.+++.+++.+++.|+||||||
T Consensus         7 ~~i~~al~~~~~lliEA~TGtGKT   30 (636)
T TIGR03117         7 LNCLTSLRQKRIGMLEASTGVGKT   30 (636)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCcHH
Confidence            567777889999999999999999

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.

>PF13173 AAA_14: AAA domain

Probab=90.18  E-value=0.14  Score=43.72  Aligned_cols=20  Identities=30%  Similarity=0.589  Sum_probs=17.1

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      |+++++|.|+.|+||||.+-
T Consensus         1 n~~~~~l~G~R~vGKTtll~   20 (128)
T PF13173_consen    1 NRKIIILTGPRGVGKTTLLK   20 (128)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            57899999999999996653

>PRK13764 ATPase; Provisional

Probab=90.16  E-value=0.19  Score=54.32  Aligned_cols=21  Identities=19%  Similarity=0.366  Sum_probs=18.0

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+.+++|+|+|||||||.+.
T Consensus       255 ~~~~~ILIsG~TGSGKTTll~  275 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTFAQ  275 (602)
T ss_pred             hcCCEEEEECCCCCCHHHHHH
Confidence            456789999999999998776

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=90.16  E-value=0.23  Score=52.01  Aligned_cols=29  Identities=14%  Similarity=0.350  Sum_probs=23.4

Q ss_pred             HHHHHHHH-------HcCCeEEEEcCCCCCcccchh
Q psy6094          62 RDAVLDMV-------RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        62 q~~il~~i-------~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |.++..++       ..|+++.++|+.||||||.+-
T Consensus        15 e~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKSTLLr   50 (504)
T TIGR03238        15 QTDLERILVKFNKELPSSSLLFLCGSSGDGKSEILA   50 (504)
T ss_pred             HHHHHHHHhCCceeecCCCEEEEECCCCCCHHHHHh
Confidence            55555554       468999999999999999887

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

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

Probab=90.12  E-value=0.14  Score=46.16  Aligned_cols=21  Identities=29%  Similarity=0.458  Sum_probs=12.4

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+++++|.|+.|+|||+.+-
T Consensus        22 ~~~~~~ll~G~~G~GKT~ll~   42 (185)
T PF13191_consen   22 GSPRNLLLTGESGSGKTSLLR   42 (185)
T ss_dssp             -----EEE-B-TTSSHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHH
Confidence            356789999999999997665

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=90.09  E-value=0.14  Score=46.88  Aligned_cols=19  Identities=26%  Similarity=0.427  Sum_probs=16.4

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+++.|+.||||||.+-
T Consensus         2 g~~i~l~G~sGsGKsTl~~   20 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLA   20 (186)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5689999999999997664

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=90.01  E-value=0.18  Score=43.80  Aligned_cols=27  Identities=15%  Similarity=0.338  Sum_probs=21.5

Q ss_pred             HHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          64 AVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        64 ~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+-..+..+.++++.|+.|+||||.+-
T Consensus        14 ~l~~~l~~~~~i~l~G~lGaGKTtl~~   40 (133)
T TIGR00150        14 AFAKPLDFGTVVLLKGDLGAGKTTLVQ   40 (133)
T ss_pred             HHHHhCCCCCEEEEEcCCCCCHHHHHH
Confidence            345556788999999999999996554

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

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

Probab=89.93  E-value=0.18  Score=49.41  Aligned_cols=29  Identities=14%  Similarity=0.227  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +-|.+++..  .++.++|.|..||||||.+.
T Consensus         3 ~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~   31 (315)
T PF00580_consen    3 DEQRRIIRS--TEGPLLVNAGAGSGKTTTLL   31 (315)
T ss_dssp             HHHHHHHHS---SSEEEEEE-TTSSHHHHHH
T ss_pred             HHHHHHHhC--CCCCEEEEeCCCCCchHHHH
Confidence            457778877  56678999999999996553

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

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

Probab=89.91  E-value=0.13  Score=43.30  Aligned_cols=20  Identities=30%  Similarity=0.230  Sum_probs=15.7

Q ss_pred             EEEEcCCCCCcccchhhhhh
Q psy6094          75 TVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~   94 (455)
                      ++|.|.+||||||..-.|..
T Consensus         1 I~i~G~~GsGKtTia~~L~~   20 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAE   20 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            57899999999987654443

...

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=89.90  E-value=0.24  Score=53.77  Aligned_cols=31  Identities=13%  Similarity=0.392  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|.+.+.....+++++|+|.+||||||.+.
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~  178 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTVA  178 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHH
Confidence            5688888888889999999999999998877

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

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=89.83  E-value=0.12  Score=49.37  Aligned_cols=46  Identities=26%  Similarity=0.350  Sum_probs=29.0

Q ss_pred             CCCChhhHhhhhcCCC----CCceEEEEeCCCCccCCCCCCeeEEEeCCC
Q psy6094         224 SMLPTVSQKSIFNTPP----EGVRKIVLATNIAETSITIDDIVYVVDCGK  269 (455)
Q Consensus       224 s~l~~~~r~~v~~~~~----~g~~kVivaTniae~gitI~~V~~VID~g~  269 (455)
                      ++|++.-+..+++...    .+...||++|--.+.-..+-|-.+|++-|.
T Consensus       167 a~LD~~~~~~l~~~l~~L~~~~~~tii~~tHd~~~~~~~ad~v~vl~~G~  216 (235)
T COG1122         167 AGLDPKGRRELLELLKKLKEEGGKTIIIVTHDLELVLEYADRVVVLDDGK  216 (235)
T ss_pred             CCCCHHHHHHHHHHHHHHHhcCCCeEEEEeCcHHHHHhhCCEEEEEECCE
Confidence            6777777776655432    234567777766666666667777776554

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

Probab=89.81  E-value=0.18  Score=48.52  Aligned_cols=29  Identities=24%  Similarity=0.287  Sum_probs=23.0

Q ss_pred             CeEEEeecCCCChhhHhhhhcCCCCCceE
Q psy6094         216 RFQIIPLHSMLPTVSQKSIFNTPPEGVRK  244 (455)
Q Consensus       216 ~~~v~~lhs~l~~~~r~~v~~~~~~g~~k  244 (455)
                      .+....||+.-..+.-.+++.=||+..+.
T Consensus       226 HLcmaTLHAN~anQaleRIinffP~Err~  254 (375)
T COG5008         226 HLCMATLHANNANQALERIINFFPEERRE  254 (375)
T ss_pred             ceEEEEeccCCchHHHHHHHhhCcHHHhh
Confidence            58889999998888888888877776544

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

Probab=89.73  E-value=0.15  Score=46.09  Aligned_cols=19  Identities=26%  Similarity=0.548  Sum_probs=15.9

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++.++|.|++||||||.+-
T Consensus         1 ~~~~~i~G~sGsGKttl~~   19 (179)
T TIGR02322         1 GRLIYVVGPSGAGKDTLLD   19 (179)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            3578999999999997664

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

>PRK08233 hypothetical protein; Provisional

Probab=89.68  E-value=0.14  Score=46.25  Aligned_cols=23  Identities=22%  Similarity=0.322  Sum_probs=18.0

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ..++.|.|.+||||||+.-.|..
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~   25 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTH   25 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            35788899999999988764443

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

Probab=89.63  E-value=0.16  Score=49.60  Aligned_cols=22  Identities=18%  Similarity=0.453  Sum_probs=18.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+++-++++|+||||||..+-
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li~   51 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLIQ   51 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHHH
Confidence            5688899999999999995443

>KOG0388|consensus

Probab=89.57  E-value=3.1  Score=45.36  Aligned_cols=112  Identities=13%  Similarity=0.098  Sum_probs=89.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCc-eEEEEeCCCCccCCCCCCee
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV-RKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~-~kVivaTniae~gitI~~V~  262 (455)
                      ..+..+|+|+.-..-++-+.+.|.-.+      +..+.|-|+....+|..+...+.... .-.+++|-....||++-..+
T Consensus      1042 aegHRvL~yfQMTkM~dl~EdYl~yr~------Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAAD 1115 (1185)
T KOG0388|consen 1042 AEGHRVLMYFQMTKMIDLIEDYLVYRG------YTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAAD 1115 (1185)
T ss_pred             cCCceEEehhHHHHHHHHHHHHHHhhc------cceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccc
Confidence            567789999998888888888887764      88999999999999999988876543 45578999999999999999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND  316 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~  316 (455)
                      .||=        ||..=+       |.--.+|.-|+-|-|.+..=.+|||.++.
T Consensus      1116 TViF--------YdSDWN-------PT~D~QAMDRAHRLGQTrdvtvyrl~~rg 1154 (1185)
T KOG0388|consen 1116 TVIF--------YDSDWN-------PTADQQAMDRAHRLGQTRDVTVYRLITRG 1154 (1185)
T ss_pred             eEEE--------ecCCCC-------cchhhHHHHHHHhccCccceeeeeecccc
Confidence            9994        443322       22234677899999999888999999954

>TIGR00235 udk uridine kinase

Probab=89.54  E-value=0.14  Score=47.82  Aligned_cols=20  Identities=30%  Similarity=0.355  Sum_probs=16.7

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+.++.|.|++||||||.+-
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~   24 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVAR   24 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHH
Confidence            46678899999999997664

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

>PF12846 AAA_10: AAA-like domain

Probab=89.44  E-value=0.16  Score=49.48  Aligned_cols=21  Identities=43%  Similarity=0.537  Sum_probs=17.2

Q ss_pred             CCeEEEEcCCCCCcccchhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~l   92 (455)
                      |..++|.|.|||||||.+-.+
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l   21 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNL   21 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHH
Confidence            457999999999999777633

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=89.41  E-value=0.14  Score=49.38  Aligned_cols=22  Identities=36%  Similarity=0.505  Sum_probs=19.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.||.||||||.+-
T Consensus        25 i~~G~i~~iiGpNG~GKSTLLk   46 (258)
T COG1120          25 IPKGEITGILGPNGSGKSTLLK   46 (258)
T ss_pred             ecCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999999876

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

Probab=89.40  E-value=0.15  Score=43.02  Aligned_cols=19  Identities=16%  Similarity=0.363  Sum_probs=14.8

Q ss_pred             EEEEcCCCCCcccchhhhh
Q psy6094          75 TVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll   93 (455)
                      +++.|++|||||+.+-.+.
T Consensus         1 ill~G~~G~GKT~l~~~la   19 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALA   19 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHH
Confidence            5899999999996654333

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

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=89.35  E-value=0.14  Score=46.85  Aligned_cols=22  Identities=18%  Similarity=0.357  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        15 i~~Ge~~~i~G~nGsGKSTLl~   36 (190)
T TIGR01166        15 AERGEVLALLGANGAGKSTLLL   36 (190)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999997764

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=89.35  E-value=0.46  Score=52.95  Aligned_cols=37  Identities=14%  Similarity=0.265  Sum_probs=32.0

Q ss_pred             ccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          54 KKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        54 ~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ........|.+.+..+..+++++|+|.+||||||.+-
T Consensus       320 ~~~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~  356 (720)
T TIGR01448       320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITR  356 (720)
T ss_pred             cCCCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHH
Confidence            3456677889999999999999999999999998776

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

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=89.30  E-value=0.31  Score=49.26  Aligned_cols=23  Identities=39%  Similarity=0.482  Sum_probs=19.6

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ++..+.+++|+|+|||||||.+.
T Consensus       174 ~v~~~~~ili~G~tGsGKTTll~  196 (340)
T TIGR03819       174 IVAARLAFLISGGTGSGKTTLLS  196 (340)
T ss_pred             HHhCCCeEEEECCCCCCHHHHHH
Confidence            45678899999999999997765

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

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=89.26  E-value=0.28  Score=53.45  Aligned_cols=31  Identities=23%  Similarity=0.404  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|.+.+.....+++++|+|++||||||.+.
T Consensus       155 d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~  185 (615)
T PRK10875        155 DWQKVAAAVALTRRISVISGGPGTGKTTTVA  185 (615)
T ss_pred             HHHHHHHHHHhcCCeEEEEeCCCCCHHHHHH
Confidence            5677887778888999999999999998876

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=89.22  E-value=0.26  Score=44.17  Aligned_cols=30  Identities=13%  Similarity=0.383  Sum_probs=22.2

Q ss_pred             HHHHHHHcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          64 AVLDMVRNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        64 ~il~~i~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ++.+.+ .++.+++.|++|.||||.+-.|+.
T Consensus        28 ~l~~~l-~~k~~vl~G~SGvGKSSLiN~L~~   57 (161)
T PF03193_consen   28 ELKELL-KGKTSVLLGQSGVGKSSLINALLP   57 (161)
T ss_dssp             HHHHHH-TTSEEEEECSTTSSHHHHHHHHHT
T ss_pred             HHHHHh-cCCEEEEECCCCCCHHHHHHHHHh
Confidence            344444 459999999999999987765543

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=89.04  E-value=5.1  Score=44.93  Aligned_cols=29  Identities=21%  Similarity=0.289  Sum_probs=22.2

Q ss_pred             CeEEEeecCCCC-hhhHhhhhcCCCCCceEEEEeCC
Q psy6094         216 RFQIIPLHSMLP-TVSQKSIFNTPPEGVRKIVLATN  250 (455)
Q Consensus       216 ~~~v~~lhs~l~-~~~r~~v~~~~~~g~~kVivaTn  250 (455)
                      ++.+..+.|+++ .++++.+..      ..|+++|+
T Consensus       147 Gl~v~~i~g~~~~~~~r~~~y~------~dIvygT~  176 (790)
T PRK09200        147 GLTVGLNFSDIDDASEKKAIYE------ADIIYTTN  176 (790)
T ss_pred             CCeEEEEeCCCCcHHHHHHhcC------CCEEEECC
Confidence            378888899999 777776543      57899986

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

Probab=88.99  E-value=0.18  Score=43.58  Aligned_cols=15  Identities=20%  Similarity=0.406  Sum_probs=12.8

Q ss_pred             eEEEEcCCCCCcccc
Q psy6094          74 ITVISGETGSGPPLH   88 (455)
Q Consensus        74 ~vii~~~TGSGKTtq   88 (455)
                      .|++.|++|+|||+.
T Consensus         1 ~vlL~G~~G~GKt~l   15 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTL   15 (139)
T ss_dssp             EEEEEESSSSSHHHH
T ss_pred             CEEEECCCCCCHHHH
Confidence            479999999999943

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

>COG3910 Predicted ATPase [General function prediction only]

Probab=88.94  E-value=0.21  Score=45.70  Aligned_cols=34  Identities=35%  Similarity=0.557  Sum_probs=23.7

Q ss_pred             cCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          55 KLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+|++.+-++-+  =-.-.+++|+|+.||||||.+-
T Consensus        22 slPa~r~l~~~L--eF~apIT~i~GENGsGKSTLLE   55 (233)
T COG3910          22 SLPAFRHLEERL--EFRAPITFITGENGSGKSTLLE   55 (233)
T ss_pred             cchHHHhhhhhc--cccCceEEEEcCCCccHHHHHH
Confidence            455555544411  1256789999999999998775

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=88.91  E-value=0.2  Score=45.47  Aligned_cols=22  Identities=32%  Similarity=0.412  Sum_probs=17.4

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ...+++.|++||||||+.-.+.
T Consensus         3 ~~ii~i~G~~GsGKsTl~~~l~   24 (188)
T TIGR01360         3 CKIIFIVGGPGSGKGTQCEKIV   24 (188)
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999998765443

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>KOG1970|consensus

Probab=88.89  E-value=0.22  Score=52.46  Aligned_cols=29  Identities=14%  Similarity=0.369  Sum_probs=22.6

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhhhcCC
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLKRSET   99 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e~~~~   99 (455)
                      .+++++++||+||||||.+-.|..+.|.+
T Consensus       109 ~~~iLLltGPsGcGKSTtvkvLskelg~~  137 (634)
T KOG1970|consen  109 GSRILLLTGPSGCGKSTTVKVLSKELGYQ  137 (634)
T ss_pred             CceEEEEeCCCCCCchhHHHHHHHhhCce
Confidence            67899999999999998886555544443

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=88.88  E-value=0.16  Score=47.11  Aligned_cols=22  Identities=18%  Similarity=0.422  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (205)
T cd03226          23 LYAGEIIALTGKNGAGKTTLAK   44 (205)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999997765

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=88.87  E-value=0.16  Score=47.33  Aligned_cols=22  Identities=18%  Similarity=0.465  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~G~~~~i~G~nGsGKSTLl~   45 (214)
T cd03292          24 ISAGEFVFLVGPSGAGKSTLLK   45 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

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

Probab=88.84  E-value=0.23  Score=42.45  Aligned_cols=28  Identities=14%  Similarity=0.479  Sum_probs=22.0

Q ss_pred             HHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          63 DAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        63 ~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+-..+..++++++.|+-|+||||.+-
T Consensus         6 ~~l~~~l~~g~vi~L~GdLGaGKTtf~r   33 (123)
T PF02367_consen    6 KKLAQILKPGDVILLSGDLGAGKTTFVR   33 (123)
T ss_dssp             HHHHHHHSS-EEEEEEESTTSSHHHHHH
T ss_pred             HHHHHhCCCCCEEEEECCCCCCHHHHHH
Confidence            4556667889999999999999996654

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

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=88.77  E-value=0.17  Score=47.17  Aligned_cols=22  Identities=23%  Similarity=0.413  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~   44 (210)
T cd03269          23 VEKGEIFGLLGPNGAGKTTTIR   44 (210)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=88.74  E-value=0.18  Score=45.99  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=17.7

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .++|.|++|||||||...|.+
T Consensus         2 riiilG~pGaGK~T~A~~La~   22 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAK   22 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999875554

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=88.74  E-value=0.18  Score=43.88  Aligned_cols=16  Identities=38%  Similarity=0.598  Sum_probs=13.3

Q ss_pred             EEEEcCCCCCcccchh
Q psy6094          75 TVISGETGSGPPLHLD   90 (455)
Q Consensus        75 vii~~~TGSGKTtqlp   90 (455)
                      ++|.|+|||||||.+-
T Consensus         2 i~i~GpsGsGKstl~~   17 (137)
T cd00071           2 IVLSGPSGVGKSTLLK   17 (137)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6789999999996543

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=88.72  E-value=0.17  Score=47.45  Aligned_cols=22  Identities=18%  Similarity=0.132  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        10 i~~Ge~~~l~G~NGsGKSTLlk   31 (213)
T PRK15177         10 MGYHEHIGILAAPGSGKTTLTR   31 (213)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PRK14530 adenylate kinase; Provisional

Probab=88.70  E-value=0.19  Score=47.19  Aligned_cols=23  Identities=13%  Similarity=0.213  Sum_probs=18.1

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +..++|.|++||||||+.-.|..
T Consensus         3 ~~~I~i~G~pGsGKsT~~~~La~   25 (215)
T PRK14530          3 QPRILLLGAPGAGKGTQSSNLAE   25 (215)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45689999999999988754443

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=88.69  E-value=0.17  Score=47.45  Aligned_cols=22  Identities=27%  Similarity=0.551  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        27 i~~G~~~~l~G~nGsGKSTLl~   48 (218)
T cd03255          27 IEKGEFVAIVGPSGSGKSTLLN   48 (218)
T ss_pred             EcCCCEEEEEcCCCCCHHHHHH
Confidence            4578999999999999998765

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.63  E-value=0.19  Score=51.29  Aligned_cols=21  Identities=19%  Similarity=0.313  Sum_probs=18.1

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+.++++.|+||+||||.+.
T Consensus       135 ~~g~ii~lvGptGvGKTTtia  155 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTA  155 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHH
Confidence            347799999999999998776

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=88.61  E-value=0.17  Score=47.90  Aligned_cols=22  Identities=27%  Similarity=0.425  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~   49 (233)
T cd03258          28 VPKGEIFGIIGRSGAGKSTLIR   49 (233)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=88.60  E-value=0.38  Score=53.39  Aligned_cols=27  Identities=30%  Similarity=0.391  Sum_probs=19.9

Q ss_pred             HHHHHHHc-----CCeEEEEcCCCCCcc--cchh
Q psy6094          64 AVLDMVRN-----NQITVISGETGSGPP--LHLD   90 (455)
Q Consensus        64 ~il~~i~~-----~~~vii~~~TGSGKT--tqlp   90 (455)
                      ++.+++.+     ++.++|.|+||+|||  +.+|
T Consensus        36 ~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlP   69 (697)
T PRK11747         36 EVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLA   69 (697)
T ss_pred             HHHHHHhcccccccceEEEECCCCcchhHHHHHH
Confidence            35555555     478999999999999  3355

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=88.59  E-value=0.21  Score=53.22  Aligned_cols=26  Identities=15%  Similarity=0.424  Sum_probs=20.2

Q ss_pred             CCeEEEEcCCCCCcccchhhhhhhhc
Q psy6094          72 NQITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      +++++++||+||||||.+-.|..+.|
T Consensus        45 ~~iLlLtGP~G~GKtttv~~La~elg   70 (519)
T PF03215_consen   45 KRILLLTGPSGCGKTTTVKVLAKELG   70 (519)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999988765555443

>PHA02244 ATPase-like protein

Probab=88.58  E-value=0.34  Score=49.25  Aligned_cols=29  Identities=21%  Similarity=0.264  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHcCCeEEEEcCCCCCcccch
Q psy6094          61 MRDAVLDMVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        61 ~q~~il~~i~~~~~vii~~~TGSGKTtql   89 (455)
                      ....+...+..+..+++.|+||||||+.+
T Consensus       108 ~~~ri~r~l~~~~PVLL~GppGtGKTtLA  136 (383)
T PHA02244        108 ETADIAKIVNANIPVFLKGGAGSGKNHIA  136 (383)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            34556677888999999999999999544

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=88.58  E-value=0.89  Score=47.38  Aligned_cols=19  Identities=26%  Similarity=0.471  Sum_probs=16.7

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +.++++.|+||+||||.+.
T Consensus       221 ~~~i~~vGptGvGKTTt~~  239 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLA  239 (424)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            6689999999999998765

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

Probab=88.53  E-value=0.58  Score=52.65  Aligned_cols=121  Identities=14%  Similarity=0.193  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHhccCCCCcCcchHHH
Q psy6094          44 RRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVI  123 (455)
Q Consensus        44 ~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~l~d~~L~~~~~D~l  123 (455)
                      .++.+..+.---.+.|..|.-.-.-+..|+..-|+||||.||||..                                  
T Consensus        69 e~~~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg----------------------------------  114 (1187)
T COG1110          69 EEFEEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFG----------------------------------  114 (1187)
T ss_pred             HHHHHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHH----------------------------------
Confidence            3444555555556999999999999999999999999999999432                                  


Q ss_pred             HHHHHHHHHhcCCCCeEEEEccCCCCCccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHH
Q psy6094         124 FSLLQHICTTQRPGAILVYCTYTFMGVSPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLH  203 (455)
Q Consensus       124 l~~lk~il~~~~~~~k~ilmSAT~~g~~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~  203 (455)
                        ++-.+                                                 ++. ..++.+++-+||..-+.+++
T Consensus       115 --~~~sl-------------------------------------------------~~a-~kgkr~yii~PT~~Lv~Q~~  142 (1187)
T COG1110         115 --LLMSL-------------------------------------------------YLA-KKGKRVYIIVPTTTLVRQVY  142 (1187)
T ss_pred             --HHHHH-------------------------------------------------HHH-hcCCeEEEEecCHHHHHHHH
Confidence              11111                                                 111 33567888889999999999


Q ss_pred             HHHHhcCCCCC-CCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         204 RSMCQSSFFNS-SRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       204 ~~L~~~~~~~~-~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      +.|.......+ ....+. +||.|+.++++.+++++.+|..+|+|+|+-
T Consensus       143 ~kl~~~~e~~~~~~~~~~-yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         143 ERLKKFAEDAGSLDVLVV-YHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHHHHHHhhcCCcceeee-eccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            88887653322 345556 999999999999999999999999999974

>PRK06526 transposase; Provisional

Probab=88.52  E-value=0.23  Score=48.09  Aligned_cols=23  Identities=22%  Similarity=0.274  Sum_probs=18.9

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -+..+.++++.|++|+|||+..-
T Consensus        94 fi~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         94 FVTGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hhhcCceEEEEeCCCCchHHHHH
Confidence            35677899999999999996654

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=88.42  E-value=0.18  Score=47.04  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~   43 (213)
T cd03235          22 VKPGEFLAIVGPNGAGKSTLLK   43 (213)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=88.36  E-value=0.18  Score=46.39  Aligned_cols=22  Identities=32%  Similarity=0.412  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (195)
T PRK13541         23 FLPSAITYIKGANGCGKSSLLR   44 (195)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

>PRK09183 transposase/IS protein; Provisional

Probab=88.36  E-value=0.23  Score=48.21  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+.++++.|++|||||+...
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH
Confidence            5678899999999999997655

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=88.36  E-value=0.17  Score=47.03  Aligned_cols=22  Identities=27%  Similarity=0.558  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~G~~~~l~G~nGsGKSTLl~   45 (211)
T cd03225          24 IKKGEFVLIVGPNGSGKSTLLR   45 (211)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=88.32  E-value=0.13  Score=46.52  Aligned_cols=25  Identities=24%  Similarity=0.255  Sum_probs=20.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ...+.++++.|..||||||+.-.+.
T Consensus         4 ~~~~~~I~i~G~~GsGKst~a~~l~   28 (176)
T PRK05541          4 KPNGYVIWITGLAGSGKTTIAKALY   28 (176)
T ss_pred             CCCCCEEEEEcCCCCCHHHHHHHHH
Confidence            3567789999999999998876443

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=88.29  E-value=0.19  Score=47.97  Aligned_cols=22  Identities=23%  Similarity=0.457  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~   46 (243)
T TIGR02315        25 INPGEFVAIIGPSGAGKSTLLR   46 (243)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=88.27  E-value=0.19  Score=46.96  Aligned_cols=22  Identities=23%  Similarity=0.401  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (213)
T cd03259          23 VEPGEFLALLGPSGCGKTTLLR   44 (213)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4588999999999999998764

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK07261 topology modulation protein; Provisional

Probab=88.27  E-value=0.2  Score=45.32  Aligned_cols=18  Identities=28%  Similarity=0.318  Sum_probs=15.0

Q ss_pred             EEEEcCCCCCcccchhhh
Q psy6094          75 TVISGETGSGPPLHLDFI   92 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~l   92 (455)
                      ++|.|++||||||..-.|
T Consensus         3 i~i~G~~GsGKSTla~~l   20 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKL   20 (171)
T ss_pred             EEEEcCCCCCHHHHHHHH
Confidence            789999999999876533

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=88.23  E-value=0.18  Score=46.68  Aligned_cols=22  Identities=32%  Similarity=0.591  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        21 i~~Ge~~~i~G~nGsGKSTLl~   42 (206)
T TIGR03608        21 IEKGKMYAIIGESGSGKSTLLN   42 (206)
T ss_pred             EeCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=88.21  E-value=0.19  Score=46.85  Aligned_cols=22  Identities=23%  Similarity=0.569  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~G~~~~l~G~nGsGKSTLl~   46 (214)
T TIGR02673        25 IRKGEFLFLTGPSGAGKTTLLK   46 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5688999999999999998765

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=88.21  E-value=0.19  Score=45.60  Aligned_cols=22  Identities=23%  Similarity=0.468  Sum_probs=18.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~   46 (178)
T cd03247          25 LKQGEKIALLGRSGSGKSTLLQ   46 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997654

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=88.12  E-value=0.18  Score=47.24  Aligned_cols=22  Identities=27%  Similarity=0.499  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (222)
T cd03224          23 VPEGEIVALLGRNGAGKTTLLK   44 (222)
T ss_pred             EcCCeEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.

>PLN02165 adenylate isopentenyltransferase

Probab=88.08  E-value=0.23  Score=49.73  Aligned_cols=20  Identities=35%  Similarity=0.493  Sum_probs=16.6

Q ss_pred             HcCCeEEEEcCCCCCcccch
Q psy6094          70 RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtql   89 (455)
                      ..+.+++|.|+||||||+..
T Consensus        41 ~~g~iivIiGPTGSGKStLA   60 (334)
T PLN02165         41 CKDKVVVIMGATGSGKSRLS   60 (334)
T ss_pred             CCCCEEEEECCCCCcHHHHH
Confidence            35678999999999999554

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

Probab=87.99  E-value=0.42  Score=46.08  Aligned_cols=21  Identities=24%  Similarity=0.487  Sum_probs=16.8

Q ss_pred             CCeEEEEcCCCCCcccchhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~l   92 (455)
                      ...+++.|++||||||.+-.+
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l   63 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNL   63 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHH
Confidence            347999999999999776533

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

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

Probab=87.98  E-value=0.51  Score=52.00  Aligned_cols=33  Identities=12%  Similarity=0.241  Sum_probs=24.4

Q ss_pred             ccCCCHHHHHHHH----HHHHcCCeEEEEcCCCCCcc
Q psy6094          54 KKLPSYQMRDAVL----DMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        54 ~~lP~~~~q~~il----~~i~~~~~vii~~~TGSGKT   86 (455)
                      .....+..|.+++    +++.++..++|.|+||+|||
T Consensus        12 ~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKT   48 (654)
T COG1199          12 PGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKT   48 (654)
T ss_pred             CCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHH
Confidence            3444555666655    45567788999999999999

>TIGR00376 DNA helicase, putative

Probab=87.94  E-value=0.39  Score=52.71  Aligned_cols=32  Identities=16%  Similarity=0.321  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHcC-CeEEEEcCCCCCcccchh
Q psy6094          59 YQMRDAVLDMVRNN-QITVISGETGSGPPLHLD   90 (455)
Q Consensus        59 ~~~q~~il~~i~~~-~~vii~~~TGSGKTtqlp   90 (455)
                      -..|.+.+..+.++ .+++|.|++|||||+.+.
T Consensus       159 n~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~  191 (637)
T TIGR00376       159 NESQKEAVSFALSSKDLFLIHGPPGTGKTRTLV  191 (637)
T ss_pred             CHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHH
Confidence            55677777776655 789999999999997766

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

>COG4136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=87.93  E-value=0.23  Score=43.89  Aligned_cols=25  Identities=20%  Similarity=0.511  Sum_probs=21.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      |..|.++-+.||.||||||.+.++.
T Consensus        25 ia~GeivtlMGPSGcGKSTLls~~~   49 (213)
T COG4136          25 IAKGEIVTLMGPSGCGKSTLLSWMI   49 (213)
T ss_pred             ecCCcEEEEECCCCccHHHHHHHHH
Confidence            5678899999999999999987543

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=87.90  E-value=0.2  Score=43.88  Aligned_cols=22  Identities=18%  Similarity=0.338  Sum_probs=18.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~   44 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLK   44 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997653

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=87.90  E-value=0.21  Score=47.41  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (236)
T cd03219          23 VRPGEIHGLIGPNGAGKTTLFN   44 (236)
T ss_pred             ecCCcEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).

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

Probab=87.87  E-value=1.5  Score=47.00  Aligned_cols=72  Identities=13%  Similarity=0.182  Sum_probs=57.8

Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCC-----CCccC-CCCCCee
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATN-----IAETS-ITIDDIV  262 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTn-----iae~g-itI~~V~  262 (455)
                      .||++||++-+..+++.+........ ++.+..++|+.+...|...++.   | ..|||||+     ..+++ ++...|.
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~-~~~~~~i~GG~~~~~q~~~l~~---~-~~ivVaTPGRllD~i~~~~l~l~~v~  176 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLG-GLRVAVVYGGVSIRKQIEALKR---G-VDIVVATPGRLLDLIKRGKLDLSGVE  176 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcC-CccEEEEECCCCHHHHHHHHhc---C-CCEEEECccHHHHHHHcCCcchhhcC
Confidence            99999999999998888887653211 5779999999999999877775   5 89999997     34444 8888998


Q ss_pred             EEE
Q psy6094         263 YVV  265 (455)
Q Consensus       263 ~VI  265 (455)
                      ++|
T Consensus       177 ~lV  179 (513)
T COG0513         177 TLV  179 (513)
T ss_pred             EEE
Confidence            877

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=87.82  E-value=0.21  Score=45.25  Aligned_cols=23  Identities=22%  Similarity=0.247  Sum_probs=17.7

Q ss_pred             eEEEEcCCCCCcccchhhhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      ++++.|++||||||+.-.|.+..
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            47899999999998876554433

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

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=87.80  E-value=0.2  Score=46.52  Aligned_cols=22  Identities=23%  Similarity=0.437  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~   44 (208)
T cd03268          23 VKKGEIYGFLGPNGAGKTTTMK   44 (208)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997765

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=87.80  E-value=0.21  Score=45.04  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=18.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKStLl~   44 (173)
T cd03230          23 VEKGEIYGLLGPNGAGKTTLIK   44 (173)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997654

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins

Probab=87.80  E-value=0.98  Score=44.15  Aligned_cols=73  Identities=16%  Similarity=0.291  Sum_probs=39.1

Q ss_pred             CeEEEEcCCCCCcccchhhhhhhhcCCCC--ChHHHHHhc------cCCCCcCcc-------hHH---HHHHHHHHHHhc
Q psy6094          73 QITVISGETGSGPPLHLDFITLKRSETQQ--YPNDVLNML------KDPELEGVN-------NDV---IFSLLQHICTTQ  134 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~e~~~~vg--~p~~ll~~l------~d~~L~~~~-------~D~---ll~~lk~il~~~  134 (455)
                      +++||+|-.||||||++- +++..|.-+-  .|-.|+..+      .+.....+-       .++   +...+..+. ..
T Consensus         2 ~~vIiTGlSGaGKs~Al~-~lED~Gy~cvDNlP~~Ll~~l~~~~~~~~~~~~~~Ai~iD~R~~~~~~~~~~~~~~l~-~~   79 (284)
T PF03668_consen    2 ELVIITGLSGAGKSTALR-ALEDLGYYCVDNLPPSLLPQLIELLAQSNSKIEKVAIVIDIRSREFFEDLFEALDELR-KK   79 (284)
T ss_pred             eEEEEeCCCcCCHHHHHH-HHHhcCeeEEcCCcHHHHHHHHHHHHhcCCCCceEEEEEeCCChHHHHHHHHHHHHHH-hc
Confidence            479999999999997763 3332222211  255544433      222222222       222   233344444 44


Q ss_pred             CCCCeEEEEccCC
Q psy6094         135 RPGAILVYCTYTF  147 (455)
Q Consensus       135 ~~~~k~ilmSAT~  147 (455)
                      .-+.++|.+-|.-
T Consensus        80 ~~~~~ilFLdA~d   92 (284)
T PF03668_consen   80 GIDVRILFLDASD   92 (284)
T ss_pred             CCceEEEEEECCh
Confidence            5677888877765

This is a family of putative P-loop ATPases [], as they contain an ATP-binding site and display ATPase and GTPase activities.; GO: 0005524 ATP binding

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=87.79  E-value=0.21  Score=46.77  Aligned_cols=22  Identities=18%  Similarity=0.545  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (216)
T TIGR00960        26 ITKGEMVFLVGHSGAGKSTFLK   47 (216)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK14527 adenylate kinase; Provisional

Probab=87.76  E-value=0.26  Score=45.24  Aligned_cols=25  Identities=16%  Similarity=0.410  Sum_probs=19.8

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      .+..+++.|++||||||+.-.+.++
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999887655443

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

Probab=87.76  E-value=0.44  Score=53.87  Aligned_cols=23  Identities=22%  Similarity=0.309  Sum_probs=20.5

Q ss_pred             HHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          64 AVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        64 ~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      ++.+++.+++.+++.|+||||||
T Consensus       256 ~V~~~l~~~~~~~~eA~tGtGKT  278 (820)
T PRK07246        256 LVGEDFHDGPASFIEAQTGIGKT  278 (820)
T ss_pred             HHHHHHhCCCcEEEECCCCCcHH
Confidence            46677788999999999999999

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=87.71  E-value=0.21  Score=47.46  Aligned_cols=22  Identities=41%  Similarity=0.588  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (235)
T cd03261          23 VRRGEILAIIGPSGSGKSTLLR   44 (235)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=87.69  E-value=0.19  Score=47.15  Aligned_cols=22  Identities=23%  Similarity=0.469  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        27 i~~G~~~~i~G~nGsGKSTLl~   48 (220)
T cd03293          27 VEEGEFVALVGPSGCGKSTLLR   48 (220)
T ss_pred             EeCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998764

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=87.68  E-value=0.21  Score=45.09  Aligned_cols=22  Identities=23%  Similarity=0.335  Sum_probs=18.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~   46 (173)
T cd03246          25 IEPGESLAIIGPSGSGKSTLAR   46 (173)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999997654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=87.68  E-value=0.21  Score=46.51  Aligned_cols=22  Identities=27%  Similarity=0.465  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (207)
T PRK13539         25 LAAGEALVLTGPNGSGKTTLLR   46 (207)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=87.66  E-value=0.27  Score=44.41  Aligned_cols=22  Identities=14%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +++++++|.+||||||..-.+.
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~   23 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQ   23 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            6789999999999997664443

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

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

Probab=87.61  E-value=0.36  Score=50.32  Aligned_cols=28  Identities=14%  Similarity=0.326  Sum_probs=24.0

Q ss_pred             HHHHHHHHHcCCeEEEEcCCCCCcccch
Q psy6094          62 RDAVLDMVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        62 q~~il~~i~~~~~vii~~~TGSGKTtql   89 (455)
                      .+.++.++..++++++.|++|+|||+.+
T Consensus       184 le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        184 IETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            4567888889999999999999999554

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=87.61  E-value=0.18  Score=45.94  Aligned_cols=23  Identities=22%  Similarity=0.492  Sum_probs=19.7

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..|..+.+.|+.||||||.+-
T Consensus        21 ~i~~Ge~~~l~G~nGsGKSTLl~   43 (177)
T cd03222          21 VVKEGEVIGIVGPNGTGKTTAVK   43 (177)
T ss_pred             EECCCCEEEEECCCCChHHHHHH
Confidence            35789999999999999997664

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=87.60  E-value=0.21  Score=47.43  Aligned_cols=22  Identities=23%  Similarity=0.472  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (236)
T TIGR03864        24 VRPGEFVALLGPNGAGKSTLFS   45 (236)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=87.58  E-value=0.22  Score=47.05  Aligned_cols=22  Identities=32%  Similarity=0.543  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        33 i~~Ge~~~i~G~nGsGKSTLl~   54 (228)
T PRK10584         33 VKRGETIALIGESGSGKSTLLA   54 (228)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=87.58  E-value=0.21  Score=46.52  Aligned_cols=22  Identities=23%  Similarity=0.522  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (213)
T cd03301          23 IADGEFVVLLGPSGCGKTTTLR   44 (213)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998764

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=87.57  E-value=0.22  Score=45.25  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=18.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~   44 (178)
T cd03229          23 IEAGEIVALLGPSGSGKSTLLR   44 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999997654

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>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=87.56  E-value=2.4  Score=44.20  Aligned_cols=83  Identities=17%  Similarity=0.212  Sum_probs=70.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC-----CCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS-----ITI  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g-----itI  258 (455)
                      ...+.+|||+|+.-+--.+.+.|.+.      ++....+|--.++.+-.++=..|-.|..+|+|-|   ||-     ..|
T Consensus       298 ~~~~~~LIfIPSYfDfVRlRN~lk~~------~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~T---ER~HFfrRy~i  368 (442)
T PF06862_consen  298 SKMSGTLIFIPSYFDFVRLRNYLKKE------NISFVQISEYTSNSDISRARSQFFHGRKPILLYT---ERFHFFRRYRI  368 (442)
T ss_pred             cCCCcEEEEecchhhhHHHHHHHHhc------CCeEEEecccCCHHHHHHHHHHHHcCCceEEEEE---hHHhhhhhcee
Confidence            56788999999999999999999965      4778888877777777777777889999999999   655     578


Q ss_pred             CCeeEEEeCCCCccccc
Q psy6094         259 DDIVYVVDCGKTKMSNF  275 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~y  275 (455)
                      .+|+.||=+|.|..+.|
T Consensus       369 rGi~~viFY~~P~~p~f  385 (442)
T PF06862_consen  369 RGIRHVIFYGPPENPQF  385 (442)
T ss_pred             cCCcEEEEECCCCChhH
Confidence            99999999999887765

; GO: 0005634 nucleus

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=87.55  E-value=0.22  Score=46.78  Aligned_cols=22  Identities=27%  Similarity=0.483  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (220)
T cd03265          23 VRRGEIFGLLGPNGAGKTTTIK   44 (220)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=87.54  E-value=0.21  Score=47.93  Aligned_cols=22  Identities=32%  Similarity=0.567  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        29 i~~Ge~~~i~G~nGsGKSTLl~   50 (253)
T PRK14242         29 FEQNQVTALIGPSGCGKSTFLR   50 (253)
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

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

Probab=87.52  E-value=0.24  Score=37.57  Aligned_cols=17  Identities=35%  Similarity=0.540  Sum_probs=13.8

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      ++.+.|+.||||||..-
T Consensus         1 ~i~i~G~~gsGKst~~~   17 (69)
T cd02019           1 IIAITGGSGSGKSTVAK   17 (69)
T ss_pred             CEEEECCCCCCHHHHHH
Confidence            36789999999997654

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

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=87.48  E-value=0.46  Score=47.41  Aligned_cols=28  Identities=18%  Similarity=0.300  Sum_probs=20.5

Q ss_pred             HHHHHHHHHcCC--eEEEEcCCCCCcccch
Q psy6094          62 RDAVLDMVRNNQ--ITVISGETGSGPPLHL   89 (455)
Q Consensus        62 q~~il~~i~~~~--~vii~~~TGSGKTtql   89 (455)
                      .+.+..++.+++  .+++.||+||||||.+
T Consensus        24 ~~~L~~~~~~~~~~~lll~Gp~GtGKT~la   53 (337)
T PRK12402         24 VERLSRAVDSPNLPHLLVQGPPGSGKTAAV   53 (337)
T ss_pred             HHHHHHHHhCCCCceEEEECCCCCCHHHHH
Confidence            344444555665  7999999999999655

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=87.48  E-value=0.29  Score=48.44  Aligned_cols=17  Identities=35%  Similarity=0.452  Sum_probs=14.8

Q ss_pred             cCCeEEEEcCCCCCccc
Q psy6094          71 NNQITVISGETGSGPPL   87 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTt   87 (455)
                      .+++++|.||||||||.
T Consensus         3 ~~~ii~I~GpTasGKS~   19 (300)
T PRK14729          3 ENKIVFIFGPTAVGKSN   19 (300)
T ss_pred             CCcEEEEECCCccCHHH
Confidence            45689999999999993

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=87.47  E-value=0.41  Score=47.83  Aligned_cols=30  Identities=20%  Similarity=0.388  Sum_probs=23.3

Q ss_pred             HHHHHHHcCCeEEEEcCCCCCcccchhhhh
Q psy6094          64 AVLDMVRNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        64 ~il~~i~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .++..+..++.+++.|++||||||.+-.+.
T Consensus        56 ~vl~~l~~~~~ilL~G~pGtGKTtla~~lA   85 (327)
T TIGR01650        56 AICAGFAYDRRVMVQGYHGTGKSTHIEQIA   85 (327)
T ss_pred             HHHHHHhcCCcEEEEeCCCChHHHHHHHHH
Confidence            366667778889999999999996654333

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=87.43  E-value=0.22  Score=46.96  Aligned_cols=22  Identities=27%  Similarity=0.514  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (227)
T cd03260          23 IPKGEITALIGPSGCGKSTLLR   44 (227)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>TIGR01978 sufC FeS assembly ATPase SufC

Probab=87.39  E-value=0.23  Score=47.23  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (243)
T TIGR01978        23 VKKGEIHAIMGPNGSGKSTLSK   44 (243)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic (PubMed:12554644) or associated with the membrane (PubMed:11943156). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.

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

Probab=87.36  E-value=0.5  Score=54.26  Aligned_cols=27  Identities=26%  Similarity=0.452  Sum_probs=21.9

Q ss_pred             HHHHHHHcCCeEEEEcCCCCCcc--cchh
Q psy6094          64 AVLDMVRNNQITVISGETGSGPP--LHLD   90 (455)
Q Consensus        64 ~il~~i~~~~~vii~~~TGSGKT--tqlp   90 (455)
                      ++.+++.+++.++|.|+||+|||  +.+|
T Consensus       268 ~v~~~l~~~~~~~iEA~TGtGKTlaYLlp  296 (928)
T PRK08074        268 EVYTALRDSEHALIEAGTGTGKSLAYLLP  296 (928)
T ss_pred             HHHHHHhcCCCEEEECCCCCchhHHHHHH
Confidence            46667778999999999999999  3355

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=87.31  E-value=0.23  Score=46.64  Aligned_cols=22  Identities=32%  Similarity=0.558  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~G~~~~i~G~nGsGKSTLl~   49 (221)
T TIGR02211        28 IGKGEIVAIVGSSGSGKSTLLH   49 (221)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=87.28  E-value=0.24  Score=44.53  Aligned_cols=22  Identities=18%  Similarity=0.449  Sum_probs=18.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (166)
T cd03223          24 IKPGDRLLITGPSGTGKSSLFR   45 (166)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999996653

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=87.27  E-value=0.23  Score=46.23  Aligned_cols=22  Identities=36%  Similarity=0.622  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        23 i~~G~~~~l~G~nGsGKSTLl~   44 (213)
T cd03262          23 VKKGEVVVIIGPSGSGKSTLLR   44 (213)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997764

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=87.23  E-value=0.25  Score=47.56  Aligned_cols=22  Identities=18%  Similarity=0.409  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        22 i~~Ge~~~i~G~NGsGKSTLlk   43 (246)
T cd03237          22 ISESEVIGILGPNGIGKTTFIK   43 (246)
T ss_pred             cCCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PRK14531 adenylate kinase; Provisional

Probab=87.20  E-value=0.28  Score=44.81  Aligned_cols=23  Identities=17%  Similarity=0.203  Sum_probs=17.9

Q ss_pred             CeEEEEcCCCCCcccchhhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      +.+++.|++||||||+.-.|.+.
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~   25 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAA   25 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35889999999999886555443

>PRK00698 tmk thymidylate kinase; Validated

Probab=87.16  E-value=0.28  Score=45.24  Aligned_cols=24  Identities=17%  Similarity=0.415  Sum_probs=19.6

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+..++|.|..||||||++-.+.+
T Consensus         2 ~~~~I~ieG~~gsGKsT~~~~L~~   25 (205)
T PRK00698          2 RGMFITIEGIDGAGKSTQIELLKE   25 (205)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999999874443

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=87.16  E-value=0.24  Score=46.75  Aligned_cols=22  Identities=27%  Similarity=0.587  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (225)
T PRK10247         30 LRAGEFKLITGPSGCGKSTLLK   51 (225)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=87.15  E-value=0.24  Score=46.33  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~   49 (218)
T cd03266          28 VKPGEVTGLLGPNGAGKTTTLR   49 (218)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=87.14  E-value=0.25  Score=49.88  Aligned_cols=22  Identities=18%  Similarity=0.475  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+-+.||.||||||.+-
T Consensus        28 i~~Gef~~lLGPSGcGKTTlLR   49 (352)
T COG3842          28 IKKGEFVTLLGPSGCGKTTLLR   49 (352)
T ss_pred             ecCCcEEEEECCCCCCHHHHHH
Confidence            5678889999999999999876

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=87.13  E-value=1.3  Score=47.13  Aligned_cols=22  Identities=18%  Similarity=0.450  Sum_probs=18.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++++.+.|+||+||||.+.
T Consensus       347 l~~G~vIaLVGPtGvGKTTtaa  368 (559)
T PRK12727        347 LERGGVIALVGPTGAGKTTTIA  368 (559)
T ss_pred             ccCCCEEEEECCCCCCHHHHHH
Confidence            3467899999999999997765

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=87.12  E-value=0.23  Score=46.49  Aligned_cols=22  Identities=23%  Similarity=0.486  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        34 i~~Ge~~~i~G~nGsGKSTLl~   55 (214)
T PRK13543         34 VDAGEALLVQGDNGAGKTTLLR   55 (214)
T ss_pred             ECCCCEEEEEcCCCCCHHHHHH
Confidence            4678999999999999997764

>PRK14247 phosphate ABC transporter ATP-binding protein; Provisional

Probab=87.12  E-value=0.23  Score=47.56  Aligned_cols=22  Identities=36%  Similarity=0.599  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (250)
T PRK14247         26 IPDNTITALMGPSGSGKSTLLR   47 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK10908 cell division protein FtsE; Provisional

Probab=87.08  E-value=0.24  Score=46.52  Aligned_cols=22  Identities=23%  Similarity=0.590  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (222)
T PRK10908         25 MRPGEMAFLTGHSGAGKSTLLK   46 (222)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=87.07  E-value=0.24  Score=47.04  Aligned_cols=22  Identities=18%  Similarity=0.439  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (241)
T cd03256          24 INPGEFVALIGPSGAGKSTLLR   45 (241)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=87.06  E-value=0.25  Score=46.54  Aligned_cols=22  Identities=23%  Similarity=0.418  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~   49 (228)
T cd03257          28 IKKGETLGLVGESGSGKSTLAR   49 (228)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>cd03279 ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends

Probab=87.03  E-value=0.31  Score=45.65  Aligned_cols=20  Identities=45%  Similarity=0.684  Sum_probs=17.4

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      ++.++.+.|++||||||.+-
T Consensus        27 ~~~~~~i~G~NGsGKSTll~   46 (213)
T cd03279          27 NNGLFLICGPTGAGKSTILD   46 (213)
T ss_pred             ccCEEEEECCCCCCHHHHHH
Confidence            46789999999999998764

They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.

>KOG1803|consensus

Probab=87.01  E-value=0.58  Score=49.80  Aligned_cols=31  Identities=26%  Similarity=0.440  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHcC-CeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNN-QITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~-~~vii~~~TGSGKTtqlp   90 (455)
                      ..|.+++....++ ...+|.||+|+|||+.+.
T Consensus       188 ~SQk~Av~~~~~~k~l~~I~GPPGTGKT~Tlv  219 (649)
T KOG1803|consen  188 SSQKAAVSFAINNKDLLIIHGPPGTGKTRTLV  219 (649)
T ss_pred             HHHHHHHHHHhccCCceEeeCCCCCCceeeHH
Confidence            4677788877777 678899999999997766

>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP

Probab=86.95  E-value=0.24  Score=46.09  Aligned_cols=22  Identities=36%  Similarity=0.572  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        21 i~~Ge~~~l~G~nGsGKSTLl~   42 (211)
T cd03298          21 FAQGEITAIVGPSGSGKSTLLN   42 (211)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=86.88  E-value=0.96  Score=43.10  Aligned_cols=22  Identities=36%  Similarity=0.495  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|+.||||||.+-
T Consensus        31 V~~Gei~~iiGgSGsGKStlLr   52 (263)
T COG1127          31 VPRGEILAILGGSGSGKSTLLR   52 (263)
T ss_pred             ecCCcEEEEECCCCcCHHHHHH
Confidence            4578899999999999998876

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=86.88  E-value=0.25  Score=46.66  Aligned_cols=22  Identities=23%  Similarity=0.430  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (232)
T cd03218          23 VKQGEIVGLLGPNGAGKTTTFY   44 (232)
T ss_pred             ecCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=86.86  E-value=0.26  Score=43.64  Aligned_cols=22  Identities=27%  Similarity=0.524  Sum_probs=18.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+|+.+.|.|++||||||.+-
T Consensus        22 i~~g~~~~i~G~nGsGKStll~   43 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLR   43 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999997654

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=86.79  E-value=0.25  Score=47.73  Aligned_cols=22  Identities=23%  Similarity=0.523  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (255)
T PRK11248         24 LESGELLVVLGPSGCGKTTLLN   45 (255)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK14262 phosphate ABC transporter ATP-binding protein; Provisional

Probab=86.78  E-value=0.27  Score=47.11  Aligned_cols=22  Identities=41%  Similarity=0.560  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (250)
T PRK14262         26 IFKNQITAIIGPSGCGKTTLLR   47 (250)
T ss_pred             ecCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK10744 pstB phosphate transporter ATP-binding protein; Provisional

Probab=86.73  E-value=0.26  Score=47.59  Aligned_cols=22  Identities=32%  Similarity=0.545  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        36 i~~Ge~~~i~G~nGsGKSTLl~   57 (260)
T PRK10744         36 IAKNQVTAFIGPSGCGKSTLLR   57 (260)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=86.71  E-value=0.26  Score=46.58  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (230)
T TIGR03410        23 VPKGEVTCVLGRNGVGKTTLLK   44 (230)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=86.69  E-value=0.26  Score=46.22  Aligned_cols=22  Identities=32%  Similarity=0.505  Sum_probs=19.5

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        27 i~~G~~~~i~G~nGsGKSTLl~   48 (220)
T cd03245          27 IRAGEKVAIIGRVGSGKSTLLK   48 (220)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4689999999999999998765

Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=86.69  E-value=0.27  Score=45.65  Aligned_cols=20  Identities=25%  Similarity=0.321  Sum_probs=17.5

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++++++.|+.||||||.+-
T Consensus        24 ~g~~~~ltGpNg~GKSTllr   43 (199)
T cd03283          24 KKNGILITGSNMSGKSTFLR   43 (199)
T ss_pred             CCcEEEEECCCCCChHHHHH
Confidence            46799999999999998765

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=86.69  E-value=0.26  Score=46.74  Aligned_cols=22  Identities=27%  Similarity=0.528  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        32 i~~Ge~~~l~G~nGsGKSTLl~   53 (233)
T PRK11629         32 IGEGEMMAIVGSSGSGKSTLLH   53 (233)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4678899999999999998765

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=86.66  E-value=0.26  Score=46.89  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (239)
T cd03296          25 IPSGELVALLGPSGSGKTTLLR   46 (239)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK08118 topology modulation protein; Reviewed

Probab=86.65  E-value=0.28  Score=44.18  Aligned_cols=21  Identities=19%  Similarity=0.223  Sum_probs=16.1

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      -++|.|+.||||||..-.|..
T Consensus         3 rI~I~G~~GsGKSTlak~L~~   23 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGE   23 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999976544443

>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL

Probab=86.65  E-value=0.26  Score=46.40  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        31 i~~Ge~~~l~G~nGsGKSTLl~   52 (224)
T TIGR02324        31 VNAGECVALSGPSGAGKSTLLK   52 (224)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=86.64  E-value=0.3  Score=44.45  Aligned_cols=20  Identities=25%  Similarity=0.366  Sum_probs=17.2

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .|.++++.|++||||||..-
T Consensus         2 ~ge~i~l~G~sGsGKSTl~~   21 (176)
T PRK09825          2 AGESYILMGVSGSGKSLIGS   21 (176)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            47789999999999997664

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=86.63  E-value=0.25  Score=45.80  Aligned_cols=22  Identities=23%  Similarity=0.448  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~   45 (204)
T PRK13538         24 LNAGELVQIEGPNGAGKTSLLR   45 (204)
T ss_pred             ECCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=86.56  E-value=0.26  Score=44.76  Aligned_cols=22  Identities=27%  Similarity=0.454  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        22 i~~G~~~~l~G~nGsGKStLl~   43 (180)
T cd03214          22 IEAGEIVGILGPNGAGKSTLLK   43 (180)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD

Probab=86.55  E-value=0.27  Score=46.53  Aligned_cols=22  Identities=27%  Similarity=0.542  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus         9 i~~Ge~~~i~G~nGsGKSTLl~   30 (230)
T TIGR02770         9 LKRGEVLALVGESGSGKSLTCL   30 (230)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997764

This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous.

>TIGR02323 CP_lyasePhnK phosphonate C-P lyase system protein PhnK

Probab=86.54  E-value=0.26  Score=47.28  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (253)
T TIGR02323        26 LYPGEVLGIVGESGSGKSTLLG   47 (253)
T ss_pred             EeCCcEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=86.51  E-value=0.25  Score=45.44  Aligned_cols=22  Identities=36%  Similarity=0.658  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~   51 (192)
T cd03232          30 VKPGTLTALMGESGAGKTTLLD   51 (192)
T ss_pred             EeCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=86.47  E-value=0.27  Score=43.98  Aligned_cols=22  Identities=27%  Similarity=0.592  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (163)
T cd03216          23 VRRGEVHALLGENGAGKSTLMK   44 (163)
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999997764

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=86.46  E-value=0.26  Score=45.42  Aligned_cols=22  Identities=18%  Similarity=0.348  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (198)
T TIGR01189        23 LNAGEALQVTGPNGIGKTTLLR   44 (198)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=86.45  E-value=0.28  Score=46.82  Aligned_cols=22  Identities=23%  Similarity=0.388  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (242)
T PRK11124         25 CPQGETLVLLGPSGAGKSSLLR   46 (242)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=86.45  E-value=2.5  Score=41.81  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=19.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|.+.=|+|..|.||||.+-
T Consensus        29 I~~GeI~GIIG~SGAGKSTLiR   50 (339)
T COG1135          29 IPKGEIFGIIGYSGAGKSTLLR   50 (339)
T ss_pred             EcCCcEEEEEcCCCCcHHHHHH
Confidence            5678889999999999999987

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=86.40  E-value=0.28  Score=44.21  Aligned_cols=22  Identities=27%  Similarity=0.487  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        25 i~~G~~~~l~G~nGsGKstLl~   46 (171)
T cd03228          25 IKPGEKVAIVGPSGSGKSTLLK   46 (171)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997664

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=86.33  E-value=0.28  Score=45.95  Aligned_cols=22  Identities=27%  Similarity=0.424  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (220)
T cd03263          25 VYKGEIFGLLGHNGAGKTTTLK   46 (220)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4678899999999999998765

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=86.32  E-value=0.28  Score=46.23  Aligned_cols=22  Identities=23%  Similarity=0.511  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~G~~~~i~G~nGsGKSTLl~   47 (229)
T cd03254          26 IKPGETVAIVGPTGAGKTTLIN   47 (229)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein

Probab=86.29  E-value=0.28  Score=46.95  Aligned_cols=22  Identities=32%  Similarity=0.567  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (247)
T TIGR00972        24 IPKNQVTALIGPSGCGKSTLLR   45 (247)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4689999999999999998765

This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters.

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=86.26  E-value=0.29  Score=46.39  Aligned_cols=22  Identities=18%  Similarity=0.492  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus         8 i~~Ge~~~i~G~nGsGKSTLl~   29 (230)
T TIGR01184         8 IQQGEFISLIGHSGCGKSTLLN   29 (230)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=86.23  E-value=0.28  Score=45.38  Aligned_cols=22  Identities=18%  Similarity=0.377  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~   45 (200)
T PRK13540         24 LPAGGLLHLKGSNGAGKTTLLK   45 (200)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997765

>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=86.22  E-value=0.28  Score=48.23  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (286)
T PRK13646         30 FEQGKYYAIVGQTGSGKSTLIQ   51 (286)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK05480 uridine/cytidine kinase; Provisional

Probab=86.20  E-value=0.32  Score=45.30  Aligned_cols=20  Identities=30%  Similarity=0.358  Sum_probs=15.9

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      ...++.|.|++||||||..-
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~   24 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVAS   24 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            34578899999999996653

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=86.19  E-value=0.81  Score=41.91  Aligned_cols=32  Identities=22%  Similarity=0.353  Sum_probs=23.4

Q ss_pred             CCHHHHHHHHHHHHcCC--eEEEEcCCCCCcccc
Q psy6094          57 PSYQMRDAVLDMVRNNQ--ITVISGETGSGPPLH   88 (455)
Q Consensus        57 P~~~~q~~il~~i~~~~--~vii~~~TGSGKTtq   88 (455)
                      |+|..-..++..+.++.  .++.-|+||||||+.
T Consensus         7 Pvf~~~~~~v~~~~~G~n~~i~~yG~tGsGKT~T   40 (186)
T cd01363           7 PVFRDVGPLLQSALDGYNVCIFAYGQTGSGKTYT   40 (186)
T ss_pred             cHHHHHHHHHHHHhCCcceeEEEECCCCCcceEe
Confidence            36666557777777764  467799999999933

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=86.16  E-value=0.29  Score=44.55  Aligned_cols=22  Identities=32%  Similarity=0.460  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~   44 (182)
T cd03215          23 VRAGEIVGIAGLVGNGQTELAE   44 (182)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK14248 phosphate ABC transporter ATP-binding protein; Provisional

Probab=86.12  E-value=0.29  Score=47.56  Aligned_cols=22  Identities=23%  Similarity=0.531  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        44 i~~Ge~~~i~G~nGsGKSTLl~   65 (268)
T PRK14248         44 IEKHAVTALIGPSGCGKSTFLR   65 (268)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

>cd03270 ABC_UvrA_I The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=86.12  E-value=0.31  Score=46.19  Aligned_cols=21  Identities=33%  Similarity=0.567  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccch
Q psy6094          69 VRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtql   89 (455)
                      |..|.++.|.|+.||||||.+
T Consensus        18 i~~Ge~~~l~G~sGsGKSTL~   38 (226)
T cd03270          18 IPRNKLVVITGVSGSGKSSLA   38 (226)
T ss_pred             cCCCcEEEEEcCCCCCHHHHH
Confidence            568899999999999999885

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=86.11  E-value=0.27  Score=45.63  Aligned_cols=22  Identities=27%  Similarity=0.511  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (202)
T cd03233          30 VKPGEMVLVLGRPGSGCSTLLK   51 (202)
T ss_pred             ECCCcEEEEECCCCCCHHHHHH
Confidence            4678999999999999997654

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=86.10  E-value=0.4  Score=43.74  Aligned_cols=24  Identities=17%  Similarity=0.364  Sum_probs=16.7

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+.+++++++.|++|+|||....
T Consensus        42 ~~~~~~~~l~l~G~~G~GKThLa~   65 (178)
T PF01695_consen   42 EFIENGENLILYGPPGTGKTHLAV   65 (178)
T ss_dssp             -S-SC--EEEEEESTTSSHHHHHH
T ss_pred             CCcccCeEEEEEhhHhHHHHHHHH
Confidence            345678999999999999995544

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

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=86.02  E-value=0.34  Score=44.35  Aligned_cols=23  Identities=22%  Similarity=0.419  Sum_probs=19.0

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      |..++|.|..||||||+.-.|.+
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~   25 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKK   25 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999774443

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PRK14738 gmk guanylate kinase; Provisional

Probab=86.01  E-value=0.35  Score=45.16  Aligned_cols=19  Identities=37%  Similarity=0.527  Sum_probs=16.1

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .++.++|+|+.||||||.+
T Consensus        12 ~~~~ivi~GpsG~GK~tl~   30 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVL   30 (206)
T ss_pred             CCeEEEEECcCCCCHHHHH
Confidence            5678999999999999654

>PRK14273 phosphate ABC transporter ATP-binding protein; Provisional

Probab=86.00  E-value=0.3  Score=46.93  Aligned_cols=22  Identities=32%  Similarity=0.551  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (254)
T PRK14273         30 ILKNSITALIGPSGCGKSTFLR   51 (254)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5689999999999999998764

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=85.99  E-value=1.3  Score=49.08  Aligned_cols=79  Identities=11%  Similarity=0.119  Sum_probs=63.3

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCC-CccCCCCCCeeE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNI-AETSITIDDIVY  263 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTni-ae~gitI~~V~~  263 (455)
                      .+..+++..|+..=+...++.+++...  .-++.+..+||+++..++..++....+|...|||+|.- ....+...++.+
T Consensus       309 ~g~q~lilaPT~~LA~Q~~~~l~~l~~--~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~l  386 (681)
T PRK10917        309 AGYQAALMAPTEILAEQHYENLKKLLE--PLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGL  386 (681)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHh--hcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccce
Confidence            456899999999999888888776431  12478999999999999999999888999999999973 344566788887


Q ss_pred             EE
Q psy6094         264 VV  265 (455)
Q Consensus       264 VI  265 (455)
                      ||
T Consensus       387 vV  388 (681)
T PRK10917        387 VI  388 (681)
T ss_pred             EE
Confidence            76

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=85.98  E-value=8.1  Score=43.76  Aligned_cols=35  Identities=11%  Similarity=0.108  Sum_probs=28.2

Q ss_pred             HHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          52 ARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        52 ~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      .|+.|-..++--+++-.+.=++--|..++||+|||
T Consensus        75 ~~R~lg~~~ydvQliGg~~Lh~G~Iaem~TGeGKT  109 (896)
T PRK13104         75 SLRTLGLRHFDVQLIGGMVLHEGNIAEMRTGEGKT  109 (896)
T ss_pred             HHHHcCCCcchHHHhhhhhhccCccccccCCCCch
Confidence            46677777777778888766666699999999999

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=85.97  E-value=0.31  Score=47.21  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        35 i~~Ge~~~I~G~NGsGKSTLlk   56 (257)
T PRK11247         35 IPAGQFVAVVGRSGCGKSTLLR   56 (257)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PRK14239 phosphate transporter ATP-binding protein; Provisional

Probab=85.80  E-value=0.31  Score=46.72  Aligned_cols=22  Identities=36%  Similarity=0.513  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~   49 (252)
T PRK14239         28 FYPNEITALIGPSGSGKSTLLR   49 (252)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=85.78  E-value=0.3  Score=52.32  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|+|++||||||.+-
T Consensus       358 i~~G~~vaIvG~SGsGKSTLl~  379 (529)
T TIGR02868       358 LPPGERVAILGPSGSGKSTLLM  379 (529)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578889999999999998764

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>KOG0060|consensus

Probab=85.72  E-value=0.36  Score=51.18  Aligned_cols=21  Identities=33%  Similarity=0.479  Sum_probs=18.1

Q ss_pred             HHcCCeEEEEcCCCCCcccch
Q psy6094          69 VRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtql   89 (455)
                      +.+|++++|+|++|||||..+
T Consensus       458 V~~g~~LLItG~sG~GKtSLl  478 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSLL  478 (659)
T ss_pred             ecCCCeEEEECCCCCchhHHH
Confidence            458999999999999999554

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=85.69  E-value=0.51  Score=42.20  Aligned_cols=37  Identities=16%  Similarity=0.159  Sum_probs=22.7

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNML  110 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~l  110 (455)
                      ++.|+|++||||||..--|.+..|-.+-..+.+.|.+
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~~vsaG~iFR~~   38 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLKLVSAGTIFREM   38 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCceeeccHHHHHH
Confidence            4778999999999876555544443322233444444

>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional

Probab=85.68  E-value=0.32  Score=46.59  Aligned_cols=22  Identities=32%  Similarity=0.542  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (250)
T PRK11264         26 VKPGEVVAIIGPSGSGKTTLLR   47 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=85.65  E-value=0.32  Score=46.41  Aligned_cols=22  Identities=23%  Similarity=0.425  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (241)
T PRK14250         26 FEGGAIYTIVGPSGAGKSTLIK   47 (241)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=85.65  E-value=0.31  Score=47.47  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        32 i~~Ge~~~l~G~nGsGKSTLl~   53 (271)
T PRK13632         32 INEGEYVAILGHNGSGKSTISK   53 (271)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional

Probab=85.61  E-value=0.33  Score=46.94  Aligned_cols=22  Identities=27%  Similarity=0.516  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (258)
T PRK13548         25 LRPGEVVAILGPNGAGKSTLLR   46 (258)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=85.56  E-value=0.31  Score=46.46  Aligned_cols=22  Identities=23%  Similarity=0.511  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (242)
T cd03295          24 IAKGEFLVLIGPSGSGKTTTMK   45 (242)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=85.52  E-value=0.34  Score=44.36  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=19.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+..++|.|+.||||||.+-
T Consensus        25 l~~Ge~~~i~G~NG~GKTtLLR   46 (209)
T COG4133          25 LNAGEALQITGPNGAGKTTLLR   46 (209)
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            4678999999999999998876

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=85.50  E-value=0.33  Score=44.15  Aligned_cols=20  Identities=35%  Similarity=0.547  Sum_probs=16.4

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+.+|.|++|+||||.+-
T Consensus        18 ~~g~~vi~G~Ng~GKStil~   37 (202)
T PF13476_consen   18 SPGLNVIYGPNGSGKSTILE   37 (202)
T ss_dssp             -SEEEEEEESTTSSHHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHH
Confidence            34589999999999997765

>PRK14237 phosphate transporter ATP-binding protein; Provisional

Probab=85.48  E-value=0.32  Score=47.24  Aligned_cols=22  Identities=36%  Similarity=0.564  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        43 i~~Ge~~~I~G~nGsGKSTLl~   64 (267)
T PRK14237         43 FEKNKITALIGPSGSGKSTYLR   64 (267)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea

Probab=85.46  E-value=0.33  Score=47.23  Aligned_cols=22  Identities=45%  Similarity=0.605  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        47 i~~Ge~~~l~G~nGsGKSTLl~   68 (269)
T cd03294          47 VREGEIFVIMGLSGSGKSTLLR   68 (269)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG0347|consensus

Probab=85.43  E-value=1.6  Score=46.10  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=49.3

Q ss_pred             CEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCC
Q psy6094         188 PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATN  250 (455)
Q Consensus       188 ~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTn  250 (455)
                      -.|||.||++-+..+++.|.....  ...+.+..+-|||+.+.|++++..-    -.|||||+
T Consensus       265 ~~LV~tPTRELa~QV~~Hl~ai~~--~t~i~v~si~GGLavqKQqRlL~~~----p~IVVATP  321 (731)
T KOG0347|consen  265 IALVVTPTRELAHQVKQHLKAIAE--KTQIRVASITGGLAVQKQQRLLNQR----PDIVVATP  321 (731)
T ss_pred             eeEEecChHHHHHHHHHHHHHhcc--ccCeEEEEeechhHHHHHHHHHhcC----CCEEEecc
Confidence            489999999999999998887653  4569999999999999999999873    46999997

>PRK06762 hypothetical protein; Provisional

Probab=85.42  E-value=0.36  Score=43.01  Aligned_cols=24  Identities=21%  Similarity=0.372  Sum_probs=18.4

Q ss_pred             CeEEEEcCCCCCcccchhhhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      ..+++.|.+||||||..-.+.+..
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999998776554443

>PRK00131 aroK shikimate kinase; Reviewed

Probab=85.41  E-value=0.38  Score=42.86  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=17.8

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..+++.|++||||||..-.+.
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La   25 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLA   25 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHH
Confidence            46789999999999997654333

>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=85.37  E-value=0.33  Score=47.26  Aligned_cols=22  Identities=18%  Similarity=0.270  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (271)
T PRK13638         24 FSLSPVTGLVGANGCGKSTLFM   45 (271)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=85.31  E-value=0.34  Score=47.14  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        32 i~~Ge~~~I~G~nGsGKSTLl~   53 (269)
T PRK13648         32 IPKGQWTSIVGHNGSGKSTIAK   53 (269)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=85.30  E-value=3.3  Score=39.69  Aligned_cols=70  Identities=10%  Similarity=0.185  Sum_probs=40.3

Q ss_pred             cCCCCEEEEcCC-HHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc-CCCCCCe
Q psy6094         184 MLVVPILVFLPG-WDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET-SITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~-~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~-gitI~~V  261 (455)
                      ...|..++|-+- ...+++||+.+.-...   +   -..+||.+..-  ++     ..|+++++|-.+.... --.||+|
T Consensus       177 k~~GatIifSsH~Me~vEeLCD~llmL~k---G---~~V~~G~v~~i--r~-----~~Gkk~~~ies~~s~eeL~~ipgi  243 (300)
T COG4152         177 KEEGATIIFSSHRMEHVEELCDRLLMLKK---G---QTVLYGTVEDI--RR-----SFGKKRLVIESDLSLEELANIPGI  243 (300)
T ss_pred             HhcCCEEEEecchHHHHHHHhhhhheecC---C---ceEEeccHHHH--HH-----hcCCceEEEeccCchHHHhcCCCc
Confidence            567888999654 5789999987764321   1   11245654221  11     1367777776443332 3457777


Q ss_pred             eEEEe
Q psy6094         262 VYVVD  266 (455)
Q Consensus       262 ~~VID  266 (455)
                      .-+..
T Consensus       244 ~~~~~  248 (300)
T COG4152         244 LKITE  248 (300)
T ss_pred             eeeee
Confidence            66663

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=85.28  E-value=0.34  Score=44.92  Aligned_cols=22  Identities=32%  Similarity=0.502  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~G~~~~i~G~nG~GKSTLl~   49 (204)
T cd03250          28 VPKGELVAIVGPVGSGKSSLLS   49 (204)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999997664

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=85.24  E-value=0.35  Score=45.93  Aligned_cols=22  Identities=23%  Similarity=0.448  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (237)
T cd03252          25 IKPGEVVGIVGRSGSGKSTLTK   46 (237)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=85.24  E-value=0.35  Score=45.96  Aligned_cols=22  Identities=14%  Similarity=0.379  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLl~   47 (238)
T cd03249          26 IPPGKTVALVGSSGCGKSTVVS   47 (238)
T ss_pred             ecCCCEEEEEeCCCCCHHHHHH
Confidence            4588999999999999998765

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=85.22  E-value=0.34  Score=44.68  Aligned_cols=22  Identities=27%  Similarity=0.557  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        32 i~~Ge~~~l~G~nGsGKStLl~   53 (194)
T cd03213          32 AKPGELTAIMGPSGAGKSTLLN   53 (194)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999997664

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>KOG1533|consensus

Probab=85.21  E-value=0.49  Score=44.76  Aligned_cols=26  Identities=19%  Similarity=0.193  Sum_probs=18.2

Q ss_pred             EEEEcCCCCCcccchh---hhhhhhcCCC
Q psy6094          75 TVISGETGSGPPLHLD---FITLKRSETQ  100 (455)
Q Consensus        75 vii~~~TGSGKTtqlp---~ll~e~~~~v  100 (455)
                      .+|+||+||||||..-   -++..+|.++
T Consensus         5 qvVIGPPgSGKsTYc~g~~~fls~~gr~~   33 (290)
T KOG1533|consen    5 QVVIGPPGSGKSTYCNGMSQFLSAIGRPV   33 (290)
T ss_pred             eEEEcCCCCCccchhhhHHHHHHHhCCce
Confidence            4789999999998765   4444455443

>PRK14240 phosphate transporter ATP-binding protein; Provisional

Probab=85.20  E-value=0.35  Score=46.37  Aligned_cols=22  Identities=32%  Similarity=0.616  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (250)
T PRK14240         26 IEENQVTALIGPSGCGKSTFLR   47 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK14269 phosphate ABC transporter ATP-binding protein; Provisional

Probab=85.19  E-value=0.34  Score=46.38  Aligned_cols=22  Identities=32%  Similarity=0.616  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (246)
T PRK14269         25 IEQNKITALIGASGCGKSTFLR   46 (246)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK14259 phosphate ABC transporter ATP-binding protein; Provisional

Probab=85.17  E-value=0.35  Score=47.09  Aligned_cols=22  Identities=23%  Similarity=0.489  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|+.||||||.+-
T Consensus        36 i~~Ge~~~l~G~nGsGKSTLl~   57 (269)
T PRK14259         36 IPRGKVTALIGPSGCGKSTVLR   57 (269)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=85.17  E-value=0.35  Score=46.05  Aligned_cols=22  Identities=32%  Similarity=0.570  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~   45 (240)
T PRK09493         24 IDQGEVVVIIGPSGSGKSTLLR   45 (240)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK14737 gmk guanylate kinase; Provisional

Probab=85.15  E-value=0.41  Score=44.01  Aligned_cols=19  Identities=21%  Similarity=0.408  Sum_probs=15.8

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .+..+|++|++||||||.+
T Consensus         3 ~~~~ivl~GpsG~GK~tl~   21 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTII   21 (186)
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4678999999999999544

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=85.12  E-value=0.34  Score=46.68  Aligned_cols=22  Identities=18%  Similarity=0.424  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~I~G~NGsGKSTLl~   48 (251)
T PRK09544         27 LKPGKILTLLGPNGAGKSTLVR   48 (251)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999997764

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=85.11  E-value=0.34  Score=44.98  Aligned_cols=22  Identities=27%  Similarity=0.367  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        31 i~~G~~~~i~G~nGsGKSTLl~   52 (207)
T cd03369          31 VKAGEKIGIVGRTGAGKSTLIL   52 (207)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=85.09  E-value=0.36  Score=42.08  Aligned_cols=17  Identities=29%  Similarity=0.382  Sum_probs=14.2

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      +++|.|++||||||.+-
T Consensus         1 ~~~i~G~~G~GKT~l~~   17 (165)
T cd01120           1 LILVFGPTGSGKTTLAL   17 (165)
T ss_pred             CeeEeCCCCCCHHHHHH
Confidence            36899999999997654

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

>PRK14244 phosphate ABC transporter ATP-binding protein; Provisional

Probab=85.06  E-value=0.35  Score=46.43  Aligned_cols=22  Identities=23%  Similarity=0.486  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~I~G~nGsGKSTLl~   49 (251)
T PRK14244         28 IYKREVTAFIGPSGCGKSTFLR   49 (251)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997765

>PRK03695 vitamin B12-transporter ATPase; Provisional

Probab=85.05  E-value=0.34  Score=46.48  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.+.|+.||||||.+-
T Consensus        19 i~~Gei~~l~G~nGsGKSTLl~   40 (248)
T PRK03695         19 VRAGEILHLVGPNGAGKSTLLA   40 (248)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=85.04  E-value=0.35  Score=45.85  Aligned_cols=22  Identities=27%  Similarity=0.422  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~   45 (236)
T cd03253          24 IPAGKKVAIVGPSGSGKSTILR   45 (236)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK14274 phosphate ABC transporter ATP-binding protein; Provisional

Probab=85.03  E-value=0.35  Score=46.68  Aligned_cols=22  Identities=27%  Similarity=0.593  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        35 i~~Ge~~~l~G~nGsGKSTLl~   56 (259)
T PRK14274         35 IPENEVTAIIGPSGCGKSTFIK   56 (259)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=84.95  E-value=0.36  Score=44.45  Aligned_cols=17  Identities=35%  Similarity=0.503  Sum_probs=13.9

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      ++.|.|++||||||..-
T Consensus         1 iigi~G~~GsGKSTl~~   17 (198)
T cd02023           1 IIGIAGGSGSGKTTVAE   17 (198)
T ss_pred             CEEEECCCCCCHHHHHH
Confidence            36789999999996654

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional

Probab=84.94  E-value=0.36  Score=45.73  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~   43 (232)
T PRK10771         22 VERGERVAILGPSGAGKSTLLN   43 (232)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998764

>PRK14532 adenylate kinase; Provisional

Probab=84.93  E-value=0.42  Score=43.62  Aligned_cols=23  Identities=13%  Similarity=0.192  Sum_probs=17.7

Q ss_pred             eEEEEcCCCCCcccchhhhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      .+++.|++||||||+.-.|....
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~   24 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEER   24 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            37899999999998876554433

>PRK14256 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.91  E-value=0.37  Score=46.30  Aligned_cols=22  Identities=32%  Similarity=0.502  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~   48 (252)
T PRK14256         27 FPENSVTAIIGPSGCGKSTVLR   48 (252)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

>PRK14255 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.91  E-value=0.37  Score=46.27  Aligned_cols=22  Identities=32%  Similarity=0.533  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~   49 (252)
T PRK14255         28 FNQNEITALIGPSGCGKSTYLR   49 (252)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=84.91  E-value=0.37  Score=44.66  Aligned_cols=21  Identities=19%  Similarity=0.330  Sum_probs=18.0

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..++.++++|+.||||||.+-
T Consensus        27 ~~~~~~~l~G~Ng~GKStll~   47 (202)
T cd03243          27 GSGRLLLITGPNMGGKSTYLR   47 (202)
T ss_pred             cCCeEEEEECCCCCccHHHHH
Confidence            356789999999999998876

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional

Probab=84.88  E-value=0.37  Score=47.10  Aligned_cols=22  Identities=23%  Similarity=0.513  Sum_probs=19.5

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+++.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~   45 (272)
T PRK13547         24 IEPGRVTALLGRNGAGKSTLLK   45 (272)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5688999999999999998765

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=84.84  E-value=0.33  Score=43.74  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|+||.||||||.+-
T Consensus        26 v~~Ge~iaitGPSG~GKStllk   47 (223)
T COG4619          26 VRAGEFIAITGPSGCGKSTLLK   47 (223)
T ss_pred             ecCCceEEEeCCCCccHHHHHH
Confidence            4578889999999999997765

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

Probab=84.84  E-value=0.77  Score=42.84  Aligned_cols=26  Identities=15%  Similarity=0.242  Sum_probs=17.5

Q ss_pred             HHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          63 DAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        63 ~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      ..+.=+..++.++++.|+.|||||+.
T Consensus        13 rAL~iAAaG~h~lLl~GppGtGKTml   38 (206)
T PF01078_consen   13 RALEIAAAGGHHLLLIGPPGTGKTML   38 (206)
T ss_dssp             HHHHHHHHCC--EEEES-CCCTHHHH
T ss_pred             HHHHHHHcCCCCeEEECCCCCCHHHH
Confidence            34444555788999999999999955

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

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=84.82  E-value=0.35  Score=45.59  Aligned_cols=22  Identities=41%  Similarity=0.622  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLlk   51 (226)
T cd03234          30 VESGQVMAILGSSGSGKTTLLD   51 (226)
T ss_pred             EcCCeEEEEECCCCCCHHHHHH
Confidence            4578899999999999997765

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>PRK14267 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.82  E-value=0.37  Score=46.30  Aligned_cols=22  Identities=23%  Similarity=0.445  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~l~G~nGsGKSTLl~   48 (253)
T PRK14267         27 IPQNGVFALMGPSGCGKSTLLR   48 (253)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=84.81  E-value=0.38  Score=45.79  Aligned_cols=22  Identities=23%  Similarity=0.450  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        44 i~~Ge~~~i~G~NGsGKSTLl~   65 (236)
T cd03267          44 IEKGEIVGFIGPNGAGKTTTLK   65 (236)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998764

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>PRK14241 phosphate transporter ATP-binding protein; Provisional

Probab=84.80  E-value=0.37  Score=46.48  Aligned_cols=22  Identities=23%  Similarity=0.442  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~   48 (258)
T PRK14241         27 IEPRSVTAFIGPSGCGKSTVLR   48 (258)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=84.78  E-value=0.4  Score=42.11  Aligned_cols=18  Identities=22%  Similarity=0.399  Sum_probs=15.2

Q ss_pred             EEEEcCCCCCcccchhhh
Q psy6094          75 TVISGETGSGPPLHLDFI   92 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~l   92 (455)
                      +++.|++||||||.+-.|
T Consensus         4 imliG~~g~GKTTL~q~L   21 (143)
T PF10662_consen    4 IMLIGPSGSGKTTLAQAL   21 (143)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            789999999999877544

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=84.77  E-value=0.36  Score=46.35  Aligned_cols=22  Identities=27%  Similarity=0.557  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~   49 (255)
T PRK11300         28 VREQEIVSLIGPNGAGKTTVFN   49 (255)
T ss_pred             EcCCeEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=84.75  E-value=0.41  Score=39.75  Aligned_cols=16  Identities=25%  Similarity=0.517  Sum_probs=13.5

Q ss_pred             EEEEcCCCCCcccchh
Q psy6094          75 TVISGETGSGPPLHLD   90 (455)
Q Consensus        75 vii~~~TGSGKTtqlp   90 (455)
                      ++|.|+.|+||||.+-
T Consensus         2 I~V~G~~g~GKTsLi~   17 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIR   17 (119)
T ss_dssp             EEEECSTTSSHHHHHH
T ss_pred             EEEECcCCCCHHHHHH
Confidence            6899999999996554

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=84.75  E-value=0.33  Score=43.17  Aligned_cols=16  Identities=31%  Similarity=0.395  Sum_probs=13.2

Q ss_pred             EEEEcCCCCCcccchh
Q psy6094          75 TVISGETGSGPPLHLD   90 (455)
Q Consensus        75 vii~~~TGSGKTtqlp   90 (455)
                      +++.|++||||||..-
T Consensus         1 i~l~G~~GsGKSTla~   16 (163)
T TIGR01313         1 FVLMGVAGSGKSTIAS   16 (163)
T ss_pred             CEEECCCCCCHHHHHH
Confidence            4688999999997654

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

>PRK14261 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.74  E-value=0.36  Score=46.42  Aligned_cols=22  Identities=27%  Similarity=0.549  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        29 i~~Ge~~~i~G~nGsGKSTLl~   50 (253)
T PRK14261         29 IPKNRVTALIGPSGCGKSTLLR   50 (253)
T ss_pred             ECCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=84.73  E-value=0.38  Score=45.27  Aligned_cols=22  Identities=27%  Similarity=0.424  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (223)
T TIGR03740        23 VPKNSVYGLLGPNGAGKSTLLK   44 (223)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=84.73  E-value=0.73  Score=45.00  Aligned_cols=18  Identities=22%  Similarity=0.146  Sum_probs=16.2

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      +++++.|+|||||||.+-
T Consensus       112 ~~~~i~g~~g~GKttl~~  129 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLR  129 (270)
T ss_pred             eEEEEEcCCCCCHHHHHH
Confidence            588999999999998776

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK15056 manganese/iron transporter ATP-binding protein; Provisional

Probab=84.71  E-value=0.37  Score=46.99  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~   51 (272)
T PRK15056         30 VPGGSIAALVGVNGSGKSTLFK   51 (272)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998764

>smart00763 AAA_PrkA PrkA AAA domain

Probab=84.71  E-value=0.84  Score=46.24  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=16.3

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++.+++.||+||||||..-
T Consensus        78 r~il~L~GPPGsGKStla~   96 (361)
T smart00763       78 KQILYLLGPVGGGKSSLVE   96 (361)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5789999999999996654

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK08356 hypothetical protein; Provisional

Probab=84.69  E-value=0.42  Score=44.07  Aligned_cols=20  Identities=20%  Similarity=0.346  Sum_probs=16.6

Q ss_pred             CeEEEEcCCCCCcccchhhh
Q psy6094          73 QITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~l   92 (455)
                      .+++++|++||||||+.-+|
T Consensus         6 ~~i~~~G~~gsGK~t~a~~l   25 (195)
T PRK08356          6 MIVGVVGKIAAGKTTVAKFF   25 (195)
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            35788999999999887655

>cd03290 ABCC_SUR1_N The SUR domain 1

Probab=84.67  E-value=0.38  Score=45.03  Aligned_cols=22  Identities=32%  Similarity=0.502  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~   45 (218)
T cd03290          24 IPTGQLTMIVGQVGCGKSSLLL   45 (218)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999997765

The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=84.67  E-value=1  Score=43.50  Aligned_cols=18  Identities=17%  Similarity=0.278  Sum_probs=14.8

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      ...+++.|++||||||..
T Consensus        42 ~~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             cceEEEEcCCCCCHHHHH
Confidence            346899999999999554

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

>PRK08181 transposase; Validated

Probab=84.66  E-value=0.56  Score=45.75  Aligned_cols=23  Identities=13%  Similarity=0.193  Sum_probs=18.9

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -+..++++++.|++|+|||...-
T Consensus       102 ~~~~~~nlll~Gp~GtGKTHLa~  124 (269)
T PRK08181        102 WLAKGANLLLFGPPGGGKSHLAA  124 (269)
T ss_pred             HHhcCceEEEEecCCCcHHHHHH
Confidence            45678899999999999995543

>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=84.66  E-value=0.35  Score=47.57  Aligned_cols=22  Identities=32%  Similarity=0.623  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        34 i~~Ge~~~l~G~nGsGKSTLl~   55 (289)
T PRK13645         34 FKKNKVTCVIGTTGSGKSTMIQ   55 (289)
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK04296 thymidine kinase; Provisional

Probab=84.59  E-value=0.38  Score=44.32  Aligned_cols=18  Identities=28%  Similarity=0.449  Sum_probs=15.3

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      +...++.|++|+||||.+
T Consensus         2 g~i~litG~~GsGKTT~~   19 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTEL   19 (190)
T ss_pred             cEEEEEECCCCCHHHHHH
Confidence            567899999999999665

>PRK11614 livF leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=84.59  E-value=0.38  Score=45.69  Aligned_cols=22  Identities=23%  Similarity=0.501  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~   49 (237)
T PRK11614         28 INQGEIVTLIGANGAGKTTLLG   49 (237)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

>PRK06217 hypothetical protein; Validated

Probab=84.58  E-value=0.4  Score=43.72  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.4

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      -++|.|.+||||||+.-
T Consensus         3 ~I~i~G~~GsGKSTla~   19 (183)
T PRK06217          3 RIHITGASGSGTTTLGA   19 (183)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            38899999999997654

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=84.58  E-value=0.38  Score=46.71  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        42 i~~Ge~~~i~G~nGsGKSTLl~   63 (267)
T PRK14235         42 IPEKTVTAFIGPSGCGKSTFLR   63 (267)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK14528 adenylate kinase; Provisional

Probab=84.56  E-value=0.45  Score=43.63  Aligned_cols=21  Identities=14%  Similarity=0.344  Sum_probs=16.7

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +.++|.|++||||||+.-.+.
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la   22 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILC   22 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            358999999999998865443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=84.53  E-value=0.47  Score=44.43  Aligned_cols=20  Identities=30%  Similarity=0.534  Sum_probs=16.3

Q ss_pred             HcCCeEEEEcCCCCCcccch
Q psy6094          70 RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtql   89 (455)
                      ..+..+++.|++|||||+.+
T Consensus        36 ~~~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        36 KGDRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCCCeEEEECCCCCCHHHHH
Confidence            35678999999999999544

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

>PRK14245 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.52  E-value=0.38  Score=46.17  Aligned_cols=22  Identities=18%  Similarity=0.468  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (250)
T PRK14245         26 IEEKSVVAFIGPSGCGKSTFLR   47 (250)
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=84.51  E-value=0.35  Score=45.14  Aligned_cols=22  Identities=32%  Similarity=0.584  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        21 i~~Ge~~~i~G~nGsGKSTLl~   42 (213)
T TIGR01277        21 VADGEIVAIMGPSGAGKSTLLN   42 (213)
T ss_pred             EeCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999997764

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>PRK13649 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=84.48  E-value=0.38  Score=47.00  Aligned_cols=22  Identities=27%  Similarity=0.490  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~   51 (280)
T PRK13649         30 IEDGSYTAFIGHTGSGKSTIMQ   51 (280)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>PRK14253 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.42  E-value=0.4  Score=45.90  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+++.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~   47 (249)
T PRK14253         26 IPARQVTALIGPSGCGKSTLLR   47 (249)
T ss_pred             ecCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PRK11231 fecE iron-dicitrate transporter ATP-binding subunit; Provisional

Probab=84.42  E-value=0.39  Score=46.25  Aligned_cols=22  Identities=27%  Similarity=0.484  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~   46 (255)
T PRK11231         25 LPTGKITALIGPNGCGKSTLLK   46 (255)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=84.39  E-value=0.39  Score=45.37  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        45 i~~Ge~~~i~G~nGsGKSTLl~   66 (224)
T cd03220          45 VPRGERIGLIGRNGAGKSTLLR   66 (224)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=84.37  E-value=0.43  Score=41.22  Aligned_cols=21  Identities=29%  Similarity=0.464  Sum_probs=16.2

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +++|+|++||||||..-.|..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            478999999999976654444

>PRK11701 phnK phosphonate C-P lyase system protein PhnK; Provisional

Probab=84.36  E-value=0.38  Score=46.38  Aligned_cols=22  Identities=32%  Similarity=0.490  Sum_probs=19.5

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        29 i~~Ge~~~i~G~nGsGKSTLl~   50 (258)
T PRK11701         29 LYPGEVLGIVGESGSGKTTLLN   50 (258)
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

>TIGR03771 anch_rpt_ABC anchored repeat-type ABC transporter, ATP-binding subunit

Probab=84.35  E-value=0.43  Score=45.01  Aligned_cols=22  Identities=18%  Similarity=0.342  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus         3 i~~Ge~~~l~G~nGsGKSTLl~   24 (223)
T TIGR03771         3 ADKGELLGLLGPNGAGKTTLLR   24 (223)
T ss_pred             cCCCcEEEEECCCCCCHHHHHH
Confidence            5678999999999999997764

This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=84.35  E-value=0.39  Score=45.76  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLl~   47 (241)
T PRK10895         26 VNSGEIVGLLGPNGAGKTTTFY   47 (241)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

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

Probab=84.34  E-value=0.45  Score=47.01  Aligned_cols=16  Identities=31%  Similarity=0.517  Sum_probs=13.6

Q ss_pred             cCCeEEEEcCCCCCcc
Q psy6094          71 NNQITVISGETGSGPP   86 (455)
Q Consensus        71 ~~~~vii~~~TGSGKT   86 (455)
                      +..++++.||||||||
T Consensus        96 ~KSNILLiGPTGsGKT  111 (408)
T COG1219          96 SKSNILLIGPTGSGKT  111 (408)
T ss_pred             eeccEEEECCCCCcHH
Confidence            3446999999999999

>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional

Probab=84.32  E-value=0.39  Score=46.71  Aligned_cols=22  Identities=36%  Similarity=0.499  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (269)
T PRK11831         30 VPRGKITAIMGPSGIGKTTLLR   51 (269)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=84.30  E-value=0.4  Score=45.36  Aligned_cols=22  Identities=18%  Similarity=0.439  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (234)
T cd03251          25 IPAGETVALVGPSGSGKSTLVN   46 (234)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=84.29  E-value=2  Score=46.02  Aligned_cols=49  Identities=20%  Similarity=0.399  Sum_probs=33.7

Q ss_pred             HhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh----hhhh
Q psy6094          40 KLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD----FITL   94 (455)
Q Consensus        40 ~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp----~ll~   94 (455)
                      ...+.+.++..+.     +-+-|++||. -..|..+||+|..||||||..-    |++.
T Consensus       200 k~ss~~mrdIV~T-----IQkEQneIIR-~ek~~ilVVQGaAGSGKTtiALHRvAyLlY  252 (747)
T COG3973         200 KNSSAKMRDIVET-----IQKEQNEIIR-FEKNKILVVQGAAGSGKTTIALHRVAYLLY  252 (747)
T ss_pred             hccchhHHHHHHH-----hhHhHHHHHh-ccCCCeEEEecCCCCCchhHHHHHHHHHHh
Confidence            3455666666554     2234777776 3567789999999999997633    7765

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=84.29  E-value=1.2  Score=49.38  Aligned_cols=37  Identities=22%  Similarity=0.270  Sum_probs=30.4

Q ss_pred             HHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          52 ARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        52 ~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      .++.|-+++++-+++.++.-++..|+..+||+|||..
T Consensus        63 ~~R~lglrpydVQlig~l~l~~G~Iaem~TGeGKTLt   99 (762)
T TIGR03714        63 DKRVLGMFPYDVQVLGAIVLHQGNIAEMKTGEGKTLT   99 (762)
T ss_pred             HHhhcCCCccHHHHHHHHHhcCCceeEecCCcchHHH
Confidence            3667777888888888887777789999999999943

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.

>PRK14238 phosphate transporter ATP-binding protein; Provisional

Probab=84.29  E-value=0.39  Score=46.79  Aligned_cols=22  Identities=27%  Similarity=0.584  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        47 i~~Ge~~~I~G~nGsGKSTLl~   68 (271)
T PRK14238         47 IHENEVTAIIGPSGCGKSTYIK   68 (271)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4688999999999999998765

>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional

Probab=84.28  E-value=0.4  Score=46.37  Aligned_cols=22  Identities=23%  Similarity=0.510  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~   48 (262)
T PRK09984         27 IHHGEMVALLGPSGSGKSTLLR   48 (262)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK10253 iron-enterobactin transporter ATP-binding protein; Provisional

Probab=84.25  E-value=0.39  Score=46.58  Aligned_cols=22  Identities=27%  Similarity=0.486  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (265)
T PRK10253         30 IPDGHFTAIIGPNGCGKSTLLR   51 (265)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>PRK13975 thymidylate kinase; Provisional

Probab=84.23  E-value=0.47  Score=43.48  Aligned_cols=24  Identities=29%  Similarity=0.475  Sum_probs=19.0

Q ss_pred             CCeEEEEcCCCCCcccchhhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      +..+++.|..||||||+.-.|.+.
T Consensus         2 ~~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          2 NKFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999987754443

>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules

Probab=84.16  E-value=0.41  Score=45.06  Aligned_cols=22  Identities=23%  Similarity=0.487  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        37 i~~Ge~~~i~G~nGsGKSTLl~   58 (226)
T cd03248          37 LHPGEVTALVGPSGSGKSTVVA   58 (226)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=84.15  E-value=0.37  Score=44.88  Aligned_cols=20  Identities=15%  Similarity=0.272  Sum_probs=17.0

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+ .+.|.|+.||||||.+-
T Consensus        24 ~~g-~~~i~G~nGsGKSTLl~   43 (211)
T cd03264          24 GPG-MYGLLGPNGAGKTTLMR   43 (211)
T ss_pred             cCC-cEEEECCCCCCHHHHHH
Confidence            456 89999999999998765

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=84.13  E-value=0.4  Score=46.97  Aligned_cols=22  Identities=32%  Similarity=0.397  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        27 I~~Ge~~~IvG~nGsGKSTLl~   48 (275)
T cd03289          27 ISPGQRVGLLGRTGSGKSTLLS   48 (275)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5688999999999999998765

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>PRK14268 phosphate ABC transporter ATP-binding protein; Provisional

Probab=84.13  E-value=0.41  Score=46.17  Aligned_cols=22  Identities=23%  Similarity=0.539  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        35 i~~Ge~~~i~G~nGsGKSTLl~   56 (258)
T PRK14268         35 IPKNSVTALIGPSGCGKSTFIR   56 (258)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>CHL00131 ycf16 sulfate ABC transporter protein; Validated

Probab=84.12  E-value=0.41  Score=45.86  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (252)
T CHL00131         30 INKGEIHAIMGPNGSGKSTLSK   51 (252)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PRK07667 uridine kinase; Provisional

Probab=84.09  E-value=0.78  Score=42.29  Aligned_cols=16  Identities=31%  Similarity=0.353  Sum_probs=13.5

Q ss_pred             eEEEEcCCCCCcccch
Q psy6094          74 ITVISGETGSGPPLHL   89 (455)
Q Consensus        74 ~vii~~~TGSGKTtql   89 (455)
                      +|-|.|.+||||||..
T Consensus        19 iIgI~G~~gsGKStla   34 (193)
T PRK07667         19 ILGIDGLSRSGKTTFV   34 (193)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            6678999999999654

>PRK09087 hypothetical protein; Validated

Probab=84.02  E-value=0.77  Score=43.55  Aligned_cols=19  Identities=26%  Similarity=0.485  Sum_probs=16.0

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+++.|++|||||+.+-
T Consensus        44 ~~~l~l~G~~GsGKThLl~   62 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLAS   62 (226)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5569999999999996654

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=84.00  E-value=0.44  Score=50.30  Aligned_cols=20  Identities=20%  Similarity=0.321  Sum_probs=17.5

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++++.+.|+||+||||.+.
T Consensus       255 ~g~Vi~LvGpnGvGKTTTia  274 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTA  274 (484)
T ss_pred             CCcEEEEECCCCccHHHHHH
Confidence            46789999999999998876

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=84.00  E-value=0.41  Score=46.40  Aligned_cols=22  Identities=27%  Similarity=0.427  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        34 i~~Ge~~~i~G~nGsGKSTLl~   55 (265)
T PRK10575         34 FPAGKVTGLIGHNGSGKSTLLK   55 (265)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998764

>PRK14265 phosphate ABC transporter ATP-binding protein; Provisional

Probab=83.98  E-value=0.42  Score=46.66  Aligned_cols=22  Identities=23%  Similarity=0.427  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        43 i~~Ge~~~IiG~nGsGKSTLl~   64 (274)
T PRK14265         43 IPAKKIIAFIGPSGCGKSTLLR   64 (274)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999998765

>PRK14251 phosphate ABC transporter ATP-binding protein; Provisional

Probab=83.98  E-value=0.42  Score=45.79  Aligned_cols=22  Identities=23%  Similarity=0.505  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~   48 (251)
T PRK14251         27 FEEKELTALIGPSGCGKSTFLR   48 (251)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999997764

>PRK13651 cobalt transporter ATP-binding subunit; Provisional

Probab=83.97  E-value=0.39  Score=47.76  Aligned_cols=22  Identities=27%  Similarity=0.587  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|++||||||.+-
T Consensus        30 i~~Ge~v~iiG~nGsGKSTLl~   51 (305)
T PRK13651         30 INQGEFIAIIGQTGSGKTTFIE   51 (305)
T ss_pred             EeCCCEEEEECCCCCcHHHHHH
Confidence            4578899999999999998764

>PRK15112 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional

Probab=83.96  E-value=0.43  Score=46.34  Aligned_cols=22  Identities=36%  Similarity=0.499  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        36 i~~Ge~~~i~G~NGsGKSTLl~   57 (267)
T PRK15112         36 LREGQTLAIIGENGSGKSTLAK   57 (267)
T ss_pred             ecCCCEEEEEcCCCCCHHHHHH
Confidence            4688999999999999998765

>TIGR02769 nickel_nikE nickel import ATP-binding protein NikE

Probab=83.91  E-value=0.42  Score=46.37  Aligned_cols=22  Identities=14%  Similarity=0.308  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        34 i~~Ge~~~i~G~nGsGKSTLl~   55 (265)
T TIGR02769        34 IEEGETVGLLGRSGCGKSTLAR   55 (265)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase.

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=83.88  E-value=0.42  Score=45.51  Aligned_cols=22  Identities=32%  Similarity=0.573  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~   46 (242)
T TIGR03411        25 VDPGELRVIIGPNGAGKTTMMD   46 (242)
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=83.87  E-value=0.41  Score=46.85  Aligned_cols=22  Identities=27%  Similarity=0.376  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+++.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGaGKSTLl~   51 (279)
T PRK13635         30 VYEGEWVAIVGHNGSGKSTLAK   51 (279)
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            4578999999999999998765

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=83.85  E-value=0.4  Score=46.93  Aligned_cols=22  Identities=27%  Similarity=0.450  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~   51 (279)
T PRK13650         30 VKQGEWLSIIGHNGSGKSTTVR   51 (279)
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998765

>cd04163 Era Era subfamily

Probab=83.85  E-value=0.5  Score=40.98  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.4

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ..+++.|++|+||||.+-
T Consensus         4 ~~i~~~G~~g~GKttl~~   21 (168)
T cd04163           4 GFVAIVGRPNVGKSTLLN   21 (168)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            358899999999998775

Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.

>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=83.84  E-value=0.4  Score=47.19  Aligned_cols=22  Identities=36%  Similarity=0.558  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        29 i~~Ge~v~i~G~nGsGKSTLl~   50 (288)
T PRK13643         29 VKKGSYTALIGHTGSGKSTLLQ   50 (288)
T ss_pred             EcCCCEEEEECCCCChHHHHHH
Confidence            4578999999999999997764

>TIGR00968 3a0106s01 sulfate ABC transporter, ATP-binding protein

Probab=83.83  E-value=0.43  Score=45.39  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~   44 (237)
T TIGR00968        23 VPTGSLVALLGPSGSGKSTLLR   44 (237)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            5688999999999999997764

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=83.83  E-value=0.43  Score=45.98  Aligned_cols=22  Identities=27%  Similarity=0.469  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~   49 (257)
T PRK10619         28 ANAGDVISIIGSSGSGKSTFLR   49 (257)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998775

>PRK14257 phosphate ABC transporter ATP-binding protein; Provisional

Probab=83.82  E-value=0.42  Score=48.09  Aligned_cols=69  Identities=14%  Similarity=0.170  Sum_probs=39.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCCCCeEEEee---cCCCChhhHhhh---hcCCCCCceEEEEeCCCCccCCCCCCeeEEEeC
Q psy6094         194 PGWDTINSLHRSMCQSSFFNSSRFQIIPL---HSMLPTVSQKSI---FNTPPEGVRKIVLATNIAETSITIDDIVYVVDC  267 (455)
Q Consensus       194 p~~~ei~~l~~~L~~~~~~~~~~~~v~~l---hs~l~~~~r~~v---~~~~~~g~~kVivaTniae~gitI~~V~~VID~  267 (455)
                      .|...--.+++.|....       .++.+   -++|+...+..+   +.....+ ..||++|.-.+.-..+-|-.+|++-
T Consensus       228 gGqkqRl~LARAl~~~p-------~IlLLDEPts~LD~~~~~~i~~~i~~l~~~-~Tii~iTH~l~~i~~~~Driivl~~  299 (329)
T PRK14257        228 GGQQQRLCIARAIALEP-------EVLLMDEPTSALDPIATAKIEELILELKKK-YSIIIVTHSMAQAQRISDETVFFYQ  299 (329)
T ss_pred             HHHHHHHHHHHHHHhCC-------CEEEEeCCcccCCHHHHHHHHHHHHHHhcC-CEEEEEeCCHHHHHHhCCEEEEEEC
Confidence            34444444566665543       23323   366666655443   3333344 6788888777766666677788876


Q ss_pred             CCC
Q psy6094         268 GKT  270 (455)
Q Consensus       268 g~~  270 (455)
                      |..
T Consensus       300 G~i  302 (329)
T PRK14257        300 GWI  302 (329)
T ss_pred             CEE
Confidence            653

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=83.79  E-value=0.44  Score=43.26  Aligned_cols=18  Identities=22%  Similarity=0.366  Sum_probs=15.6

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      .++.|+|+.||||||.+-
T Consensus         7 ~ii~ivG~sgsGKTTLi~   24 (173)
T PRK10751          7 PLLAIAAWSGTGKTTLLK   24 (173)
T ss_pred             eEEEEECCCCChHHHHHH
Confidence            368899999999998876

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=83.79  E-value=0.44  Score=44.12  Aligned_cols=22  Identities=23%  Similarity=0.395  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~   44 (201)
T cd03231          23 LAAGEALQVTGPNGSGKTTLLR   44 (201)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4678999999999999997765

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=83.73  E-value=0.43  Score=44.69  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~   48 (221)
T cd03244          27 IKPGEKVGIVGRTGSGKSSLLL   48 (221)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK13633 cobalt transporter ATP-binding subunit; Provisional

Probab=83.69  E-value=0.44  Score=46.64  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        33 i~~Ge~~~l~G~nGsGKSTLl~   54 (280)
T PRK13633         33 VKKGEFLVILGRNGSGKSTIAK   54 (280)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998765

>PRK03839 putative kinase; Provisional

Probab=83.69  E-value=0.49  Score=42.86  Aligned_cols=21  Identities=24%  Similarity=0.398  Sum_probs=16.5

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+++.|.+||||||+...+..
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~   22 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAE   22 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999987654443

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=83.68  E-value=0.87  Score=50.97  Aligned_cols=35  Identities=20%  Similarity=0.314  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHHHHHHc-CCeEEEEcCCCCCcccchh
Q psy6094          56 LPSYQMRDAVLDMVRN-NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        56 lP~~~~q~~il~~i~~-~~~vii~~~TGSGKTtqlp   90 (455)
                      .....-|.+.+..+.. +++++|+|.+|+||||.+-
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~  386 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLK  386 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHH
Confidence            4556778888888776 6899999999999998877

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

>PRK14249 phosphate ABC transporter ATP-binding protein; Provisional

Probab=83.65  E-value=0.43  Score=45.77  Aligned_cols=22  Identities=36%  Similarity=0.502  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|+.||||||.+-
T Consensus        27 i~~G~~~~i~G~nGsGKSTLl~   48 (251)
T PRK14249         27 FPERQITAIIGPSGCGKSTLLR   48 (251)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4588999999999999998765

>PRK01184 hypothetical protein; Provisional

Probab=83.65  E-value=0.5  Score=42.96  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=16.8

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      +++++|+.||||||+ ..++.+.|
T Consensus         3 ~i~l~G~~GsGKsT~-a~~~~~~g   25 (184)
T PRK01184          3 IIGVVGMPGSGKGEF-SKIAREMG   25 (184)
T ss_pred             EEEEECCCCCCHHHH-HHHHHHcC
Confidence            688999999999985 33444444

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=83.64  E-value=0.47  Score=39.46  Aligned_cols=19  Identities=21%  Similarity=0.352  Sum_probs=15.2

Q ss_pred             EEEEcCCCCCcccchhhhh
Q psy6094          75 TVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll   93 (455)
                      +++.|.||+||||.+-.++
T Consensus         2 V~iiG~~~~GKSTlin~l~   20 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALT   20 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6889999999997765443

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	455
3kx2_B	767	Crystal Structure Of Prp43p In Complex With Adp Len		2e-15
2xau_A	773	Crystal Structure Of The Prp43p Deah-Box Rna Helica		2e-15

>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp Length = 767

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/126 (40%), Positives = 68/126 (53%), Gaps = 10/126 (7%)
Query: 189 ILVFLPGWDTINSLHRSMCQSS-----FFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-- 241
           IL+FL G D I    R +                 + PL+  LP   Q+ IF   PE   
Sbjct: 306 ILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHN 365
Query: 242 ---VRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRR 298
               RK+V++TNIAETS+TID IVYVVD G +K   ++ +  + +L    IS A+A+QR 
Sbjct: 366 GRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRA 425
Query: 299 GRAGRT 304
           GRAGRT
Sbjct: 426 GRAGRT 431

>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In Complex With Adp Length = 773

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/126 (40%), Positives = 68/126 (53%), Gaps = 10/126 (7%)
Query: 189 ILVFLPGWDTINSLHRSMCQSS-----FFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-- 241
           IL+FL G D I    R +                 + PL+  LP   Q+ IF   PE   
Sbjct: 306 ILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHN 365
Query: 242 ---VRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRR 298
               RK+V++TNIAETS+TID IVYVVD G +K   ++ +  + +L    IS A+A+QR 
Sbjct: 366 GRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRA 425
Query: 299 GRAGRT 304
           GRAGRT
Sbjct: 426 GRAGRT 431

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	455
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	1e-34
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	6e-08
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	1e-28
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	2e-28
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	6e-28
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	7e-28
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	1e-27
1yks_A	440	Genome polyprotein [contains: flavivirin protease	2e-27
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	2e-25
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	1e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-11

>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* Length = 773

 Score =  136 bits (344), Expect = 1e-34
 Identities = 51/126 (40%), Positives = 68/126 (53%), Gaps = 10/126 (7%)

Query: 189 ILVFLPGWDTINSLHRSMCQ-----SSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV- 242
           IL+FL G D I    R +                 + PL+  LP   Q+ IF   PE   
Sbjct: 306 ILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHN 365

Query: 243 ----RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRR 298
               RK+V++TNIAETS+TID IVYVVD G +K   ++ +  + +L    IS A+A+QR 
Sbjct: 366 GRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRA 425

Query: 299 GRAGRT 304
           GRAGRT
Sbjct: 426 GRAGRT 431

>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* Length = 773

 Score = 54.2 bits (131), Expect = 6e-08
 Identities = 19/42 (45%), Positives = 29/42 (69%)

Query: 43  SRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSG 84
           + +Y ++L+ R++LP +  RD  L + +NNQI V  GETGSG
Sbjct: 80  TPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSG 121

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score =  116 bits (291), Expect = 1e-28
 Identities = 20/116 (17%), Positives = 41/116 (35%), Gaps = 12/116 (10%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
            + F+        +   +        +  +++ L+        +S +          V+ 
Sbjct: 174 TVWFVHSIKQGAEIGTCL------QKAGKKVLYLNRKT----FESEYPKCKSEKWDFVIT 223

Query: 249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           T+I+E          V+D     +    +   ++   P  I+ A+A QRRGR GR 
Sbjct: 224 TDISEMGANF-KADRVIDPR-KTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRN 277

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451

 Score =  115 bits (290), Expect = 2e-28
 Identities = 23/119 (19%), Positives = 41/119 (34%), Gaps = 13/119 (10%)

Query: 188 PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL 247
             + F+P     N +   +        S  ++I L          + +          V+
Sbjct: 190 KTVWFVPSIKAGNDIANCL------RKSGKRVIQLSRKT----FDTEYPKTKLTDWDFVV 239

Query: 248 ATNIAETSITIDDIVYVVDCG--KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
            T+I+E          V+D       +   D  + +    P  ++ A+A QRRGR GR 
Sbjct: 240 TTDISEMGANF-RAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRN 297

>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 Length = 618

 Score =  115 bits (290), Expect = 6e-28
 Identities = 23/118 (19%), Positives = 41/118 (34%), Gaps = 13/118 (11%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
            + F+P     N +   +        S  ++I L          + +          V+ 
Sbjct: 358 TVWFVPSIKAGNDIANCL------RKSGKRVIQLSRKT----FDTEYPKTKLTDWDFVVT 407

Query: 249 TNIAETSITIDDIVYVVDCG--KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           T+I+E          V+D       +   D  + +    P  ++ A+A QRRGR GR 
Sbjct: 408 TDISEMGANF-RAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRN 464

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673

 Score =  115 bits (290), Expect = 7e-28
 Identities = 23/118 (19%), Positives = 43/118 (36%), Gaps = 13/118 (11%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
            + F+      N + + +        +  ++I L+         + +     G    V+ 
Sbjct: 413 TVWFVASVKMSNEIAQCL------QRAGKRVIQLNRKS----YDTEYPKCKNGDWDFVIT 462

Query: 249 TNIAETSITIDDIVYVVDCG--KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           T+I+E          V+DC          + +  +    P  I+ A+A QRRGR GR 
Sbjct: 463 TDISEMGANF-GASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRN 519

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score =  113 bits (285), Expect = 1e-27
 Identities = 24/118 (20%), Positives = 43/118 (36%), Gaps = 13/118 (11%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
            + F+      N +   +        +  ++I L+         + +     G    V+ 
Sbjct: 193 TVWFVASVKMGNEIAMCL------QRAGKKVIQLNRKS----YDTEYPKCKNGDWDFVIT 242

Query: 249 TNIAETSITIDDIVYVVDCGK--TKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRT 304
           T+I+E          V+DC K        + +  +    P  I+ A+A QRRGR GR 
Sbjct: 243 TDISEMGANF-GASRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRN 299

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440

 Score =  113 bits (283), Expect = 2e-27
 Identities = 28/117 (23%), Positives = 46/117 (39%), Gaps = 12/117 (10%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
              FLP     N +  S+ ++         ++ L+         +I     +     +LA
Sbjct: 180 TAWFLPSIRAANVMAASLRKAGK------SVVVLNRKTFEREYPTI----KQKKPDFILA 229

Query: 249 TNIAETSITIDDIVYVVDCGKTKMSNFDVKDN-IATLKPEWISLANAKQRRGRAGRT 304
           T+IAE    +  +  V+DC          +   +A   P  IS ++A QRRGR GR 
Sbjct: 230 TDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRN 285

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score =  108 bits (271), Expect = 2e-25
 Identities = 24/140 (17%), Positives = 41/140 (29%), Gaps = 17/140 (12%)

Query: 190 LVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT 249
           L+F       + L   +      +      +  +  L            P     +V+AT
Sbjct: 400 LIFCHSKKKCDELAAKL------SGLGINAVAYYRGLDVSVI-------PTIGDVVVVAT 446

Query: 250 NIAETSITIDDIVYVVDCGKTKMSNFDVKDN---IATLKPEWISLANAKQRRGRAGRTLK 306
           +   T  T  D   V+DC        D   +               +  QRRGR GR  +
Sbjct: 447 DALMTGYTG-DFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRR 505

Query: 307 RSETQQYPNDVLNMLKDPEL 326
                  P +  + + D  +
Sbjct: 506 GIYRFVTPGERPSGMFDSSV 525

>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} Length = 235

 Score = 75.0 bits (185), Expect = 1e-15
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 4  PHSPKGLTHSVTSWETRQKLLNDPVLDAAFKKEMIRKLQ-SRRYQEMLEARKKLPSYQMR 62
          P S      S    E          +    K E++ +L+     Q +L+ R+ LP  +  
Sbjct: 7  PQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFE 66

Query: 63 DAVLDMVRNNQITVISGETGSG 84
            +L+ +  N + +I G TG G
Sbjct: 67 SEILEAISQNSVVIIRGATGCG 88

>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 = 66.0 bits (160), Expect = 1e-11
 Identities = 83/505 (16%), Positives = 158/505 (31%), Gaps = 175/505 (34%)

Query: 18  ETRQKLLNDPVLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVI 77
           E R +L ND         ++  K    R Q  L+ R+ L   ++R          +  +I
Sbjct: 114 EQRDRLYNDN--------QVFAKYNVSRLQPYLKLRQAL--LELRP--------AKNVLI 155

Query: 78  SGETGSGPPLHLDFITLKRSETQQYPNDVLNMLKDPELEGVNNDVIF------------- 124
            G  GSG          K           L++    +++   +  IF             
Sbjct: 156 DGVLGSG----------KTWV-------ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198

Query: 125 -SLLQHICTTQRPGAILVYCTYTFMGVS-PMKVFFCKNVLQRLMKGVGANSPKRWVKLLR 182
             +LQ +     P     + + +    +  +++   +  L+RL+K               
Sbjct: 199 LEMLQKLLYQIDPN----WTSRSDHSSNIKLRIHSIQAELRRLLK---------SKPYEN 245

Query: 183 SMLVVPIL--VFLPGWD--TINSLHRSMCQ----------SSFFNSSRFQIIPLHSMLPT 228
            +L   +L  V     +    N+ + S C+          + F +++    I L     T
Sbjct: 246 CLL---VLLNV----QNAKAWNAFNLS-CKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297

Query: 229 VSQ---KSIF----NTPPEGVRKIVLATN------IAETSITIDDIVYVVDCGKTKMSNF 275
           ++    KS+     +  P+ + + VL TN      IAE+                     
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES--------------------- 336

Query: 276 DVKDNIATLKPEWISLANAKQRRGRAG--RTLKRSETQQY-------------PNDVLNM 320
            ++D +AT    W  +   K           L+ +E ++              P  +L++
Sbjct: 337 -IRDGLATWDN-WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394

Query: 321 L------KDPELEGVNNDVIFSLLQHICTTQRPGAILVFLPG--------WDTINSLHRS 366
           +       D  +  VN    +SL++     ++P    + +P          +   +LHRS
Sbjct: 395 IWFDVIKSDVMVV-VNKLHKYSLVE-----KQPKESTISIPSIYLELKVKLENEYALHRS 448

Query: 367 MCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFE------CKPSTAKIIKELRAR-LDM 419
           +           Y      +    I    D   +             + +   R   LD 
Sbjct: 449 IVDH--------YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF 500

Query: 420 -LLAHKLSHPGTTAWGDPNEGNILH 443
             L  K+ H   TAW     G+IL+
Sbjct: 501 RFLEQKIRHDS-TAWNAS--GSILN 522

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	455
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.97
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.97
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.96
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.96
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.96
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.96
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.96
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.96
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.95
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.95
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.95
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.95
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.95
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.94
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.94
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.94
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.94
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.94
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.94
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.94
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.93
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.93
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.93
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.93
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.92
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.92
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.91
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.91
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.91
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.91
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.9
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.89
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.88
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.88
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.87
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.86
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.86
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.86
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.85
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.84
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.83
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.81
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.81
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.8
3i4u_A	270	ATP-dependent RNA helicase DHX8; splicing, ATP-bin	99.79
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.79
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.79
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.78
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.77
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.76
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.76
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.76
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.61
3h1t_A	590	Type I site-specific restriction-modification syst	99.67
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.67
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.66
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.6
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.47
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.41
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.24
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.23
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	98.93
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.91
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	98.8
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.78
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	98.78
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	98.78
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	98.77
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	98.76
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	98.75
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	98.74
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.74
3bor_A	237	Human initiation factor 4A-II; translation initiat	98.71
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	98.7
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	98.68
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	98.68
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.62
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	98.36
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.92
3b6e_A	216	Interferon-induced helicase C domain-containing P;	97.78
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	96.31
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	95.34
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	95.27
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.5
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	94.08
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	93.82
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	93.54
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	93.38
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	93.3
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	93.3
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.95
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	92.89
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.87
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	92.76
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.71
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	92.71
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	92.67
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	92.39
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	92.27
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	92.2
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	92.13
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	92.07
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	91.92
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	91.81
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	91.78
3co5_A	143	Putative two-component system transcriptional RES	91.67
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	91.64
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	91.5
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	91.39
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	91.2
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	91.0
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	90.98
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	90.96
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	90.83
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	90.79
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	90.76
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	90.76
2ewv_A	372	Twitching motility protein PILT; pilus retraction	90.69
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	90.65
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	90.63
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	90.62
1p9r_A	418	General secretion pathway protein E; bacterial typ	90.56
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	90.2
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	90.17
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	90.15
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	90.03
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.98
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	89.97
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	89.86
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	89.85
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.8
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	89.67
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	89.48
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	89.42
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	89.19
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	89.18
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	88.99
1sgw_A	214	Putative ABC transporter; structural genomics, P p	88.98
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	88.9
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	88.89
2chg_A	226	Replication factor C small subunit; DNA-binding pr	88.88
1g6h_A	257	High-affinity branched-chain amino acid transport	88.87
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	88.86
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	88.86
1b0u_A	262	Histidine permease; ABC transporter, transport pro	88.81
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	88.81
2ghi_A	260	Transport protein; multidrug resistance protein, M	88.69
1ji0_A	240	ABC transporter; ATP binding protein, structural g	88.67
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	88.62
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	88.59
3bos_A	242	Putative DNA replication factor; P-loop containing	88.56
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	88.53
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	88.47
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	88.47
4a74_A	231	DNA repair and recombination protein RADA; hydrola	88.43
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	88.43
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	88.42
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	88.38
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	88.34
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	88.32
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	88.29
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	88.27
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	88.2
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	88.12
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.1
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	88.05
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	88.0
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	88.0
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	87.95
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	87.87
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	87.71
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	87.69
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	87.69
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	87.68
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	87.58
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	87.57
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	87.52
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	87.48
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	87.46
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	87.46
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	87.35
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	87.22
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	87.1
2vli_A	183	Antibiotic resistance protein; transferase, tunica	87.05
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	86.95
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	86.92
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	86.89
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	86.89
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	86.89
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	86.84
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	86.82
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	86.78
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	86.73
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	86.64
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	86.59
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	86.5
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	86.5
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	86.48
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	86.45
3kta_A	182	Chromosome segregation protein SMC; structural mai	86.39
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	86.35
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	86.34
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	86.32
2qgz_A	308	Helicase loader, putative primosome component; str	86.28
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	86.28
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	86.25
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	86.09
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	85.97
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	85.97
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	85.88
2cvh_A	220	DNA repair and recombination protein RADB; filamen	85.87
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	85.83
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	85.81
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	85.73
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	85.73
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	85.72
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	85.69
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	85.69
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	85.68
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	85.66
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	85.59
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	85.46
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	85.35
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	85.3
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	85.14
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	85.14
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	85.11
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	85.09
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	85.07
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	85.06
2r44_A	331	Uncharacterized protein; putative ATPase, structur	85.05
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	85.03
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	85.03
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	84.96
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	84.94
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	84.92
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	84.88
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	84.79
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	84.61
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	84.59
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	84.55
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	84.55
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	84.5
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	84.5
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	84.49
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	84.48
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	84.46
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	84.43
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	84.42
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	84.35
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	84.32
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	84.22
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	84.2
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	84.16
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	84.09
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	83.97
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	83.88
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	83.86
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	83.84
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	83.81
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	83.75
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	83.68
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	83.65
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	83.6
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	83.39
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	83.26
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	83.22
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	83.19
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	83.15
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	83.12
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	83.12
2og2_A	359	Putative signal recognition particle receptor; nuc	83.1
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	83.0
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	82.98
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	82.97
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	82.92
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	82.87
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	82.86
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	82.83
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	82.71
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	82.68
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	82.48
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	82.45
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	82.44
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	82.42
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	82.42
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	82.35
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	82.33
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	82.32
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	82.29
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	82.2
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	82.14
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	82.07
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	82.06
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	81.95
1via_A	175	Shikimate kinase; structural genomics, transferase	81.91
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	81.66
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	81.65
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	81.62
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	81.57
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	81.44
3pvs_A	447	Replication-associated recombination protein A; ma	81.4
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	81.39
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	81.36
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	81.26
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	81.19
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	81.11
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	80.94
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	80.86
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	80.85
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	80.84
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	80.84
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	80.8
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	80.55
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	80.5
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	80.48
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	80.42
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	80.32
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	80.32
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	80.31
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	80.25
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	80.04
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	80.04

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=100.00  E-value=1e-65  Score=565.73  Aligned_cols=402  Identities=26%  Similarity=0.353  Sum_probs=338.2

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|.+...++++.++++.|+.+|++.+|++++.++.++++++|+|+|||||||++| +++.                    
T Consensus        73 ~f~~~~l~~~~~~~l~~r~~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~L  152 (773)
T 2xau_A           73 PFTGREFTPKYVDILKIRRELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVA  152 (773)
T ss_dssp             TTTCSBCCHHHHHHHHHHTTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHH
T ss_pred             CccccCCCHHHHHHHHHhhcCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHH
Confidence            4777888999999999999999999999999999999999999999999999999 5433                    


Q ss_pred             ----------hhcCCCC----------------------ChHHHHHhc-cCCCCcCcc-------------hHHHHHHHH
Q psy6094          95 ----------KRSETQQ----------------------YPNDVLNML-KDPELEGVN-------------NDVIFSLLQ  128 (455)
Q Consensus        95 ----------e~~~~vg----------------------~p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk  128 (455)
                                +.+..+|                      +|+.+++.+ .++.+.+++             +|.++.+++
T Consensus       153 a~q~~~~l~~~~~~~v~~~vG~~i~~~~~~~~~~~I~v~T~G~l~r~l~~~~~l~~~~~lIlDEah~R~ld~d~~~~~l~  232 (773)
T 2xau_A          153 AMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLK  232 (773)
T ss_dssp             HHHHHHHHHHHTTCCBTTTEEEEETTEEECCTTCSEEEEEHHHHHHHHHHSTTCTTEEEEEECSGGGCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchhheecceeccccccCCCCCEEEECHHHHHHHHhhCccccCCCEEEecCccccccchHHHHHHHH
Confidence                      1111111                      244466666 566666655             677788899


Q ss_pred             HHHHhcCCCCeEEEEccCC-----------------CCC-ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEE
Q psy6094         129 HICTTQRPGAILVYCTYTF-----------------MGV-SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPIL  190 (455)
Q Consensus       129 ~il~~~~~~~k~ilmSAT~-----------------~g~-~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iL  190 (455)
                      .+. ..+++.|+|+||||+                 +|+ +|++.+|.+.....+...    ....+........+|++|
T Consensus       233 ~l~-~~~~~~~iIl~SAT~~~~~l~~~~~~~~vi~v~gr~~pv~~~~~~~~~~~~~~~----~l~~l~~~~~~~~~g~iL  307 (773)
T 2xau_A          233 QVV-KRRPDLKIIIMSATLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDS----AIRTVLQIHATEEAGDIL  307 (773)
T ss_dssp             HHH-HHCTTCEEEEEESCSCCHHHHHHTTSCCEEECCCCCCCEEEECCSSCCSCHHHH----HHHHHHHHHHHSCSCEEE
T ss_pred             HHH-HhCCCceEEEEeccccHHHHHHHhcCCCcccccCcccceEEEEecCCchhHHHH----HHHHHHHHHHhcCCCCEE
Confidence            988 677899999999999                 677 888888876432111100    000122222225789999


Q ss_pred             EEcCCHHHHHHHHHHHHhcCC-----CCCCCeEEEeecCCCChhhHhhhhcCCC-----CCceEEEEeCCCCccCCCCCC
Q psy6094         191 VFLPGWDTINSLHRSMCQSSF-----FNSSRFQIIPLHSMLPTVSQKSIFNTPP-----EGVRKIVLATNIAETSITIDD  260 (455)
Q Consensus       191 VFlp~~~ei~~l~~~L~~~~~-----~~~~~~~v~~lhs~l~~~~r~~v~~~~~-----~g~~kVivaTniae~gitI~~  260 (455)
                      |||+|+++|+.+++.|.....     ....++.+.++||+|++++|.++++.|+     +|.++||||||+||+|||||+
T Consensus       308 VF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~  387 (773)
T 2xau_A          308 LFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDG  387 (773)
T ss_dssp             EECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTT
T ss_pred             EECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCC
Confidence            999999999999999985100     0123589999999999999999999999     999999999999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh----hhccCCCCcccccC-hHHHH
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND----VLNMLKDPELEGVN-NDVIF  335 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~----~~~~~~~PEi~r~~-~~~~L  335 (455)
                      |++|||+|++|.+.||+..|++.|.+.|+|+++|.||+|||||.++|.||+||+++    .+.++..|||++.+ .+++|
T Consensus       388 v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~~~G~~~~l~~~~~~~~~l~~~~~pEi~r~~L~~~~L  467 (773)
T 2xau_A          388 IVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVL  467 (773)
T ss_dssp             EEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSSSSEEEEESSCHHHHHHTSCSSCCCGGGGSCCHHHHH
T ss_pred             eEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCCCCCEEEEEecHHHhcccccccCCCccccCcHHHHHH
Confidence            99999999999999999999999999999999999999999999899999999954    36678999999999 99999


Q ss_pred             HHHh---------hhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh---------------hHH
Q psy6094         336 SLLQ---------HICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEI  391 (455)
Q Consensus       336 ~~l~---------~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~  391 (455)
                      .+..         .|++||+++++..|++.|..+||||.++++     |++|+.|+.||++|               +++
T Consensus       468 ~l~~~gi~~~~~f~~~~~p~~~~i~~a~~~L~~lgald~~~~l-----T~lG~~~a~~pl~p~~~~~l~~~~~~~c~~~~  542 (773)
T 2xau_A          468 ELKKLGIDDLVHFDFMDPPAPETMMRALEELNYLACLDDEGNL-----TPLGRLASQFPLDPMLAVMLIGSFEFQCSQEI  542 (773)
T ss_dssp             HHHHTTCCCGGGCCCSSCCCHHHHHHHHHHHHHTTSBCTTSCB-----CHHHHHHTTSSSCHHHHHHHHHGGGGTCHHHH
T ss_pred             HHHHcCCCChhhccccCCCcHHHHHHHHHHHHHcCCcccCCCc-----ChhhhhhccccCCHHHHHHHHhhcccCchhHH
Confidence            7654         688999999999999999999999999999     99999999999999               899


Q ss_pred             HHHHHhhc----CcCCcChHHHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCCC-c-hHhHHHh
Q psy6094         392 ITVRDCLS----FECKPSTAKIIKELRARLD-MLLAHKLSHPGTTAWGDPNEG-N-ILHCCSG  447 (455)
Q Consensus       392 l~iaa~ls----f~~p~~~~~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~~-~-~~~~c~~  447 (455)
                      ++|||+|+    |..|.+.+++++.+|++|. ..|||++++|+|++|.+.... . ..+||++
T Consensus       543 l~i~a~ls~~~~f~~~~~~~~~~~~~~~~f~~~~~D~~~~l~~~~~~~~~~~~~~~~~~~c~~  605 (773)
T 2xau_A          543 LTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRD  605 (773)
T ss_dssp             HHHHHHHTSCCCBCCCTTCHHHHHHHHHTTCCTTBHHHHHHHHHHHHTSHHHHHHCHHHHHHH
T ss_pred             HHHHHhcccCCcccCChHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHhccccchHHHHHHH
Confidence            99999999    8888899999999999999 899999999999999775421 1 2589997

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=1.1e-40  Score=365.63  Aligned_cols=367  Identities=13%  Similarity=0.022  Sum_probs=245.4

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHH-HHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDM-VRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~-i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      |.+..+++.+.+.++.++.-..+++|.++++. +.++++++|+|+||||||++++ +++.                    
T Consensus        10 ~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~La~   89 (715)
T 2va8_A           10 IEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTN   89 (715)
T ss_dssp             GGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHHHH
T ss_pred             HHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHHHH
Confidence            44556778888888887887899999999999 8899999999999999999987 5543                    


Q ss_pred             ----------hhcCCCC---------------------ChHHHHHhc-cCCC-CcCcc------hHH-----HHHHHHHH
Q psy6094          95 ----------KRSETQQ---------------------YPNDVLNML-KDPE-LEGVN------NDV-----IFSLLQHI  130 (455)
Q Consensus        95 ----------e~~~~vg---------------------~p~~ll~~l-~d~~-L~~~~------~D~-----ll~~lk~i  130 (455)
                                +.|..+|                     +|..+.+.+ .++. +.+++      .+.     ....++.+
T Consensus        90 q~~~~~~~~~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l~~i  169 (715)
T 2va8_A           90 EKYLTFKDWELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVVESV  169 (715)
T ss_dssp             HHHHHHGGGGGGTCCEEECCSCSSSCCGGGGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHHHHH
T ss_pred             HHHHHHHHhhcCCCEEEEEeCCCCCchhhcCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHHHHH
Confidence                      1122221                     244455555 4443 55555      221     22345555


Q ss_pred             HHhcCCCCeEEEEccCCC-----------------CC-ccceEEeehhhh------hhhhccCCC--CChHHHHHHHHc-
Q psy6094         131 CTTQRPGAILVYCTYTFM-----------------GV-SPMKVFFCKNVL------QRLMKGVGA--NSPKRWVKLLRS-  183 (455)
Q Consensus       131 l~~~~~~~k~ilmSAT~~-----------------g~-~pv~~~~l~~~~------~~~~~~~~~--~~~~~l~~~i~~-  183 (455)
                      +.+. +++|+|+||||++                 ++ +|+..++.....      -.+......  .........+.+ 
T Consensus       170 ~~~~-~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (715)
T 2va8_A          170 TIRA-KRRNLLALSATISNYKQIAKWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDS  248 (715)
T ss_dssp             HHHH-HTSEEEEEESCCTTHHHHHHHHTCEEEECCCCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHH
T ss_pred             HHhc-ccCcEEEEcCCCCCHHHHHHHhCCCccCCCCCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHH
Confidence            5232 3899999999983                 45 666554432110      000000000  000111222211 


Q ss_pred             -cCCCCEEEEcCCHHHHHHHHHHHHhcCCC---CC---------------------------CCeEEEeecCCCChhhHh
Q psy6094         184 -MLVVPILVFLPGWDTINSLHRSMCQSSFF---NS---------------------------SRFQIIPLHSMLPTVSQK  232 (455)
Q Consensus       184 -~~~g~iLVFlp~~~ei~~l~~~L~~~~~~---~~---------------------------~~~~v~~lhs~l~~~~r~  232 (455)
                       ..++++||||||+++++.+++.|......   ..                           -...+.++||+|++++|.
T Consensus       249 ~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~  328 (715)
T 2va8_A          249 LSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRD  328 (715)
T ss_dssp             HTTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHH
T ss_pred             HhcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHH
Confidence             56799999999999999999999875311   00                           012488999999999999


Q ss_pred             hhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeE
Q psy6094         233 SIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSE  309 (455)
Q Consensus       233 ~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c  309 (455)
                      .+++.|++|.++||||||++|+|||||++++|||+    ...||++.+..   ..|+|.+++.||+|||||.+   +|.|
T Consensus       329 ~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~----~~~~d~~~~~~---~~~~s~~~~~Qr~GRaGR~g~~~~G~~  401 (715)
T 2va8_A          329 LIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGD----IYRFNKKIAGY---YDEIPIMEYKQMSGRAGRPGFDQIGES  401 (715)
T ss_dssp             HHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECC----C-----------------CHHHHHHHHTTBCCTTTCSCEEE
T ss_pred             HHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeC----CeeccccCCCC---CCcCCHHHHHHHhhhcCCCCCCCCceE
Confidence            99999999999999999999999999999999997    45688766543   67999999999999999988   7999


Q ss_pred             EecCChhh-----hcc--CCCCcccccC-hH------HHHHHHh-----------hhcC------CCChhhHHhHHhhhh
Q psy6094         310 TQQYPNDV-----LNM--LKDPELEGVN-ND------VIFSLLQ-----------HICT------TQRPGAILVFLPGWD  358 (455)
Q Consensus       310 ~~L~t~~~-----~~~--~~~PEi~r~~-~~------~~L~~l~-----------~~~~------~P~~~~i~~al~~L~  358 (455)
                      |+++++..     ++.  ...||+.+++ ..      .+|..+.           ++++      +|+...+..|++.|.
T Consensus       402 ~~l~~~~~~~~~~~~~~l~~~~e~~~s~l~~~~~l~~~~l~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~~~~~al~~L~  481 (715)
T 2va8_A          402 IVVVRDKEDVDRVFKKYVLSDVEPIESKLGSERAFYTFLLGILSAEGNLSEKQLENFAYESLLAKQLVDVYFDRAIRWLL  481 (715)
T ss_dssp             EEECSCGGGHHHHHHHTTSSCCCCCCCSCCSHHHHHHHHHHHHHHHCSEEHHHHHHHHTTSSSCHHHHHHHHHHHHHHHH
T ss_pred             EEEeCCchHHHHHHHHHHcCCCCCceecCCchhHHHHHHHHHHhccccCCHHHHHHHHHhhHHHhhcchHHHHHHHHHHH
Confidence            99998432     222  4679999988 43      2332211           2222      455567999999999


Q ss_pred             hcccccCCCCCCcccCChHHHHHhhCCCCh------------------hHHHHHHHhhc-CcCCcChHHHHHHH
Q psy6094         359 TINSLHRSMCQSSFFNSCLLYEFAMVDNKP------------------KEIITVRDCLS-FECKPSTAKIIKEL  413 (455)
Q Consensus       359 ~lgald~~~~l~~~~~T~lG~~l~~lp~~p------------------~~~l~iaa~ls-f~~p~~~~~~~~~~  413 (455)
                      .+|+|+.++.  .+.+|++|+.|+.+|++|                  .+++.|+|+.+ |...+....+.+..
T Consensus       482 ~~g~i~~~~~--~~~~t~lG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~~~e~~~~~~r~~e~~~l  553 (715)
T 2va8_A          482 EHSFIKEEGN--TFALTNFGKRVADLYINPFTADIIRKGLEGHKASCELAYLHLLAFTPDGPLVSVGRNEEEEL  553 (715)
T ss_dssp             HTTSEEECSS--EEEECHHHHHHHHHTCCHHHHHHHHHHHHHSCCCCHHHHHHHHHHSTTSCCCCCCHHHHHHH
T ss_pred             HCcCEeecCC--eEeeChHHHHHHHHcCCHhHHHHHHHHhhhccCCCHHHHHHHhhcCcccccCccChHHHHHH
Confidence            9999987641  133499999999999999                  25666666666 76665555444433

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=100.00  E-value=4.1e-38  Score=344.55  Aligned_cols=325  Identities=12%  Similarity=0.070  Sum_probs=231.0

Q ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------------
Q psy6094          42 QSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------------   94 (455)
Q Consensus        42 ~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------------   94 (455)
                      +++.+.+.++.++.-..+++|.++++.+.++++++++||||||||++++ +++.                          
T Consensus        10 l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r~La~q~~~~~~   89 (702)
T 2p6r_A           10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFK   89 (702)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcHHHHHHHHHHHH
Confidence            5666777777777778899999999999999999999999999998877 5543                          


Q ss_pred             ---hhcCCCC---------------------ChHHHHHhc-cCCC-CcCcc------------------hHHHHHHHHHH
Q psy6094          95 ---KRSETQQ---------------------YPNDVLNML-KDPE-LEGVN------------------NDVIFSLLQHI  130 (455)
Q Consensus        95 ---e~~~~vg---------------------~p~~ll~~l-~d~~-L~~~~------------------~D~ll~~lk~i  130 (455)
                         +.|..+|                     +|..+.+.+ .++. +..++                  .|.++..++  
T Consensus        90 ~~~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~--  167 (702)
T 2p6r_A           90 KWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMR--  167 (702)
T ss_dssp             TTTTTTCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHH--
T ss_pred             HHHhcCCEEEEEeCCCCcchhhccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHHHHHHH--
Confidence               1111211                     244566655 4433 55555                  233333333  


Q ss_pred             HHhcCCCCeEEEEccCCC-----------------CC-ccceEEeehhhhhhhhccC-----CCCChHHHHHHHHccCCC
Q psy6094         131 CTTQRPGAILVYCTYTFM-----------------GV-SPMKVFFCKNVLQRLMKGV-----GANSPKRWVKLLRSMLVV  187 (455)
Q Consensus       131 l~~~~~~~k~ilmSAT~~-----------------g~-~pv~~~~l~~~~~~~~~~~-----~~~~~~~l~~~i~~~~~g  187 (455)
                        ..++++|+|+||||++                 ++ +|+..++.......+....     .......+...+  ..++
T Consensus       168 --~~~~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~  243 (702)
T 2p6r_A          168 --RMNKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECV--AENG  243 (702)
T ss_dssp             --HHCTTCEEEEEECCCTTHHHHHHHTTCEEEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHHH--HTTC
T ss_pred             --hcCcCceEEEECCCcCCHHHHHHHhCCCcccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHHH--hcCC
Confidence              4568999999999983                 45 6666544322110111100     000111122222  4689


Q ss_pred             CEEEEcCCHHHHHHHHHHHHhcCC--CCCC----------------------CeEEEeecCCCChhhHhhhhcCCCCCce
Q psy6094         188 PILVFLPGWDTINSLHRSMCQSSF--FNSS----------------------RFQIIPLHSMLPTVSQKSIFNTPPEGVR  243 (455)
Q Consensus       188 ~iLVFlp~~~ei~~l~~~L~~~~~--~~~~----------------------~~~v~~lhs~l~~~~r~~v~~~~~~g~~  243 (455)
                      ++||||+++++++.+++.|.....  ....                      ...+.++||+|++++|..+++.|++|.+
T Consensus       244 ~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~  323 (702)
T 2p6r_A          244 GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNI  323 (702)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHCCCC
Confidence            999999999999999999875310  0000                      1247789999999999999999999999


Q ss_pred             EEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCChhhhc-
Q psy6094         244 KIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYPNDVLN-  319 (455)
Q Consensus       244 kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t~~~~~-  319 (455)
                      +||||||++|+|||+|++++||++    ...||   |.    ..|+|.+++.||+|||||.+   +|.||.++++..+. 
T Consensus       324 ~vlvaT~~l~~Gidip~~~~VI~~----~~~yd---~~----~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~~  392 (702)
T 2p6r_A          324 KVVVATPTLAAGVNLPARRVIVRS----LYRFD---GY----SKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREI  392 (702)
T ss_dssp             CEEEECSTTTSSSCCCBSEEEECC----SEEES---SS----EEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHHH
T ss_pred             eEEEECcHHhccCCCCceEEEEcC----ceeeC---CC----CCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCccHHH
Confidence            999999999999999999999996    45676   22    57999999999999999988   79999999955432 


Q ss_pred             ---c--CCCCcccccC-hH------HHHHHHh-----------hhc---------CCCChhhHHhHHhhhhhcccccCC-
Q psy6094         320 ---M--LKDPELEGVN-ND------VIFSLLQ-----------HIC---------TTQRPGAILVFLPGWDTINSLHRS-  366 (455)
Q Consensus       320 ---~--~~~PEi~r~~-~~------~~L~~l~-----------~~~---------~~P~~~~i~~al~~L~~lgald~~-  366 (455)
                         .  ...||+.+++ ..      .+|..+.           +++         ++|..+.+..|++.|..+|+|+.+ 
T Consensus       393 ~~~~~l~~~~e~~~s~l~~~~~l~~~~l~~~~~g~~~~~~~~~~~l~~t~~~~~~~~~~~~~~~~al~~L~~~g~i~~~~  472 (702)
T 2p6r_A          393 AVKRYIFGEPERITSKLGVETHLRFHSLSIICDGYAKTLEELEDFFADTFFFKQNEISLSYELERVVRQLENWGMVVEAA  472 (702)
T ss_dssp             HHHTTTSSCCCCCCCCCCSHHHHHHHHHHHHHHTSCSSHHHHHHHHHTSTTHHHHCCCCHHHHHHHHHHHHHTTSEEESS
T ss_pred             HHHHHhcCCCCCceeecCcchhHHHHHHHHHHcCCCCCHHHHHHHHHhhhHHHhhhHHHHHHHHHHHHHHHHCcCeeECC
Confidence               1  4579999988 43      2221111           111         267889999999999999999977 


Q ss_pred             -CCCCcccCChHHHHHhhCCCCh
Q psy6094         367 -MCQSSFFNSCLLYEFAMVDNKP  388 (455)
Q Consensus       367 -~~l~~~~~T~lG~~l~~lp~~p  388 (455)
                       ..+     |++|+.++.+|++|
T Consensus       473 ~~~~-----t~lG~~~~~~~~~~  490 (702)
T 2p6r_A          473 HLAP-----TKLGSLVSRLYIDP  490 (702)
T ss_dssp             SEEE-----CHHHHHHHHTTCCH
T ss_pred             eecc-----ChHHHHHHHHhCCH
Confidence             455     99999999999999

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=100.00  E-value=6.2e-36  Score=328.17  Aligned_cols=352  Identities=14%  Similarity=0.032  Sum_probs=236.3

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHH-HHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDM-VRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~-i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      |.+..+++.+.+.++.++....+++|.++++. +.++++++++|+||||||++++ +++.                    
T Consensus         3 f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa~   82 (720)
T 2zj8_A            3 VDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAE   82 (720)
T ss_dssp             GGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGHH
T ss_pred             HhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHH
Confidence            44566788899999998888999999999998 8999999999999999998876 4442                    


Q ss_pred             ----------hhcCCCC---------------------ChHHHHHhc-cCCC-CcCcc------hHHHH-----HHHHHH
Q psy6094          95 ----------KRSETQQ---------------------YPNDVLNML-KDPE-LEGVN------NDVIF-----SLLQHI  130 (455)
Q Consensus        95 ----------e~~~~vg---------------------~p~~ll~~l-~d~~-L~~~~------~D~ll-----~~lk~i  130 (455)
                                +.|..+|                     +|..+.+.+ .++. +..++      .+.+.     ..+..+
T Consensus        83 q~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~l  162 (720)
T 2zj8_A           83 EKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVI  162 (720)
T ss_dssp             HHHHHTGGGGGGTCCEEEECSCSSCCCGGGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHH
T ss_pred             HHHHHHHHHHhcCCEEEEecCCCCccccccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHHHHH
Confidence                      1122221                     244455555 3332 55554      22111     112222


Q ss_pred             HHhcCCCCeEEEEccCCC-----------------CC-ccceEEeehhhhhhhhccC---CCCChHHHHHHHHccCCCCE
Q psy6094         131 CTTQRPGAILVYCTYTFM-----------------GV-SPMKVFFCKNVLQRLMKGV---GANSPKRWVKLLRSMLVVPI  189 (455)
Q Consensus       131 l~~~~~~~k~ilmSAT~~-----------------g~-~pv~~~~l~~~~~~~~~~~---~~~~~~~l~~~i~~~~~g~i  189 (455)
                      +...++++|+|+||||++                 ++ .|+...+.....-.+....   .......+...+  ..++++
T Consensus       163 l~~l~~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~  240 (720)
T 2zj8_A          163 LAHMLGKAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAI--RKKKGA  240 (720)
T ss_dssp             HHHHBTTBEEEEEECCCSCHHHHHHHTTEEEEECCCCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHH--HTTCCE
T ss_pred             HHHhhcCCeEEEEcCCcCCHHHHHHHhCCcccCCCCCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHH--hCCCCE
Confidence            223334899999999983                 33 4554433221110111100   111122233333  457999


Q ss_pred             EEEcCCHHHHHHHHHHHHhcCCC--CC----------C---------------CeEEEeecCCCChhhHhhhhcCCCCCc
Q psy6094         190 LVFLPGWDTINSLHRSMCQSSFF--NS----------S---------------RFQIIPLHSMLPTVSQKSIFNTPPEGV  242 (455)
Q Consensus       190 LVFlp~~~ei~~l~~~L~~~~~~--~~----------~---------------~~~v~~lhs~l~~~~r~~v~~~~~~g~  242 (455)
                      ||||+++++++.+++.|.+....  ..          .               ...+.++||+|++++|..+++.|++|.
T Consensus       241 LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~  320 (720)
T 2zj8_A          241 LIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGI  320 (720)
T ss_dssp             EEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             EEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCC
Confidence            99999999999999998763110  00          0               023899999999999999999999999


Q ss_pred             eEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCChhh--
Q psy6094         243 RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYPNDV--  317 (455)
Q Consensus       243 ~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t~~~--  317 (455)
                      ++||||||++|+|||+|++++||+.+    ..|| ..|     ..|.|.+++.||+|||||.+   +|.||.++++..  
T Consensus       321 ~~vlvaT~~l~~Gvdip~~~~VI~~~----~~yd-~~g-----~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~  390 (720)
T 2zj8_A          321 IKAVVATPTLSAGINTPAFRVIIRDI----WRYS-DFG-----MERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPR  390 (720)
T ss_dssp             SCEEEECSTTGGGCCCCBSEEEECCS----EECC-SSS-----CEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHH
T ss_pred             CeEEEECcHhhccCCCCceEEEEcCC----eeec-CCC-----CccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHH
Confidence            99999999999999999999999965    3466 223     26899999999999999987   599999999543  


Q ss_pred             -----hccCCCCcccccC-h--HH---HHH---------------HHh-hhc------CCCChhhHHhHHhhhhhccccc
Q psy6094         318 -----LNMLKDPELEGVN-N--DV---IFS---------------LLQ-HIC------TTQRPGAILVFLPGWDTINSLH  364 (455)
Q Consensus       318 -----~~~~~~PEi~r~~-~--~~---~L~---------------~l~-~~~------~~P~~~~i~~al~~L~~lgald  364 (455)
                           +-....+++...- .  .+   ++.               ++. .++      ++|..+.+..+++.|...|+|+
T Consensus       391 ~~~~~~~~~~~~~i~s~l~~~~~l~~~ll~~i~~~~~~~~~d~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~~i~  470 (720)
T 2zj8_A          391 EVMNHYIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNTFYAYQRKDTYSLEEKIRNILYFLLENEFIE  470 (720)
T ss_dssp             HHHHHHTTSCCCCCCCCTTCHHHHHHHHHHHHHHSCCCSHHHHHHHHHTSHHHHHCSCCHHHHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHhcCCCCCcEeecCchhhHHHHHHHHHHhCCCCCHHHHHHHHHhChHHHhccchHHHHHHHHHHHHHHHHCCCee
Confidence                 2222333333322 2  12   111               111 111      1222367999999999999998


Q ss_pred             -CCCCCCcccCChHHHHHhhCCCCh-------------------hHHHHHHHhhc-CcC
Q psy6094         365 -RSMCQSSFFNSCLLYEFAMVDNKP-------------------KEIITVRDCLS-FEC  402 (455)
Q Consensus       365 -~~~~l~~~~~T~lG~~l~~lp~~p-------------------~~~l~iaa~ls-f~~  402 (455)
                       .++.  .+.+|++|+.|+.+|++|                   .+++.|+|+.+ |..
T Consensus       471 ~~~~~--~~~~t~lG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~e~~~  527 (720)
T 2zj8_A          471 ISLED--KIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISLTPDITP  527 (720)
T ss_dssp             ECTTS--CEEECHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCCHHHHHHHHHTSTTCCC
T ss_pred             ECCCC--cEeeChHHHHHHHHcCCHHHHHHHHHHHHhhccCCCHHHHHHHhccCccccc
Confidence             6552  134599999999999999                   16778888777 543

>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=99.97  E-value=5.2e-31  Score=268.91  Aligned_cols=257  Identities=12%  Similarity=0.180  Sum_probs=175.0

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|.+...++.+.+.+..++..+.+++|.++++.+.+++++++.|+||||||+++. +++.                    
T Consensus        41 ~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  120 (414)
T 3eiq_A           41 SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTREL  120 (414)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHH
Confidence            4556778999999999999999999999999999999999999999999997654 3332                    


Q ss_pred             ---------hhc----CC-------------------------CCChHHHHHhc-c-CCCCcCcc------hHHHH----
Q psy6094          95 ---------KRS----ET-------------------------QQYPNDVLNML-K-DPELEGVN------NDVIF----  124 (455)
Q Consensus        95 ---------e~~----~~-------------------------vg~p~~ll~~l-~-d~~L~~~~------~D~ll----  124 (455)
                               +.+    ..                         +++|..|++.+ . ...+..++      +|.++    
T Consensus       121 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~  200 (414)
T 3eiq_A          121 AQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGF  200 (414)
T ss_dssp             HHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTT
T ss_pred             HHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCc
Confidence                     000    00                         11344566655 2 22333344      44433    


Q ss_pred             -HHHHHHHHhcCCCCeEEEEccCCCCC----------ccceEEe------ehhhhhhhhccCCCC-ChHHHHHHHHccCC
Q psy6094         125 -SLLQHICTTQRPGAILVYCTYTFMGV----------SPMKVFF------CKNVLQRLMKGVGAN-SPKRWVKLLRSMLV  186 (455)
Q Consensus       125 -~~lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~------l~~~~~~~~~~~~~~-~~~~l~~~i~~~~~  186 (455)
                       ..+..++...+++.|+|+||||++..          .++....      .+.+.+.+....... ....+...+.....
T Consensus       201 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  280 (414)
T 3eiq_A          201 KDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTI  280 (414)
T ss_dssp             HHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCCC
Confidence             33555664667899999999999321          1111110      000001111111111 22235555555677


Q ss_pred             CCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEe
Q psy6094         187 VPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVD  266 (455)
Q Consensus       187 g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID  266 (455)
                      +++|||++++++++.+++.|...+      +.+..+||++++++|.++++.|++|..+|||||+++++|+|+|++++||+
T Consensus       281 ~~~lvf~~~~~~~~~l~~~l~~~~------~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~  354 (414)
T 3eiq_A          281 TQAVIFINTRRKVDWLTEKMHARD------FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVIN  354 (414)
T ss_dssp             SSCEEECSCHHHHHHHHHHHHTTT------CCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEE
T ss_pred             CcEEEEeCCHHHHHHHHHHHHhcC------CeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEE
Confidence            899999999999999999999864      77999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         267 CGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       267 ~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ++.                  |.|.+++.||+|||||.|. |.||.+|+++
T Consensus       355 ~~~------------------p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~  387 (414)
T 3eiq_A          355 YDL------------------PTNRENYIHRIGRGGRFGRKGVAINMVTEE  387 (414)
T ss_dssp             SSC------------------CSSTHHHHHHSCCC-------CEEEEECST
T ss_pred             eCC------------------CCCHHHhhhhcCcccCCCCCceEEEEEcHH
Confidence            554                  4567889999999999975 9999999943

>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=99.97  E-value=2e-31  Score=285.53  Aligned_cols=246  Identities=16%  Similarity=0.083  Sum_probs=170.3

Q ss_pred             HHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh------------------------hhcCC---
Q psy6094          48 EMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL------------------------KRSET---   99 (455)
Q Consensus        48 ~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~------------------------e~~~~---   99 (455)
                      +.+++|..+|+|.+|+++++++.++++++++|+||||||++++ ++++                        ..+..   
T Consensus       208 e~l~~r~~lP~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~g~~vLVl~PTReLA~Qia~~l~~~~g~~vg~  287 (666)
T 3o8b_A          208 ESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNI  287 (666)
T ss_dssp             HHHHHHHHSCSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEE
T ss_pred             HhhhhhccCCcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHCCCeEEEEcchHHHHHHHHHHHHHHhCCCeeE
Confidence            3477889999999999999999999999999999999999988 6654                        11111   


Q ss_pred             -CC-------------ChHHHHHhccCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCCCCC--
Q psy6094         100 -QQ-------------YPNDVLNMLKDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTFMGV--  150 (455)
Q Consensus       100 -vg-------------~p~~ll~~l~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~~g~--  150 (455)
                       +|             +|++|++.- .-.+.+++             .+..+..+.+.+ .......+++||||++..  
T Consensus       288 ~vG~~~~~~~~~IlV~TPGrLl~~~-~l~l~~l~~lVlDEAH~l~~~~~~~l~~Il~~l-~~~~~~llil~SAT~~~~i~  365 (666)
T 3o8b_A          288 RTGVRTITTGAPVTYSTYGKFLADG-GCSGGAYDIIICDECHSTDSTTILGIGTVLDQA-ETAGARLVVLATATPPGSVT  365 (666)
T ss_dssp             ECSSCEECCCCSEEEEEHHHHHHTT-SCCTTSCSEEEETTTTCCSHHHHHHHHHHHHHT-TTTTCSEEEEEESSCTTCCC
T ss_pred             EECcEeccCCCCEEEECcHHHHhCC-CcccCcccEEEEccchhcCccHHHHHHHHHHhh-hhcCCceEEEECCCCCcccc
Confidence             11             355554321 11122222             333333344433 222333478889999665  


Q ss_pred             --ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCCh
Q psy6094         151 --SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPT  228 (455)
Q Consensus       151 --~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~  228 (455)
                        +|..... ..............    +  .+....++++|||++++++++.+++.|+..+      +.+..+||++++
T Consensus       366 ~~~p~i~~v-~~~~~~~i~~~~~~----~--~l~~~~~~~vLVFv~Tr~~ae~la~~L~~~g------~~v~~lHG~l~q  432 (666)
T 3o8b_A          366 VPHPNIEEV-ALSNTGEIPFYGKA----I--PIEAIRGGRHLIFCHSKKKCDELAAKLSGLG------INAVAYYRGLDV  432 (666)
T ss_dssp             CCCTTEEEE-ECBSCSSEEETTEE----E--CGGGSSSSEEEEECSCHHHHHHHHHHHHTTT------CCEEEECTTSCG
T ss_pred             cCCcceEEE-eecccchhHHHHhh----h--hhhhccCCcEEEEeCCHHHHHHHHHHHHhCC------CcEEEecCCCCH
Confidence              2211000 00000000000000    0  0112467899999999999999999999864      789999999998


Q ss_pred             hhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccc----cccCCCcccccccccchhhHHhhhcccCCC
Q psy6094         229 VSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSN----FDVKDNIATLKPEWISLANAKQRRGRAGRT  304 (455)
Q Consensus       229 ~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~----yd~~~~~~~l~~~~iSka~~~QR~GRaGR~  304 (455)
                      ++       ++++.++||||||+||+||||| |++|||+|+.+..+    |||..++... ..|+|.++|.||+|||||.
T Consensus       433 ~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~-~~P~s~~syiQRiGRtGRg  503 (666)
T 3o8b_A          433 SV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETT-TVPQDAVSRSQRRGRTGRG  503 (666)
T ss_dssp             GG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEE-EEECBHHHHHHHHTTBCSS
T ss_pred             HH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccc-cCcCCHHHHHHHhccCCCC
Confidence            75       2346679999999999999997 99999999988664    5677777654 6899999999999999996


Q ss_pred             CCCeEEecCChhhh
Q psy6094         305 LKRSETQQYPNDVL  318 (455)
Q Consensus       305 ~~G~c~~L~t~~~~  318 (455)
                      ++|. |.||++++.
T Consensus       504 ~~G~-i~lvt~~e~  516 (666)
T 3o8b_A          504 RRGI-YRFVTPGER  516 (666)
T ss_dssp             SCEE-EEESCCCCB
T ss_pred             CCCE-EEEEecchh
Confidence            6699 999997644

>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=99.96  E-value=3.2e-30  Score=266.63  Aligned_cols=255  Identities=16%  Similarity=0.190  Sum_probs=184.0

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hh---hhhh----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LD---FITL----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp---~ll~----------------   94 (455)
                      .|.+..+++...+.+...+....+++|.+.++.+.++++++++|+||||||.+  +|   .++.                
T Consensus        57 ~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~  136 (434)
T 2db3_A           57 HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVS  136 (434)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEEC
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEe
Confidence            35666788888998988888889999999999999999999999999999954  33   1110                


Q ss_pred             --------------h----hcCC------------------------CCChHHHHHhc--cCCCCcCcc------hHHHH
Q psy6094          95 --------------K----RSET------------------------QQYPNDVLNML--KDPELEGVN------NDVIF  124 (455)
Q Consensus        95 --------------e----~~~~------------------------vg~p~~ll~~l--~d~~L~~~~------~D~ll  124 (455)
                                    .    .+..                        +++|.+|++.+  ....+..++      +|.++
T Consensus       137 PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~  216 (434)
T 2db3_A          137 PTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRML  216 (434)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHT
T ss_pred             cCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhh
Confidence                          0    0001                        11466677766  222345555      66655


Q ss_pred             -----HHHHHHHHh--cCCCCeEEEEccCCCCC-c---------cceEEe------ehhhhhhhhccCCCCChHHHHHHH
Q psy6094         125 -----SLLQHICTT--QRPGAILVYCTYTFMGV-S---------PMKVFF------CKNVLQRLMKGVGANSPKRWVKLL  181 (455)
Q Consensus       125 -----~~lk~il~~--~~~~~k~ilmSAT~~g~-~---------pv~~~~------l~~~~~~~~~~~~~~~~~~l~~~i  181 (455)
                           ..++.++..  .+++.|+++||||++.. .         ++....      ..++.+.+.......+...+...+
T Consensus       217 ~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l  296 (434)
T 2db3_A          217 DMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEIL  296 (434)
T ss_dssp             STTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCGGGHHHHHHHHH
T ss_pred             ccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCcHHHHHHHHHHH
Confidence                 335666633  36789999999999421 1         111000      000001111111111222355555


Q ss_pred             HccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCe
Q psy6094         182 RSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDI  261 (455)
Q Consensus       182 ~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V  261 (455)
                      ... .+.+||||+++++++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|||||+|
T Consensus       297 ~~~-~~~~lVF~~t~~~a~~l~~~L~~~~------~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v  369 (434)
T 2db3_A          297 SEQ-ADGTIVFVETKRGADFLASFLSEKE------FPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNI  369 (434)
T ss_dssp             HHC-CTTEEEECSSHHHHHHHHHHHHHTT------CCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTC
T ss_pred             HhC-CCCEEEEEeCcHHHHHHHHHHHhCC------CCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccC
Confidence            533 4459999999999999999999864      789999999999999999999999999999999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      ++||+++.                  |.|.++|.||+||+||.|. |.|+.+|+.
T Consensus       370 ~~VI~~d~------------------p~~~~~y~qriGR~gR~g~~G~a~~~~~~  406 (434)
T 2db3_A          370 KHVINYDM------------------PSKIDDYVHRIGRTGRVGNNGRATSFFDP  406 (434)
T ss_dssp             CEEEESSC------------------CSSHHHHHHHHTTSSCTTCCEEEEEEECT
T ss_pred             CEEEEECC------------------CCCHHHHHHHhcccccCCCCCEEEEEEec
Confidence            99999543                  3467789999999999977 999999983

>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=99.96  E-value=5.4e-30  Score=260.97  Aligned_cols=261  Identities=13%  Similarity=0.127  Sum_probs=185.0

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC--CeEEEEcCCCCCcccchh-hhhh-------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN--QITVISGETGSGPPLHLD-FITL-------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~--~~vii~~~TGSGKTtqlp-~ll~-------------------   94 (455)
                      |.+...++...+.+...+....+++|.++++.+.++  +++++.|+||||||.++. .++.                   
T Consensus        27 f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  106 (412)
T 3fht_A           27 FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYE  106 (412)
T ss_dssp             TGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             HhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHH
Confidence            445667888888888888888999999999999987  899999999999996643 2221                   


Q ss_pred             ----------hh-----cC---------------------CCCChHHHHHhc-cCC--CCcCcc------hHHHHH----
Q psy6094          95 ----------KR-----SE---------------------TQQYPNDVLNML-KDP--ELEGVN------NDVIFS----  125 (455)
Q Consensus        95 ----------e~-----~~---------------------~vg~p~~ll~~l-~d~--~L~~~~------~D~ll~----  125 (455)
                                +.     +.                     .+++|..+++.+ ...  .+..++      +|.++.    
T Consensus       107 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~  186 (412)
T 3fht_A          107 LALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGH  186 (412)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTT
T ss_pred             HHHHHHHHHHHHHhhcccceEEEeecCcchhhhhcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCc
Confidence                      00     00                     011355566665 322  234444      454432    


Q ss_pred             --HHHHHHHhcCCCCeEEEEccCCCCC-ccc-------eE-Eeehh-------hhhhhhccCC-CCChHHHHHHHHccCC
Q psy6094         126 --LLQHICTTQRPGAILVYCTYTFMGV-SPM-------KV-FFCKN-------VLQRLMKGVG-ANSPKRWVKLLRSMLV  186 (455)
Q Consensus       126 --~lk~il~~~~~~~k~ilmSAT~~g~-~pv-------~~-~~l~~-------~~~~~~~~~~-~~~~~~l~~~i~~~~~  186 (455)
                        .+..+....+++.++++||||++.. ...       .. ..+..       ..+.+..... ......+...+....+
T Consensus       187 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  266 (412)
T 3fht_A          187 QDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITI  266 (412)
T ss_dssp             HHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcCC
Confidence              3444554567889999999999321 110       00 00000       0000000000 0011124444444677


Q ss_pred             CCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEe
Q psy6094         187 VPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVD  266 (455)
Q Consensus       187 g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID  266 (455)
                      +++||||++..+++.+++.|...+      +.+..+||++++++|..+++.|++|..+|||||+++++|+|+|++++||+
T Consensus       267 ~~~lvf~~~~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~  340 (412)
T 3fht_A          267 AQAMIFCHTRKTASWLAAELSKEG------HQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN  340 (412)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTT------CCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhCC------CeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEE
Confidence            899999999999999999999874      67899999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         267 CGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       267 ~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      ++.+....+            +.|.+++.||+|||||.+. |.||.+++.
T Consensus       341 ~~~p~~~~~------------~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~  378 (412)
T 3fht_A          341 FDLPVDKDG------------NPDNETYLHRIGRTGRFGKRGLAVNMVDS  378 (412)
T ss_dssp             SSCCBCSSS------------SBCHHHHHHHHTTSSCTTCCEEEEEEECS
T ss_pred             ECCCCCCCC------------CcchheeecccCcccCCCCCceEEEEEcC
Confidence            777644433            4678899999999999877 999999983

>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=1.5e-29  Score=258.31  Aligned_cols=258  Identities=12%  Similarity=0.198  Sum_probs=184.3

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|.+..+++...+.+...+....+++|.++++.+.+++++++.++||||||.++. .++.                    
T Consensus        38 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L  117 (410)
T 2j0s_A           38 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTREL  117 (410)
T ss_dssp             SGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHH
T ss_pred             CHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHH
Confidence            3556678888888888888888999999999999999999999999999995543 2221                    


Q ss_pred             ---------hhcC----------------------------CCCChHHHHHhc-c-CCCCcCcc------hHHHH-----
Q psy6094          95 ---------KRSE----------------------------TQQYPNDVLNML-K-DPELEGVN------NDVIF-----  124 (455)
Q Consensus        95 ---------e~~~----------------------------~vg~p~~ll~~l-~-d~~L~~~~------~D~ll-----  124 (455)
                               ..+.                            .+++|.+|++.+ . ...+..++      +|.++     
T Consensus       118 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~  197 (410)
T 2j0s_A          118 AVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFK  197 (410)
T ss_dssp             HHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTH
T ss_pred             HHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhhhH
Confidence                     0000                            011344455555 2 22333344      44432     


Q ss_pred             HHHHHHHHhcCCCCeEEEEccCCCCC-c---------cceEEeehh------hhhhhhccCCCC-ChHHHHHHHHccCCC
Q psy6094         125 SLLQHICTTQRPGAILVYCTYTFMGV-S---------PMKVFFCKN------VLQRLMKGVGAN-SPKRWVKLLRSMLVV  187 (455)
Q Consensus       125 ~~lk~il~~~~~~~k~ilmSAT~~g~-~---------pv~~~~l~~------~~~~~~~~~~~~-~~~~l~~~i~~~~~g  187 (455)
                      ..+..++...+++.++++||||++.. .         |+.......      +.+.+....... +...+...+.....+
T Consensus       198 ~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~  277 (410)
T 2j0s_A          198 EQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTIT  277 (410)
T ss_dssp             HHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCC
Confidence            34555664566889999999999432 1         111111000      000111111111 122344555555678


Q ss_pred             CEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeC
Q psy6094         188 PILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDC  267 (455)
Q Consensus       188 ~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~  267 (455)
                      ++||||++.++++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|||||+++++|+|+|++++||++
T Consensus       278 ~~lVf~~~~~~~~~l~~~L~~~~------~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~  351 (410)
T 2j0s_A          278 QAVIFCNTKRKVDWLTEKMREAN------FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY  351 (410)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTT------CCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEES
T ss_pred             cEEEEEcCHHHHHHHHHHHHhCC------CceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEE
Confidence            99999999999999999999864      678999999999999999999999999999999999999999999999995


Q ss_pred             CCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         268 GKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       268 g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      +.                  |.|.+++.||+||+||.|. |.|+.++++++
T Consensus       352 ~~------------------p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  384 (410)
T 2j0s_A          352 DL------------------PNNRELYIHRIGRSGRYGRKGVAINFVKNDD  384 (410)
T ss_dssp             SC------------------CSSHHHHHHHHTTSSGGGCCEEEEEEEEGGG
T ss_pred             CC------------------CCCHHHHHHhcccccCCCCceEEEEEecHHH
Confidence            53                  3567889999999999865 99999999543

>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=99.96  E-value=2.2e-28  Score=247.23  Aligned_cols=262  Identities=17%  Similarity=0.197  Sum_probs=183.9

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC--CeEEEEcCCCCCcccchh-hhhh------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN--QITVISGETGSGPPLHLD-FITL------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~--~~vii~~~TGSGKTtqlp-~ll~------------------   94 (455)
                      .|.+..+++...+.+...+....+++|.++++.+.++  +++++.++||||||+++. +++.                  
T Consensus         6 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~   85 (395)
T 3pey_A            6 SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSR   85 (395)
T ss_dssp             SSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             CHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCH
Confidence            3455667888888888888889999999999999988  899999999999996544 3222                  


Q ss_pred             -----------hhcC------------------------CCCChHHHHHhc-c-CCCCcCcc------hHHHH------H
Q psy6094          95 -----------KRSE------------------------TQQYPNDVLNML-K-DPELEGVN------NDVIF------S  125 (455)
Q Consensus        95 -----------e~~~------------------------~vg~p~~ll~~l-~-d~~L~~~~------~D~ll------~  125 (455)
                                 +.+.                        .+++|..+++.+ . ...+..++      +|.+.      .
T Consensus        86 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~  165 (395)
T 3pey_A           86 ELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGD  165 (395)
T ss_dssp             HHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTSCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHH
T ss_pred             HHHHHHHHHHHHHhcccCeeEEEEecCchhhhccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHH
Confidence                       0000                        011344555555 2 22344444      34333      2


Q ss_pred             HHHHHHHhcCCCCeEEEEccCCCCC-c-------cc-eEEeehh-------hhhhhhccCCC-CChHHHHHHHHccCCCC
Q psy6094         126 LLQHICTTQRPGAILVYCTYTFMGV-S-------PM-KVFFCKN-------VLQRLMKGVGA-NSPKRWVKLLRSMLVVP  188 (455)
Q Consensus       126 ~lk~il~~~~~~~k~ilmSAT~~g~-~-------pv-~~~~l~~-------~~~~~~~~~~~-~~~~~l~~~i~~~~~g~  188 (455)
                      .+..+....+++.++++||||++.. .       +- .......       ..+.+...... .....+...+.....++
T Consensus       166 ~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  245 (395)
T 3pey_A          166 QCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGS  245 (395)
T ss_dssp             HHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSE
T ss_pred             HHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccCCC
Confidence            3444454567789999999999321 0       00 0000000       00000000000 00111333444456789


Q ss_pred             EEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCC
Q psy6094         189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCG  268 (455)
Q Consensus       189 iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g  268 (455)
                      +|||+++..+++.+++.|+..+      +.+..+||++++++|.++++.|++|..+|||||+++++|+|+|++++||+++
T Consensus       246 ~lvf~~~~~~~~~l~~~l~~~~------~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~  319 (395)
T 3pey_A          246 SIIFVATKKTANVLYGKLKSEG------HEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYD  319 (395)
T ss_dssp             EEEECSCHHHHHHHHHHHHHTT------CCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESS
T ss_pred             EEEEeCCHHHHHHHHHHHHhcC------CcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcC
Confidence            9999999999999999999874      6789999999999999999999999999999999999999999999999966


Q ss_pred             CCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         269 KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       269 ~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      .++            +...+.|.+++.||+|||||.+. |.|+.+++.
T Consensus       320 ~p~------------~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~  355 (395)
T 3pey_A          320 LPT------------LANGQADPATYIHRIGRTGRFGRKGVAISFVHD  355 (395)
T ss_dssp             CCB------------CTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECS
T ss_pred             CCC------------CCcCCCCHHHhhHhccccccCCCCceEEEEEec
Confidence            543            22346789999999999999877 999999983

>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=99.96  E-value=3.9e-29  Score=260.40  Aligned_cols=231  Identities=18%  Similarity=0.190  Sum_probs=159.9

Q ss_pred             HHHHHHHHcCCeEEEEcCCCCCcccchh-hhhhh---h----------------------cCCCC----------Ch---
Q psy6094          63 DAVLDMVRNNQITVISGETGSGPPLHLD-FITLK---R----------------------SETQQ----------YP---  103 (455)
Q Consensus        63 ~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~e---~----------------------~~~vg----------~p---  103 (455)
                      +...+++.++++++++|+||||||+++. +++..   .                      |..++          +|   
T Consensus        12 ~~~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g~~v~~~~~~~~~~~t~~~~   91 (459)
T 2z83_A           12 RGSPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALRGLPVRYQTSAVQREHQGNEI   91 (459)
T ss_dssp             ---CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTTTSCEEECC--------CCCS
T ss_pred             HHHHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhcCceEeEEecccccCCCCCcE
Confidence            3345668889999999999999998744 33320   0                      11111          01   


Q ss_pred             ------HHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCCCCC-c-------cceE
Q psy6094         104 ------NDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTFMGV-S-------PMKV  155 (455)
Q Consensus       104 ------~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~~g~-~-------pv~~  155 (455)
                            ..+.+.+ .++.+.+++             .++.+++++...  ..++.|+|+||||++.. .       |+..
T Consensus        92 i~~~~~~~l~~~l~~~~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~--~~~~~~~il~SAT~~~~~~~~~~~~~pi~~  169 (459)
T 2z83_A           92 VDVMCHATLTHRLMSPNRVPNYNLFVMDEAHFTDPASIAARGYIATKV--ELGEAAAIFMTATPPGTTDPFPDSNAPIHD  169 (459)
T ss_dssp             EEEEEHHHHHHHHHSCC-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH--HTTSCEEEEECSSCTTCCCSSCCCSSCEEE
T ss_pred             EEEEchHHHHHHhhccccccCCcEEEEECCccCCchhhHHHHHHHHHh--ccCCccEEEEEcCCCcchhhhccCCCCeEE
Confidence                  1155555 556666666             255556666654  35789999999999654 2       2211


Q ss_pred             EeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhh
Q psy6094         156 FFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIF  235 (455)
Q Consensus       156 ~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~  235 (455)
                        ...   . .....   ...+..++. ..++++||||+++++++.+++.|+..+      +.+..+||.    +|.+++
T Consensus       170 --~~~---~-~~~~~---~~~~~~~l~-~~~~~~LVF~~s~~~~~~l~~~L~~~g------~~v~~lh~~----~R~~~~  229 (459)
T 2z83_A          170 --LQD---E-IPDRA---WSSGYEWIT-EYAGKTVWFVASVKMGNEIAMCLQRAG------KKVIQLNRK----SYDTEY  229 (459)
T ss_dssp             --EEC---C-CCSSC---CSSCCHHHH-HCCSCEEEECSCHHHHHHHHHHHHHTT------CCEEEESTT----CCCCCG
T ss_pred             --ecc---c-CCcch---hHHHHHHHH-hcCCCEEEEeCChHHHHHHHHHHHhcC------CcEEecCHH----HHHHHH
Confidence              100   0 00000   001123333 347899999999999999999999874      789999984    788999


Q ss_pred             cCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccc--cCCCcccccccccchhhHHhhhcccCCCC--CCeEEe
Q psy6094         236 NTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFD--VKDNIATLKPEWISLANAKQRRGRAGRTL--KRSETQ  311 (455)
Q Consensus       236 ~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd--~~~~~~~l~~~~iSka~~~QR~GRaGR~~--~G~c~~  311 (455)
                      +.|++|..+||||||++|+|||||+ ++|||+|..+.+.|+  ....+..+...|.|+++|.||+|||||.+  +|.||.
T Consensus       230 ~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~  308 (459)
T 2z83_A          230 PKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYH  308 (459)
T ss_dssp             GGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEE
T ss_pred             hhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEE
Confidence            9999999999999999999999999 999999988877764  33333333559999999999999999987  799999


Q ss_pred             cCChh
Q psy6094         312 QYPND  316 (455)
Q Consensus       312 L~t~~  316 (455)
                      +++..
T Consensus       309 ~~~~~  313 (459)
T 2z83_A          309 YGGAT  313 (459)
T ss_dssp             ECSCC
T ss_pred             EEccc
Confidence            99854

>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=99.96  E-value=1.3e-28  Score=250.34  Aligned_cols=258  Identities=11%  Similarity=0.123  Sum_probs=183.5

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|++..+++.+.+.+...+.-..+++|.++++.+.+++++++.++||||||+++. .++.                    
T Consensus        22 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  101 (400)
T 1s2m_A           22 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTREL  101 (400)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHH
Confidence            4667778888888888888888999999999999999999999999999996533 2221                    


Q ss_pred             ---------hh----cCC------------------------CCChHHHHHhc-c-CCCCcCcc------hHHH-----H
Q psy6094          95 ---------KR----SET------------------------QQYPNDVLNML-K-DPELEGVN------NDVI-----F  124 (455)
Q Consensus        95 ---------e~----~~~------------------------vg~p~~ll~~l-~-d~~L~~~~------~D~l-----l  124 (455)
                               +.    +..                        +++|..+++.+ . ...+..++      +|.+     .
T Consensus       102 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~  181 (400)
T 1s2m_A          102 ALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFK  181 (400)
T ss_dssp             HHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHH
T ss_pred             HHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhchH
Confidence                     00    000                        11244455544 2 22344444      3322     2


Q ss_pred             HHHHHHHHhcCCCCeEEEEccCCCCC----------ccceEEeehhh-----hhhhhccCCCCChHHHHHHHHccCCCCE
Q psy6094         125 SLLQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFCKNV-----LQRLMKGVGANSPKRWVKLLRSMLVVPI  189 (455)
Q Consensus       125 ~~lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l~~~-----~~~~~~~~~~~~~~~l~~~i~~~~~g~i  189 (455)
                      ..++.++...++..++++||||++..          .|......+..     .+.+.......+...+...+.....+++
T Consensus       182 ~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~  261 (400)
T 1s2m_A          182 TIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQA  261 (400)
T ss_dssp             HHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSSCBCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEE
T ss_pred             HHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccccccCCceeEEEEechhhHHHHHHHHHhhcCCCcE
Confidence            34566664556789999999999321          11111111100     0000001111111234455555677899


Q ss_pred             EEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCC
Q psy6094         190 LVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGK  269 (455)
Q Consensus       190 LVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~  269 (455)
                      ||||++.++++.+++.|...+      +.+..+||++++++|..+++.|++|..+|||||+++++|+|+|++++||+++.
T Consensus       262 lVf~~~~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~  335 (400)
T 1s2m_A          262 IIFCNSTNRVELLAKKITDLG------YSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDF  335 (400)
T ss_dssp             EEECSSHHHHHHHHHHHHHHT------CCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSC
T ss_pred             EEEEecHHHHHHHHHHHHhcC------CCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCC
Confidence            999999999999999999864      67899999999999999999999999999999999999999999999998553


Q ss_pred             CcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         270 TKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       270 ~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                                        |.|.+++.||+|||||.|. |.||.+|+.++
T Consensus       336 ------------------p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~  366 (400)
T 1s2m_A          336 ------------------PKTAETYLHRIGRSGRFGHLGLAINLINWND  366 (400)
T ss_dssp             ------------------CSSHHHHHHHHCBSSCTTCCEEEEEEECGGG
T ss_pred             ------------------CCCHHHHHHhcchhcCCCCCceEEEEeccch
Confidence                              4577889999999999865 99999999653

>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=99.95  E-value=6.3e-30  Score=274.85  Aligned_cols=249  Identities=16%  Similarity=0.166  Sum_probs=174.5

Q ss_pred             cCHHHHHHHHH--HccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh------------------------
Q psy6094          42 QSRRYQEMLEA--RKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL------------------------   94 (455)
Q Consensus        42 ~~~~~~~~l~~--R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~------------------------   94 (455)
                      .+++|.+.+.+  |+.+|+|.+   .++.+.++++++++|+||||||+++. .++.                        
T Consensus       157 ~~~~~~~~l~~~~~~~lpiq~~---~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~  233 (618)
T 2whx_A          157 KSGDYVSAITQAERIGEPDYEV---DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEE  233 (618)
T ss_dssp             -----CEECBCCCCCCCCCCCC---CGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHH
T ss_pred             chHHHHHHHhhccccCCCcccc---CHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHH
Confidence            45556665544  888999865   39999999999999999999998743 3332                        


Q ss_pred             hh-cCC----------CCChH---------HHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeE
Q psy6094          95 KR-SET----------QQYPN---------DVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAIL  140 (455)
Q Consensus        95 e~-~~~----------vg~p~---------~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~  140 (455)
                      .. +..          +++|.         .+.+++ .++.+.+++             .+..+..++..+  .+++.|+
T Consensus       234 ~l~~~~v~~~~~~l~~~~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~i~~~l--~~~~~q~  311 (618)
T 2whx_A          234 ALRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRV--EMGEAAA  311 (618)
T ss_dssp             HTTTSCEEECCTTSSCCCCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEESTTCCSHHHHHHHHHHHHHH--HHTSCEE
T ss_pred             HhcCCceeEecccceeccCCCceEEEEChHHHHHHHhccccccCCeEEEEECCCCCCccHHHHHHHHHHHh--cccCccE
Confidence            00 111          11222         255555 556666666             233444444443  2378999


Q ss_pred             EEEccCCCCC-ccceE-----EeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCC
Q psy6094         141 VYCTYTFMGV-SPMKV-----FFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNS  214 (455)
Q Consensus       141 ilmSAT~~g~-~pv~~-----~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~  214 (455)
                      |+||||+++. ..+..     ...+..   +   ..... ..+..++. ..++++||||+++++++.+++.|...+    
T Consensus       312 il~SAT~~~~~~~~~~~~~~~~~v~~~---~---~~~~~-~~ll~~l~-~~~~~~LVF~~s~~~a~~l~~~L~~~g----  379 (618)
T 2whx_A          312 IFMTATPPGSTDPFPQSNSPIEDIERE---I---PERSW-NTGFDWIT-DYQGKTVWFVPSIKAGNDIANCLRKSG----  379 (618)
T ss_dssp             EEECSSCTTCCCSSCCCSSCEEEEECC---C---CSSCC-SSSCHHHH-HCCSCEEEECSSHHHHHHHHHHHHHTT----
T ss_pred             EEEECCCchhhhhhhccCCceeeeccc---C---CHHHH-HHHHHHHH-hCCCCEEEEECChhHHHHHHHHHHHcC----
Confidence            9999999654 22111     011000   0   00000 11223333 357899999999999999999999874    


Q ss_pred             CCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCccccc--ccCCCcccccccccchh
Q psy6094         215 SRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNF--DVKDNIATLKPEWISLA  292 (455)
Q Consensus       215 ~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~y--d~~~~~~~l~~~~iSka  292 (455)
                        +.+..+||.    +|.++++.|++|..+||||||++|+||||| |++|||+|+.+.+.+  +...++......|+|.+
T Consensus       380 --~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~  452 (618)
T 2whx_A          380 --KRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPA  452 (618)
T ss_dssp             --CCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHH
T ss_pred             --CcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHH
Confidence              779999984    788899999999999999999999999997 999999999877655  44455667778899999


Q ss_pred             hHHhhhcccCCCC--CCeEEecCC
Q psy6094         293 NAKQRRGRAGRTL--KRSETQQYP  314 (455)
Q Consensus       293 ~~~QR~GRaGR~~--~G~c~~L~t  314 (455)
                      +|.||+|||||.+  +|.||.+++
T Consensus       453 ~yiQR~GRaGR~g~~~G~ai~l~~  476 (618)
T 2whx_A          453 SAAQRRGRIGRNPAQEDDQYVFSG  476 (618)
T ss_dssp             HHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             HHHHhccccCCCCCCCCeEEEEcc
Confidence            9999999999986  699999997

>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=99.95  E-value=2e-28  Score=245.04  Aligned_cols=255  Identities=16%  Similarity=0.149  Sum_probs=180.8

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC-CeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN-QITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~-~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      |.+...++...+.++..+.-..+++|.++++.+.++ +++++.|+||||||+++. .++.                    
T Consensus         8 f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~   87 (367)
T 1hv8_A            8 FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELA   87 (367)
T ss_dssp             GGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHH
T ss_pred             hhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHH
Confidence            445567788888888888888999999999998877 799999999999997644 2222                    


Q ss_pred             --------hh----cCC-----------------------CCChHHHHHhc-c-CCCCcCcc------hHHHH-----HH
Q psy6094          95 --------KR----SET-----------------------QQYPNDVLNML-K-DPELEGVN------NDVIF-----SL  126 (455)
Q Consensus        95 --------e~----~~~-----------------------vg~p~~ll~~l-~-d~~L~~~~------~D~ll-----~~  126 (455)
                              ..    +..                       +++|..+++.+ . ...+..++      +|.+.     ..
T Consensus        88 ~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~  167 (367)
T 1hv8_A           88 IQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKD  167 (367)
T ss_dssp             HHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHH
T ss_pred             HHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcCCCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchHHH
Confidence                    00    000                       11233455555 2 22344554      44332     33


Q ss_pred             HHHHHHhcCCCCeEEEEccCCCCC-cc------ceEEeeh-----hhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcC
Q psy6094         127 LQHICTTQRPGAILVYCTYTFMGV-SP------MKVFFCK-----NVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLP  194 (455)
Q Consensus       127 lk~il~~~~~~~k~ilmSAT~~g~-~p------v~~~~l~-----~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp  194 (455)
                      +..++...+++.++++||||++.. ..      ....+..     .+.+.+...........+...+. ..++.+||||+
T Consensus       168 ~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~-~~~~~~lvf~~  246 (367)
T 1hv8_A          168 VEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKINANIEQSYVEVNENERFEALCRLLK-NKEFYGLVFCK  246 (367)
T ss_dssp             HHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSSSSSEEEEEECCGGGHHHHHHHHHC-STTCCEEEECS
T ss_pred             HHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCCCCceEEEEEeChHHHHHHHHHHHh-cCCCcEEEEEC
Confidence            455554567889999999999321 10      0000000     00011111111111222444444 67789999999


Q ss_pred             CHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccc
Q psy6094         195 GWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSN  274 (455)
Q Consensus       195 ~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~  274 (455)
                      +.++++.+++.|...+      +.+..+||+++..+|.++++.|++|..+|+|||+++++|+|+|++++||+++.     
T Consensus       247 ~~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~-----  315 (367)
T 1hv8_A          247 TKRDTKELASMLRDIG------FKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHL-----  315 (367)
T ss_dssp             SHHHHHHHHHHHHHTT------CCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSC-----
T ss_pred             CHHHHHHHHHHHHhcC------CCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecC-----
Confidence            9999999999999864      67899999999999999999999999999999999999999999999999554     


Q ss_pred             cccCCCcccccccccchhhHHhhhcccCCCC-CCeEEecCChh
Q psy6094         275 FDVKDNIATLKPEWISLANAKQRRGRAGRTL-KRSETQQYPND  316 (455)
Q Consensus       275 yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~-~G~c~~L~t~~  316 (455)
                                   |.|..++.||+||+||.+ +|.||.+++.+
T Consensus       316 -------------~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~  345 (367)
T 1hv8_A          316 -------------PQNPESYMHRIGRTGRAGKKGKAISIINRR  345 (367)
T ss_dssp             -------------CSCHHHHHHHSTTTCCSSSCCEEEEEECTT
T ss_pred             -------------CCCHHHhhhcccccccCCCccEEEEEEcHH
Confidence                         457788999999999997 59999999954

>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=99.95  E-value=7.4e-30  Score=266.73  Aligned_cols=263  Identities=13%  Similarity=0.131  Sum_probs=80.0

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC--CeEEEEcCCCCCcccchh-hhhh------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN--QITVISGETGSGPPLHLD-FITL------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~--~~vii~~~TGSGKTtqlp-~ll~------------------   94 (455)
                      .|....+++...+.+...+....+++|.++++.+.++  +++++.|+||||||.++. .++.                  
T Consensus        93 ~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~  172 (479)
T 3fmp_B           93 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTY  172 (479)
T ss_dssp             CSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSH
T ss_pred             CHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChH
Confidence            3556778888888898899999999999999999987  999999999999996533 2221                  


Q ss_pred             -----------hh--------------------c------CCCCChHHHHHhc-cCC--CCcCcc------hHHHHH---
Q psy6094          95 -----------KR--------------------S------ETQQYPNDVLNML-KDP--ELEGVN------NDVIFS---  125 (455)
Q Consensus        95 -----------e~--------------------~------~~vg~p~~ll~~l-~d~--~L~~~~------~D~ll~---  125 (455)
                                 +.                    +      ..||+|.+|++++ ...  .+..++      +|.++.   
T Consensus       173 ~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~  252 (479)
T 3fmp_B          173 ELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG  252 (479)
T ss_dssp             HHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTT
T ss_pred             HHHHHHHHHHHHHHhhCCCceEEEEeCCccccccccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCC
Confidence                       00                    0      0122466677776 322  234444      554442   


Q ss_pred             ---HHHHHHHhcCCCCeEEEEccCCCCC--------ccceE-Eee-------hhhhhhhhccCC-CCChHHHHHHHHccC
Q psy6094         126 ---LLQHICTTQRPGAILVYCTYTFMGV--------SPMKV-FFC-------KNVLQRLMKGVG-ANSPKRWVKLLRSML  185 (455)
Q Consensus       126 ---~lk~il~~~~~~~k~ilmSAT~~g~--------~pv~~-~~l-------~~~~~~~~~~~~-~~~~~~l~~~i~~~~  185 (455)
                         .+..+....+++.++|+||||++..        .+... ..+       +...+.+..... ......+...+....
T Consensus       253 ~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  332 (479)
T 3fmp_B          253 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAIT  332 (479)
T ss_dssp             HHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC----------------------------------
T ss_pred             cHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhcc
Confidence               3444554556789999999999431        11110 011       111111111111 011111223333345


Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVV  265 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VI  265 (455)
                      .+++||||+++..++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|||||+++++|||+|+|++||
T Consensus       333 ~~~~lvF~~s~~~~~~l~~~L~~~~------~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI  406 (479)
T 3fmp_B          333 IAQAMIFCHTRKTASWLAAELSKEG------HQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI  406 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCceEEEeCcHHHHHHHHHHHHhCC------ccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEE
Confidence            6899999999999999999998764      7899999999999999999999999999999999999999999999999


Q ss_pred             eCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         266 DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       266 D~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +++++....+            +.|..+|.||+|||||.+. |.|+.+|+..
T Consensus       407 ~~d~p~~~~~------------~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~  446 (479)
T 3fmp_B          407 NFDLPVDKDG------------NPDNETYLHRIGRTGRFGKRGLAVNMVDSK  446 (479)
T ss_dssp             ----------------------------------------------------
T ss_pred             EecCCCCCcc------------CCCHHHHHHHhcccccCCCCceEEEEEcCc
Confidence            9666533321            4566789999999999877 9999999843

>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=3.5e-28  Score=248.37  Aligned_cols=257  Identities=15%  Similarity=0.163  Sum_probs=178.0

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhh---hh------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDF---IT------------------   93 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~---ll------------------   93 (455)
                      |.+...++...+.++..+....+++|.++++++.++++++++|+||||||..  +|.   +.                  
T Consensus        17 f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   96 (417)
T 2i4i_A           17 FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYG   96 (417)
T ss_dssp             GGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTB
T ss_pred             HhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccc
Confidence            3445577888888888888899999999999999999999999999999953  331   10                  


Q ss_pred             ------------h-------------hh----cC------------------------CCCChHHHHHhc-cC-CCCcCc
Q psy6094          94 ------------L-------------KR----SE------------------------TQQYPNDVLNML-KD-PELEGV  118 (455)
Q Consensus        94 ------------~-------------e~----~~------------------------~vg~p~~ll~~l-~d-~~L~~~  118 (455)
                                  +             +.    +.                        .+++|.+|++.+ .. ..+..+
T Consensus        97 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~  176 (417)
T 2i4i_A           97 RRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFC  176 (417)
T ss_dssp             SCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             cccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhC
Confidence                        0             00    00                        011344455555 22 234444


Q ss_pred             c------hHHHH-----HHHHHHHHh--cC--CCCeEEEEccCCCCC-c---------cceEEee------hhhhhhhhc
Q psy6094         119 N------NDVIF-----SLLQHICTT--QR--PGAILVYCTYTFMGV-S---------PMKVFFC------KNVLQRLMK  167 (455)
Q Consensus       119 ~------~D~ll-----~~lk~il~~--~~--~~~k~ilmSAT~~g~-~---------pv~~~~l------~~~~~~~~~  167 (455)
                      +      +|.++     ..++.++..  ..  ...++++||||++.. .         ++....-      +.+.+.+..
T Consensus       177 ~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  256 (417)
T 2i4i_A          177 KYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVW  256 (417)
T ss_dssp             CEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEE
T ss_pred             cEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEE
Confidence            4      55544     235555521  12  268899999999421 0         1100000      000001111


Q ss_pred             cCCCCChHHHHHHHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEE
Q psy6094         168 GVGANSPKRWVKLLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIV  246 (455)
Q Consensus       168 ~~~~~~~~~l~~~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVi  246 (455)
                      .........+...+.. ..++.+||||++.++++.+++.|...+      +.+..+||++++++|..+++.|++|..+|+
T Consensus       257 ~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~------~~~~~~h~~~~~~~r~~~~~~f~~g~~~vl  330 (417)
T 2i4i_A          257 VEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEG------YACTSIHGDRSQRDREEALHQFRSGKSPIL  330 (417)
T ss_dssp             CCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHHTSSCEE
T ss_pred             eccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCC------CCeeEecCCCCHHHHHHHHHHHHcCCCCEE
Confidence            1111112234555554 357789999999999999999999864      789999999999999999999999999999


Q ss_pred             EeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         247 LATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       247 vaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      |||+++++|+|+|++++||+++.                  |.|..++.||+||+||.+. |.||.+|++++
T Consensus       331 vaT~~~~~Gidip~v~~Vi~~~~------------------p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  384 (417)
T 2i4i_A          331 VATAVAARGLDISNVKHVINFDL------------------PSDIEEYVHRIGRTGRVGNLGLATSFFNERN  384 (417)
T ss_dssp             EECHHHHTTSCCCCEEEEEESSC------------------CSSHHHHHHHHTTBCC--CCEEEEEEECGGG
T ss_pred             EECChhhcCCCcccCCEEEEEcC------------------CCCHHHHHHhcCccccCCCCceEEEEEcccc
Confidence            99999999999999999999554                  3577889999999999976 99999999654

>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=99.95  E-value=6.8e-28  Score=243.94  Aligned_cols=256  Identities=14%  Similarity=0.148  Sum_probs=182.2

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      .|++...++.+.+.+...+.-..+++|.++++.+.+++++++.++||||||.+.. .++.                    
T Consensus         9 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L   88 (391)
T 1xti_A            9 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   88 (391)
T ss_dssp             CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHH
Confidence            3556677888888888888888999999999999999999999999999996532 2221                    


Q ss_pred             ---------hh-----cCCC-------------------------CChHHHHHhc-c-CCCCcCcc------hHHHH---
Q psy6094          95 ---------KR-----SETQ-------------------------QYPNDVLNML-K-DPELEGVN------NDVIF---  124 (455)
Q Consensus        95 ---------e~-----~~~v-------------------------g~p~~ll~~l-~-d~~L~~~~------~D~ll---  124 (455)
                               +.     +..+                         ++|..+++.+ . ...+..++      +|.++   
T Consensus        89 ~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~  168 (391)
T 1xti_A           89 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQL  168 (391)
T ss_dssp             HHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSH
T ss_pred             HHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhcc
Confidence                     00     1111                         1233344444 2 12234444      44332   


Q ss_pred             ---HHHHHHHHhcCCCCeEEEEccCCCCC-c---------cceEEeehh-------hhhhhhccCCCCChHHHHHHHHcc
Q psy6094         125 ---SLLQHICTTQRPGAILVYCTYTFMGV-S---------PMKVFFCKN-------VLQRLMKGVGANSPKRWVKLLRSM  184 (455)
Q Consensus       125 ---~~lk~il~~~~~~~k~ilmSAT~~g~-~---------pv~~~~l~~-------~~~~~~~~~~~~~~~~l~~~i~~~  184 (455)
                         ..+..++...+++.++++||||++.. .         |.....-..       ..+.+...........+...+...
T Consensus       169 ~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~  248 (391)
T 1xti_A          169 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVL  248 (391)
T ss_dssp             HHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHHHHHHHS
T ss_pred             chHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHHHHHHhc
Confidence               23455554556789999999999432 1         111111000       000011111111222355566556


Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYV  264 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~V  264 (455)
                      ..+++|||+++.++++.+++.|...+      +.+..+||++++++|..+++.|++|..+|||||+++++|+|+|++++|
T Consensus       249 ~~~~~lvf~~~~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~V  322 (391)
T 1xti_A          249 EFNQVVIFVKSVQRCIALAQLLVEQN------FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIA  322 (391)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEE
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhCC------CcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEE
Confidence            78899999999999999999999864      678999999999999999999999999999999999999999999999


Q ss_pred             EeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         265 VDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       265 ID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      |+++.                  |.|.+++.||+||+||.+. |.|+.+++.
T Consensus       323 i~~~~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~  356 (391)
T 1xti_A          323 FNYDM------------------PEDSDTYLHRVARAGRFGTKGLAITFVSD  356 (391)
T ss_dssp             EESSC------------------CSSHHHHHHHHCBCSSSCCCCEEEEEECS
T ss_pred             EEeCC------------------CCCHHHHHHhcccccCCCCceEEEEEEcc
Confidence            99554                  3477889999999999875 999999984

>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=99.95  E-value=1.9e-28  Score=254.57  Aligned_cols=194  Identities=15%  Similarity=0.097  Sum_probs=138.5

Q ss_pred             hHHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhhhhhhc
Q psy6094         103 PNDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVLQRLMK  167 (455)
Q Consensus       103 p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~~~~~~  167 (455)
                      ++.+.+++ .++.+.+++             .+.++..+...  ...++.|+|+||||++.. .....   .+.......
T Consensus        95 ~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~~~~~--~~~~~~~~i~~SAT~~~~~~~~~~---~~~~~~~~~  169 (451)
T 2jlq_A           95 HATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTR--VEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIE  169 (451)
T ss_dssp             HHHHHHHHHHCSCCCCCSEEEEETTTCCSHHHHHHHHHHHHH--HHTTSCEEEEECSSCTTCCCSSCC---CSSCEEEEE
T ss_pred             hHHHHHHhhCcccccCCCEEEEeCCccCCcchHHHHHHHHHh--hcCCCceEEEEccCCCccchhhhc---CCCceEecC
Confidence            33466666 666666666             23333333322  245789999999999654 22110   000000000


Q ss_pred             cCCCCC-hHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEE
Q psy6094         168 GVGANS-PKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIV  246 (455)
Q Consensus       168 ~~~~~~-~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVi  246 (455)
                      ...+.. -..+..++. ...+++||||+++++++.+++.|+..+      +.+..+||.+    +.++++.|++|..+||
T Consensus       170 ~~~p~~~~~~~~~~l~-~~~~~~lVF~~s~~~a~~l~~~L~~~g------~~~~~lh~~~----~~~~~~~f~~g~~~vL  238 (451)
T 2jlq_A          170 REIPERSWNTGFDWIT-DYQGKTVWFVPSIKAGNDIANCLRKSG------KRVIQLSRKT----FDTEYPKTKLTDWDFV  238 (451)
T ss_dssp             CCCCSSCCSSSCHHHH-HCCSCEEEECSSHHHHHHHHHHHHTTT------CCEEEECTTT----HHHHGGGGGSSCCSEE
T ss_pred             ccCCchhhHHHHHHHH-hCCCCEEEEcCCHHHHHHHHHHHHHcC------CeEEECCHHH----HHHHHHhhccCCceEE
Confidence            000000 000123333 457899999999999999999998764      7788999964    4578999999999999


Q ss_pred             EeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccc---cccchhhHHhhhcccCCCC--CCeEEecCC
Q psy6094         247 LATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKP---EWISLANAKQRRGRAGRTL--KRSETQQYP  314 (455)
Q Consensus       247 vaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~---~~iSka~~~QR~GRaGR~~--~G~c~~L~t  314 (455)
                      ||||++|+|||||+ ++|||+|+.+...|| ..+...+..   .|.|.++|.||+|||||.+  +|.||.++.
T Consensus       239 VaT~v~~~GiDip~-~~VI~~~~~~~~~~d-~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~  309 (451)
T 2jlq_A          239 VTTDISEMGANFRA-GRVIDPRRCLKPVIL-TDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSG  309 (451)
T ss_dssp             EECGGGGSSCCCCC-SEEEECCEEEEEEEE-CSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             EECCHHHhCcCCCC-CEEEECCCccccccc-ccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeC
Confidence            99999999999999 999999999999988 556666665   9999999999999999988  689998876

>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=99.94  E-value=1.7e-27  Score=246.63  Aligned_cols=175  Identities=20%  Similarity=0.175  Sum_probs=122.2

Q ss_pred             HHHHHHHHHHHhcCCCCeEEEEccCCCCC-ccceEEe--ehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHH
Q psy6094         122 VIFSLLQHICTTQRPGAILVYCTYTFMGV-SPMKVFF--CKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDT  198 (455)
Q Consensus       122 ~ll~~lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~--l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~e  198 (455)
                      ..++.+..+.  .+++.++++||||++.. .......  ..... ...  ...... .+...+. ..++++|||||++++
T Consensus       117 ~~~~~~~~~~--~~~~~~~l~~SAT~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~-~~~~~l~-~~~~~~lVF~~s~~~  189 (440)
T 1yks_A          117 AARGWAAHRA--RANESATILMTATPPGTSDEFPHSNGEIEDVQ-TDI--PSEPWN-TGHDWIL-ADKRPTAWFLPSIRA  189 (440)
T ss_dssp             HHHHHHHHHH--HTTSCEEEEECSSCTTCCCSSCCCSSCEEEEE-CCC--CSSCCS-SSCHHHH-HCCSCEEEECSCHHH
T ss_pred             HHHHHHHHHh--ccCCceEEEEeCCCCchhhhhhhcCCCeeEee-ecc--ChHHHH-HHHHHHH-hcCCCEEEEeCCHHH
Confidence            4455666654  25679999999999544 2111000  00000 000  000001 1223333 347899999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCccccc-cc
Q psy6094         199 INSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNF-DV  277 (455)
Q Consensus       199 i~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~y-d~  277 (455)
                      ++.+++.|+..+      +.+..+||    ++|.++++.|++|..+|||||+++|+||||| +++|||+|..+.+.| +.
T Consensus       190 a~~l~~~L~~~~------~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~  258 (440)
T 1yks_A          190 ANVMAASLRKAG------KSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDE  258 (440)
T ss_dssp             HHHHHHHHHHTT------CCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETT
T ss_pred             HHHHHHHHHHcC------CCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeeccc
Confidence            999999999864      78999999    5788999999999999999999999999999 999999999888776 44


Q ss_pred             CCCcccccccccchhhHHhhhcccCCC-C-CCeEEecCC
Q psy6094         278 KDNIATLKPEWISLANAKQRRGRAGRT-L-KRSETQQYP  314 (455)
Q Consensus       278 ~~~~~~l~~~~iSka~~~QR~GRaGR~-~-~G~c~~L~t  314 (455)
                      ..++......|.|.++|.||+||+||. + +|.||.+|+
T Consensus       259 ~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~  297 (440)
T 1yks_A          259 GRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSE  297 (440)
T ss_dssp             TTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             ccceeeccccccCHHHHHHhccccCCCCCCCceEEEEec
Confidence            456666677899999999999999997 3 599999984

>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=99.94  E-value=1.7e-27  Score=253.69  Aligned_cols=112  Identities=18%  Similarity=0.199  Sum_probs=99.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++++||||+++..++.+++.|....   ..++.+..+||++++.+|..+++.|++|..+|||||+++++|||+|+|++
T Consensus       337 ~~~~~~iVF~~s~~~~~~l~~~L~~~~---~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~  413 (563)
T 3i5x_A          337 DSNYKAIIFAPTVKFTSFLCSILKNEF---KKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHE  413 (563)
T ss_dssp             TTCCEEEEECSCHHHHHHHHHHHHHHH---TTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCE
T ss_pred             CCCCcEEEEcCcHHHHHHHHHHHHHhc---cCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCE
Confidence            567899999999999999999998752   11478999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||+++.                  |.|..+|.||+|||||.+. |.|+.+++..
T Consensus       414 VI~~~~------------------p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~  449 (563)
T 3i5x_A          414 VLQIGV------------------PSELANYIHRIGRTARSGKEGSSVLFICKD  449 (563)
T ss_dssp             EEEESC------------------CSSTTHHHHHHTTSSCTTCCEEEEEEEEGG
T ss_pred             EEEECC------------------CCchhhhhhhcCccccCCCCceEEEEEchh
Confidence            999554                  3466789999999999985 9999999954

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.94  E-value=1.1e-27  Score=256.28  Aligned_cols=112  Identities=18%  Similarity=0.199  Sum_probs=99.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++.+||||+++..++.+++.|....   ..++.+..+||++++.+|.++++.|+.|..+|||||+++++|||+|+|++
T Consensus       286 ~~~~~~iVF~~t~~~~~~l~~~L~~~~---~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~  362 (579)
T 3sqw_A          286 DSNYKAIIFAPTVKFTSFLCSILKNEF---KKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHE  362 (579)
T ss_dssp             TTCCEEEEECSSHHHHHHHHHHHHHHH---TTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCE
T ss_pred             CCCCcEEEECCcHHHHHHHHHHHHHhh---cCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCE
Confidence            557789999999999999999998752   11377999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||+++.                  |.|..+|.||+|||||.+. |.|+.+++.+
T Consensus       363 VI~~~~------------------p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~  398 (579)
T 3sqw_A          363 VLQIGV------------------PSELANYIHRIGRTARSGKEGSSVLFICKD  398 (579)
T ss_dssp             EEEESC------------------CSSTTHHHHHHTTSSCTTCCEEEEEEEEGG
T ss_pred             EEEcCC------------------CCCHHHhhhhccccccCCCCceEEEEEccc
Confidence            999554                  3466789999999999986 9999999954

>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=99.94  E-value=7.3e-28  Score=243.76  Aligned_cols=257  Identities=14%  Similarity=0.174  Sum_probs=76.7

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------   94 (455)
                      |++...++...+.+...+.-..+++|.++++.+.+++++++.++||||||.+.. .++.                     
T Consensus        23 f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~  102 (394)
T 1fuu_A           23 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELA  102 (394)
T ss_dssp             SGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHH
T ss_pred             hhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHH
Confidence            445667888888888888888999999999999999999999999999996532 2221                     


Q ss_pred             --------hh----cCC-----------------------CCChHHHHHhc-c-CCCCcCcc------hHHHH-----HH
Q psy6094          95 --------KR----SET-----------------------QQYPNDVLNML-K-DPELEGVN------NDVIF-----SL  126 (455)
Q Consensus        95 --------e~----~~~-----------------------vg~p~~ll~~l-~-d~~L~~~~------~D~ll-----~~  126 (455)
                              ..    +..                       +++|..+++.+ . ...+..++      +|.++     ..
T Consensus       103 ~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~~~  182 (394)
T 1fuu_A          103 LQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQ  182 (394)
T ss_dssp             HHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHHHCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcHHH
Confidence                    00    000                       11233355544 2 22233444      44433     23


Q ss_pred             HHHHHHhcCCCCeEEEEccCCCCC----------ccceEEeehh------hhhhhhccCCCC-ChHHHHHHHHccCCCCE
Q psy6094         127 LQHICTTQRPGAILVYCTYTFMGV----------SPMKVFFCKN------VLQRLMKGVGAN-SPKRWVKLLRSMLVVPI  189 (455)
Q Consensus       127 lk~il~~~~~~~k~ilmSAT~~g~----------~pv~~~~l~~------~~~~~~~~~~~~-~~~~l~~~i~~~~~g~i  189 (455)
                      +..++...+++.++++||||++..          .|+......+      +.+.+....... ....+...+.....+++
T Consensus       183 ~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  262 (394)
T 1fuu_A          183 IYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQA  262 (394)
T ss_dssp             HHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC-------------------------------------
T ss_pred             HHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcE
Confidence            455554667889999999999421          1222111111      111111111111 11123333433567899


Q ss_pred             EEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCC
Q psy6094         190 LVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGK  269 (455)
Q Consensus       190 LVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~  269 (455)
                      ||||++.++++.+++.|...+      +.+..+||++++++|..+++.|++|..+|+|||+++++|+|+|++++||+++.
T Consensus       263 lVf~~~~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~  336 (394)
T 1fuu_A          263 VIFCNTRRKVEELTTKLRNDK------FTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDL  336 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEECCHHHHHHHHHHHHHcC------CeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCC
Confidence            999999999999999998763      78999999999999999999999999999999999999999999999998553


Q ss_pred             CcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         270 TKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       270 ~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                                        |.|.+++.||+||+||.+. |.||.++++++
T Consensus       337 ------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  367 (394)
T 1fuu_A          337 ------------------PANKENYIHRIGRGGRFGRKGVAINFVTNED  367 (394)
T ss_dssp             -------------------------------------------------
T ss_pred             ------------------CCCHHHHHHHcCcccCCCCCceEEEEEchhH
Confidence                              4567788999999999865 99999999654

>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=99.94  E-value=2e-27  Score=269.90  Aligned_cols=252  Identities=17%  Similarity=0.169  Sum_probs=170.0

Q ss_pred             ccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh--------------------------hhcCCCC-----
Q psy6094          54 KKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL--------------------------KRSETQQ-----  101 (455)
Q Consensus        54 ~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~--------------------------e~~~~vg-----  101 (455)
                      ...+.+++|.++++++.++++++|+|+||||||+++. .++.                          +....+|     
T Consensus       181 ~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~PtraLa~Q~~~~l~~~~~~VglltGd  260 (1108)
T 3l9o_A          181 YPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGD  260 (1108)
T ss_dssp             CSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHTSSEEEECSS
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcHHHHHHHHHHHHHHhCCccEEeCc
Confidence            3456789999999999999999999999999997654 3322                          1111111     


Q ss_pred             ------------ChHHHHHhc-cCC-CCcCcc------hHHHH-----HHHHHHHHhcCCCCeEEEEccCCC--------
Q psy6094         102 ------------YPNDVLNML-KDP-ELEGVN------NDVIF-----SLLQHICTTQRPGAILVYCTYTFM--------  148 (455)
Q Consensus       102 ------------~p~~ll~~l-~d~-~L~~~~------~D~ll-----~~lk~il~~~~~~~k~ilmSAT~~--------  148 (455)
                                  +|.+|++++ .+. .+..++      +|.+.     ..+..++...+++.|+|+||||++        
T Consensus       261 ~~~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~  340 (1108)
T 3l9o_A          261 ITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEW  340 (1108)
T ss_dssp             CBCCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHH
T ss_pred             cccCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHH
Confidence                        466677766 333 244444      33332     224555546788999999999982        


Q ss_pred             ---------------CC-ccceEEeehhhh------------------hhhhccCCC-----------------------
Q psy6094         149 ---------------GV-SPMKVFFCKNVL------------------QRLMKGVGA-----------------------  171 (455)
Q Consensus       149 ---------------g~-~pv~~~~l~~~~------------------~~~~~~~~~-----------------------  171 (455)
                                     .+ .|+..++.....                  ...+.....                       
T Consensus       341 l~~~~~~~~~vi~~~~rp~pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  420 (1108)
T 3l9o_A          341 ICKIHSQPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGS  420 (1108)
T ss_dssp             HHHHTCSCEEEEEECCCSSCEEEEEEETTSSCCEEEEETTTEECHHHHHHHHTTC-------------------------
T ss_pred             HHhhcCCCeEEEecCCCcccceEEEeecCCcceeeeeccccchhhhhHHHHHHHHHhhhccccccccccccccccccccc
Confidence                           22 344333321100                  000000000                       


Q ss_pred             C---ChHH---HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCC------------------------------
Q psy6094         172 N---SPKR---WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSS------------------------------  215 (455)
Q Consensus       172 ~---~~~~---l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~------------------------------  215 (455)
                      .   ....   ++..+.....+++|||++++.+++.++..|...+.....                              
T Consensus       421 ~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~  500 (1108)
T 3l9o_A          421 AKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHIL  500 (1108)
T ss_dssp             ----CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHT
T ss_pred             ccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHH
Confidence            0   0111   333333356779999999999999999988652110000                              


Q ss_pred             ---CeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchh
Q psy6094         216 ---RFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLA  292 (455)
Q Consensus       216 ---~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka  292 (455)
                         ...+..+||+|++.+|..+++.|++|..+|||||+++++|||||++++||++..+    ||..      ...|+|.+
T Consensus       501 ~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~----~d~~------~~r~iS~~  570 (1108)
T 3l9o_A          501 PLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRK----WDGQ------QFRWVSGG  570 (1108)
T ss_dssp             HHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEE----ESSS------CEEECCHH
T ss_pred             HhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcc----cCcc------ccccCCHH
Confidence               0118899999999999999999999999999999999999999999999985542    4332      23589999


Q ss_pred             hHHhhhcccCCCC---CCeEEecCCh
Q psy6094         293 NAKQRRGRAGRTL---KRSETQQYPN  315 (455)
Q Consensus       293 ~~~QR~GRaGR~~---~G~c~~L~t~  315 (455)
                      +|.||+|||||.+   .|.||.++++
T Consensus       571 eyiQr~GRAGR~G~d~~G~~ill~~~  596 (1108)
T 3l9o_A          571 EYIQMSGRAGRRGLDDRGIVIMMIDE  596 (1108)
T ss_dssp             HHHHHHHHSCCSSSCSSEEEEEEECC
T ss_pred             HHHHhhcccCCCCCCCceEEEEEecC
Confidence            9999999999988   6999999984

>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=99.94  E-value=4.4e-26  Score=225.55  Aligned_cols=242  Identities=17%  Similarity=0.190  Sum_probs=171.1

Q ss_pred             CHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh-----------------------hhc-
Q psy6094          43 SRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL-----------------------KRS-   97 (455)
Q Consensus        43 ~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~-----------------------e~~-   97 (455)
                      ++...+.++..+.-..+++|.++++.+.+++++++.++||||||.++. .++.                       +.+ 
T Consensus         2 ~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~   81 (337)
T 2z0m_A            2 NEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTRELTRQVASHIRDIGR   81 (337)
T ss_dssp             CHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHHHHHHHhh
Confidence            456677788888888999999999999999999999999999996544 3332                       000 


Q ss_pred             ---CC-----------------------CCChHHHHHhc-c-CCCCcCcc------hHHHH-----HHHHHHHHhcCCCC
Q psy6094          98 ---ET-----------------------QQYPNDVLNML-K-DPELEGVN------NDVIF-----SLLQHICTTQRPGA  138 (455)
Q Consensus        98 ---~~-----------------------vg~p~~ll~~l-~-d~~L~~~~------~D~ll-----~~lk~il~~~~~~~  138 (455)
                         ..                       +++|..+++.+ . ...+..++      +|.+.     ..++.++...+...
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~  161 (337)
T 2z0m_A           82 YMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRK  161 (337)
T ss_dssp             TSCCCEEEECTTSCHHHHHHHHTTCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHHHHHCTTCS
T ss_pred             hcCCcEEEEECCcchHHHHhhcCCCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHHHhhCCccc
Confidence               11                       11344455555 2 22344444      44443     33555564566788


Q ss_pred             eEEEEccCCCCC-cc---------ceEE-e--ehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHH
Q psy6094         139 ILVYCTYTFMGV-SP---------MKVF-F--CKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRS  205 (455)
Q Consensus       139 k~ilmSAT~~g~-~p---------v~~~-~--l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~  205 (455)
                      ++++||||++.. ..         .... .  .......+..  ...........+....++++|||+++.++++.+++.
T Consensus       162 ~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~lvf~~~~~~~~~l~~~  239 (337)
T 2z0m_A          162 ITGLFSATIPEEIRKVVKDFITNYEEIEACIGLANVEHKFVH--VKDDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRL  239 (337)
T ss_dssp             EEEEEESCCCHHHHHHHHHHSCSCEEEECSGGGGGEEEEEEE--CSSSSHHHHHHHHTCCCSSEEEECSCHHHHHHHHTT
T ss_pred             EEEEEeCcCCHHHHHHHHHhcCCceeeecccccCCceEEEEE--eChHHHHHHHHHHhCCCCcEEEEEcCHHHHHHHHHH
Confidence            999999999321 00         0000 0  0000001111  111122234555557788999999999999998877


Q ss_pred             HHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCccccc
Q psy6094         206 MCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLK  285 (455)
Q Consensus       206 L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~  285 (455)
                      |.          .+..+||+++..+|.++++.|++|..+|||||+++++|+|+|++++||+++.                
T Consensus       240 l~----------~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~----------------  293 (337)
T 2z0m_A          240 FD----------NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDA----------------  293 (337)
T ss_dssp             CT----------TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSC----------------
T ss_pred             hh----------hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecC----------------
Confidence            65          2678999999999999999999999999999999999999999999999553                


Q ss_pred             ccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         286 PEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       286 ~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                        |.|.+++.||+|||||.+. |.|+.+++
T Consensus       294 --~~s~~~~~Q~~GR~gR~g~~g~~~~~~~  321 (337)
T 2z0m_A          294 --PQDLRTYIHRIGRTGRMGRKGEAITFIL  321 (337)
T ss_dssp             --CSSHHHHHHHHTTBCGGGCCEEEEEEES
T ss_pred             --CCCHHHhhHhcCccccCCCCceEEEEEe
Confidence              3467889999999999865 99999988

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.94  E-value=1.3e-26  Score=250.97  Aligned_cols=228  Identities=18%  Similarity=0.194  Sum_probs=160.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh-hhhh---hh----------------------cC----------CCCChHH-------
Q psy6094          69 VRNNQITVISGETGSGPPLHLD-FITL---KR----------------------SE----------TQQYPND-------  105 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp-~ll~---e~----------------------~~----------~vg~p~~-------  105 (455)
                      +.++++++++|+||||||+++. .++.   ..                      +.          .+++|.+       
T Consensus       238 l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~La~Q~~~~l~~~~i~~~~~~l~~v~tp~~ll~~l~~  317 (673)
T 2wv9_A          238 LKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRGLPVRYLTPAVQREHSGNEIVDVMCH  317 (673)
T ss_dssp             GSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCCEECCC---CCCCSCCCEEEEEH
T ss_pred             HhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHHHHHHHHHHhcCCeeeecccccccCCHHHHHHHHHh
Confidence            3489999999999999998743 3332   00                      00          0222322       


Q ss_pred             --HHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCCCCC-c--cceEEeehhhhhhhh
Q psy6094         106 --VLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTFMGV-S--PMKVFFCKNVLQRLM  166 (455)
Q Consensus       106 --ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~~g~-~--pv~~~~l~~~~~~~~  166 (455)
                        +.+.+ .+..+.+++             .+..+..++.++  .+++.++++||||++.. .  +....-...+...+ 
T Consensus       318 ~~l~~~l~~~~~l~~l~lvViDEaH~~~~~~~~~~~~l~~~~--~~~~~~vl~~SAT~~~~i~~~~~~~~~i~~v~~~~-  394 (673)
T 2wv9_A          318 ATLTHRLMSPLRVPNYNLFVMDEAHFTDPASIAARGYIATRV--EAGEAAAIFMTATPPGTSDPFPDTNSPVHDVSSEI-  394 (673)
T ss_dssp             HHHHHHHHSSSCCCCCSEEEEESTTCCCHHHHHHHHHHHHHH--HTTSCEEEEECSSCTTCCCSSCCCSSCEEEEECCC-
T ss_pred             hhhHHHHhcccccccceEEEEeCCcccCccHHHHHHHHHHhc--cccCCcEEEEcCCCChhhhhhcccCCceEEEeeec-
Confidence              44444 444555555             334556666655  23689999999999544 1  11100000000000 


Q ss_pred             ccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEE
Q psy6094         167 KGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIV  246 (455)
Q Consensus       167 ~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVi  246 (455)
                        ..... ..+...+. ..++++|||||++++++.+++.|+..+      +.+..+||    ++|.++++.|++|..+||
T Consensus       395 --~~~~~-~~~l~~l~-~~~~~~lVF~~s~~~~e~la~~L~~~g------~~v~~lHg----~eR~~v~~~F~~g~~~VL  460 (673)
T 2wv9_A          395 --PDRAW-SSGFEWIT-DYAGKTVWFVASVKMSNEIAQCLQRAG------KRVIQLNR----KSYDTEYPKCKNGDWDFV  460 (673)
T ss_dssp             --CSSCC-SSCCHHHH-SCCSCEEEECSSHHHHHHHHHHHHTTT------CCEEEECS----SSHHHHGGGGGTCCCSEE
T ss_pred             --CHHHH-HHHHHHHH-hCCCCEEEEECCHHHHHHHHHHHHhCC------CeEEEeCh----HHHHHHHHHHHCCCceEE
Confidence              00000 11223333 468899999999999999999999863      78999999    488899999999999999


Q ss_pred             EeCCCCccCCCCCCeeEEEeCCCCccc--ccccCCCcccccccccchhhHHhhhcccCCC-C-CCeEEecCC
Q psy6094         247 LATNIAETSITIDDIVYVVDCGKTKMS--NFDVKDNIATLKPEWISLANAKQRRGRAGRT-L-KRSETQQYP  314 (455)
Q Consensus       247 vaTniae~gitI~~V~~VID~g~~k~~--~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~-~-~G~c~~L~t  314 (455)
                      ||||++|+||||| +++|||+|....+  .||...++..+...|.|.++|.||+|||||. + +|.||.+|.
T Consensus       461 VaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~  531 (673)
T 2wv9_A          461 ITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGG  531 (673)
T ss_dssp             EECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECS
T ss_pred             EECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEe
Confidence            9999999999999 9999999976654  3676667777778999999999999999998 3 599999985

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.93  E-value=9.4e-27  Score=251.54  Aligned_cols=165  Identities=14%  Similarity=0.085  Sum_probs=122.9

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCC--CceEEEEeCCCCccCCCCCCee
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPE--GVRKIVLATNIAETSITIDDIV  262 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~--g~~kVivaTniae~gitI~~V~  262 (455)
                      .+|+ +||++++++++.+++.|...+      +.+.++||+|++++|.++++.|.+  |.++||||||++|+|||| +|+
T Consensus       320 ~~g~-iIf~~s~~~ie~la~~L~~~g------~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~  391 (677)
T 3rc3_A          320 RPGD-CIVCFSKNDIYSVSRQIEIRG------LESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIR  391 (677)
T ss_dssp             CTTE-EEECSSHHHHHHHHHHHHHTT------CCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBS
T ss_pred             CCCC-EEEEcCHHHHHHHHHHHHhcC------CCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-Ccc
Confidence            3444 677888999999999999863      789999999999999988888877  899999999999999999 999


Q ss_pred             EEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC----CCeEEecCChh-----hhccCCCCcccccC-hH
Q psy6094         263 YVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL----KRSETQQYPND-----VLNMLKDPELEGVN-ND  332 (455)
Q Consensus       263 ~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~----~G~c~~L~t~~-----~~~~~~~PEi~r~~-~~  332 (455)
                      +|||+|..|. .||+..+.   ...|+|.++|.||+|||||.+    +|.||.+++++     .+.....|+|.+.+ ..
T Consensus       392 ~VI~~~~~k~-~~~~~G~~---~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~~d~~~~~~~~~~~~~~i~~~~l~p  467 (677)
T 3rc3_A          392 RIIFYSLIKP-SINEKGER---ELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLSLLKEILKRPVDPIRAAGLHP  467 (677)
T ss_dssp             EEEESCSBC---------------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESSTTHHHHHHHHHHSCCCCCCCEEECC
T ss_pred             EEEECCcccc-ccccCCcc---ccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEecchHHHHHHHHhcCcchhhhccCCC
Confidence            9999999988 88877443   257999999999999999988    48999999854     35567889999866 33


Q ss_pred             HHH--HHHhhhcCCCChhhHHhHHhhhhhccccc
Q psy6094         333 VIF--SLLQHICTTQRPGAILVFLPGWDTINSLH  364 (455)
Q Consensus       333 ~~L--~~l~~~~~~P~~~~i~~al~~L~~lgald  364 (455)
                      ..+  ..+...+   +...+...++.+..++.++
T Consensus       468 ~~~~l~~~~~~l---~~~~l~ell~~l~~~~~vd  498 (677)
T 3rc3_A          468 TAEQIEMFAYHL---PDATLSNLIDIFVDFSQVD  498 (677)
T ss_dssp             CHHHHHHHHHHS---TTSCHHHHHHHHHHHCBCC
T ss_pred             hHHHHHHHhccC---CcchHHHHHHHHHHhhccc
Confidence            333  3333222   2234455555566565555

>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=99.93  E-value=2e-26  Score=243.65  Aligned_cols=249  Identities=13%  Similarity=0.109  Sum_probs=166.1

Q ss_pred             CHHHHHHHHH-HccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc--chhhhh-h---------------------hhc
Q psy6094          43 SRRYQEMLEA-RKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPL--HLDFIT-L---------------------KRS   97 (455)
Q Consensus        43 ~~~~~~~l~~-R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt--qlp~ll-~---------------------e~~   97 (455)
                      ++...+.++. -+.-...++|.++++++.+++++++.++||||||.  ++|.+. .                     +.|
T Consensus        10 ~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~~g~~lvi~P~~aL~~q~~~~l~~~g   89 (523)
T 1oyw_A           10 ESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISLMKDQVDQLQANG   89 (523)
T ss_dssp             HHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHhCCCEEEECChHHHHHHHHHHHHHcC
Confidence            3444445544 34455678899999999999999999999999995  566221 1                     111


Q ss_pred             CCCC----------------------------ChHHHH-----Hhc---------cCC--CCcCcchHH--HHHHHHHHH
Q psy6094          98 ETQQ----------------------------YPNDVL-----NML---------KDP--ELEGVNNDV--IFSLLQHIC  131 (455)
Q Consensus        98 ~~vg----------------------------~p~~ll-----~~l---------~d~--~L~~~~~D~--ll~~lk~il  131 (455)
                      ..++                            +|.+|+     +.+         -|.  .+...+.|+  ....+..+.
T Consensus        90 i~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~  169 (523)
T 1oyw_A           90 VAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLR  169 (523)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHH
T ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHH
Confidence            1111                            122221     111         000  000001111  112233344


Q ss_pred             HhcCCCCeEEEEccCCCCC-c---------cceEEeehhh---hhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCHHH
Q psy6094         132 TTQRPGAILVYCTYTFMGV-S---------PMKVFFCKNV---LQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDT  198 (455)
Q Consensus       132 ~~~~~~~k~ilmSAT~~g~-~---------pv~~~~l~~~---~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~e  198 (455)
                       ...++.++++||||++.. .         .-...+....   .-.+...........+..++....++++||||+++++
T Consensus       170 -~~~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~~l~~~v~~~~~~~~~l~~~l~~~~~~~~IVf~~sr~~  248 (523)
T 1oyw_A          170 -QRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAK  248 (523)
T ss_dssp             -HHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCCCCTTEEEEEEECSSHHHHHHHHHHHTTTCCEEEECSSHHH
T ss_pred             -HhCCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCCCCCceEEEEEeCCCHHHHHHHHHHhcCCCcEEEEeCCHHH
Confidence             445789999999999221 0         0000010000   0000001111223346666665667899999999999


Q ss_pred             HHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccC
Q psy6094         199 INSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVK  278 (455)
Q Consensus       199 i~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~  278 (455)
                      ++.+++.|...+      +.+..+||++++++|..+++.|.+|..+|||||+++++|||+|+|++||+++.         
T Consensus       249 ~e~l~~~L~~~g------~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~---------  313 (523)
T 1oyw_A          249 VEDTAARLQSKG------ISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDI---------  313 (523)
T ss_dssp             HHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSC---------
T ss_pred             HHHHHHHHHHCC------CCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECC---------
Confidence            999999999874      77999999999999999999999999999999999999999999999999554         


Q ss_pred             CCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         279 DNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       279 ~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                               |.|.++|.||+|||||.+. |.|+.+|+.+
T Consensus       314 ---------p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~  343 (523)
T 1oyw_A          314 ---------PRNIESYYQETGRAGRDGLPAEAMLFYDPA  343 (523)
T ss_dssp             ---------CSSHHHHHHHHTTSCTTSSCEEEEEEECHH
T ss_pred             ---------CCCHHHHHHHhccccCCCCCceEEEEeCHH
Confidence                     3577889999999999885 9999999954

>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=99.93  E-value=7.2e-26  Score=242.34  Aligned_cols=116  Identities=18%  Similarity=0.161  Sum_probs=102.8

Q ss_pred             HHHHHHc-cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         177 WVKLLRS-MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       177 l~~~i~~-~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      +..++.. ..++++||||+++++++.+++.|...+      +.+.++||+|++++|.++++.|..|..+|||||+++++|
T Consensus       257 l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g------~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~G  330 (591)
T 2v1x_A          257 IVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLG------IHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG  330 (591)
T ss_dssp             HHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTT
T ss_pred             HHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCC------CCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcC
Confidence            4444543 367889999999999999999999864      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      ||+|+|++||+++.+                  -|.++|.||+|||||.|. |.|+.+|+..
T Consensus       331 ID~p~V~~VI~~~~p------------------~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~  374 (591)
T 2v1x_A          331 IDKPDVRFVIHHSMS------------------KSMENYYQESGRAGRDDMKADCILYYGFG  374 (591)
T ss_dssp             CCCSCEEEEEESSCC------------------SSHHHHHHHHTTSCTTSSCEEEEEEECHH
T ss_pred             CCcccccEEEEeCCC------------------CCHHHHHHHhccCCcCCCCceEEEEEChH
Confidence            999999999996654                  367889999999999875 9999999954

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.93  E-value=6.8e-26  Score=234.06  Aligned_cols=170  Identities=18%  Similarity=0.158  Sum_probs=129.5

Q ss_pred             HHHHHHHHHHHHhcCCCCeEEEEccCCCCC--------ccceEEeehhhhhhhhccCCCCChHHHHHHHHccCCCCEEEE
Q psy6094         121 DVIFSLLQHICTTQRPGAILVYCTYTFMGV--------SPMKVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVF  192 (455)
Q Consensus       121 D~ll~~lk~il~~~~~~~k~ilmSAT~~g~--------~pv~~~~l~~~~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVF  192 (455)
                      +.....++.+.  .+++.++++||||++..        .|+...  +.   . ..   ......+...+. ..+|++|||
T Consensus       110 ~~~~~~l~~~~--~~~~~~~l~~SAT~~~~~~~~~~~~~~i~~~--~~---~-~~---~~~~~~~~~~l~-~~~~~~lVF  177 (431)
T 2v6i_A          110 VAARGYIETRV--SMGDAGAIFMTATPPGTTEAFPPSNSPIIDE--ET---R-IP---DKAWNSGYEWIT-EFDGRTVWF  177 (431)
T ss_dssp             HHHHHHHHHHH--HTTSCEEEEEESSCTTCCCSSCCCSSCCEEE--EC---C-CC---SSCCSSCCHHHH-SCSSCEEEE
T ss_pred             HHHHHHHHHHh--hCCCCcEEEEeCCCCcchhhhcCCCCceeec--cc---c-CC---HHHHHHHHHHHH-cCCCCEEEE
Confidence            44555566554  35789999999999543        222111  00   0 00   000011223444 457899999


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcc
Q psy6094         193 LPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKM  272 (455)
Q Consensus       193 lp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~  272 (455)
                      ||++++++.+++.|+..+      +.+..+||+    +|.++++.|++|..+|||||+++|+||||| +.+|||+|.++.
T Consensus       178 ~~~~~~~~~l~~~L~~~~------~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~  246 (431)
T 2v6i_A          178 VHSIKQGAEIGTCLQKAG------KKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIK  246 (431)
T ss_dssp             CSSHHHHHHHHHHHHHTT------CCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEE
T ss_pred             eCCHHHHHHHHHHHHHcC------CeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCcccc
Confidence            999999999999999863      779999997    677899999999999999999999999999 999999999999


Q ss_pred             cccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         273 SNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       273 ~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      +.|| ..++......|.|.+++.||+||+||.++ +.|+.+|.
T Consensus       247 ~v~d-~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          247 PILL-DGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEE-TTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             ceec-ccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            9998 67777788899999999999999999874 44555554

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.92  E-value=3.4e-25  Score=249.55  Aligned_cols=128  Identities=20%  Similarity=0.148  Sum_probs=103.4

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCC---------------------------------CCeEEEeec
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNS---------------------------------SRFQIIPLH  223 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~---------------------------------~~~~v~~lh  223 (455)
                      +..++.....+++|||++++++++.++..|...+....                                 -...+.++|
T Consensus       327 li~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H  406 (997)
T 4a4z_A          327 IVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHH  406 (997)
T ss_dssp             HHHHHHHTTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEEC
T ss_pred             HHHHHHhCCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeec
Confidence            45555556778999999999999999999876431000                                 011478999


Q ss_pred             CCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCC
Q psy6094         224 SMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR  303 (455)
Q Consensus       224 s~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR  303 (455)
                      |+|++.+|..+++.|..|..+|||||+++++|||+|+ +.||..+.++   ||..      ...|+|.++|.||+|||||
T Consensus       407 ~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k---~dg~------~~~~~s~~~y~Qr~GRAGR  476 (997)
T 4a4z_A          407 GGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRK---HDGN------GLRELTPGEFTQMAGRAGR  476 (997)
T ss_dssp             TTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEE---EETT------EEEECCHHHHHHHHGGGCC
T ss_pred             CCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEecccc---ccCc------cCCCCCHHHHhHHhccccc
Confidence            9999999999999999999999999999999999999 6666666654   4432      2358999999999999999


Q ss_pred             CC---CCeEEecCC
Q psy6094         304 TL---KRSETQQYP  314 (455)
Q Consensus       304 ~~---~G~c~~L~t  314 (455)
                      .|   .|.||.++.
T Consensus       477 ~G~~~~G~vi~l~~  490 (997)
T 4a4z_A          477 RGLDSTGTVIVMAY  490 (997)
T ss_dssp             TTTCSSEEEEEECC
T ss_pred             CCCCcceEEEEecC
Confidence            87   599999995

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.91  E-value=5.1e-25  Score=206.01  Aligned_cols=160  Identities=15%  Similarity=0.152  Sum_probs=130.0

Q ss_pred             hHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCc
Q psy6094         174 PKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAE  253 (455)
Q Consensus       174 ~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae  253 (455)
                      ...+...+....++++||||+++.+++.+++.|...+      +.+.++||++++.+|.++++.|++|..+|+||||+++
T Consensus        19 ~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~------~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~   92 (212)
T 3eaq_A           19 LEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLG------HPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAA   92 (212)
T ss_dssp             HHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHT------CCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTT
T ss_pred             HHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcC------CCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhh
Confidence            3345556665678999999999999999999999864      7899999999999999999999999999999999999


Q ss_pred             cCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC-CCeEEecCChhh--------------h
Q psy6094         254 TSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL-KRSETQQYPNDV--------------L  318 (455)
Q Consensus       254 ~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~-~G~c~~L~t~~~--------------~  318 (455)
                      +|+|||++++|||+|.                  |.|.++|.||+|||||.| +|.||.+|+..+              +
T Consensus        93 ~Gidi~~v~~Vi~~~~------------------p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~  154 (212)
T 3eaq_A           93 RGLDIPQVDLVVHYRL------------------PDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRF  154 (212)
T ss_dssp             CSSSCCCBSEEEESSC------------------CSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCC
T ss_pred             cCCCCccCcEEEECCC------------------CcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcC
Confidence            9999999999999665                  357789999999999997 499999999543              2


Q ss_pred             c---cCCCCcccccC-hHHHHHH--------------HhhhcCCCChhhHHhHHhhh
Q psy6094         319 N---MLKDPELEGVN-NDVIFSL--------------LQHICTTQRPGAILVFLPGW  357 (455)
Q Consensus       319 ~---~~~~PEi~r~~-~~~~L~~--------------l~~~~~~P~~~~i~~al~~L  357 (455)
                      .   ....|||.+.. ..+++.+              +..++++|+++++..|+..|
T Consensus       155 ~~~~~~~~~ei~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~l~~al~~l  211 (212)
T 3eaq_A          155 KRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVEVVAALLALL  211 (212)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHHHTTSCHHHHTTTHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             eecCCCCHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhcCCHHHHHHHHHhh
Confidence            2   22345666666 5555522              23567788888888887665

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.91  E-value=4.1e-25  Score=240.92  Aligned_cols=130  Identities=18%  Similarity=0.135  Sum_probs=75.5

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEee--------cCCCChhhHhhhhcCCCC-CceEEEEeCCCCccC
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPL--------HSMLPTVSQKSIFNTPPE-GVRKIVLATNIAETS  255 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~l--------hs~l~~~~r~~v~~~~~~-g~~kVivaTniae~g  255 (455)
                      .++++|||++++.+++.+++.|...+.+  ..+.+..+        ||+|++++|.++++.|++ |..+|||||+++++|
T Consensus       397 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~--~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~G  474 (696)
T 2ykg_A          397 PETITILFVKTRALVDALKNWIEGNPKL--SFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEG  474 (696)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHCTTC--CSCCEEC-----------------------------CCSCSEEEESSCCC
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhCCCc--cccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcC
Confidence            5789999999999999999999987532  12566667        669999999999999998 999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhh-------------hccCC
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV-------------LNMLK  322 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~-------------~~~~~  322 (455)
                      ||||++++||+        ||++          .|..+|.||+|| ||.++|.||.|++...             +....
T Consensus       475 iDip~v~~VI~--------~d~p----------~s~~~~~Qr~GR-GR~~~g~~~~l~~~~~~~~~~~~~~~~e~~~~~~  535 (696)
T 2ykg_A          475 IDIAQCNLVIL--------YEYV----------GNVIKMIQTRGR-GRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDS  535 (696)
T ss_dssp             ---CCCSEEEE--------ESCC------------CCCC----------CCCEEEEEESCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCccCCEEEE--------eCCC----------CCHHHHHHhhcc-CcCCCceEEEEecCCCHHHHHHHHHHHHHHHHHH
Confidence            99999999999        5543          344566799999 9998899999999432             23445


Q ss_pred             CCcccccC-hHHHH
Q psy6094         323 DPELEGVN-NDVIF  335 (455)
Q Consensus       323 ~PEi~r~~-~~~~L  335 (455)
                      .||+.+.+ +.++.
T Consensus       536 ~~~~~~~~~~~~~~  549 (696)
T 2ykg_A          536 ILRLQTWDEAVFRE  549 (696)
T ss_dssp             HHHHTTSCHHHHHH
T ss_pred             HHHhhccCHHHHHH
Confidence            67777777 66644

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.91  E-value=3e-24  Score=241.89  Aligned_cols=129  Identities=22%  Similarity=0.210  Sum_probs=103.6

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCC---------------------------------CeEEEeec
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSS---------------------------------RFQIIPLH  223 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~---------------------------------~~~v~~lh  223 (455)
                      +...+.....+++|||++++.+++.+++.|...+.....                                 ...+..+|
T Consensus       334 l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~H  413 (1010)
T 2xgj_A          334 IVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHH  413 (1010)
T ss_dssp             HHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEES
T ss_pred             HHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEEC
Confidence            334444355679999999999999999988763211000                                 01278899


Q ss_pred             CCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCC
Q psy6094         224 SMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGR  303 (455)
Q Consensus       224 s~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR  303 (455)
                      |+|++.+|..+++.|++|..+|||||+++++|||+|++++||+.    ...||...      ..|.|.++|.||+|||||
T Consensus       414 ggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~----~~kfd~~~------~rp~s~~~y~Qr~GRAGR  483 (1010)
T 2xgj_A          414 SGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTS----VRKWDGQQ------FRWVSGGEYIQMSGRAGR  483 (1010)
T ss_dssp             TTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESC----SEEECSSC------EEECCHHHHHHHHTTBCC
T ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeC----CcccCCcC------CccCCHHHHhHhhhhccc
Confidence            99999999999999999999999999999999999999999983    22355332      358899999999999999


Q ss_pred             CCC---CeEEecCCh
Q psy6094         304 TLK---RSETQQYPN  315 (455)
Q Consensus       304 ~~~---G~c~~L~t~  315 (455)
                      .|.   |.||.++++
T Consensus       484 ~G~d~~G~vi~l~~~  498 (1010)
T 2xgj_A          484 RGLDDRGIVIMMIDE  498 (1010)
T ss_dssp             TTTCSSEEEEEEECS
T ss_pred             CCCCCceEEEEEECC
Confidence            884   999999983

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.91  E-value=1.3e-24  Score=222.70  Aligned_cols=237  Identities=15%  Similarity=0.119  Sum_probs=157.2

Q ss_pred             HHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccch-hhhhh--------------------------hh--
Q psy6094          46 YQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHL-DFITL--------------------------KR--   96 (455)
Q Consensus        46 ~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtql-p~ll~--------------------------e~--   96 (455)
                      +.++++.......+++|.++++.+.++++++++|+||||||... +.++.                          ..  
T Consensus        10 ~~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~   89 (414)
T 3oiy_A           10 FRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLAD   89 (414)
T ss_dssp             HHHHHHHHHSSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHcc
Confidence            44556555566778999999999999999999999999999531 11111                          11  


Q ss_pred             -cCCCC----------------------------ChHHHHHhccCCCCcCcc------h----------HHHHH------
Q psy6094          97 -SETQQ----------------------------YPNDVLNMLKDPELEGVN------N----------DVIFS------  125 (455)
Q Consensus        97 -~~~vg----------------------------~p~~ll~~l~d~~L~~~~------~----------D~ll~------  125 (455)
                       +..++                            +|.+|++.+....+..++      +          |.++.      
T Consensus        90 ~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~~~~  169 (414)
T 3oiy_A           90 EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPE  169 (414)
T ss_dssp             SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSEEEESCHHHHHHCHHHHHHHHHHTTCCH
T ss_pred             CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccEEEEeChHhhhhccchhhhHHhhcCCcH
Confidence             11111                            233343333111122333      2          55554      


Q ss_pred             H-HHHHHHhcC-----------CCCeEEEEccCC-CCC-cc-ceE-----------EeehhhhhhhhccCCCCChHHHHH
Q psy6094         126 L-LQHICTTQR-----------PGAILVYCTYTF-MGV-SP-MKV-----------FFCKNVLQRLMKGVGANSPKRWVK  179 (455)
Q Consensus       126 ~-lk~il~~~~-----------~~~k~ilmSAT~-~g~-~p-v~~-----------~~l~~~~~~~~~~~~~~~~~~l~~  179 (455)
                      - ++.++...+           ++.++++||||+ +.. .. ...           ...+.+.+.+..   ......+..
T Consensus       170 ~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~---~~~~~~l~~  246 (414)
T 3oiy_A          170 EIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRIS---SRSKEKLVE  246 (414)
T ss_dssp             HHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHSCCSSCCCCCCCSEEEEEES---SCCHHHHHH
T ss_pred             HHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhccCcCccccccccchheeec---cCHHHHHHH
Confidence            1 445543333           789999999994 322 10 000           000000011111   123334555


Q ss_pred             HHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEE-eecCCCChhhHhhhhcCCCCCceEEEEe----CCCCcc
Q psy6094         180 LLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQII-PLHSMLPTVSQKSIFNTPPEGVRKIVLA----TNIAET  254 (455)
Q Consensus       180 ~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~-~lhs~l~~~~r~~v~~~~~~g~~kViva----Tniae~  254 (455)
                      .+.. .++++||||+++.+++.+++.|...+      +.+. .+||.    +| + ++.|++|..+|+||    |+++++
T Consensus       247 ~l~~-~~~~~lVF~~~~~~~~~l~~~L~~~~------~~~~~~~h~~----~r-~-~~~f~~g~~~vLvat~s~T~~~~~  313 (414)
T 3oiy_A          247 LLEI-FRDGILIFAQTEEEGKELYEYLKRFK------FNVGETWSEF----EK-N-FEDFKVGKINILIGVQAYYGKLTR  313 (414)
T ss_dssp             HHHH-HCSSEEEEESSHHHHHHHHHHHHHTT------CCEEESSSCH----HH-H-HHHHHTTSCSEEEEECCTTCCCCC
T ss_pred             HHHH-cCCCEEEEECCHHHHHHHHHHHHHcC------CceehhhcCc----ch-H-HHHHhCCCCeEEEEecCcCchhhc
Confidence            5553 56899999999999999999999864      6777 89985    33 3 88899999999999    999999


Q ss_pred             CCCCCC-eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC-----CCeEEecCC
Q psy6094         255 SITIDD-IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL-----KRSETQQYP  314 (455)
Q Consensus       255 gitI~~-V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~-----~G~c~~L~t  314 (455)
                      |+|||+ |++||++|.++.                .|..+|.||+|||||.+     .|.||.++.
T Consensus       314 GiDip~~v~~VI~~~~p~~----------------~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~~  363 (414)
T 3oiy_A          314 GVDLPERIKYVIFWGTPSG----------------PDVYTYIQASGRSSRILNGVLVKGVSVIFEE  363 (414)
T ss_dssp             CCCCTTTCCEEEEESCCTT----------------TCHHHHHHHHGGGCCEETTEECCEEEEEECC
T ss_pred             cCccccccCEEEEECCCCC----------------CCHHHHHHHhCccccCCCCCCcceEEEEEEc
Confidence            999999 999999665421                56788999999999975     699999995

>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=99.91  E-value=2.4e-24  Score=252.92  Aligned_cols=199  Identities=13%  Similarity=0.057  Sum_probs=138.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCC-------C-C-------------CC-------CeEEEeecCCCChhhHhhhh
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSF-------F-N-------------SS-------RFQIIPLHSMLPTVSQKSIF  235 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~-------~-~-------------~~-------~~~v~~lhs~l~~~~r~~v~  235 (455)
                      ...+++||||+++..++.++..|.....       + .             .+       ..-|..+||+|++++|..++
T Consensus      1153 ~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE 1232 (1724)
T 4f92_B         1153 SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVE 1232 (1724)
T ss_dssp             CSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHH
T ss_pred             cCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHH
Confidence            5678999999999999998877653210       0 0             00       12378899999999999999


Q ss_pred             cCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEec
Q psy6094         236 NTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQ  312 (455)
Q Consensus       236 ~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L  312 (455)
                      +.|++|..+|||||+++++||++|.+.+||.+.    ..||...+    ...+.|..++.||+|||||.|   .|.|+.+
T Consensus      1233 ~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~----~~~dg~~~----~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll 1304 (1724)
T 4f92_B         1233 QLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDT----QYYNGKIH----AYVDYPIYDVLQMVGHANRPLQDDEGRCVIM 1304 (1724)
T ss_dssp             HHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECS----EEEETTTT----EEEECCHHHHHHHHTTBCCTTTCSCEEEEEE
T ss_pred             HHHHCCCCeEEEEChHHHcCCCCCccEEEEecC----ccccCccc----ccCCCCHHHHHHhhccccCCCCCCceEEEEE
Confidence            999999999999999999999999999999643    34554432    235788999999999999987   4999999


Q ss_pred             CChhh---hcc-CCCCcccccC-----hHHHH---------------HHHh------h------h--cCCCC--------
Q psy6094         313 YPNDV---LNM-LKDPELEGVN-----NDVIF---------------SLLQ------H------I--CTTQR--------  346 (455)
Q Consensus       313 ~t~~~---~~~-~~~PEi~r~~-----~~~~L---------------~~l~------~------~--~~~P~--------  346 (455)
                      .+...   +.. ...|+-.++.     .+.++               .++.      .      +  +....        
T Consensus      1305 ~~~~~~~~~~~ll~~~~pveS~L~~~l~~~l~~eI~~~~i~~~~d~~~~l~~Tfl~~r~~~nP~~y~l~~~~~~~~~~~l 1384 (1724)
T 4f92_B         1305 CQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHL 1384 (1724)
T ss_dssp             EEGGGHHHHHHHTTSCBCCCCCGGGSCHHHHHHHHHTTSCCBHHHHHHHHTTSSHHHHHHHSGGGTTCSCCSHHHHHHHH
T ss_pred             ecchHHHHHHHHhCCCCceeeecccchHHHHHHHHHhcccCCHHHHHHHHHhhHHHHHHhcCcccccccccchhhHHHHH
Confidence            88322   111 1222222222     22222               2221      0      0  11111        


Q ss_pred             hhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCChhHH
Q psy6094         347 PGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEI  391 (455)
Q Consensus       347 ~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p~~~  391 (455)
                      .+.++.+++.|.+.|+|+.+++- .+.+|++|+.++..+++|..+
T Consensus      1385 ~~lv~~~l~~L~~~~~I~~~~~~-~l~~T~lG~i~s~~yi~~~t~ 1428 (1724)
T 4f92_B         1385 SELVEQTLSDLEQSKCISIEDEM-DVAPLNLGMIAAYYYINYTTI 1428 (1724)
T ss_dssp             HHHHHHHHHHHHHTTSEEEETTT-EEEECHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHHHHCCCEEEcCCC-CEeecHHHHHHHHHCCCHHHH
Confidence            24467889999999999643321 245699999999999999443

>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=99.91  E-value=1.5e-24  Score=254.61  Aligned_cols=197  Identities=13%  Similarity=0.072  Sum_probs=139.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcC----C---C---CC---------------------CCeEEEeecCCCChhhHh
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSS----F---F---NS---------------------SRFQIIPLHSMLPTVSQK  232 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~----~---~---~~---------------------~~~~v~~lhs~l~~~~r~  232 (455)
                      ..++++||||+++++++.+++.|.+..    .   +   ..                     -..-+..+||+|++++|.
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~  394 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRT  394 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHH
Confidence            456789999999999999998886421    0   0   00                     012277889999999999


Q ss_pred             hhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeE
Q psy6094         233 SIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSE  309 (455)
Q Consensus       233 ~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c  309 (455)
                      .+.+.|++|..+|||||+.++.|||+|.+++||..    ...||+..|.    ..++|.+++.||+|||||.|   .|.+
T Consensus       395 ~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~----~~~~~~~~~~----~~~ls~~~~~Qm~GRAGR~g~d~~G~~  466 (1724)
T 4f92_B          395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKG----TQVYSPEKGR----WTELGALDILQMLGRAGRPQYDTKGEG  466 (1724)
T ss_dssp             HHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEEC----CEEEETTTTE----EEECCHHHHHHHHTTBSCTTTCSCEEE
T ss_pred             HHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeC----CEEecCcCCC----cccCCHHHHHHhhhhccCCCCCCccEE
Confidence            99999999999999999999999999999999963    2458877663    35789999999999999976   4999


Q ss_pred             EecCChhhhc------cCCCC-cccccC--h-----HHHH----------HHHh------hhcCC--------------C
Q psy6094         310 TQQYPNDVLN------MLKDP-ELEGVN--N-----DVIF----------SLLQ------HICTT--------------Q  345 (455)
Q Consensus       310 ~~L~t~~~~~------~~~~P-Ei~r~~--~-----~~~L----------~~l~------~~~~~--------------P  345 (455)
                      |.+.+.++..      ....| |-...+  .     ++++          .++.      .....              |
T Consensus       467 ii~~~~~~~~~~~~ll~~~~pieS~l~~~l~d~L~aeI~~g~i~~~~~a~~~l~~T~~~~r~~~~p~~y~~~~~~~~~d~  546 (1724)
T 4f92_B          467 ILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDP  546 (1724)
T ss_dssp             EEEEESTTCCHHHHHTTTCSCCCCCTTTTHHHHHHHHHHHTSCCBHHHHHHHHHHSHHHHHHHHCTTTTTCCHHHHHHCT
T ss_pred             EEEecchhHHHHHHHHcCCCcchhhccccHHHHHHHHHHHhhcCCHHHHHHHHhccHHHHHhhhChhhhccCccccccch
Confidence            9887743321      11111 111111  1     1222          1211      01111              1


Q ss_pred             C-----hhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh
Q psy6094         346 R-----PGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP  388 (455)
Q Consensus       346 ~-----~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p  388 (455)
                      .     .+.+..++..|...|.+..+..-..+.+|++|+.++.+++++
T Consensus       547 ~l~~~~~~~i~~~~~~L~~~~li~~d~~~~~~~~T~lGr~~s~~yi~~  594 (1724)
T 4f92_B          547 LLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITN  594 (1724)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTSEEECTTTCBEEECHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCeeeecCCCccccchHHHHHHHhcCCH
Confidence            1     234678899999999996544333456799999999999999

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.90  E-value=1.8e-24  Score=212.58  Aligned_cols=165  Identities=14%  Similarity=0.137  Sum_probs=132.9

Q ss_pred             hHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCc
Q psy6094         174 PKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAE  253 (455)
Q Consensus       174 ~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae  253 (455)
                      ...+...+....++++||||+++.+++.+++.|...+      +.+.++||++++.+|..+++.|++|..+|+||||+|+
T Consensus        16 ~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g------~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~   89 (300)
T 3i32_A           16 LEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLG------HPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAA   89 (300)
T ss_dssp             HHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTT------CCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTT
T ss_pred             HHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCC------CCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhh
Confidence            3345566655678999999999999999999998764      7899999999999999999999999999999999999


Q ss_pred             cCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC-CCeEEecCChhh--------------h
Q psy6094         254 TSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL-KRSETQQYPNDV--------------L  318 (455)
Q Consensus       254 ~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~-~G~c~~L~t~~~--------------~  318 (455)
                      +|+|||+|++|||++++                  .|.++|.||+|||||.| +|.||.+|+..+              +
T Consensus        90 ~Gidi~~v~~VI~~d~p------------------~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~  151 (300)
T 3i32_A           90 RGLDIPQVDLVVHYRMP------------------DRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRF  151 (300)
T ss_dssp             CSTTCCCCSEEEESSCC------------------SSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCC
T ss_pred             cCccccceeEEEEcCCC------------------CCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcc
Confidence            99999999999996653                  46778999999999997 599999999432              2


Q ss_pred             c---cCCCCcccccC-hHHHHHH--------------HhhhcCCCChhhHHhHHhhhhhccc
Q psy6094         319 N---MLKDPELEGVN-NDVIFSL--------------LQHICTTQRPGAILVFLPGWDTINS  362 (455)
Q Consensus       319 ~---~~~~PEi~r~~-~~~~L~~--------------l~~~~~~P~~~~i~~al~~L~~lga  362 (455)
                      .   ....|||.+.+ ..+++++              +..++++|+++.+..|+..|.....
T Consensus       152 ~~~~~~~~~ei~~~~~~~~~~~l~~~~~~~~~~f~~~~~~l~~~~~~e~laaal~~l~~~~~  213 (300)
T 3i32_A          152 KRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVEVVAALLALLLGGAP  213 (300)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHHHTTSCHHHHHTTHHHHHHHHHHTCHHHHHHHHHHHHTCCC
T ss_pred             eEeCCCCHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhcCcHHHHHHHHHHHhcCCc
Confidence            2   23456777777 6666632              2356778999999999999865443

>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=99.89  E-value=1.8e-23  Score=221.20  Aligned_cols=115  Identities=18%  Similarity=0.175  Sum_probs=55.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC------CCCeEEEeecCCCChhhHhhhhcCCCC-CceEEEEeCCCCccCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFN------SSRFQIIPLHSMLPTVSQKSIFNTPPE-GVRKIVLATNIAETSI  256 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~------~~~~~v~~lhs~l~~~~r~~v~~~~~~-g~~kVivaTniae~gi  256 (455)
                      ..++.+|||++++..++.+++.|.......      -.+.....+||++++++|.++++.|++ |..+|+|||+++++||
T Consensus       388 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~Gi  467 (556)
T 4a2p_A          388 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  467 (556)
T ss_dssp             CTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC------
T ss_pred             CCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCC
Confidence            467899999999999999999998752110      012345567889999999999999999 9999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV  317 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~  317 (455)
                      |+|++++||+        ||+          |-|..++.||+|| ||.++|.||.|++...
T Consensus       468 Dip~v~~VI~--------~d~----------p~s~~~~~Qr~GR-gR~~~g~~~~l~~~~~  509 (556)
T 4a2p_A          468 DIVQCNLVVL--------YEY----------SGNVTKMIQVRGR-GRAAGSKCILVTSKTE  509 (556)
T ss_dssp             -----CEEEE--------ETC----------CSCHHHHHHC---------CCEEEEESCHH
T ss_pred             CchhCCEEEE--------eCC----------CCCHHHHHHhcCC-CCCCCceEEEEEeCcc
Confidence            9999999998        553          3466788999999 9998899999999553

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.88  E-value=2.2e-22  Score=212.38  Aligned_cols=114  Identities=16%  Similarity=0.209  Sum_probs=73.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC------CCCeEEEeecCCCChhhHhhhhcCCCC-CceEEEEeCCCCccCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFN------SSRFQIIPLHSMLPTVSQKSIFNTPPE-GVRKIVLATNIAETSI  256 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~------~~~~~v~~lhs~l~~~~r~~v~~~~~~-g~~kVivaTniae~gi  256 (455)
                      ..++.+|||+++...++.+++.|...+...      -.+.....+||++++++|.++++.|++ |..+|+|||+++++||
T Consensus       387 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~Gl  466 (555)
T 3tbk_A          387 KPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGI  466 (555)
T ss_dssp             CTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCE
T ss_pred             CCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCC
Confidence            456899999999999999999999764210      012344556789999999999999999 9999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~  316 (455)
                      |+|++++||+        ||++.          |..++.||+|| ||..+|.||.|++..
T Consensus       467 Dlp~v~~VI~--------~d~p~----------s~~~~~Qr~GR-gR~~~g~~~~l~~~~  507 (555)
T 3tbk_A          467 DIAECNLVIL--------YEYVG----------NVIKMIQTRGR-GRARDSKCFLLTSSA  507 (555)
T ss_dssp             ETTSCSEEEE--------ESCCS----------SCCCEECSSCC-CTTTSCEEEEEESCH
T ss_pred             ccccCCEEEE--------eCCCC----------CHHHHHHhcCc-CcCCCceEEEEEcCC
Confidence            9999999999        55443          33456699999 999889999999954

>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=99.88  E-value=2.1e-22  Score=207.71  Aligned_cols=110  Identities=20%  Similarity=0.237  Sum_probs=96.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecC--------CCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHS--------MLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs--------~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      ..++.+|||+++...++.+++.|...+      +.+..+||        +++.++|.++++.|.+|..+|+|||+++++|
T Consensus       359 ~~~~k~lVF~~~~~~~~~l~~~L~~~~------~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~G  432 (494)
T 1wp9_A          359 KQNSKIIVFTNYRETAKKIVNELVKDG------IKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEG  432 (494)
T ss_dssp             CTTCCEEEECSCHHHHHHHHHHHHHTT------CCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGG
T ss_pred             CCCCeEEEEEccHHHHHHHHHHHHHcC------CCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccC
Confidence            468899999999999999999999874      77999999        9999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV  317 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~  317 (455)
                      +|+|++++||.++.                  |-+.+.+.||+||+||.++|.||+|+++..
T Consensus       433 ldl~~~~~Vi~~d~------------------~~~~~~~~Qr~GR~~R~g~g~~~~l~~~~t  476 (494)
T 1wp9_A          433 LDVPEVDLVVFYEP------------------VPSAIRSIQRRGRTGRHMPGRVIILMAKGT  476 (494)
T ss_dssp             GGSTTCCEEEESSC------------------CHHHHHHHHHHTTSCSCCCSEEEEEEETTS
T ss_pred             CCchhCCEEEEeCC------------------CCCHHHHHHHHhhccCCCCceEEEEEecCC
Confidence            99999999998443                  346678999999999999999999999543

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.87  E-value=4.7e-23  Score=234.07  Aligned_cols=212  Identities=15%  Similarity=0.136  Sum_probs=141.2

Q ss_pred             HHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccch-hhhhh--------------------------hh
Q psy6094          44 RRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHL-DFITL--------------------------KR   96 (455)
Q Consensus        44 ~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtql-p~ll~--------------------------e~   96 (455)
                      ..+.+.++..-....+++|.++++.+.++++++++|+||||||+.. +.++.                          ..
T Consensus        65 ~~~~~~~~~~~gf~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~l  144 (1104)
T 4ddu_A           65 EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKL  144 (1104)
T ss_dssp             HHHHHHHHHHSSSCCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHHh
Confidence            3445555555555788999999999999999999999999999632 22111                          10


Q ss_pred             c---CC----------------------------CCChHHHHHhccCCCCcCcc------h----------HHHHH----
Q psy6094          97 S---ET----------------------------QQYPNDVLNMLKDPELEGVN------N----------DVIFS----  125 (455)
Q Consensus        97 ~---~~----------------------------vg~p~~ll~~l~d~~L~~~~------~----------D~ll~----  125 (455)
                      +   ..                            ||+|.+|++.+....+.+++      +          |.+|.    
T Consensus       145 ~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf  224 (1104)
T 4ddu_A          145 ADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGI  224 (1104)
T ss_dssp             SCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSC
T ss_pred             hCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEEEEeCCCccccccccchhhhHhcCC
Confidence            0   01                            12344554443101122222      2          77776    


Q ss_pred             --H-HHHHHHhcC-----------CCCeEEEEccCC-CCC-cc------ce------EEeehhhhhhhhccCCCCChHHH
Q psy6094         126 --L-LQHICTTQR-----------PGAILVYCTYTF-MGV-SP------MK------VFFCKNVLQRLMKGVGANSPKRW  177 (455)
Q Consensus       126 --~-lk~il~~~~-----------~~~k~ilmSAT~-~g~-~p------v~------~~~l~~~~~~~~~~~~~~~~~~l  177 (455)
                        . ++.++...+           ++.|+++||||+ +.. ..      +.      ....+.+.+.+...   .....+
T Consensus       225 ~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~i~v~~~~~~~~~i~~~~~~~---~k~~~L  301 (1104)
T 4ddu_A          225 PEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISS---RSKEKL  301 (1104)
T ss_dssp             CHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTCCCCCBCCCCCCCEEEEEESC---CCHHHH
T ss_pred             CHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcceeEEeccCCCCcCCceeEEEec---CHHHHH
Confidence              2 556654434           789999999994 322 10      00      00001111111111   233345


Q ss_pred             HHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEE-eecCCCChhhHhhhhcCCCCCceEEEEe----CCCC
Q psy6094         178 VKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQII-PLHSMLPTVSQKSIFNTPPEGVRKIVLA----TNIA  252 (455)
Q Consensus       178 ~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~-~lhs~l~~~~r~~v~~~~~~g~~kViva----Tnia  252 (455)
                      ...+.. .++++||||+++..++.+++.|...+      +.+. .+||     +|.+ ++.|++|..+||||    ||++
T Consensus       302 ~~ll~~-~~~~~LVF~~s~~~a~~l~~~L~~~g------~~~~~~lhg-----~rr~-l~~F~~G~~~VLVatas~Tdvl  368 (1104)
T 4ddu_A          302 VELLEI-FRDGILIFAQTEEEGKELYEYLKRFK------FNVGETWSE-----FEKN-FEDFKVGKINILIGVQAYYGKL  368 (1104)
T ss_dssp             HHHHHH-HCSSEEEEESSSHHHHHHHHHHHHTT------CCEEESSSS-----HHHH-HHHHHHTSCSEEEEETTTHHHH
T ss_pred             HHHHHh-cCCCEEEEECcHHHHHHHHHHHHhCC------CCeeeEecC-----cHHH-HHHHHCCCCCEEEEecCCCCee
Confidence            555553 46999999999999999999999864      6787 9999     2555 88999999999999    9999


Q ss_pred             ccCCCCCC-eeEEEeCCCCc
Q psy6094         253 ETSITIDD-IVYVVDCGKTK  271 (455)
Q Consensus       253 e~gitI~~-V~~VID~g~~k  271 (455)
                      ++|||||+ |++||++|+|+
T Consensus       369 arGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          369 TRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             CCSCCCTTTCCEEEEESCCE
T ss_pred             EecCcCCCCCCEEEEECCCC
Confidence            99999999 99999999998

>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=99.86  E-value=7.4e-22  Score=215.30  Aligned_cols=109  Identities=17%  Similarity=0.205  Sum_probs=87.5

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCC--------CChhhHhhhhcCCCCCceEEEEeCCCCccCCC
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSM--------LPTVSQKSIFNTPPEGVRKIVLATNIAETSIT  257 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~--------l~~~~r~~v~~~~~~g~~kVivaTniae~git  257 (455)
                      ++.+|||+++++.++.+++.|.....+...++.+..+||+        |++.+|.++++.|++|..+|||||+++++|||
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            7899999999999999999999864333335889999999        99999999999999999999999999999999


Q ss_pred             CCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         258 IDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       258 I~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      +|++++||+        ||+          |-|.+++.||+|||||.+  .++.++.
T Consensus       480 ip~v~~VI~--------~d~----------p~s~~~~~Qr~GRArr~g--~~~~l~~  516 (699)
T 4gl2_A          480 IKECNIVIR--------YGL----------VTNEIAMVQARGRARADE--STYVLVA  516 (699)
T ss_dssp             CCSCCCCEE--------ESC----------CCCHHHHHHHHTTSCSSS--CEEEEEE
T ss_pred             cccCCEEEE--------eCC----------CCCHHHHHHHcCCCCCCC--ceEEEEE
Confidence            999999998        543          345678899999988754  4555544

>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=99.86  E-value=1.2e-22  Score=222.53  Aligned_cols=117  Identities=18%  Similarity=0.195  Sum_probs=92.4

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHH--------HHHHHHHHHHh-cCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEE
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWD--------TINSLHRSMCQ-SSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKI  245 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~--------ei~~l~~~L~~-~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kV  245 (455)
                      +...+..  ..+++++||||..+        .++.+++.|.. ..    +++.+..+||+|++++|..+++.|++|..+|
T Consensus       567 l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~----~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~I  642 (780)
T 1gm5_A          567 VYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVF----PEFKLGLMHGRLSQEEKDRVMLEFAEGRYDI  642 (780)
T ss_dssp             HHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC-------CBCCCCSSSCCSCSHHHHHHHTTTSSSB
T ss_pred             HHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhc----CCCcEEEEeCCCCHHHHHHHHHHHHCCCCeE
Confidence            4444443  46788999999654        45666776765 21    2477899999999999999999999999999


Q ss_pred             EEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         246 VLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       246 ivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      +|||+++|+|||+|++++||+.+.        +.         .+.+++.||+||+||.+. |.||.+++
T Consensus       643 LVaT~vie~GIDiP~v~~VIi~d~--------~r---------~~l~~l~Qr~GRaGR~g~~g~~ill~~  695 (780)
T 1gm5_A          643 LVSTTVIEVGIDVPRANVMVIENP--------ER---------FGLAQLHQLRGRVGRGGQEAYCFLVVG  695 (780)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSC--------SS---------SCTTHHHHHHHTSCCSSTTCEEECCCC
T ss_pred             EEECCCCCccccCCCCCEEEEeCC--------CC---------CCHHHHHHHhcccCcCCCCCEEEEEEC
Confidence            999999999999999999998443        21         134678899999999775 99999997

>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=99.86  E-value=2.6e-21  Score=214.31  Aligned_cols=115  Identities=18%  Similarity=0.176  Sum_probs=61.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCC------CCeEEEeecCCCChhhHhhhhcCCCC-CceEEEEeCCCCccCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNS------SRFQIIPLHSMLPTVSQKSIFNTPPE-GVRKIVLATNIAETSI  256 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~------~~~~v~~lhs~l~~~~r~~v~~~~~~-g~~kVivaTniae~gi  256 (455)
                      ..++.+|||++++..++.+++.|........      .+.....+||++++.+|..+++.|++ |..+|+|||+++++||
T Consensus       629 ~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GI  708 (797)
T 4a2q_A          629 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  708 (797)
T ss_dssp             CSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-----
T ss_pred             CCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCC
Confidence            4568999999999999999999987532110      12345667999999999999999999 9999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV  317 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~  317 (455)
                      |+|++++||+        ||+          |-|..++.||+|| ||..+|.||.|++...
T Consensus       709 Dlp~v~~VI~--------yd~----------p~s~~~~iQr~GR-GR~~~g~~i~l~~~~~  750 (797)
T 4a2q_A          709 DIVQCNLVVL--------YEY----------SGNVTKMIQVRGR-GRAAGSKCILVTSKTE  750 (797)
T ss_dssp             --CCCSEEEE--------ESC----------CSCHHHHHTC--------CCCEEEEECCHH
T ss_pred             CchhCCEEEE--------eCC----------CCCHHHHHHhcCC-CCCCCceEEEEEeCCc
Confidence            9999999998        543          3466788999999 9998899999999543

>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=99.85  E-value=7.7e-22  Score=223.84  Aligned_cols=199  Identities=11%  Similarity=0.053  Sum_probs=126.1

Q ss_pred             HccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc-chhhhhh------------------------------hhcC---
Q psy6094          53 RKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPL-HLDFITL------------------------------KRSE---   98 (455)
Q Consensus        53 R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt-qlp~ll~------------------------------e~~~---   98 (455)
                      .+.. . ++|.++++.+.+|++++++|+||||||+ ++|.+..                              ..+.   
T Consensus        54 ~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~  131 (1054)
T 1gku_B           54 VGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTE  131 (1054)
T ss_dssp             TCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGG
T ss_pred             cCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCcc
Confidence            3444 5 9999999999999999999999999994 4442211                              1111   


Q ss_pred             -CC----C----------------------ChHHHHHhccCCCCcCcc------hHHHHH---HHHHHHHhc--------
Q psy6094          99 -TQ----Q----------------------YPNDVLNMLKDPELEGVN------NDVIFS---LLQHICTTQ--------  134 (455)
Q Consensus        99 -~v----g----------------------~p~~ll~~l~d~~L~~~~------~D~ll~---~lk~il~~~--------  134 (455)
                       .+    |                      +|.+|++.+..  |..++      +|.++.   .++.++...        
T Consensus       132 ~~v~~~~Gg~~~~~~~~~~~~l~~~~IlV~TP~~L~~~l~~--L~~l~~lViDEah~~l~~~~~~~~i~~~lgf~~~~~~  209 (1054)
T 1gku_B          132 NLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE--LGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKT  209 (1054)
T ss_dssp             GSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTT--SCCCSEEEESCHHHHHTSTHHHHHHHHHTTEEEETTT
T ss_pred             ceEEEEeCCCChhhHHHHHhhccCCCEEEEcHHHHHHHHHH--hccCCEEEEeChhhhhhccccHHHHHHHhCcchhhhh
Confidence             11    1                      24445555522  44555      666664   233333222        


Q ss_pred             ---CCCCeEEEEccCCCCCccceEEeehhh---------------hhhhhccCCCCChHHHHHHHHccCCCCEEEEcCCH
Q psy6094         135 ---RPGAILVYCTYTFMGVSPMKVFFCKNV---------------LQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGW  196 (455)
Q Consensus       135 ---~~~~k~ilmSAT~~g~~pv~~~~l~~~---------------~~~~~~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~  196 (455)
                         +...++++||||++........++.++               .+.+.   .......+...+. ..++++||||+++
T Consensus       210 ~~~~~~~q~~l~SAT~t~~~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~---~~~k~~~L~~ll~-~~~~~~LVF~~t~  285 (1054)
T 1gku_B          210 KSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDIGSSRITVRNVEDVAV---NDESISTLSSILE-KLGTGGIIYARTG  285 (1054)
T ss_dssp             TEEEECCSSEEEECCCCSCCCTTHHHHHHHHCCCCSCCEECCCCEEEEEE---SCCCTTTTHHHHT-TSCSCEEEEESSH
T ss_pred             hhcccCCceEEEEecCCCchhHHHHHhhcceEEEccCcccCcCCceEEEe---chhHHHHHHHHHh-hcCCCEEEEEcCH
Confidence               356789999999943200000011110               01111   0111222444444 4468899999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEe----CCCCccCCCCCCe-eEEEeCCCCc
Q psy6094         197 DTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA----TNIAETSITIDDI-VYVVDCGKTK  271 (455)
Q Consensus       197 ~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViva----Tniae~gitI~~V-~~VID~g~~k  271 (455)
                      ++++.+++.|...       +.+..+||++.     .+++.|++|..+||||    ||++++|||||+| ++||++|.++
T Consensus       286 ~~a~~l~~~L~~~-------~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~  353 (1054)
T 1gku_B          286 EEAEEIYESLKNK-------FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS  353 (1054)
T ss_dssp             HHHHHHHHTTTTS-------SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCE
T ss_pred             HHHHHHHHHHhhc-------cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCCc
Confidence            9999999988764       67999999983     5677788999999999    9999999999995 9999999993

>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=99.84  E-value=7.8e-21  Score=217.01  Aligned_cols=111  Identities=17%  Similarity=0.170  Sum_probs=96.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+++++|||++.++++.+++.|+...    +++.+..+||++++.+|.++++.|.+|..+|+|||+++|+|||||++++
T Consensus       810 ~~g~qvlvf~~~v~~~~~l~~~L~~~~----p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~  885 (1151)
T 2eyq_A          810 LRGGQVYYLYNDVENIQKAAERLAELV----PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  885 (1151)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHC----TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEE
T ss_pred             hcCCeEEEEECCHHHHHHHHHHHHHhC----CCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcE
Confidence            467899999999999999999998863    2477999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      ||.        +++.         +.+.+++.||+||+||.+. |.||.+++.
T Consensus       886 VIi--------~~~~---------~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~  921 (1151)
T 2eyq_A          886 III--------ERAD---------HFGLAQLHQLRGRVGRSHHQAYAWLLTPH  921 (1151)
T ss_dssp             EEE--------TTTT---------SSCHHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             EEE--------eCCC---------CCCHHHHHHHHhccCcCCCceEEEEEECC
Confidence            995        3221         1234678899999999875 999999984

>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=99.84  E-value=7.4e-21  Score=213.72  Aligned_cols=114  Identities=18%  Similarity=0.182  Sum_probs=61.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCC------CCCeEEEeecCCCChhhHhhhhcCCCC-CceEEEEeCCCCccCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFN------SSRFQIIPLHSMLPTVSQKSIFNTPPE-GVRKIVLATNIAETSI  256 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~------~~~~~v~~lhs~l~~~~r~~v~~~~~~-g~~kVivaTniae~gi  256 (455)
                      ..++.+|||+++++.++.+++.|.....+.      -.+.....+||++++.+|.++++.|+. |..+|||||+++++||
T Consensus       629 ~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGI  708 (936)
T 4a2w_A          629 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  708 (936)
T ss_dssp             CTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC-----
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCC
Confidence            356899999999999999999999863211      012345567999999999999999999 9999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~  316 (455)
                      |||++++||+        ||+          |-|..++.||+|| ||.++|.||.|++..
T Consensus       709 Dlp~v~~VI~--------yD~----------p~s~~~~iQr~GR-GR~~~g~vi~Li~~~  749 (936)
T 4a2w_A          709 DIVQCNLVVL--------YEY----------SGNVTKMIQVRGR-GRAAGSKCILVTSKT  749 (936)
T ss_dssp             -CCCCSEEEE--------ESC----------CSCSHHHHCC--------CCCEEEEESCH
T ss_pred             cchhCCEEEE--------eCC----------CCCHHHHHHhcCC-CCCCCCEEEEEEeCC
Confidence            9999999998        554          3456778899999 999889999999954

>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=99.83  E-value=2.5e-20  Score=201.93  Aligned_cols=104  Identities=20%  Similarity=0.152  Sum_probs=91.4

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC-----
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID-----  259 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~-----  259 (455)
                      .+.++|||+.+.+.++.+++.|...+      +.+..|||.+.+.++..+.+.++.|  .|+||||+|+||+||+     
T Consensus       431 ~~~pvLVft~s~~~se~Ls~~L~~~g------i~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V  502 (844)
T 1tf5_A          431 TGQPVLVGTVAVETSELISKLLKNKG------IPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGV  502 (844)
T ss_dssp             HTCCEEEEESCHHHHHHHHHHHHTTT------CCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTS
T ss_pred             cCCcEEEEECCHHHHHHHHHHHHHCC------CCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchh
Confidence            46789999999999999999999875      7788999999998888777777766  5999999999999999     


Q ss_pred             ---CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         260 ---DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       260 ---~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                         ++.+||++.+                  |-|...+.||+||+||.|. |.++.+++
T Consensus       503 ~~~ggl~VIn~d~------------------p~s~r~y~hr~GRTGRqG~~G~s~~~vs  543 (844)
T 1tf5_A          503 KELGGLAVVGTER------------------HESRRIDNQLRGRSGRQGDPGITQFYLS  543 (844)
T ss_dssp             GGGTSEEEEESSC------------------CSSHHHHHHHHTTSSGGGCCEEEEEEEE
T ss_pred             hhcCCcEEEEecC------------------CCCHHHHHhhcCccccCCCCCeEEEEec
Confidence               8999999655                  4566778899999999887 99998888

>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=99.81  E-value=3.5e-20  Score=167.62  Aligned_cols=122  Identities=20%  Similarity=0.229  Sum_probs=101.4

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      +...+....++++|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|+
T Consensus        25 L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~------~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gi   98 (175)
T 2rb4_A           25 LCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDG------HQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGI   98 (175)
T ss_dssp             HHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTT------CCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTT
T ss_pred             HHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcC------CcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCC
Confidence            5555555667899999999999999999999864      7799999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+|++++||+++.+...            ....+..++.||+|||||.+. |.||.+++..
T Consensus        99 d~~~~~~Vi~~d~p~~~------------~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~  147 (175)
T 2rb4_A           99 DVKQVTIVVNFDLPVKQ------------GEEPDYETYLHRIGRTGRFGKKGLAFNMIEVD  147 (175)
T ss_dssp             CCTTEEEEEESSCCC--------------CCSCCHHHHHHHHCBC----CCEEEEEEECGG
T ss_pred             CcccCCEEEEeCCCCCc------------cccCCHHHHHHHhcccccCCCCceEEEEEccc
Confidence            99999999996654111            123678899999999999865 9999999954

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.81  E-value=4e-20  Score=165.39  Aligned_cols=117  Identities=16%  Similarity=0.197  Sum_probs=104.5

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+...+....++++|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|
T Consensus        25 ~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~------~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   98 (163)
T 2hjv_A           25 LLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLG------YPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG   98 (163)
T ss_dssp             HHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTT
T ss_pred             HHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcC------CcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcC
Confidence            35566666678899999999999999999999864      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|+|++++||+++.                  |.|.+++.||+||+||.+. |.|+.+++..
T Consensus        99 ld~~~~~~Vi~~~~------------------p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~  142 (163)
T 2hjv_A           99 IDIENISLVINYDL------------------PLEKESYVHRTGRTGRAGNKGKAISFVTAF  142 (163)
T ss_dssp             CCCSCCSEEEESSC------------------CSSHHHHHHHTTTSSCTTCCEEEEEEECGG
T ss_pred             CchhcCCEEEEeCC------------------CCCHHHHHHhccccCcCCCCceEEEEecHH
Confidence            99999999999543                  4577889999999999875 9999999954

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.80  E-value=2.3e-20  Score=167.15  Aligned_cols=117  Identities=19%  Similarity=0.299  Sum_probs=100.5

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+...+....++++|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|
T Consensus        20 ~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   93 (165)
T 1fuk_A           20 CLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDK------FTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG   93 (165)
T ss_dssp             HHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTT
T ss_pred             HHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcC------CCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcC
Confidence            35566665678899999999999999999999864      779999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|+|++++||+++.                  |.|.+++.||+||+||.+. |.||.+++.+
T Consensus        94 ~d~~~~~~Vi~~~~------------------p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~  137 (165)
T 1fuk_A           94 IDVQQVSLVINYDL------------------PANKENYIHRIGRGGRFGRKGVAINFVTNE  137 (165)
T ss_dssp             CCCCSCSEEEESSC------------------CSSGGGGGGSSCSCC-----CEEEEEEETT
T ss_pred             CCcccCCEEEEeCC------------------CCCHHHHHHHhcccccCCCCceEEEEEcch
Confidence            99999999999554                  3466778899999999865 9999999844

>3i4u_A ATP-dependent RNA helicase DHX8; splicing, ATP-binding, hydrolase, mRNA processing, splicing, nucleotide-binding, nucleus, phosphoprotein, SPLI; 2.10A {Homo sapiens}

Probab=99.79  E-value=1.7e-19  Score=174.05  Aligned_cols=105  Identities=13%  Similarity=0.103  Sum_probs=92.2

Q ss_pred             HHhhhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCCh---------------hHHHHHHHhhc--
Q psy6094         337 LLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKP---------------KEIITVRDCLS--  399 (455)
Q Consensus       337 ~l~~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p---------------~~~l~iaa~ls--  399 (455)
                      ++..++|||+.+++..|++.|..+||||.+|+|     |++|+.|+.||+||               +++++|||+||  
T Consensus         7 ~l~~~ldpP~~~~l~~A~~~L~~LgAld~~g~l-----T~lG~~ma~lPl~P~lakmLl~a~~~~c~~~~l~iaA~Ls~~   81 (270)
T 3i4u_A            7 EFELGTRGSPMETLITAMEQLYTLGALDDEGLL-----TRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQ   81 (270)
T ss_dssp             -------CCHHHHHHHHHHHHHHHTSBCTTSCB-----CHHHHHHTTSCSCHHHHHHHHHHHHTTCHHHHHHHHHHHTSS
T ss_pred             ccccCCCCcCHHHHHHHHHHHHHcCCcCCCCCc-----cHHHHHHHhCCCCHHHHHHHHHhhhcCCHHHHHHHHHHHCCC
Confidence            344459999999999999999999999999999     99999999999999               89999999999  


Q ss_pred             --CcCCcChHHHHHHHHhhhC-CCCcHHHHHHHHHHHhcCCCCchHhHHHhh
Q psy6094         400 --FECKPSTAKIIKELRARLD-MLLAHKLSHPGTTAWGDPNEGNILHCCSGF  448 (455)
Q Consensus       400 --f~~p~~~~~~~~~~~~~~~-~~sD~~~~~~~~~~~~~~~~~~~~~~c~~~  448 (455)
                        |..|.+++++++++|++|. ..|||++++|+|++|.+.+.+  ++||++|
T Consensus        82 ~~f~~p~~~~~~a~~~~~~f~~~~sD~ltlLn~~~~~~~~~~~--~~wC~~~  131 (270)
T 3i4u_A           82 NVFYRPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKNNKFS--NPWCYEN  131 (270)
T ss_dssp             CCBCCCGGGHHHHHHHHHTTCBTTBHHHHHHHHHHHHHHTTTC--HHHHHHT
T ss_pred             ccccCCchhHHHHHHHHHHccCCCChHHHHHHHHHHHHHcCch--hhHHHHh
Confidence              8889999999999999999 999999999999999986543  6899973

>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=99.79  E-value=8.8e-20  Score=164.73  Aligned_cols=116  Identities=17%  Similarity=0.229  Sum_probs=103.6

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+...+....++++|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|
T Consensus        21 ~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~------~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G   94 (172)
T 1t5i_A           21 KLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQN------FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG   94 (172)
T ss_dssp             HHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTT
T ss_pred             HHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcC------CCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcC
Confidence            45566666677899999999999999999999864      779999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      +|+|++++||+++.                  |.|.+++.||+||+||.|. |.|+.+++.
T Consensus        95 ldi~~~~~Vi~~d~------------------p~~~~~~~qr~GR~~R~g~~g~~~~~~~~  137 (172)
T 1t5i_A           95 MDIERVNIAFNYDM------------------PEDSDTYLHRVARAGRFGTKGLAITFVSD  137 (172)
T ss_dssp             CCGGGCSEEEESSC------------------CSSHHHHHHHHHHHTGGGCCCEEEEEECS
T ss_pred             cchhhCCEEEEECC------------------CCCHHHHHHHhcccccCCCCcEEEEEEcC
Confidence            99999999999443                  3567889999999999876 999999983

>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=99.79  E-value=9.7e-20  Score=189.59  Aligned_cols=113  Identities=14%  Similarity=0.094  Sum_probs=94.2

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      +...+....++++|||+++.+.++.+++.|.           +..+||+++..+|.++++.|++|..+|||||+++++|+
T Consensus       340 l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----------~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gl  408 (472)
T 2fwr_A          340 LREILERHRKDKIIIFTRHNELVYRISKVFL-----------IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  408 (472)
T ss_dssp             HHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----------CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----------cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCc
Confidence            4444554668899999999999999998774           33589999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCC----eEEecCChhhh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR----SETQQYPNDVL  318 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G----~c~~L~t~~~~  318 (455)
                      |+|++++||+        ||+          |-|..++.||+||+||.++|    .+|.++++...
T Consensus       409 dlp~~~~Vi~--------~~~----------~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t~  456 (472)
T 2fwr_A          409 DVPDANVGVI--------MSG----------SGSAREYIQRLGRILRPSKGKKEAVLYELISRGTG  456 (472)
T ss_dssp             CSCCBSEEEE--------ECC----------SSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSCC
T ss_pred             ccccCcEEEE--------ECC----------CCCHHHHHHHHhhccCCCCCCceEEEEEEEeCCCc
Confidence            9999999998        432          34567889999999998877    56677765443

>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=99.78  E-value=1.5e-19  Score=165.26  Aligned_cols=118  Identities=18%  Similarity=0.222  Sum_probs=89.8

Q ss_pred             HHHHHHHcc-CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         176 RWVKLLRSM-LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       176 ~l~~~i~~~-~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      .+...+... .++++|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++
T Consensus        35 ~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g------~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~  108 (185)
T 2jgn_A           35 FLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEG------YACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAAR  108 (185)
T ss_dssp             HHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTT------CCEEEEC--------CHHHHHHHHTSSSEEEEEC----
T ss_pred             HHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcC------CceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhc
Confidence            355666543 57899999999999999999999864      78999999999999999999999999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      |+|+|++++||+++.                  |.|.+++.||+||+||.|. |.|+.+++..+
T Consensus       109 Gldi~~~~~VI~~d~------------------p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~  154 (185)
T 2jgn_A          109 GLDISNVKHVINFDL------------------PSDIEEYVHRIGRTGRVGNLGLATSFFNERN  154 (185)
T ss_dssp             --CCCSBSEEEESSC------------------CSSHHHHHHHHTTBCCTTSCEEEEEEECGGG
T ss_pred             CCCcccCCEEEEeCC------------------CCCHHHHHHHccccCCCCCCcEEEEEEchhh
Confidence            999999999999443                  3467889999999999875 99999999553

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.77  E-value=1.9e-19  Score=165.39  Aligned_cols=115  Identities=17%  Similarity=0.254  Sum_probs=99.2

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      +...+. ..++++|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|+
T Consensus        46 L~~~l~-~~~~~~lVF~~~~~~~~~l~~~L~~~g------~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gl  118 (191)
T 2p6n_A           46 LLECLQ-KTPPPVLIFAEKKADVDAIHEYLLLKG------VEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGL  118 (191)
T ss_dssp             HHHHHT-TSCSCEEEECSCHHHHHHHHHHHHHHT------CCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTC
T ss_pred             HHHHHH-hCCCCEEEEECCHHHHHHHHHHHHHcC------CcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCC
Confidence            555554 456789999999999999999998864      7799999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+|++++||+++.                  |.+..++.||+||+||.|. |.|+.+++..
T Consensus       119 di~~v~~VI~~d~------------------p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~  161 (191)
T 2p6n_A          119 DFPAIQHVINYDM------------------PEEIENYVHRIGRTGCSGNTGIATTFINKA  161 (191)
T ss_dssp             CCCCCSEEEESSC------------------CSSHHHHHHHHTTSCC---CCEEEEEECTT
T ss_pred             CcccCCEEEEeCC------------------CCCHHHHHHHhCccccCCCCcEEEEEEcCc
Confidence            9999999999443                  3567789999999999875 9999999843

>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=99.76  E-value=6.9e-18  Score=182.89  Aligned_cols=105  Identities=20%  Similarity=0.162  Sum_probs=90.8

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCe--
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDI--  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V--  261 (455)
                      ..+.++|||+.+.+.++.+++.|...+      +.+..|||...+.++..+.+.+++|  .|+||||+|.||+||+.+  
T Consensus       458 ~~gqpvLVft~Sie~sE~Ls~~L~~~G------i~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~  529 (922)
T 1nkt_A          458 AKGQPVLIGTTSVERSEYLSRQFTKRR------IPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGN  529 (922)
T ss_dssp             HTTCCEEEEESCHHHHHHHHHHHHHTT------CCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCC
T ss_pred             hcCCcEEEEECCHHHHHHHHHHHHHCC------CCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCC
Confidence            345689999999999999999999875      7788899998888888888888888  699999999999999975  


Q ss_pred             --------------------------------------------------eEEEeCCCCcccccccCCCcccccccccch
Q psy6094         262 --------------------------------------------------VYVVDCGKTKMSNFDVKDNIATLKPEWISL  291 (455)
Q Consensus       262 --------------------------------------------------~~VID~g~~k~~~yd~~~~~~~l~~~~iSk  291 (455)
                                                                        .|||++.+                  |-|+
T Consensus       530 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~------------------pes~  591 (922)
T 1nkt_A          530 VDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTER------------------HESR  591 (922)
T ss_dssp             HHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSC------------------CSSH
T ss_pred             HHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccC------------------CCCH
Confidence                                                              59999655                  4566


Q ss_pred             hhHHhhhcccCCCCC-CeEEecCC
Q psy6094         292 ANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       292 a~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ..+.||+||+||.|. |.+..+.+
T Consensus       592 riy~qr~GRTGRqGdpG~s~fflS  615 (922)
T 1nkt_A          592 RIDNQLRGRSGRQGDPGESRFYLS  615 (922)
T ss_dssp             HHHHHHHHTSSGGGCCEEEEEEEE
T ss_pred             HHHHHHhcccccCCCCeeEEEEec
Confidence            778899999999887 99888777

>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=99.76  E-value=3e-18  Score=185.34  Aligned_cols=105  Identities=16%  Similarity=0.141  Sum_probs=91.8

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCC---
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDD---  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~---  260 (455)
                      ..+.++|||+++...++.+++.|...+      +.+..|||...+.++..+.+.+++|  .|+||||+|.||+||+.   
T Consensus       439 ~~gqpvLVft~sie~se~Ls~~L~~~g------i~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn  510 (853)
T 2fsf_A          439 AKGQPVLVGTISIEKSELVSNELTKAG------IKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGS  510 (853)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHTT------CCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCC
T ss_pred             cCCCCEEEEECcHHHHHHHHHHHHHCC------CCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCc
Confidence            356789999999999999999999875      7788899999888888888889888  69999999999999997   


Q ss_pred             -----------------------------e-----eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC
Q psy6094         261 -----------------------------I-----VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK  306 (455)
Q Consensus       261 -----------------------------V-----~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~  306 (455)
                                                   |     .+||++.+                  |-|+..+.||+||+||.|.
T Consensus       511 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~------------------pes~riy~qr~GRTGRqGd  572 (853)
T 2fsf_A          511 WQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTER------------------HESRRIDNQLRGRSGRQGD  572 (853)
T ss_dssp             HHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSC------------------CSSHHHHHHHHTTSSGGGC
T ss_pred             hHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccC------------------CCCHHHHHhhccccccCCC
Confidence                                         4     69999665                  4566778899999999887


Q ss_pred             -CeEEecCC
Q psy6094         307 -RSETQQYP  314 (455)
Q Consensus       307 -G~c~~L~t  314 (455)
                       |.+..+.+
T Consensus       573 ~G~s~~fls  581 (853)
T 2fsf_A          573 AGSSRFYLS  581 (853)
T ss_dssp             CEEEEEEEE
T ss_pred             CeeEEEEec
Confidence             99888777

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.76  E-value=3.2e-19  Score=187.48  Aligned_cols=105  Identities=13%  Similarity=0.078  Sum_probs=88.7

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC-CCCccCCCCCCeeE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT-NIAETSITIDDIVY  263 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT-niae~gitI~~V~~  263 (455)
                      .+..++||++ .++++.+++.|...+      ..+..+||++++.+|.++++.|.+|..+|+||| +++++|+|+|++++
T Consensus       347 ~~~~~ivf~~-~~~~~~l~~~L~~~~------~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~  419 (510)
T 2oca_A          347 DENAFVMFKH-VSHGKAIFDLIKNEY------DKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHH  419 (510)
T ss_dssp             TCEEEEEESS-HHHHHHHHHHHHTTC------SSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEE
T ss_pred             CCCeEEEEec-HHHHHHHHHHHHHcC------CCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcE
Confidence            3445666666 889999999998764      368899999999999999999999999999999 99999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCC-eEEecCC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR-SETQQYP  314 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G-~c~~L~t  314 (455)
                      ||..+.        .          .|.+++.||+||+||.++| .++.+|+
T Consensus       420 vi~~~~--------~----------~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          420 VVLAHG--------V----------KSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             EEESSC--------C----------CSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             EEEeCC--------C----------CCHHHHHHHHhcccccCCCCceEEEEE
Confidence            997432        2          3457788999999999885 4777777

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.61  E-value=6e-20  Score=165.37  Aligned_cols=116  Identities=18%  Similarity=0.203  Sum_probs=101.7

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCC
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSI  256 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gi  256 (455)
                      +..++....++.+|||+++...++.+++.|...+      +.+..+||++++.+|..+++.|++|..+|+|||+++++|+
T Consensus        21 l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~------~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gi   94 (170)
T 2yjt_D           21 LVHLLKQPEATRSIVFVRKRERVHELANWLREAG------INNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGI   94 (170)
Confidence            4455554567899999999999999999998763      7899999999999999999999999999999999999999


Q ss_pred             CCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         257 TIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       257 tI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      |+|++++||+++.                  |.|.+++.||+||+||.+. |.|+.+++..
T Consensus        95 d~~~~~~Vi~~~~------------------p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~  137 (170)
T 2yjt_D           95 DIPDVSHVFNFDM------------------PRSGDTYLHRIGRTARAGRKGTAISLVEAH  137 (170)
Confidence            9999999998553                  3466778899999999875 9999999854

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.67  E-value=5.8e-17  Score=173.51  Aligned_cols=104  Identities=16%  Similarity=0.068  Sum_probs=82.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCC--CCCCeEEEeecCCCChhhHhhhhcCCCCCceE---EEEeCCCCccCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFF--NSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRK---IVLATNIAETSITI  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~k---VivaTniae~gitI  258 (455)
                      ...+++||||++.+.++.+++.|......  ....-.+..+||+++. +|..+++.|.+|..+   |++||+++++|||+
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDi  515 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDA  515 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCC
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccc
Confidence            45689999999999999999999875310  0011237778998764 688899999887665   89999999999999


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK  306 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~  306 (455)
                      |++++||.        |++          +-|...+.||+||+||.++
T Consensus       516 p~v~~Vi~--------~~~----------~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          516 PTCKNVVL--------ARV----------VNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             TTEEEEEE--------ESC----------CCCHHHHHHHHTTSCCCBG
T ss_pred             hheeEEEE--------Eec----------CCChHHHHHHHhhhcccCc
Confidence            99999997        432          3466788999999999775

>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=99.67  E-value=1.5e-16  Score=172.45  Aligned_cols=113  Identities=15%  Similarity=0.082  Sum_probs=101.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++.+|||++++..++.+++.|...+      +.+..+||++++.+|.++++.|+.|..+|+||||++++|+|+|+|++
T Consensus       437 ~~~~~vlVf~~t~~~ae~L~~~L~~~g------i~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~l  510 (664)
T 1c4o_A          437 ARGERTLVTVLTVRMAEELTSFLVEHG------IRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSL  510 (664)
T ss_dssp             HTTCEEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEE
T ss_pred             hcCCEEEEEECCHHHHHHHHHHHHhcC------CCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCE
Confidence            457899999999999999999999874      67888999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~  315 (455)
                      ||+++..+.       |      .|.|..++.||+|||||.++|.|+.+++.
T Consensus       511 VI~~d~d~~-------G------~p~s~~~~iQr~GRagR~~~G~~i~~~~~  549 (664)
T 1c4o_A          511 VAILDADKE-------G------FLRSERSLIQTIGRAARNARGEVWLYADR  549 (664)
T ss_dssp             EEETTTTSC-------S------GGGSHHHHHHHHGGGTTSTTCEEEEECSS
T ss_pred             EEEeCCccc-------C------CCCCHHHHHHHHCccCcCCCCEEEEEEcC
Confidence            999664322       1      26688899999999999999999999984

>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=99.66  E-value=1.3e-16  Score=172.81  Aligned_cols=113  Identities=17%  Similarity=0.105  Sum_probs=100.8

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++.+|||+++...++.+++.|...+      +.+..+||++++.+|.++++.|++|..+|+||||++++|+|+|+|++
T Consensus       443 ~~~~~vlVf~~t~~~ae~L~~~L~~~g------i~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~l  516 (661)
T 2d7d_A          443 ERNERVLVTTLTKKMSEDLTDYLKEIG------IKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSL  516 (661)
T ss_dssp             TTTCEEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEE
T ss_pred             hcCCeEEEEECCHHHHHHHHHHHHhcC------CCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCE
Confidence            457799999999999999999999874      67888999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~  315 (455)
                      ||+++..+.       |      .|.|..++.||+|||||.++|.|+.+++.
T Consensus       517 Vi~~d~d~~-------G------~p~s~~~~iQr~GRagR~~~G~~i~~~~~  555 (661)
T 2d7d_A          517 VAILDADKE-------G------FLRSERSLIQTIGRAARNAEGRVIMYADK  555 (661)
T ss_dssp             EEETTTTCC-------T------TTTSHHHHHHHHHTTTTSTTCEEEEECSS
T ss_pred             EEEeCcccc-------c------CCCCHHHHHHHhCcccCCCCCEEEEEEeC
Confidence            999664321       1      25688899999999999988999999984

>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=99.60  E-value=2e-15  Score=170.00  Aligned_cols=115  Identities=17%  Similarity=0.144  Sum_probs=97.2

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCc--eEEEEeCCCCcc
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV--RKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~--~kVivaTniae~  254 (455)
                      +..++....++.+||||++...++.+++.|....     ++.+..+||++++.+|.++++.|.+|.  .+|+|||+++++
T Consensus       494 L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~-----g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~  568 (968)
T 3dmq_A          494 LMGYLTSHRSQKVLVICAKAATALQLEQVLRERE-----GIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSE  568 (968)
T ss_dssp             HHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTT-----CCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTC
T ss_pred             HHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhc
Confidence            4445554678899999999999999999999532     378999999999999999999999997  999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-C--eEEecCC
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-R--SETQQYP  314 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G--~c~~L~t  314 (455)
                      |+|+|++++||+        ||+.          -+.+.+.||.||+||.|. |  .+|.++.
T Consensus       569 GlDl~~~~~VI~--------~d~p----------~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~  613 (968)
T 3dmq_A          569 GRNFQFASHMVM--------FDLP----------FNPDLLEQRIGRLDRIGQAHDIQIHVPYL  613 (968)
T ss_dssp             SSCCTTCCEEEC--------SSCC----------SSHHHHHHHHHTTSCSSSCSCCEEEEEEE
T ss_pred             CCCcccCcEEEE--------ecCC----------CCHHHHHHHhhccccCCCCceEEEEEecC
Confidence            999999999998        5433          355778899999999876 5  4555555

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.47  E-value=4.9e-14  Score=150.09  Aligned_cols=112  Identities=18%  Similarity=0.162  Sum_probs=91.1

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      +...+..  ..+.++|||+++...++.+++.|...+      +.+..|||+..+.++..+...+++|  .|+||||+|+|
T Consensus       463 l~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~G------i~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgR  534 (822)
T 3jux_A          463 IVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKG------IPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGR  534 (822)
T ss_dssp             HHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTT------CCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTT
T ss_pred             HHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCC------CCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhC
Confidence            4444443  356789999999999999999999875      7788899997666666565556666  59999999999


Q ss_pred             CCCCC--------CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         255 SITID--------DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       255 gitI~--------~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      |+||+        ++.+||++.+                  |-|...+.||+|||||.|. |.++.+++
T Consensus       535 GtDI~lg~~V~~~GglhVInte~------------------Pes~r~y~qriGRTGRqG~~G~a~~fvs  585 (822)
T 3jux_A          535 GTDIKLGPGVAELGGLCIIGTER------------------HESRRIDNQLRGRAGRQGDPGESIFFLS  585 (822)
T ss_dssp             TCCCCCCTTTTTTTSCEEEESSC------------------CSSHHHHHHHHTTSSCSSCCCEEEEEEE
T ss_pred             CcCccCCcchhhcCCCEEEecCC------------------CCCHHHHHHhhCccccCCCCeeEEEEec
Confidence            99998        7779999665                  4566678899999999987 99988888

>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=99.41  E-value=7.5e-13  Score=124.96  Aligned_cols=118  Identities=23%  Similarity=0.415  Sum_probs=90.0

Q ss_pred             hHHHHHHHHHHH-hcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh------------
Q psy6094          29 LDAAFKKEMIRK-LQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL------------   94 (455)
Q Consensus        29 ~~~~~~~~~~~~-~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~------------   94 (455)
                      .++.+.+.|.+. ..++.+.++++.|+.+|++.+|.++++.+.+|+++++.|+|||||||+++ ++++            
T Consensus        32 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~  111 (235)
T 3llm_A           32 ISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECN  111 (235)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCE
T ss_pred             hcHHHHHHHHHHhhcCHHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceE
Confidence            456677777755 47899999999999999999999999999999999999999999999877 4443            


Q ss_pred             --------------------hhcCC-----------------------CCChHHHHHhc-cCCCCcCcc-----------
Q psy6094          95 --------------------KRSET-----------------------QQYPNDVLNML-KDPELEGVN-----------  119 (455)
Q Consensus        95 --------------------e~~~~-----------------------vg~p~~ll~~l-~d~~L~~~~-----------  119 (455)
                                          ..+..                       +++|++|++.+ .  .+.+++           
T Consensus       112 ~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~Ivv~Tpg~l~~~l~~--~l~~~~~lVlDEah~~~  189 (235)
T 3llm_A          112 IVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERD  189 (235)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCSSSEEEEEEHHHHHHHHHH--CCTTCCEEEECCTTSCC
T ss_pred             EEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhccCCCCCeEEEECHHHHHHHHHh--hhcCCcEEEEECCccCC
Confidence                                11111                       12466666665 3  133333           


Q ss_pred             --hHHHHHHHHHHHHhcCCCCeEEEEccCCCC
Q psy6094         120 --NDVIFSLLQHICTTQRPGAILVYCTYTFMG  149 (455)
Q Consensus       120 --~D~ll~~lk~il~~~~~~~k~ilmSAT~~g  149 (455)
                        .|+++..++.++ ...++.|+++||||++.
T Consensus       190 ~~~~~~~~~l~~i~-~~~~~~~~il~SAT~~~  220 (235)
T 3llm_A          190 INTDFLLVVLRDVV-QAYPEVRIVLMSATIDT  220 (235)
T ss_dssp             HHHHHHHHHHHHHH-HHCTTSEEEEEECSSCC
T ss_pred             cchHHHHHHHHHHH-hhCCCCeEEEEecCCCH
Confidence              677777888888 66789999999999953

>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=99.24  E-value=7.4e-11  Score=132.79  Aligned_cols=110  Identities=6%  Similarity=0.003  Sum_probs=79.5

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCC------CCCCCeEE-EeecCC----------C----------Chh---------
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSF------FNSSRFQI-IPLHSM----------L----------PTV---------  229 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~------~~~~~~~v-~~lhs~----------l----------~~~---------  229 (455)
                      ++.+||||+++..+..+++.|.....      .....+.+ +.+||+          +          ++.         
T Consensus       537 g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I  616 (1038)
T 2w00_A          537 GFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAI  616 (1038)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHH
Confidence            46799999999999999999986530      01112444 445542          2          221         


Q ss_pred             --------------------hHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCccccccccc
Q psy6094         230 --------------------SQKSIFNTPPEGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWI  289 (455)
Q Consensus       230 --------------------~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~i  289 (455)
                                          +|..+.++|++|..+|+|+||++.||+|+|.+. |+.        +|          .|.
T Consensus       617 ~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l~-tly--------lD----------kpl  677 (1038)
T 2w00_A          617 REYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTLN-TLF--------VD----------KNL  677 (1038)
T ss_dssp             HHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTEE-EEE--------EE----------SCC
T ss_pred             HHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCccccc-EEE--------Ec----------cCC
Confidence                                366788889999999999999999999999994 553        33          234


Q ss_pred             chhhHHhhhcccCCCCC-----CeEEecCC
Q psy6094         290 SLANAKQRRGRAGRTLK-----RSETQQYP  314 (455)
Q Consensus       290 Ska~~~QR~GRaGR~~~-----G~c~~L~t  314 (455)
                      +...+.||.||+||..+     |..+-+..
T Consensus       678 ~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          678 RYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             CHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             CccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            55678899999999875     55555554

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.23  E-value=7.7e-12  Score=120.82  Aligned_cols=112  Identities=18%  Similarity=0.060  Sum_probs=81.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ceE-EEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VRK-IVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~k-VivaTniae~gitI~~V  261 (455)
                      ..+..+|||+.....++.+.+.|....     ++.+..+||++++++|.++++.|.+| ..+ +++||+++++|+|++++
T Consensus       110 ~~~~kvlIFs~~~~~~~~l~~~L~~~~-----g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~a  184 (271)
T 1z5z_A          110 DEGDKIAIFTQFVDMGKIIRNIIEKEL-----NTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSA  184 (271)
T ss_dssp             HTTCCEEEEESCHHHHHHHHHHHHHHH-----CSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTC
T ss_pred             hCCCeEEEEeccHHHHHHHHHHHHHhc-----CCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCcccC
Confidence            367899999999999999999998741     25677899999999999999999877 555 78999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEEecCChhhh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSETQQYPNDVL  318 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~~L~t~~~~  318 (455)
                      ++||+        ||++-+          .+.+.||.||++|.|.   -.+|+|++...+
T Consensus       185 ~~VI~--------~d~~wn----------p~~~~Q~~gR~~R~Gq~~~v~v~~li~~~Ti  226 (271)
T 1z5z_A          185 NRVIH--------FDRWWN----------PAVEDQATDRVYRIGQTRNVIVHKLISVGTL  226 (271)
T ss_dssp             SEEEE--------CSCCSC----------TTTC--------------CCEEEEEEETTSH
T ss_pred             CEEEE--------ECCCCC----------hhHHHHHHHhccccCCCCceEEEEEeeCCCH
Confidence            99998        544333          3445699999999765   456888886543

>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=99.00  E-value=2.7e-10  Score=118.95  Aligned_cols=111  Identities=15%  Similarity=0.020  Sum_probs=87.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC-ce-EEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG-VR-KIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g-~~-kVivaTniae~gitI~~V  261 (455)
                      ..+..+|||+.....++.+.+.|....     ++.+..+||++++++|.++++.|.+| .. .+++||++++.|+|++++
T Consensus       339 ~~~~k~lvF~~~~~~~~~l~~~l~~~~-----~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~  413 (500)
T 1z63_A          339 DEGDKIAIFTQFVDMGKIIRNIIEKEL-----NTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSA  413 (500)
T ss_dssp             TTTCCEEEECSCHHHHHHHHHHHHHHH-----TCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTC
T ss_pred             ccCCcEEEEEehHHHHHHHHHHHHHhh-----CCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhC
Confidence            467899999999999999999998742     25677899999999999999999877 34 489999999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEEecCChhh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSETQQYPNDV  317 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~~L~t~~~  317 (455)
                      ++||.        ||+.-          +.+.+.||.||++|.|.   ..+|+|++...
T Consensus       414 ~~vi~--------~d~~~----------~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~t  454 (500)
T 1z63_A          414 NRVIH--------FDRWW----------NPAVEDQATDRVYRIGQTRNVIVHKLISVGT  454 (500)
T ss_dssp             SEEEE--------SSCCS----------CC---CHHHHTTTTTTTTSCEEEEEEEETTS
T ss_pred             CEEEE--------eCCCC----------CcchHHHHHHHHHHcCCCCeeEEEEEEeCCC
Confidence            99998        44332          33456699999999776   35688877543

>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=98.93  E-value=2.4e-09  Score=101.78  Aligned_cols=63  Identities=11%  Similarity=0.034  Sum_probs=55.1

Q ss_pred             chHHHHHHHHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          28 VLDAAFKKEMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .....-...|++...++.+.+.++..+....+++|.++++.+.+++++++.|+||||||.++.
T Consensus        36 ~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~   98 (249)
T 3ber_A           36 IVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA   98 (249)
T ss_dssp             CHHHHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH
T ss_pred             cCcccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhH
Confidence            344455567888889999999999999999999999999999999999999999999996543

>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=1.6e-09  Score=117.02  Aligned_cols=109  Identities=11%  Similarity=0.054  Sum_probs=93.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCce---EEEEeCCCCccCCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVR---KIVLATNIAETSITIDD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~---kVivaTniae~gitI~~  260 (455)
                      ..+..+|||+.....++.+.+.|...+      +.+..+||++++++|.++++.|.+|..   .+++||++++.|||+++
T Consensus       414 ~~~~k~lIFs~~~~~~~~l~~~l~~~g------~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~  487 (644)
T 1z3i_X          414 TTSDKVVLVSNYTQTLDLFEKLCRNRR------YLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIG  487 (644)
T ss_dssp             HCCCEEEEEESCHHHHHHHHHHHHHHT------CCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTT
T ss_pred             cCCCEEEEEEccHHHHHHHHHHHHHCC------CCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCccccc
Confidence            457899999999999999999998764      678999999999999999999987754   58999999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEEecCChh
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSETQQYPND  316 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~~L~t~~  316 (455)
                      +++||.        ||+          |-+.+.+.||.||++|.|.   ..+|+|++..
T Consensus       488 a~~Vi~--------~d~----------~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~  528 (644)
T 1z3i_X          488 ANRLVM--------FDP----------DWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  528 (644)
T ss_dssp             EEEEEE--------CSC----------CSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             CCEEEE--------ECC----------CCCccHHHHHHHhhhhcCCCCceEEEEEEECC
Confidence            999998        543          3456778899999999775   4788888754

>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=98.80  E-value=2.3e-08  Score=93.17  Aligned_cols=48  Identities=13%  Similarity=0.124  Sum_probs=43.7

Q ss_pred             HhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc
Q psy6094          40 KLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPL   87 (455)
Q Consensus        40 ~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt   87 (455)
                      ...++...+.+...+....+++|.++++.+.++++++++|+||||||.
T Consensus        25 ~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~   72 (228)
T 3iuy_A           25 FQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTL   72 (228)
T ss_dssp             HTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHH
T ss_pred             hccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHH
Confidence            567788888888888888999999999999999999999999999995

>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=98.78  E-value=9.7e-09  Score=100.39  Aligned_cols=114  Identities=12%  Similarity=0.099  Sum_probs=81.8

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC--CeEEEEcCCCCCcccchh-hhhh------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN--QITVISGETGSGPPLHLD-FITL------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~--~~vii~~~TGSGKTtqlp-~ll~------------------   94 (455)
                      .|.+..+++...+.+...+....+++|.++++.+.++  ++++++|+||||||..+. .++.                  
T Consensus        93 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~Ptr  172 (300)
T 3fmo_B           93 SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTY  172 (300)
T ss_dssp             CSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcH
Confidence            3566778888899998899999999999999999987  999999999999995422 2221                  


Q ss_pred             -----------hhc--------------------------CCCCChHHHHHhc-cCC--CCcCcc------hHHHHH---
Q psy6094          95 -----------KRS--------------------------ETQQYPNDVLNML-KDP--ELEGVN------NDVIFS---  125 (455)
Q Consensus        95 -----------e~~--------------------------~~vg~p~~ll~~l-~d~--~L~~~~------~D~ll~---  125 (455)
                                 ..+                          ..||+|.+|++.+ ...  .+..++      +|.++.   
T Consensus       173 eLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~  252 (300)
T 3fmo_B          173 ELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQG  252 (300)
T ss_dssp             HHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTT
T ss_pred             HHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhhcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccC
Confidence                       000                          1122577788877 322  344444      676664   


Q ss_pred             ---HHHHHHHhcCCCCeEEEEccCCCC
Q psy6094         126 ---LLQHICTTQRPGAILVYCTYTFMG  149 (455)
Q Consensus       126 ---~lk~il~~~~~~~k~ilmSAT~~g  149 (455)
                         .+..++...+++.|+++||||++.
T Consensus       253 ~~~~~~~i~~~~~~~~q~i~~SAT~~~  279 (300)
T 3fmo_B          253 HQDQSIRIQRMLPRNCQMLLFSATFED  279 (300)
T ss_dssp             HHHHHHHHHTTSCTTCEEEEEESCCCH
T ss_pred             cHHHHHHHHHhCCCCCEEEEEeccCCH
Confidence               255566456788999999999954

>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=98.78  E-value=1.9e-08  Score=93.34  Aligned_cols=52  Identities=4%  Similarity=-0.055  Sum_probs=45.7

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |.+...++.+.+.+...+....+++|.++++.+.+++++++.++||||||..
T Consensus        16 f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~   67 (224)
T 1qde_A           16 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT   67 (224)
T ss_dssp             GGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             hhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHH
Confidence            4455677888888888888889999999999999999999999999999965

>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=98.78  E-value=1.6e-08  Score=92.46  Aligned_cols=52  Identities=17%  Similarity=0.151  Sum_probs=46.0

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |.+...++...+.++..+....+++|.++++.+.+++++++.++||||||..
T Consensus         3 f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~   54 (207)
T 2gxq_A            3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLA   54 (207)
T ss_dssp             GGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             hhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHH
Confidence            4455677888888888888899999999999999999999999999999964

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=98.77  E-value=1.5e-08  Score=94.91  Aligned_cols=52  Identities=13%  Similarity=0.132  Sum_probs=47.2

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |.+...++...+.++.++....+++|.++++.+.+++++++.++||||||++
T Consensus        27 f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~   78 (236)
T 2pl3_A           27 FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLA   78 (236)
T ss_dssp             GGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             HhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHH
Confidence            5566688888888999999999999999999999999999999999999964

>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=98.76  E-value=1.2e-08  Score=96.14  Aligned_cols=51  Identities=12%  Similarity=0.059  Sum_probs=43.7

Q ss_pred             HHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          38 IRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        38 ~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      .+...++...+.+...+....+++|.++++.+.++++++++|+||||||..
T Consensus        32 ~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~   82 (242)
T 3fe2_A           32 YEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLS   82 (242)
T ss_dssp             TTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHH
T ss_pred             hhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHH
Confidence            345567777777877788878999999999999999999999999999944

>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=98.75  E-value=1.7e-08  Score=92.32  Aligned_cols=52  Identities=6%  Similarity=-0.011  Sum_probs=46.1

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |++...++...+.+...+....+++|.++++.+.+++++++.++||||||..
T Consensus         5 f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~   56 (206)
T 1vec_A            5 FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGA   56 (206)
T ss_dssp             GGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHH
T ss_pred             hhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHH
Confidence            5566678888888888888889999999999999999999999999999943

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=98.74  E-value=1.4e-08  Score=94.17  Aligned_cols=52  Identities=12%  Similarity=0.106  Sum_probs=46.0

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |.+...++...+.++..+....+++|.++++.+.+++++++.++||||||..
T Consensus         6 f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~   57 (219)
T 1q0u_A            6 FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHA   57 (219)
T ss_dssp             GGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHH
T ss_pred             HhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHH
Confidence            4455677888888888888889999999999999999999999999999964

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.74  E-value=8.4e-09  Score=114.06  Aligned_cols=111  Identities=15%  Similarity=0.089  Sum_probs=93.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCc---eEEEEeCCCCccCCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV---RKIVLATNIAETSITIDD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~---~kVivaTniae~gitI~~  260 (455)
                      ..+..+|||+.....++.+.+.|...+      +.+..+||+++..+|.++++.|..|.   ..+|+||.+++.||+++.
T Consensus       570 ~~g~kvLIFsq~~~~ld~L~~~L~~~g------~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~  643 (800)
T 3mwy_W          570 KDGHRVLIFSQMVRMLDILGDYLSIKG------INFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMT  643 (800)
T ss_dssp             TTTCCEEEEESCHHHHHHHHHHHHHHT------CCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTT
T ss_pred             hCCCeEEEEechHHHHHHHHHHHHhCC------CCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccc
Confidence            456799999999999999999998774      77889999999999999999998754   359999999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEEecCChhhh
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSETQQYPNDVL  318 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~~L~t~~~~  318 (455)
                      +++||.        ||+.          -+.+...||.||++|.|.   ..+|+|+++..+
T Consensus       644 a~~VI~--------~D~~----------wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~Ti  686 (800)
T 3mwy_W          644 ADTVVI--------FDSD----------WNPQADLQAMARAHRIGQKNHVMVYRLVSKDTV  686 (800)
T ss_dssp             CCEEEE--------SSCC----------SCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSH
T ss_pred             cceEEE--------ecCC----------CChhhHHHHHHHHHhcCCCceEEEEEEecCCCH
Confidence            999998        5433          244667799999999654   678899885543

>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=98.71  E-value=2e-08  Score=94.47  Aligned_cols=53  Identities=6%  Similarity=-0.038  Sum_probs=46.0

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccch
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtql   89 (455)
                      |.+...++...+.+...+.-..+++|.++++.+.+++++++.|+||||||..+
T Consensus        32 f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~   84 (237)
T 3bor_A           32 FDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATF   84 (237)
T ss_dssp             GGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHH
T ss_pred             hhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHH
Confidence            55666788888888888887789999999999999999999999999999553

>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=98.70  E-value=1.3e-08  Score=94.14  Aligned_cols=52  Identities=6%  Similarity=-0.042  Sum_probs=44.7

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |++...++...+.+...+.-..+++|.++++.+.+++++++.++||||||..
T Consensus        16 f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~   67 (220)
T 1t6n_A           16 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV   67 (220)
T ss_dssp             STTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             HhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhh
Confidence            4556677888888877777778999999999999999999999999999954

>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=98.68  E-value=4.4e-08  Score=91.54  Aligned_cols=52  Identities=17%  Similarity=0.105  Sum_probs=46.4

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      |.+...++...+.++..+.-..+++|.++++.+.+++++++.++||||||.+
T Consensus        26 f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~   77 (230)
T 2oxc_A           26 FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCV   77 (230)
T ss_dssp             GGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             HhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHH
Confidence            5666788888888888888778999999999999999999999999999955

>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=98.68  E-value=3.1e-08  Score=94.71  Aligned_cols=47  Identities=11%  Similarity=0.116  Sum_probs=42.9

Q ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          42 QSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        42 ~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      .++...+.+...+....+++|.++++.+.++++++++|+||||||..
T Consensus        61 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~  107 (262)
T 3ly5_A           61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLA  107 (262)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHH
Confidence            67888888888888889999999999999999999999999999953

>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=98.62  E-value=1.7e-07  Score=88.14  Aligned_cols=51  Identities=14%  Similarity=0.078  Sum_probs=45.7

Q ss_pred             HHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          38 IRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        38 ~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      .....++...+.+...+....+++|.++++.+.+++++++.|+||||||..
T Consensus        32 ~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~   82 (245)
T 3dkp_A           32 QEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLA   82 (245)
T ss_dssp             HHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             hccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHH
Confidence            345688888888888888889999999999999999999999999999954

>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=98.36  E-value=1.8e-07  Score=88.60  Aligned_cols=49  Identities=8%  Similarity=0.066  Sum_probs=39.0

Q ss_pred             HhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          40 KLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        40 ~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      ...++...+.+...+.-..+++|.++++.+.+++++++.++||||||..
T Consensus        28 l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~   76 (253)
T 1wrb_A           28 LKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAA   76 (253)
T ss_dssp             GSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHH
Confidence            3344444455555666778999999999999999999999999999953

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.92  E-value=4.9e-06  Score=87.79  Aligned_cols=116  Identities=14%  Similarity=0.118  Sum_probs=67.7

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEE--eCCCCccCCCCCC-
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVL--ATNIAETSITIDD-  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kViv--aTniae~gitI~~-  260 (455)
                      ..+|.+|||+|+...++.+++.+...        . +..++..  .++.++++.|+.|. .|++  +|+.+..|||+|| 
T Consensus       382 ~~~g~~lvff~S~~~~~~v~~~l~~~--------~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~  449 (540)
T 2vl7_A          382 NSSKSVLVFFPSYEMLESVRIHLSGI--------P-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREK  449 (540)
T ss_dssp             TCSSEEEEEESCHHHHHHHHTTCTTS--------C-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC-------------
T ss_pred             hCCCCEEEEeCCHHHHHHHHHHhccC--------c-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCC
Confidence            56889999999999999998777542        1 2335443  35666777776653 5777  8999999999998 


Q ss_pred             ---eeEEEeCCCCcccccccCC-------------CcccccccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         261 ---IVYVVDCGKTKMSNFDVKD-------------NIATLKPEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       261 ---V~~VID~g~~k~~~yd~~~-------------~~~~l~~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                         ++.||..|+|.....|+..             +...+. .+..--...|-.||+-|...  |..+-+
T Consensus       450 ~~~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~-~~~~~~~~~Q~~GR~iR~~~D~g~v~ll  518 (540)
T 2vl7_A          450 ENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSII-HDLTAIVIKQTIGRAFRDPNDYVKIYLC  518 (540)
T ss_dssp             --CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHH-HHHHHHHHHHHHHHHCCSTTCCCEEEEE
T ss_pred             cccccEEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHH-HHHHHHHHHHHhCCcccCCCccEEEEEE
Confidence               8999999999655433321             111011 11124567899999999654  765544

>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=97.78  E-value=1.8e-05  Score=72.16  Aligned_cols=39  Identities=18%  Similarity=0.077  Sum_probs=34.2

Q ss_pred             HHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          52 ARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        52 ~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .....+.+++|.++++.+.+++++++.++||||||+.+.
T Consensus        28 ~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~   66 (216)
T 3b6e_A           28 PEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAV   66 (216)
T ss_dssp             CSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHH
T ss_pred             ccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHH
Confidence            345678999999999999999999999999999996544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=96.31  E-value=0.012  Score=64.64  Aligned_cols=30  Identities=13%  Similarity=0.220  Sum_probs=26.1

Q ss_pred             CCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          57 PSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        57 P~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      -.+..|...+..+..|+  |+.+.||||||..
T Consensus        79 ~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLv  108 (997)
T 2ipc_A           79 RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLV  108 (997)
T ss_dssp             CCCHHHHHHHHHHHTTS--EEECCSTHHHHHH
T ss_pred             CCcHHHHhhcccccCCc--eeeccCCCchHHH
Confidence            55888999999999998  8999999999943

>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=95.34  E-value=0.0073  Score=56.25  Aligned_cols=34  Identities=18%  Similarity=0.125  Sum_probs=29.6

Q ss_pred             CCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccch
Q psy6094          56 LPSYQMRDAVLDMVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        56 lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtql   89 (455)
                      ....++|.+.++.+.+++.+++.|+||+|||.+.
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a  125 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVA  125 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHH
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHH
Confidence            3568899999999999989999999999999443

>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=95.27  E-value=0.0058  Score=58.23  Aligned_cols=31  Identities=10%  Similarity=0.021  Sum_probs=28.0

Q ss_pred             CCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          56 LPSYQMRDAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        56 lP~~~~q~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      +..+++|.+.++.+.++...++.++||||||
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT  142 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRS  142 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHH
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcH
Confidence            5788999999998887788899999999999

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.50  E-value=0.023  Score=51.87  Aligned_cols=34  Identities=24%  Similarity=0.263  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          57 PSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        57 P~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |-.--+..+++.+..|+.+.|.|+.||||||.+-
T Consensus         7 pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl~   40 (208)
T 3b85_A            7 PKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLAM   40 (208)
T ss_dssp             CCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHHH
T ss_pred             cCCHhHHHHHHhccCCCEEEEECCCCCCHHHHHH
Confidence            3333456788889999999999999999997764

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=94.08  E-value=0.028  Score=59.07  Aligned_cols=30  Identities=27%  Similarity=0.397  Sum_probs=24.4

Q ss_pred             CCHHHHHHHHH----HHHcCCeEEEEcCCCCCcc
Q psy6094          57 PSYQMRDAVLD----MVRNNQITVISGETGSGPP   86 (455)
Q Consensus        57 P~~~~q~~il~----~i~~~~~vii~~~TGSGKT   86 (455)
                      ..++.|.++++    ++.+++++++.++||||||
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT   36 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKT   36 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHH
Confidence            35667777655    5668999999999999999

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=93.82  E-value=0.059  Score=57.46  Aligned_cols=117  Identities=9%  Similarity=0.064  Sum_probs=71.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC--CCCccCCCCCC-
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT--NIAETSITIDD-  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT--niae~gitI~~-  260 (455)
                      ..+|.+|||+|+....+.+++.+. ..     ...   ...+++..++..+++.|. +..-|++++  ....-|||+++ 
T Consensus       446 ~~~g~~lvlF~Sy~~l~~v~~~l~-~~-----~~~---~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~  515 (620)
T 4a15_A          446 KVKKNTIVYFPSYSLMDRVENRVS-FE-----HMK---EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGN  515 (620)
T ss_dssp             HHCSCEEEEESCHHHHHHHTSSCC-SC-----CEE---CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------C
T ss_pred             hCCCCEEEEeCCHHHHHHHHHHHH-hc-----chh---ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCC
Confidence            568889999999999999887776 11     122   445555667788888887 788899997  47778999985 


Q ss_pred             -eeEEEeCCCCcccccccC-------------CCcccccccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         261 -IVYVVDCGKTKMSNFDVK-------------DNIATLKPEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       261 -V~~VID~g~~k~~~yd~~-------------~~~~~l~~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                       .+.||-.|+|-... ||.             .+...-...| .--...|=.||+=|...  |..+-+
T Consensus       516 ~l~~viI~~lPfp~~-~p~~~ar~~~~~~~~g~~~~~~y~~p-a~~~l~Qa~GRlIR~~~D~G~v~ll  581 (620)
T 4a15_A          516 ELEMIILAGLPFPRP-DAINRSLFDYYERKYGKGWEYSVVYP-TAIKIRQEIGRLIRSAEDTGACVIL  581 (620)
T ss_dssp             CCCEEEESSCCCCCC-CHHHHHHHHHHHHHHSCHHHHHTHHH-HHHHHHHHHHTTCCSTTCCEEEEEE
T ss_pred             ceEEEEEEcCCCCCC-CHHHHHHHHHHHHhhCCCchHHhHHH-HHHHHHHHhCccccCCCceEEEEEE
Confidence             56888889884432 221             1111001223 33456799999988554  766544

>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=93.54  E-value=0.031  Score=59.45  Aligned_cols=32  Identities=22%  Similarity=0.356  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchhh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLDF   91 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp~   91 (455)
                      ..|.+.+..+..+++++|+|++||||||.+.+
T Consensus       152 ~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~  183 (608)
T 1w36_D          152 NWQKVAAAVALTRRISVISGGPGTGKTTTVAK  183 (608)
T ss_dssp             CHHHHHHHHHHTBSEEEEECCTTSTHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHH
Confidence            45888888888999999999999999987663

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=93.38  E-value=0.043  Score=48.17  Aligned_cols=20  Identities=15%  Similarity=0.131  Sum_probs=17.6

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++.+++.|++||||||.+-
T Consensus        37 ~g~~~~l~G~~G~GKTtL~~   56 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLAV   56 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57899999999999997765

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=93.30  E-value=0.025  Score=50.01  Aligned_cols=20  Identities=20%  Similarity=0.244  Sum_probs=17.1

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++.++++|++||||||.+-
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~   23 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKN   23 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57889999999999997653

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=93.30  E-value=0.044  Score=58.44  Aligned_cols=23  Identities=17%  Similarity=0.228  Sum_probs=20.1

Q ss_pred             HHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          64 AVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        64 ~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      ++.+++.+++++++.|+||||||
T Consensus        14 ~v~~~l~~~~~~~~~apTGtGKT   36 (620)
T 4a15_A           14 FLRSSLQKSYGVALESPTGSGKT   36 (620)
T ss_dssp             HHHHHHHHSSEEEEECCTTSCHH
T ss_pred             HHHHHHHcCCCEEEECCCCCCHH
Confidence            34467789999999999999999

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.95  E-value=0.03  Score=55.62  Aligned_cols=23  Identities=35%  Similarity=0.601  Sum_probs=20.3

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..|..++|+|+|||||||.+-
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTll~  193 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTLMK  193 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHHHH
Confidence            47789999999999999997765

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=92.89  E-value=0.027  Score=50.37  Aligned_cols=21  Identities=19%  Similarity=0.385  Sum_probs=18.3

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|.++.+.|++||||||.+-
T Consensus         5 ~~g~ii~l~Gp~GsGKSTl~~   25 (205)
T 3tr0_A            5 NKANLFIISAPSGAGKTSLVR   25 (205)
T ss_dssp             CCCCEEEEECCTTSCHHHHHH
T ss_pred             CCCcEEEEECcCCCCHHHHHH
Confidence            468899999999999998765

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.87  E-value=0.021  Score=54.09  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+..+.|+|+|||||||.+-
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll~   43 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTIA   43 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHHH
Confidence            5688899999999999998764

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=92.76  E-value=0.033  Score=50.34  Aligned_cols=23  Identities=17%  Similarity=0.291  Sum_probs=18.3

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..|+++.+.|++||||||.+-
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl~   38 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVVR   38 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHHH
Confidence            57899999999999999998764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.71  E-value=0.043  Score=57.10  Aligned_cols=24  Identities=25%  Similarity=0.394  Sum_probs=20.6

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -.+..+.+++|+|+|||||||.+-
T Consensus       255 ~~v~~g~~i~I~GptGSGKTTlL~  278 (511)
T 2oap_1          255 LAIEHKFSAIVVGETASGKTTTLN  278 (511)
T ss_dssp             HHHHTTCCEEEEESTTSSHHHHHH
T ss_pred             HHHhCCCEEEEECCCCCCHHHHHH
Confidence            346789999999999999997765

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=92.71  E-value=0.045  Score=57.37  Aligned_cols=30  Identities=13%  Similarity=0.293  Sum_probs=23.1

Q ss_pred             CCHHHHHHHH----HHHHcCCeEEEEcCCCCCcc
Q psy6094          57 PSYQMRDAVL----DMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        57 P~~~~q~~il----~~i~~~~~vii~~~TGSGKT   86 (455)
                      +.++.|.+++    +++.+++++++.++||||||
T Consensus         7 ~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT   40 (540)
T 2vl7_A            7 QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKT   40 (540)
T ss_dssp             --CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHH
Confidence            4455677654    55678999999999999999

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=92.67  E-value=0.031  Score=50.05  Aligned_cols=22  Identities=23%  Similarity=0.320  Sum_probs=18.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+..+++.|++||||||++-
T Consensus         3 i~~g~~i~l~G~~GsGKSTl~~   24 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTVRK   24 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999997764

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=92.39  E-value=0.022  Score=50.06  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=18.4

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..+.+.|++||||||.+-
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            467889999999999998875

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=92.27  E-value=0.04  Score=54.03  Aligned_cols=23  Identities=22%  Similarity=0.358  Sum_probs=20.1

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..+.++.|.|+|||||||.+-
T Consensus       167 ~i~~g~~v~i~G~~GsGKTTll~  189 (330)
T 2pt7_A          167 GIAIGKNVIVCGGTGSGKTTYIK  189 (330)
T ss_dssp             HHHHTCCEEEEESTTSCHHHHHH
T ss_pred             hccCCCEEEEECCCCCCHHHHHH
Confidence            46789999999999999998765

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=92.20  E-value=0.039  Score=50.49  Aligned_cols=22  Identities=27%  Similarity=0.342  Sum_probs=17.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~   41 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIK   41 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHH
Confidence            5678999999999999996653

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=92.13  E-value=0.025  Score=50.00  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=20.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      +..+..+++.|+.||||||.+-.|
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~L   29 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEAL   29 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHH
Confidence            567889999999999999876544

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=92.07  E-value=0.039  Score=49.67  Aligned_cols=20  Identities=30%  Similarity=0.498  Sum_probs=16.0

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++.++++|++||||||.+-
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~   22 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLK   22 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57789999999999997664

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=91.92  E-value=0.048  Score=49.38  Aligned_cols=20  Identities=25%  Similarity=0.410  Sum_probs=17.4

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..+++.|++||||||.+-
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~   26 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVRE   26 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHH
Confidence            57899999999999997654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=91.81  E-value=0.083  Score=56.55  Aligned_cols=32  Identities=13%  Similarity=0.297  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHH-HcCCeEEEEcCCCCCcccchh
Q psy6094          59 YQMRDAVLDMV-RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        59 ~~~q~~il~~i-~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -..|.+++..+ .+....+|+||+|||||+.+.
T Consensus       191 N~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~  223 (646)
T 4b3f_X          191 DTSQKEAVLFALSQKELAIIHGPPGTGKTTTVV  223 (646)
T ss_dssp             CHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCceEEECCCCCCHHHHHH
Confidence            34566666554 456799999999999997665

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=91.78  E-value=0.04  Score=50.62  Aligned_cols=24  Identities=21%  Similarity=0.242  Sum_probs=15.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      +..|.++.+.|++||||||.+-.|
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~L   47 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANKL   47 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHH
Confidence            457889999999999999877544

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=91.67  E-value=0.072  Score=45.11  Aligned_cols=22  Identities=18%  Similarity=0.215  Sum_probs=17.7

Q ss_pred             HHHcCCeEEEEcCCCCCcccch
Q psy6094          68 MVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtql   89 (455)
                      +...+..+++.|++|||||+..
T Consensus        23 ~~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           23 AAKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HHTCSSCEEEEEETTCCHHHHH
T ss_pred             HhCCCCcEEEECCCCccHHHHH
Confidence            3456778999999999999544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=91.64  E-value=0.073  Score=45.17  Aligned_cols=21  Identities=14%  Similarity=0.191  Sum_probs=17.1

Q ss_pred             HHcCCeEEEEcCCCCCcccch
Q psy6094          69 VRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtql   89 (455)
                      ...+..+++.|++|||||+..
T Consensus        21 a~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           21 SETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TTCCSCEEEESSTTSSHHHHH
T ss_pred             hCCCCCEEEECCCCCCHHHHH
Confidence            456778999999999999443

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=91.50  E-value=0.052  Score=49.92  Aligned_cols=41  Identities=17%  Similarity=0.245  Sum_probs=27.5

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNM  109 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~  109 (455)
                      +...+++++.|++||||+||...|.+..|...=..++++|.
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~~g~~hIstGdllR~   66 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQKFHFNHLSSGDLLRA   66 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHHHCCEEECHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHCCceEcHHHHHHH
Confidence            44567899999999999999876665444321124445543

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=91.20  E-value=0.051  Score=53.83  Aligned_cols=21  Identities=29%  Similarity=0.501  Sum_probs=17.8

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..++|+|+|||||||.+-
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~  141 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLA  141 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHH
Confidence            456689999999999998775

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=91.00  E-value=0.069  Score=48.29  Aligned_cols=20  Identities=20%  Similarity=0.343  Sum_probs=17.3

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++.++++|++|+||||.+-
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~   37 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKN   37 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHH
Confidence            68899999999999996553

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=90.98  E-value=0.13  Score=45.93  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=15.8

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      +.+++.|++|+|||+.+-
T Consensus        55 ~~~~l~G~~GtGKT~la~   72 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA   72 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            789999999999996654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=90.96  E-value=0.12  Score=44.82  Aligned_cols=27  Identities=19%  Similarity=0.428  Sum_probs=19.2

Q ss_pred             HHHHHHHc--CCeEEEEcCCCCCcccchh
Q psy6094          64 AVLDMVRN--NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        64 ~il~~i~~--~~~vii~~~TGSGKTtqlp   90 (455)
                      ++...+..  ...+++.|++|+|||+.+-
T Consensus        33 ~l~~~l~~~~~~~~ll~G~~G~GKT~l~~   61 (195)
T 1jbk_A           33 RTIQVLQRRTKNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             HHHHHHTSSSSCEEEEECCTTSCHHHHHH
T ss_pred             HHHHHHhcCCCCceEEECCCCCCHHHHHH
Confidence            34444433  4679999999999996654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=90.83  E-value=0.073  Score=47.67  Aligned_cols=26  Identities=12%  Similarity=0.051  Sum_probs=19.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +..++.+++.|++||||||..-.+..
T Consensus        22 ~~~~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             cCCCCEEEEEcCCCCCHHHHHHHHHH
Confidence            34678999999999999987654443

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=90.79  E-value=0.13  Score=46.28  Aligned_cols=27  Identities=19%  Similarity=0.208  Sum_probs=19.4

Q ss_pred             HHHHHHHcCC---eEEEEcCCCCCcccchh
Q psy6094          64 AVLDMVRNNQ---ITVISGETGSGPPLHLD   90 (455)
Q Consensus        64 ~il~~i~~~~---~vii~~~TGSGKTtqlp   90 (455)
                      .+...+..++   .+++.|++|+||||.+-
T Consensus        34 ~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~   63 (250)
T 1njg_A           34 ALANGLSLGRIHHAYLFSGTRGVGKTSIAR   63 (250)
T ss_dssp             HHHHHHHHTCCCSEEEEECSTTSCHHHHHH
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHH
Confidence            3344445454   79999999999996654

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=90.76  E-value=0.074  Score=46.71  Aligned_cols=25  Identities=20%  Similarity=0.393  Sum_probs=19.4

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      .+..+++.|+.||||||+.-.|.+.
T Consensus         2 ~~~~I~i~G~~GsGKsT~~~~L~~~   26 (192)
T 1kht_A            2 KNKVVVVTGVPGVGSTTSSQLAMDN   26 (192)
T ss_dssp             -CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999887655443

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=90.76  E-value=0.093  Score=44.98  Aligned_cols=20  Identities=30%  Similarity=0.479  Sum_probs=17.4

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++.+++.|++||||||.+-
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~   54 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQ   54 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            68899999999999996654

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=90.69  E-value=0.05  Score=54.20  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+..++|+|+|||||||.+-
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~  154 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIA  154 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHHH
Confidence            4678899999999999997764

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=90.65  E-value=0.11  Score=54.72  Aligned_cols=33  Identities=21%  Similarity=0.424  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          58 SYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        58 ~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ....|.+++..+.++++++|+|++||||||.+-
T Consensus       190 L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~  222 (574)
T 3e1s_A          190 LSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK  222 (574)
T ss_dssp             CCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH
Confidence            457899999999999999999999999998776

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=90.63  E-value=0.077  Score=48.72  Aligned_cols=21  Identities=14%  Similarity=0.411  Sum_probs=17.1

Q ss_pred             HHcCCeEEEEcCCCCCcccch
Q psy6094          69 VRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtql   89 (455)
                      ...|+.++|+||.||||||.+
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            467899999999999999655

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=90.62  E-value=0.053  Score=50.35  Aligned_cols=22  Identities=27%  Similarity=0.573  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        28 i~~Ge~~~iiG~nGsGKSTLl~   49 (235)
T 3tif_A           28 IKEGEFVSIMGPSGSGKSTMLN   49 (235)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998876

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=90.56  E-value=0.12  Score=52.26  Aligned_cols=21  Identities=38%  Similarity=0.591  Sum_probs=17.6

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..++|+|+|||||||.+-
T Consensus       165 ~~ggii~I~GpnGSGKTTlL~  185 (418)
T 1p9r_A          165 RPHGIILVTGPTGSGKSTTLY  185 (418)
T ss_dssp             SSSEEEEEECSTTSCHHHHHH
T ss_pred             hcCCeEEEECCCCCCHHHHHH
Confidence            356689999999999997765

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=90.20  E-value=0.099  Score=45.29  Aligned_cols=19  Identities=16%  Similarity=0.436  Sum_probs=16.0

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ...+++.|++|+|||+.+-
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            5679999999999996554

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=90.17  E-value=0.09  Score=47.09  Aligned_cols=24  Identities=21%  Similarity=0.275  Sum_probs=19.3

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ..+.++++.|+.||||||.+-.|.
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~   50 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVA   50 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHH
Confidence            457899999999999998876443

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=90.15  E-value=0.082  Score=47.52  Aligned_cols=21  Identities=19%  Similarity=0.273  Sum_probs=17.7

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..++++|++||||||+.-
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~   30 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIK   30 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHHH
Confidence            457789999999999997654

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=90.03  E-value=0.097  Score=47.59  Aligned_cols=24  Identities=21%  Similarity=0.347  Sum_probs=19.1

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      ++++.|++||||+||...|.+..|
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g   25 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG   25 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478899999999999876665443

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=89.98  E-value=0.086  Score=45.27  Aligned_cols=20  Identities=25%  Similarity=0.541  Sum_probs=16.5

Q ss_pred             CeEEEEcCCCCCcccchhhh
Q psy6094          73 QITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~l   92 (455)
                      .++++.|++||||||+.-.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            36889999999999877544

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=89.97  E-value=0.089  Score=47.48  Aligned_cols=21  Identities=29%  Similarity=0.465  Sum_probs=17.5

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..+.|.|++||||||.+-
T Consensus        20 ~~g~~v~I~G~sGsGKSTl~~   40 (208)
T 3c8u_A           20 PGRQLVALSGAPGSGKSTLSN   40 (208)
T ss_dssp             CSCEEEEEECCTTSCTHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHH
Confidence            356789999999999997764

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=89.86  E-value=0.16  Score=54.16  Aligned_cols=32  Identities=16%  Similarity=0.297  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          59 YQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        59 ~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -..|.+++..+..+..++|+|++|||||+.+.
T Consensus       182 n~~Q~~av~~~l~~~~~li~GppGTGKT~~~~  213 (624)
T 2gk6_A          182 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA  213 (624)
T ss_dssp             CHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH
Confidence            46788888888888899999999999997665

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=89.85  E-value=0.067  Score=49.71  Aligned_cols=22  Identities=18%  Similarity=0.459  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~   49 (237)
T 2cbz_A           28 IPEGALVAVVGQVGCGKSSLLS   49 (237)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998765

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=89.67  E-value=0.099  Score=47.76  Aligned_cols=24  Identities=33%  Similarity=0.246  Sum_probs=17.8

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .....+++.|.+||||||+.-.|.
T Consensus         5 ~~~~~I~l~G~~GsGKsT~a~~La   28 (227)
T 1zd8_A            5 ARLLRAVIMGAPGSGKGTVSSRIT   28 (227)
T ss_dssp             --CCEEEEEECTTSSHHHHHHHHH
T ss_pred             ccCcEEEEECCCCCCHHHHHHHHH
Confidence            345689999999999998765443

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=89.48  E-value=0.07  Score=49.12  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|+.||||||.+-
T Consensus        27 i~~Ge~~~iiG~nGsGKSTLl~   48 (224)
T 2pcj_A           27 VKKGEFVSIIGASGSGKSTLLY   48 (224)
T ss_dssp             EETTCEEEEEECTTSCHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998865

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=89.42  E-value=0.1  Score=45.21  Aligned_cols=19  Identities=16%  Similarity=0.216  Sum_probs=16.1

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +.++++.|+.||||||..-
T Consensus         4 ~~~i~l~G~~GsGKSTl~~   22 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGR   22 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5679999999999997654

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=89.19  E-value=0.15  Score=45.03  Aligned_cols=27  Identities=26%  Similarity=0.330  Sum_probs=20.7

Q ss_pred             HHHcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          68 MVRNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+.....+++.|.+||||||+.-.+.+
T Consensus         8 ~~~~~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A            8 DLRKCKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             HHHHSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            345577899999999999987654443

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=89.18  E-value=0.078  Score=50.55  Aligned_cols=22  Identities=23%  Similarity=0.513  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|++||||||.+-
T Consensus        31 i~~Ge~~~iiGpnGsGKSTLl~   52 (275)
T 3gfo_A           31 IKRGEVTAILGGNGVGKSTLFQ   52 (275)
T ss_dssp             EETTSEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3568899999999999998876

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=88.99  E-value=0.16  Score=44.10  Aligned_cols=21  Identities=14%  Similarity=0.336  Sum_probs=18.2

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|+++.+.|+.||||||.+-
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr   51 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTR   51 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHH
Confidence            678899999999999997654

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=88.98  E-value=0.076  Score=48.64  Aligned_cols=22  Identities=18%  Similarity=0.394  Sum_probs=18.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        32 i~~Ge~~~iiG~NGsGKSTLlk   53 (214)
T 1sgw_A           32 IEKGNVVNFHGPNGIGKTTLLK   53 (214)
T ss_dssp             EETTCCEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578889999999999997764

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=88.90  E-value=0.12  Score=44.39  Aligned_cols=21  Identities=5%  Similarity=0.021  Sum_probs=16.8

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+++.|+.||||||+.-.+.+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            688999999999987654443

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=88.89  E-value=0.1  Score=45.41  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=18.4

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+.++++.|+.||||||+.-.+.
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~   29 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVA   29 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHH
Confidence            35689999999999998765443

>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=88.88  E-value=0.22  Score=44.16  Aligned_cols=16  Identities=25%  Similarity=0.401  Sum_probs=13.8

Q ss_pred             eEEEEcCCCCCcccch
Q psy6094          74 ITVISGETGSGPPLHL   89 (455)
Q Consensus        74 ~vii~~~TGSGKTtql   89 (455)
                      .+++.|++|+|||+.+
T Consensus        40 ~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           40 HLLFSGPPGTGKTATA   55 (226)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5999999999999554

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=88.87  E-value=0.086  Score=49.60  Aligned_cols=22  Identities=32%  Similarity=0.592  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~liG~nGsGKSTLlk   51 (257)
T 1g6h_A           30 VNKGDVTLIIGPNGSGKSTLIN   51 (257)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EeCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998875

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=88.86  E-value=0.086  Score=49.32  Aligned_cols=22  Identities=23%  Similarity=0.463  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        32 i~~Ge~~~i~G~nGsGKSTLl~   53 (247)
T 2ff7_A           32 IKQGEVIGIVGRSGSGKSTLTK   53 (247)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3478899999999999998875

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=88.86  E-value=0.13  Score=45.08  Aligned_cols=23  Identities=13%  Similarity=0.020  Sum_probs=18.2

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+.+++.|++||||||..-.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            56799999999999987654443

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=88.81  E-value=0.089  Score=49.69  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|+.||||||.+-
T Consensus        29 i~~Ge~~~liG~nGsGKSTLlk   50 (262)
T 1b0u_A           29 ARAGDVISIIGSSGSGKSTFLR   50 (262)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998865

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=88.81  E-value=0.087  Score=48.65  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        31 i~~Ge~~~i~G~nGsGKSTLl~   52 (229)
T 2pze_A           31 IERGQLLAVAGSTGAGKTSLLM   52 (229)
T ss_dssp             EETTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3478899999999999998765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=88.69  E-value=0.092  Score=49.53  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        43 i~~Ge~~~i~G~nGsGKSTLl~   64 (260)
T 2ghi_A           43 IPSGTTCALVGHTGSGKSTIAK   64 (260)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998875

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=88.67  E-value=0.091  Score=48.90  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|+.||||||.+-
T Consensus        29 i~~Ge~~~l~G~nGsGKSTLl~   50 (240)
T 1ji0_A           29 VPRGQIVTLIGANGAGKTTTLS   50 (240)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998875

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=88.62  E-value=0.14  Score=45.56  Aligned_cols=24  Identities=21%  Similarity=0.158  Sum_probs=19.4

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+..+++.|..||||||+.-.+.+
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L~~   26 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNIME   26 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            467899999999999998764443

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=88.59  E-value=0.13  Score=44.70  Aligned_cols=22  Identities=23%  Similarity=0.228  Sum_probs=17.6

Q ss_pred             CeEEEEcCCCCCcccchhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ..+++.|.+||||||+.-.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            3688999999999988765543

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=88.56  E-value=0.26  Score=44.61  Aligned_cols=19  Identities=21%  Similarity=0.176  Sum_probs=16.1

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .++.+++.|++||||||.+
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999544

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=88.53  E-value=0.08  Score=49.34  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~   46 (243)
T 1mv5_A           25 AQPNSIIAFAGPSGGGKSTIFS   46 (243)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578889999999999998765

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=88.47  E-value=0.15  Score=44.89  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=19.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ...+..+++.|..||||||+.-.+.
T Consensus         6 m~~~~~I~l~G~~GsGKsT~~~~La   30 (196)
T 2c95_A            6 LKKTNIIFVVGGPGSGKGTQCEKIV   30 (196)
T ss_dssp             HTTSCEEEEEECTTSSHHHHHHHHH
T ss_pred             CcCCCEEEEECCCCCCHHHHHHHHH
Confidence            3456789999999999998765443

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=88.47  E-value=0.094  Score=49.68  Aligned_cols=22  Identities=23%  Similarity=0.478  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|+.||||||.+-
T Consensus        34 i~~Ge~~~liG~nGsGKSTLl~   55 (266)
T 4g1u_C           34 IASGEMVAIIGPNGAGKSTLLR   55 (266)
T ss_dssp             EETTCEEEEECCTTSCHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998875

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=88.43  E-value=0.078  Score=48.08  Aligned_cols=22  Identities=32%  Similarity=0.425  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++++.|.|++||||||.+-
T Consensus        22 i~~G~~~~l~G~nGsGKSTll~   43 (231)
T 4a74_A           22 IETQAITEVFGEFGSGKTQLAH   43 (231)
T ss_dssp             EESSEEEEEEESTTSSHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999998866

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=88.43  E-value=0.15  Score=44.30  Aligned_cols=22  Identities=9%  Similarity=0.347  Sum_probs=17.3

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +..++++|..||||||..-.+.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La   24 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQ   24 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHH
Confidence            5679999999999997654433

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=88.42  E-value=0.12  Score=46.45  Aligned_cols=20  Identities=25%  Similarity=0.225  Sum_probs=16.2

Q ss_pred             HcCCeEEEEcCCCCCcccch
Q psy6094          70 RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtql   89 (455)
                      ..+.++.|.|++||||||.+
T Consensus         4 ~~~~~i~i~G~~GsGKSTl~   23 (211)
T 3asz_A            4 PKPFVIGIAGGTASGKTTLA   23 (211)
T ss_dssp             -CCEEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHH
Confidence            45678889999999999665

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=88.38  E-value=0.1  Score=45.74  Aligned_cols=24  Identities=17%  Similarity=0.254  Sum_probs=18.7

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+..+++.|..||||||+.-.+..
T Consensus         3 ~g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            456789999999999988754443

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=88.34  E-value=0.098  Score=48.98  Aligned_cols=22  Identities=18%  Similarity=0.354  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLlk   47 (250)
T 2d2e_A           26 VPKGEVHALMGPNGAGKSTLGK   47 (250)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998876

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=88.32  E-value=0.1  Score=49.20  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        38 i~~Gei~~l~G~NGsGKSTLlk   59 (256)
T 1vpl_A           38 IEEGEIFGLIGPNGAGKTTTLR   59 (256)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCcEEEEECCCCCCHHHHHH
Confidence            3578899999999999998865

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=88.29  E-value=0.1  Score=49.40  Aligned_cols=22  Identities=32%  Similarity=0.662  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        47 i~~Gei~~liG~NGsGKSTLlk   68 (263)
T 2olj_A           47 IREGEVVVVIGPSGSGKSTFLR   68 (263)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEEcCCCCcHHHHHH
Confidence            3578899999999999998875

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=88.27  E-value=0.14  Score=44.16  Aligned_cols=22  Identities=27%  Similarity=0.187  Sum_probs=17.2

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      -|++++.|..||||||+.-.|.
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La   28 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELG   28 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHH
Confidence            3789999999999997664443

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=88.20  E-value=0.1  Score=49.40  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        43 i~~Ge~~~l~G~NGsGKSTLlk   64 (267)
T 2zu0_C           43 VHPGEVHAIMGPNGSGKSTLSA   64 (267)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            4578899999999999998876

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=88.12  E-value=0.11  Score=45.86  Aligned_cols=22  Identities=18%  Similarity=0.427  Sum_probs=17.6

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +.++++.|++||||||.+-.+.
T Consensus         2 g~ii~l~G~~GaGKSTl~~~L~   23 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTTCKRLA   23 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHh
Confidence            3578899999999998876443

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=88.10  E-value=0.13  Score=49.98  Aligned_cols=19  Identities=21%  Similarity=0.267  Sum_probs=16.0

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+++|+|||||||||..-
T Consensus         3 ~~~i~i~GptgsGKt~la~   21 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSV   21 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHH
Confidence            4578999999999997654

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=88.05  E-value=0.11  Score=49.40  Aligned_cols=22  Identities=23%  Similarity=0.388  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        42 i~~Ge~~~i~G~nGsGKSTLlk   63 (271)
T 2ixe_A           42 LYPGKVTALVGPNGSGKSTVAA   63 (271)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            4578999999999999998875

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=88.00  E-value=0.12  Score=50.00  Aligned_cols=21  Identities=10%  Similarity=0.245  Sum_probs=18.2

Q ss_pred             HHcCCeEEEEcCCCCCcccch
Q psy6094          69 VRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtql   89 (455)
                      |..|+.+.|.|++||||||.+
T Consensus       123 i~~Ge~vaIvGpsGsGKSTLl  143 (305)
T 2v9p_A          123 IPKKNCLAFIGPPNTGKSMLC  143 (305)
T ss_dssp             CTTCSEEEEECSSSSSHHHHH
T ss_pred             ecCCCEEEEECCCCCcHHHHH
Confidence            457899999999999999665

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=88.00  E-value=0.15  Score=44.60  Aligned_cols=24  Identities=13%  Similarity=0.079  Sum_probs=19.0

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ....++++.|.+||||||+.-.+.
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~~l~   32 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGKELA   32 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHHHHH
Confidence            356789999999999998765443

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=87.95  E-value=0.11  Score=49.15  Aligned_cols=22  Identities=27%  Similarity=0.560  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.|.|+.||||||.+-
T Consensus        30 i~~Ge~~~liG~nGsGKSTLl~   51 (266)
T 2yz2_A           30 INEGECLLVAGNTGSGKSTLLQ   51 (266)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998765

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=87.87  E-value=0.14  Score=45.12  Aligned_cols=27  Identities=7%  Similarity=0.204  Sum_probs=20.3

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhhhc
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      .+..+++.|..||||||+.-.+.+..+
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l~   30 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGLR   30 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            356789999999999998765544433

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=87.71  E-value=0.14  Score=44.67  Aligned_cols=22  Identities=14%  Similarity=0.163  Sum_probs=18.1

Q ss_pred             cCCeEEEEcCCCCCcccchhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      .+..+++.|..||||||+.-.+
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L   25 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMAL   25 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHH
Confidence            4678899999999999876533

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=87.69  E-value=0.11  Score=48.72  Aligned_cols=22  Identities=27%  Similarity=0.537  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.|.|+.||||||.+-
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~   49 (253)
T 2nq2_C           28 LNKGDILAVLGQNGCGKSTLLD   49 (253)
T ss_dssp             EETTCEEEEECCSSSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998765

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=87.69  E-value=0.14  Score=46.95  Aligned_cols=25  Identities=24%  Similarity=0.343  Sum_probs=20.1

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ..|..+.|.|+.||||||++-.|..
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~   42 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEK   42 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHh
Confidence            3567899999999999999874443

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=87.68  E-value=0.11  Score=49.48  Aligned_cols=22  Identities=18%  Similarity=0.367  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        44 i~~Ge~~~liG~NGsGKSTLlk   65 (279)
T 2ihy_A           44 IAKGDKWILYGLNGAGKTTLLN   65 (279)
T ss_dssp             EETTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998865

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=87.58  E-value=0.15  Score=44.85  Aligned_cols=22  Identities=18%  Similarity=0.283  Sum_probs=17.4

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +..+++.|.+||||||+.-.+.
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~   24 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIV   24 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999998765443

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=87.57  E-value=0.27  Score=53.92  Aligned_cols=32  Identities=16%  Similarity=0.297  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          59 YQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        59 ~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -..|.+++..+..+.+++|+|++||||||.+.
T Consensus       358 n~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~  389 (800)
T 2wjy_A          358 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA  389 (800)
T ss_dssp             CHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH
T ss_pred             CHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH
Confidence            46788888888888999999999999997665

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=87.52  E-value=0.12  Score=48.51  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.|.|+.||||||.+-
T Consensus        23 i~~Ge~~~liG~NGsGKSTLlk   44 (249)
T 2qi9_C           23 VRAGEILHLVGPNGAGKSTLLA   44 (249)
T ss_dssp             EETTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578889999999999998875

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=87.48  E-value=0.18  Score=46.71  Aligned_cols=23  Identities=30%  Similarity=0.242  Sum_probs=18.5

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ....++|.|+.||||||++-.|.
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La   48 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIA   48 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            35789999999999998875443

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=87.46  E-value=0.15  Score=45.54  Aligned_cols=21  Identities=19%  Similarity=0.283  Sum_probs=17.8

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+.++++.|+.||||||..-
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~   43 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLAC   43 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHH
Confidence            467889999999999997654

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=87.46  E-value=0.17  Score=44.72  Aligned_cols=17  Identities=29%  Similarity=0.530  Sum_probs=14.6

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+.+.|+.||||||.+-
T Consensus         2 ~i~l~G~nGsGKTTLl~   18 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVK   18 (178)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998764

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=87.35  E-value=0.15  Score=49.93  Aligned_cols=19  Identities=26%  Similarity=0.473  Sum_probs=15.6

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .+.+++|+|+|||||||..
T Consensus        39 ~~~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3458999999999999654

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=87.22  E-value=0.24  Score=50.58  Aligned_cols=30  Identities=17%  Similarity=0.388  Sum_probs=21.5

Q ss_pred             HHHHHHHHH----HcCC-eEEEEcCCCCCcccchh
Q psy6094          61 MRDAVLDMV----RNNQ-ITVISGETGSGPPLHLD   90 (455)
Q Consensus        61 ~q~~il~~i----~~~~-~vii~~~TGSGKTtqlp   90 (455)
                      .|.+++..+    .+++ .++|.|+.||||||.+-
T Consensus        29 ~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~   63 (459)
T 3upu_A           29 GQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK   63 (459)
T ss_dssp             HHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH
Confidence            345555543    3334 99999999999998766

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=87.10  E-value=0.28  Score=53.83  Aligned_cols=32  Identities=16%  Similarity=0.335  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          59 YQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        59 ~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -..|.+++..+..+..++|.|++|||||+.+.
T Consensus       362 n~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~  393 (802)
T 2xzl_A          362 NSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSA  393 (802)
T ss_dssp             CHHHHHHHHHHTTCSEEEEECSTTSSHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            37788999988888899999999999997665

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=87.05  E-value=0.21  Score=43.53  Aligned_cols=24  Identities=21%  Similarity=0.235  Sum_probs=14.4

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ....+++.|..||||||+.-.+.+
T Consensus         4 ~~~~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             -CCEEEEECCC----CHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356799999999999988654443

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=86.95  E-value=0.19  Score=45.48  Aligned_cols=22  Identities=18%  Similarity=0.347  Sum_probs=17.6

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +.++.|.|++||||||..-.+.
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~   26 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMA   26 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999998775443

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=86.92  E-value=0.17  Score=44.25  Aligned_cols=22  Identities=23%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             eEEEEcCCCCCcccchhhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      .+++.|..||||||+.-.|.+.
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~   24 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999987655443

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=86.89  E-value=0.17  Score=45.11  Aligned_cols=23  Identities=17%  Similarity=0.365  Sum_probs=18.3

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..+++.|..||||||+.-.|.
T Consensus         3 ~~~~I~i~G~~GsGKsT~~~~L~   25 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQATLLK   25 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHH
Confidence            35678999999999998875443

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=86.89  E-value=0.092  Score=50.86  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        77 i~~Ge~vaivG~sGsGKSTLl~   98 (306)
T 3nh6_A           77 VMPGQTLALVGPSGAGKSTILR   98 (306)
T ss_dssp             ECTTCEEEEESSSCHHHHHHHH
T ss_pred             EcCCCEEEEECCCCchHHHHHH
Confidence            3467889999999999998875

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=86.89  E-value=0.14  Score=46.38  Aligned_cols=22  Identities=18%  Similarity=0.404  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++++.|++||||||.+-
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~   41 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSL   41 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             CcCCCEEEEEcCCCCCHHHHHH
Confidence            4568899999999999998765

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=86.84  E-value=0.12  Score=46.28  Aligned_cols=22  Identities=32%  Similarity=0.206  Sum_probs=18.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+..+.|.|++||||||..-
T Consensus        18 ~~~~~~i~i~G~~GsGKSTl~~   39 (207)
T 2qt1_A           18 GSKTFIIGISGVTNSGKTTLAK   39 (207)
T ss_dssp             SCCCEEEEEEESTTSSHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHH
Confidence            4567788999999999997654

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=86.82  E-value=0.17  Score=45.13  Aligned_cols=21  Identities=29%  Similarity=0.313  Sum_probs=17.2

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .++++.|+.||||||+.-.|.
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~   39 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIA   39 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            479999999999998765443

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=86.78  E-value=0.18  Score=47.14  Aligned_cols=17  Identities=29%  Similarity=0.217  Sum_probs=14.4

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      +++|.|+|||||||..-
T Consensus         3 li~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            58899999999997653

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=86.73  E-value=0.33  Score=46.36  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=18.5

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +..++++|++||||||..-.+..
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999988765543

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=86.64  E-value=0.21  Score=43.99  Aligned_cols=22  Identities=23%  Similarity=0.421  Sum_probs=17.6

Q ss_pred             cCCeEEEEcCCCCCcccchhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      .+..++++|..||||||..-.+
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~L   30 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMI   30 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            4678999999999999765433

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=86.59  E-value=0.2  Score=44.33  Aligned_cols=21  Identities=24%  Similarity=0.205  Sum_probs=16.9

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+++.|..||||||+.-.|..
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            578999999999988764443

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=86.50  E-value=0.21  Score=44.64  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=18.5

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..+++.|..||||||+.-.+.
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~   31 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLV   31 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHH
Confidence            46789999999999998765443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=86.48  E-value=0.19  Score=44.25  Aligned_cols=23  Identities=17%  Similarity=0.268  Sum_probs=18.8

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..+++.|..||||||+.-.+.
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~   34 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLA   34 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHH
Confidence            46789999999999998876443

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=86.45  E-value=0.21  Score=44.99  Aligned_cols=23  Identities=13%  Similarity=0.033  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDF   91 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~   91 (455)
                      +..+.++++.|..||||||+.-.
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~   44 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVE   44 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHH
Confidence            45678899999999999987653

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=86.39  E-value=0.19  Score=43.84  Aligned_cols=17  Identities=41%  Similarity=0.472  Sum_probs=15.3

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      ..+|.|++||||||.+-
T Consensus        28 ~~~i~G~NGsGKStll~   44 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGD   44 (182)
T ss_dssp             EEEEEECTTSSHHHHHH
T ss_pred             cEEEECCCCCCHHHHHH
Confidence            78999999999998765

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=86.35  E-value=0.21  Score=45.22  Aligned_cols=19  Identities=21%  Similarity=0.330  Sum_probs=15.5

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .++.++|.|+|||||||..
T Consensus        33 ~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            3566899999999999654

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=86.34  E-value=0.29  Score=43.81  Aligned_cols=19  Identities=21%  Similarity=0.183  Sum_probs=15.8

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .+.++.|.|++||||||.+
T Consensus        21 ~~~~i~i~G~~GsGKstl~   39 (201)
T 1rz3_A           21 GRLVLGIDGLSRSGKTTLA   39 (201)
T ss_dssp             SSEEEEEEECTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3568899999999999655

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=86.32  E-value=0.2  Score=44.69  Aligned_cols=18  Identities=39%  Similarity=0.580  Sum_probs=14.7

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      +-+||+||+|+||||.+-
T Consensus         2 RpIVi~GPSG~GK~Tl~~   19 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLK   19 (186)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            458999999999996553

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=86.28  E-value=0.39  Score=46.31  Aligned_cols=19  Identities=21%  Similarity=0.315  Sum_probs=16.2

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      ++.+++.|++|+|||+.+-
T Consensus       152 ~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            6899999999999995543

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=86.28  E-value=0.21  Score=44.68  Aligned_cols=19  Identities=16%  Similarity=0.375  Sum_probs=16.3

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      |+.+.+.|++||||||.+-
T Consensus         1 G~~i~i~G~nG~GKTTll~   19 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIH   19 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHH
Confidence            4578899999999998775

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=86.25  E-value=0.15  Score=48.91  Aligned_cols=21  Identities=29%  Similarity=0.472  Sum_probs=18.3

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|+.+.|.|+.||||||.+-
T Consensus        62 ~~Ge~~~i~G~NGsGKSTLlk   82 (290)
T 2bbs_A           62 ERGQLLAVAGSTGAGKTSLLM   82 (290)
T ss_dssp             CTTCEEEEEESTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHH
Confidence            467889999999999998765

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=86.09  E-value=0.16  Score=50.37  Aligned_cols=22  Identities=27%  Similarity=0.442  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        27 i~~Ge~~~llGpsGsGKSTLLr   48 (359)
T 3fvq_A           27 LDPGEILFIIGASGCGKTTLLR   48 (359)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCchHHHHHH
Confidence            3568899999999999999866

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=85.97  E-value=0.2  Score=46.13  Aligned_cols=25  Identities=16%  Similarity=0.279  Sum_probs=20.6

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      .+..+++.|+.|||||||+..+.+.
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            5678999999999999998755443

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=85.97  E-value=0.3  Score=45.57  Aligned_cols=20  Identities=30%  Similarity=0.424  Sum_probs=16.2

Q ss_pred             HcCCeEEEEcCCCCCcccch
Q psy6094          70 RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtql   89 (455)
                      ..+..+++.|++|||||+.+
T Consensus        27 ~~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHHH
T ss_pred             CCCCCEEEECCCCCcHHHHH
Confidence            45678999999999999443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=85.88  E-value=0.15  Score=49.13  Aligned_cols=20  Identities=25%  Similarity=0.463  Sum_probs=17.2

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+.++.+.|++||||||.+.
T Consensus        99 ~g~vi~lvG~nGsGKTTll~  118 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLG  118 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHH
Confidence            35678899999999998876

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=85.87  E-value=0.17  Score=45.42  Aligned_cols=22  Identities=18%  Similarity=0.110  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+..+++.|++||||||.+-
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~   38 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLAL   38 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHH
T ss_pred             CcCCEEEEEECCCCCCHHHHHH
Confidence            4568899999999999997765

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=85.83  E-value=0.24  Score=44.27  Aligned_cols=23  Identities=13%  Similarity=0.252  Sum_probs=18.8

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..+++.|..||||||+.-.+.
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~   30 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLV   30 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            46789999999999998875443

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=85.81  E-value=0.39  Score=45.49  Aligned_cols=18  Identities=22%  Similarity=0.257  Sum_probs=15.1

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      ...+++.|++|||||+.+
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            567999999999999544

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=85.73  E-value=0.25  Score=44.73  Aligned_cols=22  Identities=18%  Similarity=0.250  Sum_probs=17.6

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +..+++.|..||||||+.-.|.
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La   25 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQ   25 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999998875443

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=85.73  E-value=0.12  Score=46.40  Aligned_cols=19  Identities=21%  Similarity=0.436  Sum_probs=16.1

Q ss_pred             eEEEEcCCCCCcccchhhh
Q psy6094          74 ITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~l   92 (455)
                      .++|.|+.||||||++-.|
T Consensus         2 ~I~i~G~~GsGKsTl~~~L   20 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKL   20 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHH
Confidence            5789999999999987643

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=85.72  E-value=0.36  Score=45.74  Aligned_cols=18  Identities=22%  Similarity=0.333  Sum_probs=15.5

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      .+.+++.|++||||||.+
T Consensus        54 ~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            568999999999999554

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=85.69  E-value=0.41  Score=46.55  Aligned_cols=26  Identities=19%  Similarity=0.379  Sum_probs=19.9

Q ss_pred             HHHHHHcCCe--EEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQI--TVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~--vii~~~TGSGKTtqlp   90 (455)
                      +-..+.+++.  +++.|++|+||||.+-
T Consensus        37 L~~~i~~g~~~~~ll~Gp~G~GKTtla~   64 (340)
T 1sxj_C           37 VRKFVDEGKLPHLLFYGPPGTGKTSTIV   64 (340)
T ss_dssp             HHHHHHTTCCCCEEEECSSSSSHHHHHH
T ss_pred             HHHHHhcCCCceEEEECCCCCCHHHHHH
Confidence            3345666766  8999999999997654

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=85.69  E-value=0.23  Score=44.71  Aligned_cols=23  Identities=26%  Similarity=0.265  Sum_probs=17.6

Q ss_pred             eEEEEcCCCCCcccchhhhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      .+++.|+.||||||+.-.+.++.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37889999999998876554433

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=85.68  E-value=0.24  Score=47.79  Aligned_cols=20  Identities=15%  Similarity=0.459  Sum_probs=17.5

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+.++.+.|++||||||.+-
T Consensus       101 ~g~vi~lvG~nGsGKTTll~  120 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIA  120 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHH
Confidence            35789999999999998876

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=85.66  E-value=0.36  Score=46.43  Aligned_cols=26  Identities=19%  Similarity=0.262  Sum_probs=20.1

Q ss_pred             HHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+.+.++++++|.|+.|+|||+.+-
T Consensus        24 L~~~l~~~~~v~i~G~~G~GKT~Ll~   49 (350)
T 2qen_A           24 LEESLENYPLTLLLGIRRVGKSSLLR   49 (350)
T ss_dssp             HHHHHHHCSEEEEECCTTSSHHHHHH
T ss_pred             HHHHHhcCCeEEEECCCcCCHHHHHH
Confidence            33344456899999999999997765

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=85.59  E-value=0.17  Score=49.99  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.+.|++||||||.+-
T Consensus        38 i~~Ge~~~llGpnGsGKSTLLr   59 (355)
T 1z47_A           38 IREGEMVGLLGPSGSGKTTILR   59 (355)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999999876

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=85.46  E-value=0.22  Score=48.29  Aligned_cols=20  Identities=20%  Similarity=0.165  Sum_probs=16.0

Q ss_pred             CeEEEEcCCCCCcccchhhh
Q psy6094          73 QITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~l   92 (455)
                      ..++|+|||||||||..-.+
T Consensus        11 ~~i~i~GptgsGKt~la~~L   30 (316)
T 3foz_A           11 KAIFLMGPTASGKTALAIEL   30 (316)
T ss_dssp             EEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCccCHHHHHHHH
Confidence            47889999999999765433

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=85.35  E-value=0.24  Score=43.35  Aligned_cols=21  Identities=24%  Similarity=0.366  Sum_probs=16.8

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ..+++.|..||||||+.-.+.
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~   27 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIV   27 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            468899999999998765443

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=85.30  E-value=0.18  Score=50.26  Aligned_cols=22  Identities=23%  Similarity=0.490  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.+.|++||||||.+-
T Consensus        26 i~~Ge~~~llGpsGsGKSTLLr   47 (381)
T 3rlf_A           26 IHEGEFVVFVGPSGCGKSTLLR   47 (381)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             ECCCCEEEEEcCCCchHHHHHH
Confidence            3568899999999999999876

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=85.14  E-value=0.27  Score=44.86  Aligned_cols=24  Identities=21%  Similarity=0.346  Sum_probs=19.8

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .|..+++.|..|||||||+-.+.+
T Consensus         2 ~g~~i~~eG~~gsGKsT~~~~l~~   25 (213)
T 4tmk_A            2 RSKYIVIEGLEGAGKTTARNVVVE   25 (213)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            477899999999999999874433

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=85.14  E-value=0.19  Score=49.76  Aligned_cols=22  Identities=23%  Similarity=0.471  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr   47 (359)
T 2yyz_A           26 VKDGEFVALLGPSGCGKTTTLL   47 (359)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEEcCCCchHHHHHH
Confidence            3468899999999999999876

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=85.11  E-value=0.22  Score=45.23  Aligned_cols=22  Identities=27%  Similarity=0.368  Sum_probs=17.5

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ...+++.|+.||||||+.-.|.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La   26 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIK   26 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3568999999999998875443

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=85.09  E-value=0.43  Score=46.45  Aligned_cols=17  Identities=24%  Similarity=0.274  Sum_probs=15.0

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      ++-|.|++||||||.+-
T Consensus        94 iigI~GpsGSGKSTl~~  110 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSR  110 (321)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            78899999999997764

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=85.07  E-value=0.25  Score=44.44  Aligned_cols=22  Identities=27%  Similarity=0.246  Sum_probs=17.0

Q ss_pred             eEEEEcCCCCCcccchhhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      .+++.|+.||||||+.-.+.++
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~   23 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEK   23 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3788999999999887655433

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=85.06  E-value=0.19  Score=47.81  Aligned_cols=26  Identities=12%  Similarity=0.236  Sum_probs=21.2

Q ss_pred             HHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.--+..|..++|.|++||||||.+-
T Consensus        28 i~~~l~~G~~~~i~G~~G~GKTTl~~   53 (296)
T 1cr0_A           28 KTLGARGGEVIMVTSGSGMGKSTFVR   53 (296)
T ss_dssp             HHCSBCTTCEEEEEESTTSSHHHHHH
T ss_pred             HhcCCCCCeEEEEEeCCCCCHHHHHH
Confidence            33346688999999999999998765

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=85.05  E-value=0.3  Score=47.22  Aligned_cols=29  Identities=17%  Similarity=0.228  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHcCCeEEEEcCCCCCcccch
Q psy6094          61 MRDAVLDMVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        61 ~q~~il~~i~~~~~vii~~~TGSGKTtql   89 (455)
                      ....+..++..+..+++.|++|+|||+.+
T Consensus        35 ~~~~l~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           35 MINRLLIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCeEEEECCCCCcHHHHH
Confidence            34455566677889999999999999443

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=85.03  E-value=0.19  Score=49.78  Aligned_cols=22  Identities=23%  Similarity=0.487  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr   47 (362)
T 2it1_A           26 IKDGEFMALLGPSGSGKSTLLY   47 (362)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCchHHHHHH
Confidence            3468899999999999999876

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=85.03  E-value=0.19  Score=47.54  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=18.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +. |+.+.|.|+.||||||.+-
T Consensus        28 i~-Ge~~~i~G~NGsGKSTLlk   48 (263)
T 2pjz_A           28 VN-GEKVIILGPNGSGKTTLLR   48 (263)
T ss_dssp             EC-SSEEEEECCTTSSHHHHHH
T ss_pred             EC-CEEEEEECCCCCCHHHHHH
Confidence            35 7889999999999998865

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=84.96  E-value=0.25  Score=42.59  Aligned_cols=21  Identities=14%  Similarity=0.145  Sum_probs=16.6

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ..+++.|..||||||+.-.+.
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La   23 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELA   23 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            468999999999997765443

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=84.94  E-value=0.26  Score=43.19  Aligned_cols=21  Identities=19%  Similarity=0.260  Sum_probs=16.9

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+++.|..||||||+.-.+.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999988764443

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=84.92  E-value=0.27  Score=43.21  Aligned_cols=19  Identities=16%  Similarity=0.191  Sum_probs=16.1

Q ss_pred             CeEEEEcCCCCCcccchhh
Q psy6094          73 QITVISGETGSGPPLHLDF   91 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~   91 (455)
                      .++.+.|+.||||||.+..
T Consensus         5 ~~i~i~G~sGsGKTTl~~~   23 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEK   23 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            4688999999999987763

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=84.88  E-value=0.21  Score=46.19  Aligned_cols=22  Identities=23%  Similarity=0.208  Sum_probs=17.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+.++-|.|+.||||||.+-
T Consensus        22 i~~g~iigI~G~~GsGKSTl~k   43 (245)
T 2jeo_A           22 SMRPFLIGVSGGTASGKSTVCE   43 (245)
T ss_dssp             -CCSEEEEEECSTTSSHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHH
Confidence            4567788899999999997764

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=84.79  E-value=0.3  Score=43.50  Aligned_cols=24  Identities=17%  Similarity=0.209  Sum_probs=18.4

Q ss_pred             CCeEEEEcCCCCCcccchhhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      +..+++.|..||||||+.-.|.+.
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~   43 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEK   43 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            346899999999999887555443

>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=84.61  E-value=0.39  Score=49.16  Aligned_cols=33  Identities=9%  Similarity=0.052  Sum_probs=26.5

Q ss_pred             CCHHHHHHHHHHH----HcCCeEEEEcCCCCCcccch
Q psy6094          57 PSYQMRDAVLDMV----RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        57 P~~~~q~~il~~i----~~~~~vii~~~TGSGKTtql   89 (455)
                      ..+++|.+.++.+    ..+...|+..+||+|||.+.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~a   73 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT   73 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHH
Confidence            3678898887766    46778999999999999553

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=84.59  E-value=0.2  Score=46.67  Aligned_cols=20  Identities=30%  Similarity=0.571  Sum_probs=17.1

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .. .++.+.|+.||||||.+-
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~   42 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLE   42 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHH
T ss_pred             CC-EEEEEECCCCCCHHHHHH
Confidence            35 788899999999998765

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=84.55  E-value=0.28  Score=43.67  Aligned_cols=21  Identities=14%  Similarity=0.357  Sum_probs=16.8

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      ..+++.|..||||||+.-.+.
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~   36 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLV   36 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            468899999999998765443

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=84.55  E-value=0.28  Score=41.89  Aligned_cols=18  Identities=44%  Similarity=0.671  Sum_probs=15.3

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ...+|.|++||||||.+-
T Consensus        24 g~~~I~G~NGsGKStil~   41 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLD   41 (149)
T ss_dssp             EEEEEECCTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            478999999999997665

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=84.50  E-value=0.4  Score=45.07  Aligned_cols=20  Identities=20%  Similarity=0.318  Sum_probs=16.1

Q ss_pred             HcCCeEEEEcCCCCCcccch
Q psy6094          70 RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtql   89 (455)
                      .....+++.|++|||||+.+
T Consensus        49 ~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHHH
Confidence            34667999999999999544

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=84.50  E-value=0.21  Score=49.74  Aligned_cols=22  Identities=23%  Similarity=0.563  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++.+.|+.||||||.+-
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr   47 (372)
T 1g29_1           26 VKDGEFMILLGPSGCGKTTTLR   47 (372)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCcHHHHHHH
Confidence            3478899999999999999876

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=84.49  E-value=0.21  Score=49.69  Aligned_cols=22  Identities=23%  Similarity=0.552  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        34 i~~Ge~~~llGpnGsGKSTLLr   55 (372)
T 1v43_A           34 IKDGEFLVLLGPSGCGKTTTLR   55 (372)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCChHHHHHH
Confidence            3578899999999999999876

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=84.48  E-value=0.27  Score=45.35  Aligned_cols=26  Identities=19%  Similarity=0.414  Sum_probs=17.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          69 VRNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ...+..+++.|+.|||||||+-.+.+
T Consensus        22 m~~g~~I~~eG~~GsGKsT~~~~l~~   47 (227)
T 3v9p_A           22 MARGKFITFEGIDGAGKTTHLQWFCD   47 (227)
T ss_dssp             -CCCCEEEEECCC---CHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34688899999999999999874433

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=84.46  E-value=3.6  Score=42.76  Aligned_cols=115  Identities=16%  Similarity=0.055  Sum_probs=74.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC--CCCccCCCCC--
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT--NIAETSITID--  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT--niae~gitI~--  259 (455)
                      ..+|.+|||+|+....+.+++.   .      +..++.=..+++..+..+.|+  ..+ .-|+++|  .-..-|||++  
T Consensus       391 ~~~g~~lvlF~Sy~~l~~v~~~---~------~~~v~~q~~~~~~~~~~~~~~--~~~-~~vl~~v~gg~~~EGiD~~d~  458 (551)
T 3crv_A          391 QAKANVLVVFPSYEIMDRVMSR---I------SLPKYVESEDSSVEDLYSAIS--ANN-KVLIGSVGKGKLAEGIELRNN  458 (551)
T ss_dssp             HCSSEEEEEESCHHHHHHHHTT---C------CSSEEECCSSCCHHHHHHHTT--SSS-SCEEEEESSCCSCCSSCCEET
T ss_pred             hCCCCEEEEecCHHHHHHHHHh---c------CCcEEEcCCCCCHHHHHHHHH--hcC-CeEEEEEecceeccccccccc
Confidence            6789999999999999988862   1      123333223455555555554  223 4799998  5677799999  


Q ss_pred             ---CeeEEEeCCCCcccccccCC-----------Ccccc---cccccchhhHHhhhcccCCCCC--CeEEec
Q psy6094         260 ---DIVYVVDCGKTKMSNFDVKD-----------NIATL---KPEWISLANAKQRRGRAGRTLK--RSETQQ  312 (455)
Q Consensus       260 ---~V~~VID~g~~k~~~yd~~~-----------~~~~l---~~~~iSka~~~QR~GRaGR~~~--G~c~~L  312 (455)
                         ..+.||-.|+|-... ||..           |...+   ...| .--...|=.||.=|...  |..+-|
T Consensus       459 ~g~~l~~viI~~lPfp~~-dp~~~ar~~~~~~~~g~~~~~~~y~~p-a~~~l~Qa~GRlIR~~~D~G~v~ll  528 (551)
T 3crv_A          459 DRSLISDVVIVGIPYPPP-DDYLKILAQRVSLKMNRENEEFLFKIP-ALVTIKQAIGRAIRDVNDKCNVWLL  528 (551)
T ss_dssp             TEESEEEEEEESCCCCCC-SHHHHHHHHHTTCCSSTTTHHHHTHHH-HHHHHHHHHHTTCCSTTCEEEEEEE
T ss_pred             CCcceeEEEEEcCCCCCC-CHHHHHHHHHHHHhhCCchhHHHHHHH-HHHHHHHHhccCccCCCccEEEEEe
Confidence               378888889886554 4421           22111   2333 44557788899988654  755544

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=84.43  E-value=0.21  Score=50.06  Aligned_cols=22  Identities=32%  Similarity=0.397  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.+.|++||||||.+-
T Consensus        44 i~~Ge~~~llGpsGsGKSTLLr   65 (390)
T 3gd7_A           44 ISPGQRVGLLGRTGSGKSTLLS   65 (390)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCChHHHHHH
Confidence            4578899999999999998876

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=84.42  E-value=0.27  Score=44.85  Aligned_cols=25  Identities=16%  Similarity=0.399  Sum_probs=20.0

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ..+..+++.|..|||||||+-.+.+
T Consensus         4 m~g~~i~~eG~~gsGKsT~~~~l~~   28 (213)
T 4edh_A            4 MTGLFVTLEGPEGAGKSTNRDYLAE   28 (213)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCceEEEEEcCCCCCHHHHHHHHHH
Confidence            4577899999999999999874443

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=84.35  E-value=0.28  Score=45.49  Aligned_cols=25  Identities=16%  Similarity=0.129  Sum_probs=19.1

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      ....+++.|+.||||||+.-.|.+.
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3447899999999999887655443

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=84.32  E-value=0.39  Score=46.70  Aligned_cols=18  Identities=17%  Similarity=0.320  Sum_probs=15.4

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ..+++.|++||||||.+-
T Consensus        52 ~~~ll~Gp~G~GKTTLa~   69 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAH   69 (334)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            579999999999996654

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=84.22  E-value=0.28  Score=44.20  Aligned_cols=20  Identities=20%  Similarity=0.330  Sum_probs=16.2

Q ss_pred             eEEEEcCCCCCcccchhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+++.|+.||||||+.-.|.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~   21 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIM   21 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            37899999999998875444

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=84.20  E-value=0.32  Score=43.11  Aligned_cols=19  Identities=37%  Similarity=0.525  Sum_probs=16.2

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .++..++.|+.||||||.+
T Consensus         2 ~g~i~vi~G~~gsGKTT~l   20 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTEL   20 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHH
T ss_pred             ccEEEEEECCCCCCHHHHH
Confidence            4678999999999999654

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=84.16  E-value=0.21  Score=45.53  Aligned_cols=22  Identities=23%  Similarity=0.283  Sum_probs=18.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+.++.+.|++||||||.+-
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~   42 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICH   42 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHH
T ss_pred             CcCCeEEEEECCCCCcHHHHHH
Confidence            4568899999999999997765

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=84.09  E-value=0.78  Score=44.49  Aligned_cols=23  Identities=13%  Similarity=0.099  Sum_probs=17.6

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..++|.|++|||||+.+-.++
T Consensus        44 ~~~~lli~GpPGTGKT~~v~~v~   66 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVNDVM   66 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHH
Confidence            45689999999999996554443

>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=83.97  E-value=4  Score=39.54  Aligned_cols=108  Identities=6%  Similarity=-0.065  Sum_probs=60.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCC-----C
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSIT-----I  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~git-----I  258 (455)
                      ..+..||||.......+-+.+.+...      ++....+-|.....++ +.    .++...|.+.|.-+.-|++     .
T Consensus       123 ~~~~kVLIfsq~t~~LDilE~~l~~~------~~~y~RlDG~~~~~~~-k~----~~~~~~i~Lltsag~~gin~~~~nl  191 (328)
T 3hgt_A          123 EYETETAIVCRPGRTMDLLEALLLGN------KVHIKRYDGHSIKSAA-AA----NDFSCTVHLFSSEGINFTKYPIKSK  191 (328)
T ss_dssp             TSCEEEEEEECSTHHHHHHHHHHTTS------SCEEEESSSCCC------------CCSEEEEEEESSCCCTTTSCCCCC
T ss_pred             hCCCEEEEEECChhHHHHHHHHHhcC------CCceEeCCCCchhhhh-hc----ccCCceEEEEECCCCCCcCcccccC
Confidence            56778999999999988888888765      4888899888444332 21    2345677776664444454     4


Q ss_pred             CCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhccc--CCCCCCeEEecCChh
Q psy6094         259 DDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRA--GRTLKRSETQQYPND  316 (455)
Q Consensus       259 ~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRa--GR~~~G~c~~L~t~~  316 (455)
                      -..+.||=        ||+.-+...-      --++..|+-|.  |+..+=..|||.+..
T Consensus       192 ~~aD~VI~--------~DsdwNp~~d------~iQa~~r~~R~~~gq~k~v~V~RLvt~~  237 (328)
T 3hgt_A          192 ARFDMLIC--------LDTTVDTSQK------DIQYLLQYKRERKGLERYAPIVRLVAIN  237 (328)
T ss_dssp             SCCSEEEE--------CSTTCCTTSH------HHHHHHCCC---------CCEEEEEETT
T ss_pred             CCCCEEEE--------ECCCCCCCCh------HHHHHHHHhhhccCCCCcceEEEEeCCC
Confidence            45566663        4433221110      01233355555  334456899998844

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=83.88  E-value=0.31  Score=41.81  Aligned_cols=20  Identities=15%  Similarity=0.081  Sum_probs=16.2

Q ss_pred             eEEEEcCCCCCcccchhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+++.|..||||||+.-.+.
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~   21 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLS   21 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            47899999999998765443

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=83.86  E-value=0.3  Score=44.47  Aligned_cols=21  Identities=24%  Similarity=0.292  Sum_probs=16.9

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+++.|..||||||+.-.|.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999988764443

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=83.84  E-value=0.55  Score=45.95  Aligned_cols=19  Identities=21%  Similarity=0.291  Sum_probs=15.9

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      .+.+++.|++|+|||+.+-
T Consensus        45 ~~~vll~G~~G~GKT~la~   63 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSK   63 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            5679999999999996554

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=83.81  E-value=0.34  Score=44.33  Aligned_cols=24  Identities=17%  Similarity=0.228  Sum_probs=18.8

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ....+++.|.+||||||+.-.|.+
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            346799999999999988754443

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=83.75  E-value=0.17  Score=44.45  Aligned_cols=18  Identities=28%  Similarity=0.355  Sum_probs=15.2

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      +.+.|+|++||||||.+-
T Consensus         3 ~~v~IvG~SGsGKSTL~~   20 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLIT   20 (171)
T ss_dssp             CEEEEEESCHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            467899999999997764

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=83.68  E-value=0.29  Score=47.39  Aligned_cols=22  Identities=14%  Similarity=0.083  Sum_probs=18.5

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+.++.|.|++||||||.+-
T Consensus        87 ~~~g~ivgI~G~sGsGKSTL~~  108 (312)
T 3aez_A           87 RPVPFIIGVAGSVAVGKSTTAR  108 (312)
T ss_dssp             SCCCEEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEECCCCchHHHHHH
Confidence            4567889999999999997654

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=83.65  E-value=0.52  Score=43.65  Aligned_cols=18  Identities=22%  Similarity=0.385  Sum_probs=14.6

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      .+.+++.|++||||||.+
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            446999999999999443

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=83.60  E-value=0.35  Score=45.08  Aligned_cols=25  Identities=12%  Similarity=0.215  Sum_probs=19.6

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ..+.++.|.|++||||||..-.|..
T Consensus        25 ~~g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           25 AIAPVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             TTSCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3567899999999999987654443

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=83.39  E-value=0.25  Score=49.00  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|.++.|.|+.||||||.+-
T Consensus        51 i~~Gei~~IiGpnGaGKSTLlr   72 (366)
T 3tui_C           51 VPAGQIYGVIGASGAGKSTLIR   72 (366)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEEcCCCchHHHHHH
Confidence            3578899999999999998876

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=83.26  E-value=0.17  Score=49.81  Aligned_cols=22  Identities=41%  Similarity=0.640  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        23 i~~Ge~~~llGpnGsGKSTLLr   44 (348)
T 3d31_A           23 VESGEYFVILGPTGAGKTLFLE   44 (348)
T ss_dssp             ECTTCEEEEECCCTHHHHHHHH
T ss_pred             EcCCCEEEEECCCCccHHHHHH
Confidence            3578899999999999999876

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=83.22  E-value=0.37  Score=43.58  Aligned_cols=23  Identities=26%  Similarity=0.465  Sum_probs=17.9

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +..+++.|..||||||+.-.|.+
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            35688999999999988754443

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=83.19  E-value=0.31  Score=44.07  Aligned_cols=23  Identities=17%  Similarity=0.296  Sum_probs=18.4

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ++.+++.|.-|||||||+-.|.+
T Consensus         2 ~kFI~~EG~dGsGKsTq~~~L~~   24 (205)
T 4hlc_A            2 SAFITFEGPEGSGKTTVINEVYH   24 (205)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHHH
Confidence            45788999999999999874433

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=83.15  E-value=0.37  Score=44.71  Aligned_cols=24  Identities=25%  Similarity=0.457  Sum_probs=20.1

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+..+++.|..|||||||+..+.+
T Consensus        26 ~~~~i~~eG~~GsGKsT~~~~l~~   49 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTAIQVVVE   49 (236)
T ss_dssp             CCCEEEEEESTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            578899999999999999874443

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=83.12  E-value=0.37  Score=44.04  Aligned_cols=24  Identities=13%  Similarity=0.296  Sum_probs=20.2

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .+..+++.|..|||||||+-.+.+
T Consensus         4 ~g~~i~~eG~~g~GKst~~~~l~~   27 (216)
T 3tmk_A            4 RGKLILIEGLDRTGKTTQCNILYK   27 (216)
T ss_dssp             CCCEEEEEECSSSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            478899999999999999875544

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=83.12  E-value=0.98  Score=49.73  Aligned_cols=24  Identities=17%  Similarity=0.061  Sum_probs=22.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHH
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMC  207 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~  207 (455)
                      ..+.+|||++.+.++.+.+.++|.
T Consensus       441 ~~GqPVLVgT~SIe~SE~LS~~L~  464 (997)
T 2ipc_A          441 ERGQPVLVGTISIEKSERLSQMLK  464 (997)
T ss_dssp             HHTCCEEEECSSHHHHHHHHHHHH
T ss_pred             HCCCCEEEEeCCHHHHHHHHHHHh
Confidence            457899999999999999999998

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=83.10  E-value=0.24  Score=49.05  Aligned_cols=19  Identities=26%  Similarity=0.473  Sum_probs=16.8

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +.++.+.|++||||||.+.
T Consensus       157 g~vi~lvG~nGsGKTTll~  175 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLG  175 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHH
Confidence            5578899999999998876

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=83.00  E-value=0.33  Score=44.66  Aligned_cols=21  Identities=24%  Similarity=0.224  Sum_probs=17.0

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..+++.|++||||||.+-
T Consensus        10 ~~G~i~litG~mGsGKTT~ll   30 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELI   30 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHH
T ss_pred             CCcEEEEEECCCCCcHHHHHH
Confidence            457789999999999997653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=82.98  E-value=0.25  Score=45.10  Aligned_cols=22  Identities=18%  Similarity=0.540  Sum_probs=18.6

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.+++|.|++||||||.+-
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~   41 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQ   41 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHH
Confidence            4578899999999999997644

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=82.97  E-value=0.34  Score=42.31  Aligned_cols=20  Identities=25%  Similarity=0.235  Sum_probs=15.8

Q ss_pred             CeEEEEcCCCCCcccchhhh
Q psy6094          73 QITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~l   92 (455)
                      ..+++.|..||||||..-.|
T Consensus         3 ~~I~l~G~~GsGKsT~a~~L   22 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRL   22 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45889999999999765433

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=82.92  E-value=0.36  Score=42.92  Aligned_cols=20  Identities=15%  Similarity=0.282  Sum_probs=16.1

Q ss_pred             eEEEEcCCCCCcccchhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+.|.|+.||||||..-.+.
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~   22 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFR   22 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHH
Confidence            58899999999997765443

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=82.87  E-value=0.64  Score=45.62  Aligned_cols=19  Identities=32%  Similarity=0.443  Sum_probs=15.5

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      ....+++.|++|||||+..
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3467999999999999543

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=82.86  E-value=0.67  Score=44.10  Aligned_cols=26  Identities=15%  Similarity=0.234  Sum_probs=18.4

Q ss_pred             HHHHHHcCC--eEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQ--ITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~--~vii~~~TGSGKTtqlp   90 (455)
                      +...+.+++  .+++.|++|+||||.+-
T Consensus        37 l~~~l~~~~~~~~ll~G~~G~GKT~la~   64 (327)
T 1iqp_A           37 LKHYVKTGSMPHLLFAGPPGVGKTTAAL   64 (327)
T ss_dssp             HHHHHHHTCCCEEEEESCTTSSHHHHHH
T ss_pred             HHHHHHcCCCCeEEEECcCCCCHHHHHH
Confidence            334444444  69999999999996553

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=82.83  E-value=0.42  Score=46.24  Aligned_cols=28  Identities=11%  Similarity=0.234  Sum_probs=20.1

Q ss_pred             HHHHHHHHcC--CeEEEEcCCCCCcccchh
Q psy6094          63 DAVLDMVRNN--QITVISGETGSGPPLHLD   90 (455)
Q Consensus        63 ~~il~~i~~~--~~vii~~~TGSGKTtqlp   90 (455)
                      +.+...+..+  ..+++.|++|+||||.+-
T Consensus        47 ~~l~~~l~~~~~~~~ll~G~~G~GKT~la~   76 (353)
T 1sxj_D           47 TVLKKTLKSANLPHMLFYGPPGTGKTSTIL   76 (353)
T ss_dssp             HHHHHHTTCTTCCCEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHhcCCCCEEEEECCCCCCHHHHHH
Confidence            3455555555  459999999999996553

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=82.71  E-value=0.35  Score=47.06  Aligned_cols=18  Identities=17%  Similarity=0.115  Sum_probs=15.2

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ..++|+|+|||||||..-
T Consensus         6 ~~i~i~GptGsGKTtla~   23 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAM   23 (323)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            478999999999997644

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=82.68  E-value=0.36  Score=43.51  Aligned_cols=21  Identities=24%  Similarity=0.379  Sum_probs=16.8

Q ss_pred             CCeEEEEcCCCCCcccchhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~l   92 (455)
                      +.++.|.|..||||||+.-.+
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L   24 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAF   24 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHH
Confidence            347889999999999876544

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=82.48  E-value=0.38  Score=47.14  Aligned_cols=18  Identities=33%  Similarity=0.239  Sum_probs=15.1

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      .+++|.|+|||||||..-
T Consensus         8 ~lI~I~GptgSGKTtla~   25 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSI   25 (340)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHH
Confidence            478999999999997644

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=82.45  E-value=0.34  Score=45.38  Aligned_cols=23  Identities=22%  Similarity=0.289  Sum_probs=19.0

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .++.+++.|+.||||||..-.+.
T Consensus        47 ~g~~i~l~G~~GsGKSTl~~~La   69 (250)
T 3nwj_A           47 NGRSMYLVGMMGSGKTTVGKIMA   69 (250)
T ss_dssp             TTCCEEEECSTTSCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
Confidence            38899999999999998765443

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=82.44  E-value=0.27  Score=46.43  Aligned_cols=22  Identities=9%  Similarity=0.187  Sum_probs=19.4

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+.+++|.|++||||||.+-
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~   48 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLAL   48 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHH
Confidence            5678999999999999998765

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=82.42  E-value=0.71  Score=44.07  Aligned_cols=20  Identities=20%  Similarity=0.295  Sum_probs=16.3

Q ss_pred             HcCCeEEEEcCCCCCcccch
Q psy6094          70 RNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtql   89 (455)
                      ..++.+++.|++|||||+.+
T Consensus        47 ~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHHH
T ss_pred             CCCceEEEECCCCcCHHHHH
Confidence            35678999999999999443

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=82.42  E-value=0.34  Score=47.24  Aligned_cols=20  Identities=20%  Similarity=0.356  Sum_probs=17.6

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+.++.+.|++||||||.+.
T Consensus       128 ~g~vi~lvG~nGaGKTTll~  147 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIA  147 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            36789999999999999876

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=82.35  E-value=0.38  Score=42.87  Aligned_cols=19  Identities=26%  Similarity=0.450  Sum_probs=15.5

Q ss_pred             eEEEEcCCCCCcccchhhh
Q psy6094          74 ITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~l   92 (455)
                      ++.+.|+.||||||..-.+
T Consensus         4 ~i~l~G~~GsGKST~~~~L   22 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLF   22 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5788999999999776544

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=82.33  E-value=0.56  Score=45.91  Aligned_cols=17  Identities=24%  Similarity=0.499  Sum_probs=15.2

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .++|.|++|+||||.+-
T Consensus        46 ~~li~G~~G~GKTtl~~   62 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR   62 (389)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            79999999999997664

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=82.32  E-value=0.37  Score=47.64  Aligned_cols=17  Identities=35%  Similarity=0.679  Sum_probs=15.2

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      ..+|+|+|||||||.+-
T Consensus        25 ~~~i~G~NGaGKTTll~   41 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLFE   41 (365)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            67899999999998875

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=82.29  E-value=0.69  Score=47.82  Aligned_cols=30  Identities=13%  Similarity=0.071  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          61 MRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        61 ~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ....++.++..+..+++.|++|+|||+.+-
T Consensus        30 ~i~~l~~al~~~~~VLL~GpPGtGKT~LAr   59 (500)
T 3nbx_X           30 AIRLCLLAALSGESVFLLGPPGIAKSLIAR   59 (500)
T ss_dssp             HHHHHHHHHHHTCEEEEECCSSSSHHHHHH
T ss_pred             HHHHHHHHHhcCCeeEeecCchHHHHHHHH
Confidence            345566677788999999999999995443

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=82.20  E-value=0.5  Score=44.89  Aligned_cols=17  Identities=24%  Similarity=0.200  Sum_probs=14.4

Q ss_pred             CeEEEEcCCCCCcccch
Q psy6094          73 QITVISGETGSGPPLHL   89 (455)
Q Consensus        73 ~~vii~~~TGSGKTtql   89 (455)
                      ..+++.|++|||||+.+
T Consensus        48 ~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             EEEEEESCSSSSHHHHH
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            47999999999999544

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=82.14  E-value=0.37  Score=50.98  Aligned_cols=22  Identities=27%  Similarity=0.483  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.|.|++||||||.+-
T Consensus       378 i~~G~~~~ivG~sGsGKSTll~  399 (598)
T 3qf4_B          378 IKPGQKVALVGPTGSGKTTIVN  399 (598)
T ss_dssp             CCTTCEEEEECCTTSSTTHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3568889999999999998875

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=82.07  E-value=0.66  Score=44.32  Aligned_cols=18  Identities=17%  Similarity=0.176  Sum_probs=14.9

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      ...+++.|++|+|||+.+
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            367999999999999544

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=82.06  E-value=0.28  Score=51.40  Aligned_cols=46  Identities=22%  Similarity=0.318  Sum_probs=28.3

Q ss_pred             HHHHHHHHHccCCCHHHHHHHHH--------HHHcCCeEEEEcCCCCCcccchh
Q psy6094          45 RYQEMLEARKKLPSYQMRDAVLD--------MVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        45 ~~~~~l~~R~~lP~~~~q~~il~--------~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+++..-...|.|....++..        .+..+.+++++|+.||||||..-
T Consensus       334 ~ir~~Lr~G~~~p~~f~~peV~~vLR~~~~~~~~~G~iI~LiG~sGSGKSTLar  387 (552)
T 3cr8_A          334 EFQRRMRAGLKIPEWYSFPEVLAELHRQTPPRERQGFTVFFTGLSGAGKSTLAR  387 (552)
T ss_dssp             HHHHHHTTTCCCCTTTSCHHHHHHHHHHSCCGGGSCEEEEEEESSCHHHHHHHH
T ss_pred             HHHHHHhcCCCCCccccccchhhhhhhhcccccccceEEEEECCCCChHHHHHH
Confidence            44555555445554433233333        23467899999999999997553

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=81.95  E-value=0.42  Score=45.87  Aligned_cols=20  Identities=30%  Similarity=0.516  Sum_probs=17.4

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++++++.|++|+||||.+.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~  123 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLA  123 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            36789999999999998776

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=81.91  E-value=0.39  Score=41.67  Aligned_cols=17  Identities=29%  Similarity=0.233  Sum_probs=14.3

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .++|.|+.||||||..-
T Consensus         6 ~i~i~G~~GsGKsTla~   22 (175)
T 1via_A            6 NIVFIGFMGSGKSTLAR   22 (175)
T ss_dssp             CEEEECCTTSCHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHH
Confidence            58899999999996543

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=81.66  E-value=0.47  Score=41.78  Aligned_cols=18  Identities=17%  Similarity=0.311  Sum_probs=15.8

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ..++++|++||||||.+.
T Consensus         7 ~~i~i~G~sGsGKTTl~~   24 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLLK   24 (174)
T ss_dssp             CEEEEECCTTSCHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHH
Confidence            578999999999998765

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=81.65  E-value=0.18  Score=49.77  Aligned_cols=22  Identities=23%  Similarity=0.394  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|..+.+.|+.||||||.+-
T Consensus        28 i~~Ge~~~llGpnGsGKSTLLr   49 (353)
T 1oxx_K           28 IENGERFGILGPSGAGKTTFMR   49 (353)
T ss_dssp             ECTTCEEEEECSCHHHHHHHHH
T ss_pred             ECCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999999876

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=81.62  E-value=0.58  Score=45.17  Aligned_cols=17  Identities=24%  Similarity=0.315  Sum_probs=14.3

Q ss_pred             CeEEEEcCCCCCcccch
Q psy6094          73 QITVISGETGSGPPLHL   89 (455)
Q Consensus        73 ~~vii~~~TGSGKTtql   89 (455)
                      ..+++.|++|||||+.+
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            46999999999999543

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=81.57  E-value=0.68  Score=46.63  Aligned_cols=24  Identities=25%  Similarity=0.443  Sum_probs=18.3

Q ss_pred             HHHHcCCeEEEEcCCCCCcccchh
Q psy6094          67 DMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        67 ~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+...+.++.+.|++|+||||.+-
T Consensus        64 ~~~~~~~~valvG~nGaGKSTLln   87 (413)
T 1tq4_A           64 EIDSSVLNVAVTGETGSGKSSFIN   87 (413)
T ss_dssp             HHHHCCEEEEEEECTTSSHHHHHH
T ss_pred             hcccCCeEEEEECCCCCcHHHHHH
Confidence            334445588899999999998765

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=81.44  E-value=0.43  Score=44.64  Aligned_cols=23  Identities=13%  Similarity=0.247  Sum_probs=18.0

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      ...+++.|.+||||||+.-.+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            45789999999999988764443

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=81.40  E-value=0.58  Score=47.62  Aligned_cols=28  Identities=14%  Similarity=0.300  Sum_probs=20.4

Q ss_pred             HHHHHcCC--eEEEEcCCCCCcccchhhhh
Q psy6094          66 LDMVRNNQ--ITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        66 l~~i~~~~--~vii~~~TGSGKTtqlp~ll   93 (455)
                      ...+..++  .+++.|++||||||.+-.+.
T Consensus        42 ~~~i~~~~~~~vLL~GppGtGKTtlAr~ia   71 (447)
T 3pvs_A           42 PRAIEAGHLHSMILWGPPGTGKTTLAEVIA   71 (447)
T ss_dssp             HHHHHHTCCCEEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHcCCCcEEEEECCCCCcHHHHHHHHH
Confidence            35566665  49999999999997655443

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=81.39  E-value=0.4  Score=44.33  Aligned_cols=17  Identities=18%  Similarity=0.231  Sum_probs=14.3

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      -+++.|++||||||.+-
T Consensus        51 g~ll~G~~G~GKTtl~~   67 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLAR   67 (254)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            48999999999996554

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=81.36  E-value=0.46  Score=45.95  Aligned_cols=21  Identities=29%  Similarity=0.474  Sum_probs=17.6

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+++|+|+.||||||.+-.++
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~   25 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHIL   25 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHH
T ss_pred             cEEEEEecCCCCHHHHHHHHH
Confidence            478999999999999987443

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=81.26  E-value=0.29  Score=43.48  Aligned_cols=21  Identities=14%  Similarity=0.286  Sum_probs=17.5

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+..+++.|++|+||||.+-
T Consensus        24 ~~~~~v~lvG~~g~GKSTLl~   44 (210)
T 1pui_A           24 DTGIEVAFAGRSNAGKSSALN   44 (210)
T ss_dssp             SCSEEEEEEECTTSSHHHHHT
T ss_pred             CCCcEEEEECCCCCCHHHHHH
Confidence            456679999999999997664

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=81.19  E-value=0.43  Score=46.56  Aligned_cols=20  Identities=20%  Similarity=0.275  Sum_probs=16.5

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .+..+++.|++|+||||.+-
T Consensus        43 ~~~~vll~G~~G~GKT~l~~   62 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVAR   62 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHH
Confidence            45679999999999996554

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=81.11  E-value=0.76  Score=44.73  Aligned_cols=17  Identities=24%  Similarity=0.286  Sum_probs=14.5

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+++.|++|+||||.+-
T Consensus        40 ~~ll~G~~G~GKT~la~   56 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIAR   56 (373)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999996654

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=80.94  E-value=0.44  Score=42.07  Aligned_cols=19  Identities=32%  Similarity=0.405  Sum_probs=15.2

Q ss_pred             CeEEEEcCCCCCcccchhh
Q psy6094          73 QITVISGETGSGPPLHLDF   91 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~   91 (455)
                      .++.|.|++||||||..-.
T Consensus         9 ~~I~i~G~~GsGKST~~~~   27 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAAL   27 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4678899999999976543

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=80.85  E-value=0.51  Score=45.97  Aligned_cols=19  Identities=26%  Similarity=0.321  Sum_probs=16.3

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++|.|++|+||||.+-
T Consensus        45 ~~~vli~G~~G~GKTtl~~   63 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVK   63 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5689999999999997654

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=80.84  E-value=0.75  Score=44.84  Aligned_cols=20  Identities=20%  Similarity=0.333  Sum_probs=15.9

Q ss_pred             CeEEEEcCCCCCcccchhhh
Q psy6094          73 QITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~l   92 (455)
                      +.+++.|++|+|||+.+-.+
T Consensus        71 ~~vLl~GppGtGKT~la~~l   90 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIAMGM   90 (368)
T ss_dssp             CEEEEEESTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            47999999999999654433

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=80.84  E-value=0.35  Score=50.93  Aligned_cols=21  Identities=14%  Similarity=0.384  Sum_probs=18.4

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|+.+.+.|++||||||.+-
T Consensus       365 ~~G~~~~ivG~sGsGKSTll~  385 (578)
T 4a82_A          365 EKGETVAFVGMSGGGKSTLIN  385 (578)
T ss_dssp             CTTCEEEEECSTTSSHHHHHT
T ss_pred             CCCCEEEEECCCCChHHHHHH
Confidence            467889999999999998875

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=80.80  E-value=0.51  Score=43.51  Aligned_cols=19  Identities=21%  Similarity=0.298  Sum_probs=15.5

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      ....+++.|++|||||+.+
T Consensus        38 ~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCCEEEEESCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4567999999999999544

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=80.55  E-value=0.4  Score=50.51  Aligned_cols=22  Identities=18%  Similarity=0.415  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|++||||||.+-
T Consensus       366 i~~G~~~~ivG~sGsGKSTll~  387 (582)
T 3b5x_A          366 IPQGKTVALVGRSGSGKSTIAN  387 (582)
T ss_pred             ECCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998875

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.50  E-value=2.4  Score=42.39  Aligned_cols=18  Identities=22%  Similarity=0.397  Sum_probs=14.7

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      .+-+++.||+|||||+.+
T Consensus       182 prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          182 PKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CCCEEEESCSSSSHHHHH
T ss_pred             CCceEEeCCCCCCHHHHH
Confidence            356999999999999543

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=80.48  E-value=0.46  Score=44.36  Aligned_cols=25  Identities=12%  Similarity=0.256  Sum_probs=19.5

Q ss_pred             HcCCeEEEEcCCCCCcccchhhhhh
Q psy6094          70 RNNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .....+++.|..||||||+.-.|.+
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~   46 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQ   46 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGG
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHH
Confidence            3456789999999999999875544

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=80.42  E-value=0.46  Score=45.70  Aligned_cols=19  Identities=26%  Similarity=0.359  Sum_probs=15.6

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+++.|++||||||.+-
T Consensus        37 ~~~lll~G~~GtGKT~la~   55 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ   55 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            4579999999999996543

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=80.32  E-value=0.41  Score=44.56  Aligned_cols=23  Identities=13%  Similarity=0.267  Sum_probs=18.1

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+..+++.|++||||||..-.|.
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~   53 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQ   53 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            45678999999999998765443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=80.32  E-value=0.52  Score=44.76  Aligned_cols=18  Identities=17%  Similarity=0.278  Sum_probs=15.0

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      +..+++.|++|||||+.+
T Consensus        67 ~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            347999999999999554

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=80.31  E-value=0.47  Score=47.60  Aligned_cols=18  Identities=33%  Similarity=0.447  Sum_probs=15.2

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      .+++|+|+|||||||..-
T Consensus         3 ~~i~i~GptgsGKttla~   20 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSI   20 (409)
T ss_dssp             EEEEEEECSSSSHHHHHH
T ss_pred             cEEEEECcchhhHHHHHH
Confidence            468899999999997654

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=80.25  E-value=0.44  Score=47.12  Aligned_cols=18  Identities=39%  Similarity=0.586  Sum_probs=15.6

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ...+|+|+||+|||+.+-
T Consensus        26 gl~vi~G~NGaGKT~ile   43 (371)
T 3auy_A           26 GIVAIIGENGSGKSSIFE   43 (371)
T ss_dssp             EEEEEEECTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            578999999999997765

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=80.04  E-value=0.46  Score=45.69  Aligned_cols=21  Identities=24%  Similarity=0.262  Sum_probs=17.1

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+.++-|.|++||||||.+-
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~   98 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTAR   98 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            455688899999999997654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=80.04  E-value=0.5  Score=44.69  Aligned_cols=17  Identities=18%  Similarity=0.429  Sum_probs=14.9

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+.+.|++||||||.+-
T Consensus         4 ~v~lvG~nGaGKSTLln   20 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVN   20 (270)
T ss_dssp             EEEEEESSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47789999999998876

---

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	455
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	9e-22
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	8e-14

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 93.1 bits (231), Expect = 9e-22
 Identities = 32/121 (26%), Positives = 48/121 (39%), Gaps = 12/121 (9%)

Query: 189 ILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLA 248
              FLP     N +  S+ ++         ++ L+         +I    P      +LA
Sbjct: 39  TAWFLPSIRAANVMAASLRKAGK------SVVVLNRKTFEREYPTIKQKKP----DFILA 88

Query: 249 TNIAETSITIDDIVYVVDCGKT-KMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR 307
           T+IAE    +  +  V+DC    K    D    +A   P  IS ++A QRRGR GR   R
Sbjct: 89  TDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNR 147

Query: 308 S 308
            
Sbjct: 148 D 148

>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 = 69.6 bits (169), Expect = 8e-14
 Identities = 35/295 (11%), Positives = 75/295 (25%), Gaps = 60/295 (20%)

Query: 67  DMVRNNQITVISGETGSG------PPLHLDFITLKR-----SETQQYPNDVLNMLKDPEL 115
           D+ R  ++T++    G+G      P +  + I         + T+    ++   L+   +
Sbjct: 4   DIFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPI 63

Query: 116 EGVNNDVIFSLLQHICTTQRPGAILV----------------------YCTYTFMGVSPM 153
                 +               A                             +      +
Sbjct: 64  RYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYI 123

Query: 154 KVFFCKNVLQRLMKGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQ----- 208
                      +   + A  P       +S   +          + NS H  +       
Sbjct: 124 STRVEMGEAAGIF--MTATPPGSRDPFPQSNAPIMDEEREIPERSWNSGHEWVTDFKGKT 181

Query: 209 -------------SSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS 255
                        ++    +  ++I L                       V+ T+I+E  
Sbjct: 182 VWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIKTRTND----WDFVVTTDISEMG 237

Query: 256 ITIDDIVYVVDCG--KTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS 308
                   V+D       +   D ++ +    P  ++ ++A QRRGR GR  K  
Sbjct: 238 ANF-KAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNE 291

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	455
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.95
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.93
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.83
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.83
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.83
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.82
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.82
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.82
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.81
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.81
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.79
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.76
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.63
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.62
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.61
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.58
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.54
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.44
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.3
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.26
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.25
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.22
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.2
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.2
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.18
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.09
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.01
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.81
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.62
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.31
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.29
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.22
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.2
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.16
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	98.15
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	98.09
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.62
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.56
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	97.36
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.3
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	95.66
d1ls1a2	207	GTPase domain of the signal sequence recognition p	95.32
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.06
d1okkd2	207	GTPase domain of the signal recognition particle r	94.96
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	94.73
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	94.64
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.14
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.13
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.76
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	93.49
d2qy9a2	211	GTPase domain of the signal recognition particle r	93.44
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	93.36
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	93.36
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	93.3
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.07
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.04
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	92.92
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.77
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	92.37
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	92.31
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	92.24
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	92.15
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	92.14
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	91.88
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	91.77
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	91.49
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	91.45
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	91.42
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	91.25
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	91.18
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	91.12
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	91.08
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	91.06
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	91.06
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	90.9
d1vmaa2	213	GTPase domain of the signal recognition particle r	90.78
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	90.75
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	90.73
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	90.73
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	90.64
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	90.63
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	90.51
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	90.51
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	90.28
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	90.25
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	90.24
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	89.92
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	89.76
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	89.71
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	89.69
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	89.58
d2awna2	232	Maltose transport protein MalK, N-terminal domain	89.55
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	89.48
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	89.43
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	89.39
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	89.25
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	88.95
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	88.88
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	88.83
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	88.59
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	88.4
d2p6ra1	85	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	88.38
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	88.37
d1g2912	240	Maltose transport protein MalK, N-terminal domain	88.33
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	88.31
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	88.22
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	88.16
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	88.12
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	87.6
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	87.54
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	87.38
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	87.11
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	86.79
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	86.78
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	86.73
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	86.59
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	86.59
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	86.43
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	86.35
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	85.94
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	85.87
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	85.8
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	85.71
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	85.62
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	85.55
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	85.48
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	85.47
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	85.42
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	85.18
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	85.18
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	85.15
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	84.94
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	84.81
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	84.77
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	84.7
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	84.64
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	83.58
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	83.51
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	83.42
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	83.32
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	82.98
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	82.81
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	82.61
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	82.5
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	80.98
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	80.69
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	80.08

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.95  E-value=1.2e-30  Score=252.58  Aligned_cols=226  Identities=19%  Similarity=0.115  Sum_probs=165.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+|++||||||..+++.+++.|+..+      +.|++|||.++.+++.+    +++|.++|||||||||+|+|| ||++
T Consensus        34 ~~~g~~~~F~~s~~~~~~~a~~L~~~g------~~V~~l~~~~~~~e~~~----~~~~~~~~~~~t~~~~~~~~~-~~~~  102 (299)
T d1yksa2          34 ADKRPTAWFLPSIRAANVMAASLRKAG------KSVVVLNRKTFEREYPT----IKQKKPDFILATDIAEMGANL-CVER  102 (299)
T ss_dssp             HCCSCEEEECSCHHHHHHHHHHHHHTT------CCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSE
T ss_pred             hcCCCEEEEeCCHHHHHHHHHHHHhcC------CeEEEEcCcCcHhHHhh----hhcCCcCEEEEechhhhceec-CceE
Confidence            458999999999999999999999875      67999999999988765    457889999999999999999 6999


Q ss_pred             EEeCCCC-cccccccCCCcccccccccchhhHHhhhcccCCCCCC-eEEecCChhhhccC------CCCcccccChHHHH
Q psy6094         264 VVDCGKT-KMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR-SETQQYPNDVLNML------KDPELEGVNNDVIF  335 (455)
Q Consensus       264 VID~g~~-k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G-~c~~L~t~~~~~~~------~~PEi~r~~~~~~L  335 (455)
                      |||+|+. |...||+.+++..+...|+|++++.||+||+||.+.+ .||.+|+....++.      +.++|...+-.+.+
T Consensus       103 vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~~~~~~d~~~~~~~te~~i~l~~i~l~~  182 (299)
T d1yksa2         103 VLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRG  182 (299)
T ss_dssp             EEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCGG
T ss_pred             EEecCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeCCCCCCcccchhhhhhHHHHhhCccccc
Confidence            9999995 8889999999999999999999999999999998653 56777774322111      11233332200011


Q ss_pred             -------HHHhhhcCCCChhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCCChhHHHHHHHhhcCcCCcChHH
Q psy6094         336 -------SLLQHICTTQRPGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDNKPKEIITVRDCLSFECKPSTAK  408 (455)
Q Consensus       336 -------~~l~~~~~~P~~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~~p~~~l~iaa~lsf~~p~~~~~  408 (455)
                             ....+++++|+.+....+++.+..+|||+..+..     +.+|+.++.+++.+...     -..|+.|....-
T Consensus       183 ~~~g~~~~~e~~~~~~p~g~~~L~~~~~l~~l~aL~~~d~p-----~~La~~va~~~~~~~~~-----~~~f~~P~e~~i  252 (299)
T d1yksa2         183 GMVAPLYGVEGTKTPVSPGEMRLRDDQRKVFRELVRNCDLP-----VWLSWQVAKAGLKTNDR-----KWCFEGPEEHEI  252 (299)
T ss_dssp             GCCCCCSTTHHHHSSSCTTTTCCCHHHHHHHHHHHHTTCCC-----HHHHHHHHHTTCCTTCC-----GGGSCSCGGGCC
T ss_pred             ccccccchhhhccccCCCchhhhhHhHHHHHHHHHhhcCCC-----cchHHHHHhcccccccc-----cceeECchhchh
Confidence                   0112577888888777889999999999887766     89999999998876111     122666655432


Q ss_pred             HHHHHH-hhhC-CCCcHHHHHHHH
Q psy6094         409 IIKELR-ARLD-MLLAHKLSHPGT  430 (455)
Q Consensus       409 ~~~~~~-~~~~-~~sD~~~~~~~~  430 (455)
                      ..+..+ .+|. +.|||+++++.|
T Consensus       253 ~~~~~~~~~f~~~~Gd~~~L~~r~  276 (299)
T d1yksa2         253 LNDSGETVKCRAPGGAKKPLRPRW  276 (299)
T ss_dssp             BCTTSCBCEEECTTSCEEECCCSS
T ss_pred             hhhhccccceeCCCcceeeeeeeE
Confidence            222222 3466 899999988765

>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=99.93  E-value=7.8e-27  Score=226.44  Aligned_cols=232  Identities=16%  Similarity=0.146  Sum_probs=159.1

Q ss_pred             HHHcCCeEEEEcCCCCCcccchh-hhhh---hhcCC----------------------CC-------------------C
Q psy6094          68 MVRNNQITVISGETGSGPPLHLD-FITL---KRSET----------------------QQ-------------------Y  102 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp-~ll~---e~~~~----------------------vg-------------------~  102 (455)
                      ++++++++++.|+||||||+++. .++.   ..+..                      ++                   +
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~t   84 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMC   84 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSCCBCCC--------CCCSEEEEE
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEeecccCccccccCC
Confidence            35689999999999999997643 3332   00100                      11                   1


Q ss_pred             hHHHHHhc-cCCCCcCcc-------------hHHHHHHHHHHHHhcCCCCeEEEEccCCCCC-ccceEEeehhhh-hhhh
Q psy6094         103 PNDVLNML-KDPELEGVN-------------NDVIFSLLQHICTTQRPGAILVYCTYTFMGV-SPMKVFFCKNVL-QRLM  166 (455)
Q Consensus       103 p~~ll~~l-~d~~L~~~~-------------~D~ll~~lk~il~~~~~~~k~ilmSAT~~g~-~pv~~~~l~~~~-~~~~  166 (455)
                      +..+..++ .+..+.+++             .+.+.++++.+.  .+++.++++||||+++. .+....+..... ....
T Consensus        85 ~~~l~~~~~~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~--~~~~~~~v~~SAT~~~~~~~~~~~~~~~~~~~~~~  162 (305)
T d2bmfa2          85 HATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRV--EMGEAAGIFMTATPPGSRDPFPQSNAPIMDEEREI  162 (305)
T ss_dssp             HHHHHHHHTSSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHH--HHTSCEEEEECSSCTTCCCSSCCCSSCEEEEECCC
T ss_pred             cHHHHHHHhcCccccceeEEEeeeeeecchhhHHHHHHHHHhh--ccccceEEEeecCCCcceeeecccCCcceEEEEec
Confidence            22244444 555555565             333445555543  35788999999999765 333222111000 0000


Q ss_pred             ccCCCCChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEE
Q psy6094         167 KGVGANSPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIV  246 (455)
Q Consensus       167 ~~~~~~~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVi  246 (455)
                      .....   ......+. ..++++||||+++++++.+++.|++.+      +.+..+||+++++.+.    .+++|.++++
T Consensus       163 ~~~~~---~~~~~~~~-~~~~~~lvf~~~~~~~~~l~~~L~~~~------~~~~~l~~~~~~~~~~----~~~~~~~~~l  228 (305)
T d2bmfa2         163 PERSW---NSGHEWVT-DFKGKTVWFVPSIKAGNDIAACLRKNG------KKVIQLSRKTFDSEYI----KTRTNDWDFV  228 (305)
T ss_dssp             CCSCC---SSCCHHHH-SSCSCEEEECSCHHHHHHHHHHHHHHT------CCCEECCTTCHHHHGG----GGGTSCCSEE
T ss_pred             cHHHH---HHHHHHHH-hhCCCEEEEeccHHHHHHHHHHHHhCC------CCEEEeCCcChHHHHh----hhhccchhhh
Confidence            00000   00112233 567899999999999999999999875      6788999999776554    4567899999


Q ss_pred             EeCCCCccCCCCCCeeEEEeCCCCccc--ccccCCCcccccccccchhhHHhhhcccCCCCCCe-EEecCChh
Q psy6094         247 LATNIAETSITIDDIVYVVDCGKTKMS--NFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRS-ETQQYPND  316 (455)
Q Consensus       247 vaTniae~gitI~~V~~VID~g~~k~~--~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~-c~~L~t~~  316 (455)
                      +|||++++|+|+ ++++|||+|.....  .||+.++...+...|+|++++.||+|||||.+.|. ..-+|..+
T Consensus       229 vaT~~~~~G~~~-~~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         229 VTTDISEMGANF-KAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             EECGGGGTTCCC-CCSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             hhhHHHHhcCCC-CccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence            999999999999 68999999986544  58999999999999999999999999999999854 44566643

>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=99.83  E-value=3.8e-21  Score=171.51  Aligned_cols=119  Identities=12%  Similarity=0.183  Sum_probs=105.7

Q ss_pred             hHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCc
Q psy6094         174 PKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAE  253 (455)
Q Consensus       174 ~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae  253 (455)
                      ...|..++...+.+++||||+++..++.++..|...+      +.+..+||++++++|..+++.|+.|..+|+|||++++
T Consensus        20 ~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g------~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~   93 (171)
T d1s2ma2          20 LHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLG------YSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLT   93 (171)
T ss_dssp             HHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHT------CCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSS
T ss_pred             HHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhccc------ccccccccccchhhhhhhhhhcccCccccccchhHhh
Confidence            3346777777778899999999999999999999875      7889999999999999999999999999999999999


Q ss_pred             cCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         254 TSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       254 ~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|+|+|++++||+++.                  |-+..+|.||+||+||.|. |.|+.+++..
T Consensus        94 ~Gid~~~v~~VI~~d~------------------p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~  139 (171)
T d1s2ma2          94 RGIDIQAVNVVINFDF------------------PKTAETYLHRIGRSGRFGHLGLAINLINWN  139 (171)
T ss_dssp             SSCCCTTEEEEEESSC------------------CSSHHHHHHHHCBSSCTTCCEEEEEEECGG
T ss_pred             hccccceeEEEEecCC------------------cchHHHHHHHhhhcccCCCccEEEEEeCHH
Confidence            9999999999999443                  3455678899999999876 9999999954

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=99.83  E-value=1.3e-20  Score=166.96  Aligned_cols=119  Identities=15%  Similarity=0.095  Sum_probs=102.6

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~  254 (455)
                      ++..+.+  ..+.++||||++.+.++.+++.|...+      +.+..+||++++.+|.++++.|+.|+.+|||||+++++
T Consensus        20 ll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~G------i~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~   93 (174)
T d1c4oa2          20 LMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHG------IRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLRE   93 (174)
T ss_dssp             HHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCT
T ss_pred             HHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcC------CceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeee
Confidence            4444433  467789999999999999999999975      88999999999999999999999999999999999999


Q ss_pred             CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         255 SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       255 gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      |||+|+|++||+++.++        .     ..+.|..+|.||.|||||.++|.++.++.
T Consensus        94 GiDip~V~~Vi~~~~~~--------~-----~~~~~~~~~iq~~GR~gR~~~g~~~~~~~  140 (174)
T d1c4oa2          94 GLDIPEVSLVAILDADK--------E-----GFLRSERSLIQTIGRAARNARGEVWLYAD  140 (174)
T ss_dssp             TCCCTTEEEEEETTTTS--------C-----SGGGSHHHHHHHHGGGTTSTTCEEEEECS
T ss_pred             eccCCCCcEEEEecccc--------c-----cccchhHHHHHHhhhhhhcCCCeeEEeec
Confidence            99999999999944432        1     13567788999999999999998877665

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.82  E-value=1.6e-20  Score=168.58  Aligned_cols=112  Identities=17%  Similarity=0.109  Sum_probs=98.2

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++.+||||++..+++.++..|+..+      +.+..+||+|++.+|.++++.|++|+.+||||||++++|||||+|++
T Consensus        29 ~~~~~~iif~~~~~~~~~~~~~l~~~g------~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~  102 (181)
T d1t5la2          29 ERNERTLVTTLTKKMAEDLTDYLKEAG------IKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSL  102 (181)
T ss_dssp             HTTCEEEEECSSHHHHHHHHHHHHTTT------CCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEE
T ss_pred             hcCCeEEEEeehhhhhHHHHHHHHhCC------cceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCE
Confidence            457789999999999999999999875      88999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                      ||+++.++..             .+-|..+|.||.|||||.+.|.++.++.
T Consensus       103 VI~~d~p~~~-------------~~~s~~~yi~R~GRagR~g~~~~~~~~~  140 (181)
T d1t5la2         103 VAILDADKEG-------------FLRSERSLIQTIGRAARNANGHVIMYAD  140 (181)
T ss_dssp             EEETTTTSCS-------------GGGSHHHHHHHHGGGTTSTTCEEEEECS
T ss_pred             EEEecCCccc-------------ccccHHHHHHHHHhhccccCceeEeecc
Confidence            9996665421             1235577899999999998877766665

>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=99.82  E-value=1.2e-20  Score=172.32  Aligned_cols=118  Identities=14%  Similarity=0.118  Sum_probs=105.4

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+..++....+..+|||+++...++.++..|...+      +.+..+||++++++|.++++.|..|+.+|||||+++++|
T Consensus        20 ~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~------~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~G   93 (200)
T d1oywa3          20 QLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKG------ISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMG   93 (200)
T ss_dssp             HHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTT
T ss_pred             HHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCC------ceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhc
Confidence            46667766677789999999999999999999874      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChhh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPNDV  317 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~~  317 (455)
                      ||+|+|++||+++.                  |-|..+|.||+|||||.|. |.|+.+|+..+
T Consensus        94 iD~p~v~~VI~~~~------------------P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d  138 (200)
T d1oywa3          94 INKPNVRFVVHFDI------------------PRNIESYYQETGRAGRDGLPAEAMLFYDPAD  138 (200)
T ss_dssp             TCCTTCCEEEESSC------------------CSSHHHHHHHHTTSCTTSSCEEEEEEECHHH
T ss_pred             cCCCCCCEEEECCC------------------ccchHHHHHHhhhhhcCCCCceEEEecCHHH
Confidence            99999999999554                  3456778899999999877 99999999543

>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=99.82  E-value=4.3e-21  Score=170.63  Aligned_cols=117  Identities=15%  Similarity=0.291  Sum_probs=104.1

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .|...+......++||||++++.++.+++.|...+      +.+..+||++++++|..+++.|++|..+|+|||+++++|
T Consensus        24 ~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~------~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rG   97 (168)
T d2j0sa2          24 TLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREAN------FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARG   97 (168)
T ss_dssp             HHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTT------CCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSS
T ss_pred             HHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcc------cchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhccc
Confidence            35666666677899999999999999999999875      678999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|+|+|++||+++.                  |-|...|.||+||+||.+. |.||.+++.+
T Consensus        98 iDi~~v~~VIn~d~------------------P~~~~~yihR~GR~gR~g~~G~~i~~~~~~  141 (168)
T d2j0sa2          98 LDVPQVSLIINYDL------------------PNNRELYIHRIGRSGRYGRKGVAINFVKND  141 (168)
T ss_dssp             CCCTTEEEEEESSC------------------CSSHHHHHHHHTTSSGGGCCEEEEEEEEGG
T ss_pred             ccccCcceEEEecC------------------CcCHHHHHhhhccccccCCCcEEEEEECHH
Confidence            99999999999443                  4556778999999999877 9999999854

>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=99.81  E-value=1e-20  Score=167.24  Aligned_cols=117  Identities=20%  Similarity=0.351  Sum_probs=100.0

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .|..++.+....++||||+++..++.+++.|...+      +.+..+||++++++|..+++.|+.|..+|+||||++++|
T Consensus        17 ~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~------~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rG   90 (162)
T d1fuka_          17 CLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDK------FTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG   90 (162)
T ss_dssp             HHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTT
T ss_pred             HHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcC------ceEEEeccCCchhhHHHHHHHHhhcccceeecccccccc
Confidence            35566666778899999999999999999999875      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|+|+|++||+        ||.+          .+...|.||+||+||.+. |.|+.+++++
T Consensus        91 iDi~~v~~VI~--------~d~P----------~~~~~yihR~GR~gR~g~~g~~i~~~~~~  134 (162)
T d1fuka_          91 IDVQQVSLVIN--------YDLP----------ANKENYIHRIGRGGRFGRKGVAINFVTNE  134 (162)
T ss_dssp             CCCCSCSEEEE--------SSCC----------SSGGGGGGSSCSCC-----CEEEEEEETT
T ss_pred             ccCCCceEEEE--------eccc----------hhHHHHHhhccccccCCCccEEEEEcCHH
Confidence            99999999999        5433          344567799999999888 9999999853

>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=99.81  E-value=1.1e-20  Score=165.68  Aligned_cols=116  Identities=18%  Similarity=0.202  Sum_probs=102.9

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+...+. ..++.+||||++.+.++.+++.|+..+      +.+..+||++++.+|..+++.|+.|..+|+|||+++++|
T Consensus        19 ~L~~ll~-~~~~k~IIF~~s~~~~~~l~~~L~~~g------~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~G   91 (155)
T d1hv8a2          19 ALCRLLK-NKEFYGLVFCKTKRDTKELASMLRDIG------FKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRG   91 (155)
T ss_dssp             HHHHHHC-STTCCEEEECSSHHHHHHHHHHHHHTT------CCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHH
T ss_pred             HHHHHHc-cCCCCEEEEECchHHHHHHHhhhcccc------cccccccccchhhhhhhhhhhhhcccceeeeehhHHhhh
Confidence            3555554 567889999999999999999999874      789999999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCChh
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPND  316 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~~  316 (455)
                      +|+|++++||+++.                  |-|..+|.||.||+||.|. |.|+.+++..
T Consensus        92 id~~~v~~Vi~~d~------------------p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  135 (155)
T d1hv8a2          92 IDVNDLNCVINYHL------------------PQNPESYMHRIGRTGRAGKKGKAISIINRR  135 (155)
T ss_dssp             CCCSCCSEEEESSC------------------CSCHHHHHHHSTTTCCSSSCCEEEEEECTT
T ss_pred             hhhccCcEEEEecC------------------CCCHHHHHHHHHhcCcCCCCceEEEEEchH
Confidence            99999999999554                  3466788999999999876 9999999854

>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=99.79  E-value=3.5e-20  Score=164.69  Aligned_cols=119  Identities=17%  Similarity=0.229  Sum_probs=105.0

Q ss_pred             ChHHHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCC
Q psy6094         173 SPKRWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIA  252 (455)
Q Consensus       173 ~~~~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTnia  252 (455)
                      +...+...+.....+.+||||++...++.+++.|...+      +.+..+||++++++|..+++.|.+|..+|+|||+++
T Consensus        14 K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~------~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~   87 (168)
T d1t5ia_          14 KNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQN------FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLF   87 (168)
T ss_dssp             HHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCC
T ss_pred             HHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhcccc------ccccccccccchhhhhhhhhhhccccceeeeccccc
Confidence            34446777766778899999999999999999999875      779999999999999999999999999999999999


Q ss_pred             ccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         253 ETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       253 e~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      ++|+|+|++++||++++                  |.|..++.||.||+||.+. |.||.+++.
T Consensus        88 ~~Gid~~~~~~vi~~~~------------------p~~~~~yiqr~GR~gR~g~~g~~i~l~~~  133 (168)
T d1t5ia_          88 GRGMDIERVNIAFNYDM------------------PEDSDTYLHRVARAGRFGTKGLAITFVSD  133 (168)
T ss_dssp             STTCCGGGCSEEEESSC------------------CSSHHHHHHHHHHHTGGGCCCEEEEEECS
T ss_pred             cchhhcccchhhhhhhc------------------ccchhhHhhhhhhcccCCCccEEEEEECc
Confidence            99999999999999443                  3455678899999999876 999999984

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.76  E-value=1.6e-18  Score=148.45  Aligned_cols=103  Identities=20%  Similarity=0.201  Sum_probs=87.6

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..++++||||+++.+++.+++.|...+      +.+..+||++++++       |.+|..+|+||||++++||| ++|+.
T Consensus        33 ~~~~k~IVFc~t~~~ae~la~~L~~~G------~~~~~~H~~~~~~~-------~~~~~~~vlvaTd~~~~GiD-~~v~~   98 (138)
T d1jr6a_          33 IKGGRHLIFCHSKKKCDELAAKLVALG------INAVAYYRGLDVSV-------IPTNGDVVVVATDALMTGFT-GDFDS   98 (138)
T ss_dssp             HTTSCEEEECSCHHHHHHHHHHHHHHT------CEEEEECTTCCSCC-------CTTSSCEEEEESSSSCSSSC-CCBSE
T ss_pred             cCCCCEEEEeCcHHHHHHHHHHHhccc------cchhhhhccchhhh-------hhhhhcceeehhHHHHhccc-cccce
Confidence            457899999999999999999999875      88999999998644       56899999999999999999 99999


Q ss_pred             EEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCCh
Q psy6094         264 VVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~  315 (455)
                      |||++..    |+          .|-+..+|.||.|||||.++|. |.++++
T Consensus        99 Vi~~~~~----~~----------~P~~~~~y~qr~GR~gRg~~G~-~~~i~~  135 (138)
T d1jr6a_          99 VIDCNTS----DG----------KPQDAVSRTQRRGRTGRGKPGI-YRFVAP  135 (138)
T ss_dssp             EEECSEE----TT----------EECCHHHHHHHHTTBCSSSCEE-EEECCS
T ss_pred             EEEEEec----CC----------CCCCHHHHHhHhccccCCCCcE-EEEEcC
Confidence            9996642    32          3567788999999999955685 777764

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.63  E-value=1.3e-16  Score=153.03  Aligned_cols=113  Identities=20%  Similarity=0.270  Sum_probs=92.5

Q ss_pred             HHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEee--------cCCCChhhHhhhhcCCCCCceEEEEeCCC
Q psy6094         180 LLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPL--------HSMLPTVSQKSIFNTPPEGVRKIVLATNI  251 (455)
Q Consensus       180 ~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~l--------hs~l~~~~r~~v~~~~~~g~~kVivaTni  251 (455)
                      ++....++.+|||+++.+.++.+++.|...+      +.+..+        |+++++.+|..+++.|++|..+|+|||++
T Consensus       155 ~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~  228 (286)
T d1wp9a2         155 QLQRKQNSKIIVFTNYRETAKKIVNELVKDG------IKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSV  228 (286)
T ss_dssp             HHHHCTTCCEEEECSCHHHHHHHHHHHHHTT------CCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGG
T ss_pred             HHHhCCCCcEEEEeCcHHhHHHHHHHHHHcC------CceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccc
Confidence            3344678899999999999999999998864      444445        45677789999999999999999999999


Q ss_pred             CccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChh
Q psy6094         252 AETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPND  316 (455)
Q Consensus       252 ae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~  316 (455)
                      ++.|||+|++++||+        ||+          |-+...+.||+||+||.++|.+|.|+++.
T Consensus       229 ~~~Gld~~~~~~Vi~--------~d~----------~~~~~~~~Qr~GR~gR~~~~~~~~l~~~~  275 (286)
T d1wp9a2         229 GEEGLDVPEVDLVVF--------YEP----------VPSAIRSIQRRGRTGRHMPGRVIILMAKG  275 (286)
T ss_dssp             GGGGGGSTTCCEEEE--------SSC----------CHHHHHHHHHHTTSCSCCCSEEEEEEETT
T ss_pred             eeccccCCCCCEEEE--------eCC----------CCCHHHHHHHHHhCCCCCCCEEEEEEeCC
Confidence            999999999999999        443          23557788999999999999999999853

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.62  E-value=6.7e-17  Score=147.16  Aligned_cols=118  Identities=18%  Similarity=0.208  Sum_probs=87.2

Q ss_pred             HHHHHHc--cCCCCEEEEcCCHHHHHHHH--------HHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEE
Q psy6094         177 WVKLLRS--MLVVPILVFLPGWDTINSLH--------RSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIV  246 (455)
Q Consensus       177 l~~~i~~--~~~g~iLVFlp~~~ei~~l~--------~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVi  246 (455)
                      +...|..  ..++++-+.||-.++.+.+.        +.|.+.   ..+++.+..+||.|+++++.+++..|.+|+.+|+
T Consensus        18 v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~---~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iL   94 (206)
T d1gm5a4          18 VYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKE---VFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDIL   94 (206)
T ss_dssp             HHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGS---CC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBC
T ss_pred             HHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHh---cCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEE
Confidence            4455544  56788888899876665432        222221   1245788899999999999999999999999999


Q ss_pred             EeCCCCccCCCCCCeeEEEeCCCCcccccccCC-CcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         247 LATNIAETSITIDDIVYVVDCGKTKMSNFDVKD-NIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       247 vaTniae~gitI~~V~~VID~g~~k~~~yd~~~-~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      |||+|+|+|||||++++||.        ||++. |+          +++.|++||+||.+. |.||.+|++
T Consensus        95 VaTtViE~GIDip~a~~iii--------~~a~~fgl----------sqlhQlrGRvGR~~~~~~~~l~~~~  147 (206)
T d1gm5a4          95 VSTTVIEVGIDVPRANVMVI--------ENPERFGL----------AQLHQLRGRVGRGGQEAYCFLVVGD  147 (206)
T ss_dssp             CCSSCCCSCSCCTTCCEEEB--------CSCSSSCT----------THHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             EEehhhhccccccCCcEEEE--------EccCCccH----------HHHHhhhhheeeccccceeEeeecc
Confidence            99999999999999999886        55442 44          456699999999887 999999974

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.61  E-value=2.5e-16  Score=143.52  Aligned_cols=122  Identities=17%  Similarity=0.104  Sum_probs=97.1

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCC--CCCC----------------------eEEEeecCCCChhhHhhhhcCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFF--NSSR----------------------FQIIPLHSMLPTVSQKSIFNTPP  239 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~--~~~~----------------------~~v~~lhs~l~~~~r~~v~~~~~  239 (455)
                      ..++++|||||++++++.++..|......  ....                      .-|..+||+|++++|..+.+.|+
T Consensus        38 ~~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~  117 (201)
T d2p6ra4          38 AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFR  117 (201)
T ss_dssp             HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHH
T ss_pred             HcCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHh
Confidence            35789999999999999999888753210  0000                      11677899999999999999999


Q ss_pred             CCceEEEEeCCCCccCCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCC---CCeEEecCChh
Q psy6094         240 EGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTL---KRSETQQYPND  316 (455)
Q Consensus       240 ~g~~kVivaTniae~gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~---~G~c~~L~t~~  316 (455)
                      +|..+|||||+.++.||++|...+||.. .   ..||..       ..+.+.+++.||+|||||.|   .|.||.++...
T Consensus       118 ~g~i~vlvaT~~l~~Gin~p~~~vvi~~-~---~~~d~~-------~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~  186 (201)
T d2p6ra4         118 RGNIKVVVATPTLAAGVNLPARRVIVRS-L---YRFDGY-------SKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR  186 (201)
T ss_dssp             TTSCCEEEECSTTTSSSCCCBSEEEECC-S---EEESSS-------EEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGG
T ss_pred             CCCceEEEechHHHhhcCCCCceEEEec-c---eeccCC-------cCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCC
Confidence            9999999999999999999999999963 2   234321       23678899999999999976   49999988743

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.58  E-value=1.3e-15  Score=143.86  Aligned_cols=106  Identities=17%  Similarity=0.093  Sum_probs=88.2

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhH----------hhhhcCCCCCceEEEEeCCCCcc
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQ----------KSIFNTPPEGVRKIVLATNIAET  254 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r----------~~v~~~~~~g~~kVivaTniae~  254 (455)
                      .++++||||+++++++++++.|.+.+      +.+..+||+++++.|          ..+++.+..|..+++|+|+++++
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~G------i~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~  108 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALG------INAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVT  108 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTT------CCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEE
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCC------CCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhc
Confidence            37899999999999999999999875      788999999999876          45778888999999999999999


Q ss_pred             ---CCCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCC
Q psy6094         255 ---SITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYP  314 (455)
Q Consensus       255 ---gitI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t  314 (455)
                         ++|++.|..||+        ||          .|.|.++|.||+||+||.++|.++.++.
T Consensus       109 g~~giDid~V~~VI~--------~d----------~P~SvesyIQRiGRTGRGr~G~~~~l~~  153 (299)
T d1a1va2         109 QTVDFSLDPTFTIET--------TT----------LPQDAVSRTQRRGRTGRGKPGIYRFVAP  153 (299)
T ss_dssp             EEEECCCSSSCEEEE--------EE----------EECBHHHHHHHHTTBCSSSCEEEEESCS
T ss_pred             cCCCCCCCcceEEEe--------CC----------CCCCHHHHHhhccccCCCCCceEEEEec
Confidence               567777778997        32          5788899999999999966687776655

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.54  E-value=4.1e-15  Score=134.40  Aligned_cols=110  Identities=16%  Similarity=0.154  Sum_probs=96.4

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCCCeeE
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITIDDIVY  263 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~~V~~  263 (455)
                      ..+|++-+.||..++++.+.+.+.+..    +++.+..+||.|+++++.+++..|.+|+.+|+|||.|.|.|||||+++.
T Consensus        29 ~rGgQvy~V~p~I~~~e~~~~~l~~~~----p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~  104 (211)
T d2eyqa5          29 LRGGQVYYLYNDVENIQKAAERLAELV----PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  104 (211)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHC----TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEE
T ss_pred             HcCCeEEEEEcCccchhhHHHHHHHhC----CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcE
Confidence            678999999999999999999998864    3688999999999999999999999999999999999999999999998


Q ss_pred             EEeCCCCcccccccC-CCcccccccccchhhHHhhhcccCCCCC-CeEEecCCh
Q psy6094         264 VVDCGKTKMSNFDVK-DNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYPN  315 (455)
Q Consensus       264 VID~g~~k~~~yd~~-~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t~  315 (455)
                      +|-        +|.. -|+          ++..|.+||+||.+. |.||-+++.
T Consensus       105 iiI--------~~a~rfGL----------aQLhQLRGRVGR~~~~s~c~l~~~~  140 (211)
T d2eyqa5         105 III--------ERADHFGL----------AQLHQLRGRVGRSHHQAYAWLLTPH  140 (211)
T ss_dssp             EEE--------TTTTSSCH----------HHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             EEE--------ecchhccc----------cccccccceeeecCccceEEEEecC
Confidence            884        3322 243          556799999999776 999999874

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.44  E-value=1.7e-15  Score=142.38  Aligned_cols=103  Identities=12%  Similarity=0.103  Sum_probs=84.2

Q ss_pred             HHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeC----CCC
Q psy6094         177 WVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLAT----NIA  252 (455)
Q Consensus       177 l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaT----nia  252 (455)
                      +..++. ..++.+|||+++++.++.+++.|...            +||++++.+|.++++.|.+|..+|+|||    |+|
T Consensus        17 l~~~l~-~~~~~~iif~~~~~~~~~l~~~l~~~------------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~   83 (248)
T d1gkub2          17 LSSILE-KLGTGGIIYARTGEEAEEIYESLKNK------------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTL   83 (248)
T ss_dssp             THHHHT-TSCSCEEEEESSHHHHHHHHHTTTTS------------SCEEECTTSSSHHHHHHHHTSCSEEEEECC-----
T ss_pred             HHHHHH-HhCCCEEEEECCHHHHHHHHHHHHHh------------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchh
Confidence            555555 34567999999999999999988752            7999999999999999999999999999    899


Q ss_pred             ccCCCCCC-eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         253 ETSITIDD-IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       253 e~gitI~~-V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                      ++|||+|+ |++||+++.|+                      +.||.||+||.+. |.++.++.
T Consensus        84 ~rGlDip~~v~~VI~~d~P~----------------------~~~r~gR~~R~g~~~~~~~~~~  125 (248)
T d1gkub2          84 VRGLDLPERIRFAVFVGCPS----------------------FRVTIEDIDSLSPQMVKLLAYL  125 (248)
T ss_dssp             -CCSCCTTTCCEEEEESCCE----------------------EEEECSCGGGSCHHHHHHHHTT
T ss_pred             hhccCccccccEEEEeCCCc----------------------chhhhhhhhccCcceEeeeecc
Confidence            99999996 99999966552                      3389999999877 88877776

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.30  E-value=3e-13  Score=122.51  Aligned_cols=103  Identities=15%  Similarity=0.125  Sum_probs=87.1

Q ss_pred             HHHHHHHccCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccC
Q psy6094         176 RWVKLLRSMLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETS  255 (455)
Q Consensus       176 ~l~~~i~~~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~g  255 (455)
                      .+...+....+..+|||+.....++.+++.|..           ..+||++++.+|..+++.|.+|..+|+|||++++.|
T Consensus        83 ~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~~-----------~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~G  151 (200)
T d2fwra1          83 KLREILERHRKDKIIIFTRHNELVYRISKVFLI-----------PAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEG  151 (200)
T ss_dssp             HHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTTC-----------CBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSS
T ss_pred             HHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcCc-----------ceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcc
Confidence            355666656677999999999999988877643           247999999999999999999999999999999999


Q ss_pred             CCCCCeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCC
Q psy6094         256 ITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKR  307 (455)
Q Consensus       256 itI~~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G  307 (455)
                      +|+|++++||.        ||+          |-|...+.||.||++|.++|
T Consensus       152 idl~~~~~vi~--------~~~----------~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         152 IDVPDANVGVI--------MSG----------SGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             SCSCCBSEEEE--------ECC----------SSCCHHHHHHHHHSBCCCTT
T ss_pred             cCCCCCCEEEE--------eCC----------CCCHHHHHHHHHhcCCCCCC
Confidence            99999999997        432          23567788999999998875

>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=99.26  E-value=2.1e-12  Score=118.77  Aligned_cols=113  Identities=9%  Similarity=0.127  Sum_probs=85.7

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhhh-------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFITL-------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll~-------------------   94 (455)
                      .|++..++++..+.++..+..-.+++|.+.++++.+|++++++|+||||||.+  +| ++.                   
T Consensus        18 sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllP-il~~l~~~~~~~~~lil~Ptre   96 (222)
T d2j0sa1          18 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSIS-VLQCLDIQVRETQALILAPTRE   96 (222)
T ss_dssp             SGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHH-HHHTCCTTSCSCCEEEECSSHH
T ss_pred             CHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccc-ccccccccccCceeEEecchHH
Confidence            36777899999999999999999999999999999999999999999999933  33 111                   


Q ss_pred             ----------h--------------------------hc--CCCCChHHHHHhc--cCCCCcCcc------hHHHHH---
Q psy6094          95 ----------K--------------------------RS--ETQQYPNDVLNML--KDPELEGVN------NDVIFS---  125 (455)
Q Consensus        95 ----------e--------------------------~~--~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~---  125 (455)
                                .                          .+  .-+|+|+++.+.+  ....+....      +|.|++   
T Consensus        97 La~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f  176 (222)
T d2j0sa1          97 LAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGF  176 (222)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTT
T ss_pred             HHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcCc
Confidence                      0                          00  1123577777766  333455555      788774   


Q ss_pred             --HHHHHHHhcCCCCeEEEEccCCCC
Q psy6094         126 --LLQHICTTQRPGAILVYCTYTFMG  149 (455)
Q Consensus       126 --~lk~il~~~~~~~k~ilmSAT~~g  149 (455)
                        .+..+++..+++.|++++|||++.
T Consensus       177 ~~~i~~I~~~l~~~~Q~ilfSAT~~~  202 (222)
T d2j0sa1         177 KEQIYDVYRYLPPATQVVLISATLPH  202 (222)
T ss_dssp             HHHHHHHHTTSCTTCEEEEEESCCCH
T ss_pred             HHHHHHHHHhCCCCCEEEEEEEeCCH
Confidence              367777677889999999999954

>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=99.25  E-value=2.9e-12  Score=116.62  Aligned_cols=114  Identities=11%  Similarity=0.045  Sum_probs=84.2

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------   94 (455)
                      |++..++++..+.+.+.+.--.++.|.+.++++.+|++++++|+||||||.++- .++.                     
T Consensus         3 F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~   82 (207)
T d1t6na_           3 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELA   82 (207)
T ss_dssp             STTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHH
T ss_pred             ccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchhh
Confidence            456678899999999999999999999999999999999999999999994322 2221                     


Q ss_pred             ------------------------------------hh--cCCCCChHHHHHhc--cCCCCcCcc------hHHHHH---
Q psy6094          95 ------------------------------------KR--SETQQYPNDVLNML--KDPELEGVN------NDVIFS---  125 (455)
Q Consensus        95 ------------------------------------e~--~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~---  125 (455)
                                                          ..  ..-||+|+++.+.+  ..-.+++..      +|.|+.   
T Consensus        83 ~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~  162 (207)
T d1t6na_          83 FQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD  162 (207)
T ss_dssp             HHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHH
T ss_pred             HHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcCC
Confidence                                                00  01133577777777  223455555      787773   


Q ss_pred             ---HHHHHHHhcCCCCeEEEEccCCCCC
Q psy6094         126 ---LLQHICTTQRPGAILVYCTYTFMGV  150 (455)
Q Consensus       126 ---~lk~il~~~~~~~k~ilmSAT~~g~  150 (455)
                         .++.+++..+++.|++++|||++..
T Consensus       163 ~~~~i~~I~~~~~~~~Q~il~SAT~~~~  190 (207)
T d1t6na_         163 MRRDVQEIFRMTPHEKQVMMFSATLSKE  190 (207)
T ss_dssp             HHHHHHHHHHTSCSSSEEEEEESCCCTT
T ss_pred             cHHHHHHHHHhCCCCCEEEEEeeeCCHH
Confidence               2667776777899999999999654

>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=99.22  E-value=3.1e-12  Score=116.18  Aligned_cols=114  Identities=10%  Similarity=0.110  Sum_probs=83.8

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh-hhhh---------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHLD-FITL---------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp-~ll~---------------------   94 (455)
                      |++..++++..+.++..+.-...++|.+.++++.+|++++++|+||||||.++- .++.                     
T Consensus         3 F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~   82 (209)
T d1q0ua_           3 FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELA   82 (209)
T ss_dssp             GGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHH
T ss_pred             cccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccchh
Confidence            667778999999999999999999999999999999999999999999994422 2221                     


Q ss_pred             --------------------------------------hhc--CCCCChHHHHHhc--cCCCCcCcc------hHHHHHH
Q psy6094          95 --------------------------------------KRS--ETQQYPNDVLNML--KDPELEGVN------NDVIFSL  126 (455)
Q Consensus        95 --------------------------------------e~~--~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~~  126 (455)
                                                            ..+  .-+|+|.+++..+  ....+.+..      +|.+++.
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~  162 (209)
T d1q0ua_          83 TQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDM  162 (209)
T ss_dssp             HHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHT
T ss_pred             HHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeeccccccc
Confidence                                                  000  0022566666665  333444444      7887743


Q ss_pred             -----HHHHHHhcCCCCeEEEEccCCCCC
Q psy6094         127 -----LQHICTTQRPGAILVYCTYTFMGV  150 (455)
Q Consensus       127 -----lk~il~~~~~~~k~ilmSAT~~g~  150 (455)
                           +..++...+++.|+++||||++..
T Consensus       163 ~f~~~v~~I~~~~~~~~Q~il~SATl~~~  191 (209)
T d1q0ua_         163 GFITDVDQIAARMPKDLQMLVFSATIPEK  191 (209)
T ss_dssp             TCHHHHHHHHHTSCTTCEEEEEESCCCGG
T ss_pred             ccHHHHHHHHHHCCCCCEEEEEEccCCHH
Confidence                 677776778999999999999654

>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=99.20  E-value=1.1e-11  Score=112.63  Aligned_cols=115  Identities=12%  Similarity=0.162  Sum_probs=86.2

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhh---h----------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFIT---L----------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll---~----------------   94 (455)
                      +|++..++++..+.+...+.--..+.|.+.++.+.+|++++++|+||||||..  +|.+.   .                
T Consensus         4 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el   83 (206)
T d1veca_           4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTREL   83 (206)
T ss_dssp             SGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHH
T ss_pred             ChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchh
Confidence            46677889999999999899899999999999999999999999999999933  33111   0                


Q ss_pred             ------------------------------------hh--cCCCCChHHHHHhc--cCCCCcCcc------hHHHHH---
Q psy6094          95 ------------------------------------KR--SETQQYPNDVLNML--KDPELEGVN------NDVIFS---  125 (455)
Q Consensus        95 ------------------------------------e~--~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~---  125 (455)
                                                          ..  ...+|+|+++.+.+  ....+....      +|.|++   
T Consensus        84 ~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f  163 (206)
T d1veca_          84 ALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDF  163 (206)
T ss_dssp             HHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTT
T ss_pred             hHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccch
Confidence                                                00  01133677788777  334455555      787773   


Q ss_pred             --HHHHHHHhcCCCCeEEEEccCCCCC
Q psy6094         126 --LLQHICTTQRPGAILVYCTYTFMGV  150 (455)
Q Consensus       126 --~lk~il~~~~~~~k~ilmSAT~~g~  150 (455)
                        .+..+++..+++.|+++||||++..
T Consensus       164 ~~~i~~I~~~~~~~~Q~~l~SAT~~~~  190 (206)
T d1veca_         164 VQIMEDIILTLPKNRQILLYSATFPLS  190 (206)
T ss_dssp             HHHHHHHHHHSCTTCEEEEEESCCCHH
T ss_pred             HHHHHHHHHhCCCCCEEEEEEecCCHH
Confidence              4777777788999999999999543

>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=99.20  E-value=3.4e-12  Score=117.12  Aligned_cols=113  Identities=12%  Similarity=0.071  Sum_probs=83.9

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll~--------------------   94 (455)
                      |++..++++..+.+...+.--..++|.+.++.+.+|++++++|+||||||..  +| ++.                    
T Consensus        14 F~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp-~l~~i~~~~~~~~alil~Pt~eL   92 (218)
T d2g9na1          14 FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAIS-ILQQIELDLKATQALVLAPTREL   92 (218)
T ss_dssp             GGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHH-HHHHCCTTCCSCCEEEECSSHHH
T ss_pred             HHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhh-hhheecccccCccEEEEcccchh
Confidence            4455688888888888888888999999999999999999999999999933  33 111                    


Q ss_pred             -----------------------------h--h-------cCCCCChHHHHHhc--cCCCCcCcc------hHHHHHH--
Q psy6094          95 -----------------------------K--R-------SETQQYPNDVLNML--KDPELEGVN------NDVIFSL--  126 (455)
Q Consensus        95 -----------------------------e--~-------~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~~--  126 (455)
                                                   +  .       ..-||+|+++.+.+  ....+....      +|.|++.  
T Consensus        93 ~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~f  172 (218)
T d2g9na1          93 AQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGF  172 (218)
T ss_dssp             HHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTC
T ss_pred             hhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCch
Confidence                                         0  0       01133688888887  444555555      7888743  


Q ss_pred             ---HHHHHHhcCCCCeEEEEccCCCCC
Q psy6094         127 ---LQHICTTQRPGAILVYCTYTFMGV  150 (455)
Q Consensus       127 ---lk~il~~~~~~~k~ilmSAT~~g~  150 (455)
                         +..+++..+++.|++++|||++..
T Consensus       173 ~~~~~~Il~~~~~~~Q~il~SAT~~~~  199 (218)
T d2g9na1         173 KDQIYDIFQKLNSNTQVVLLSATMPSD  199 (218)
T ss_dssp             HHHHHHHHHHSCTTCEEEEEESCCCHH
T ss_pred             HHHHHHHHHhCCCCCeEEEEEecCCHH
Confidence               666676778899999999999654

>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=99.18  E-value=8.8e-12  Score=113.80  Aligned_cols=113  Identities=10%  Similarity=0.064  Sum_probs=84.6

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll~--------------------   94 (455)
                      |++..++++..+.+...+..-..++|.+.++++.+|++++++|+||||||..  +| ++.                    
T Consensus        12 F~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp-~i~~l~~~~~~~~~lil~pt~el   90 (212)
T d1qdea_          12 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIA-ALQRIDTSVKAPQALMLAPTREL   90 (212)
T ss_dssp             GGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHH-HHHHCCTTCCSCCEEEECSSHHH
T ss_pred             hhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhh-hHhhhhccCCCcceEEEcccHHH
Confidence            3456789999999999999999999999999999999999999999999943  33 111                    


Q ss_pred             ------------------------------h-----h-cCCCCChHHHHHhc--cCCCCcCcc------hHHHHHH----
Q psy6094          95 ------------------------------K-----R-SETQQYPNDVLNML--KDPELEGVN------NDVIFSL----  126 (455)
Q Consensus        95 ------------------------------e-----~-~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~~----  126 (455)
                                                    +     . ..-||+|.++...+  ....|....      +|.+++.    
T Consensus        91 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f~~  170 (212)
T d1qdea_          91 ALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKE  170 (212)
T ss_dssp             HHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHH
T ss_pred             hhhhhhhhcccccccccceeeEeeccchhHHHHHhcCCcEEEECCCccccccccCceecCcceEEeehhhhhhcccchHH
Confidence                                          0     0 11123577777766  333555555      7877743    


Q ss_pred             -HHHHHHhcCCCCeEEEEccCCCCC
Q psy6094         127 -LQHICTTQRPGAILVYCTYTFMGV  150 (455)
Q Consensus       127 -lk~il~~~~~~~k~ilmSAT~~g~  150 (455)
                       +..+++..+++.|++++|||++..
T Consensus       171 ~v~~I~~~~~~~~Q~vl~SAT~~~~  195 (212)
T d1qdea_         171 QIYQIFTLLPPTTQVVLLSATMPND  195 (212)
T ss_dssp             HHHHHHHHSCTTCEEEEEESSCCHH
T ss_pred             HHHHHHHhCCCCCeEEEEEeeCCHH
Confidence             666776778899999999999653

>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=99.09  E-value=8.7e-11  Score=106.43  Aligned_cols=114  Identities=12%  Similarity=0.132  Sum_probs=85.2

Q ss_pred             HHHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc--hhhhhh-------------------
Q psy6094          36 EMIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH--LDFITL-------------------   94 (455)
Q Consensus        36 ~~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq--lp~ll~-------------------   94 (455)
                      .|.+..+++...+.+.+.+.--.++.|.+.++++.+|++++++|+||||||..  +|.+..                   
T Consensus         2 sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~   81 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTREL   81 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             ChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchhh
Confidence            35677889999999999999999999999999999999999999999999933  221110                   


Q ss_pred             -----------------------------------hh--cCCCCChHHHHHhc--cCCCCcCcc------hHHHHH----
Q psy6094          95 -----------------------------------KR--SETQQYPNDVLNML--KDPELEGVN------NDVIFS----  125 (455)
Q Consensus        95 -----------------------------------e~--~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll~----  125 (455)
                                                         ..  ..-+++|++|.+.+  ..-.|....      +|.|++    
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f~  161 (206)
T d1s2ma1          82 ALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFK  161 (206)
T ss_dssp             HHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHH
T ss_pred             hhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhhH
Confidence                                               00  00122577788877  333455555      777763    


Q ss_pred             -HHHHHHHhcCCCCeEEEEccCCCC
Q psy6094         126 -LLQHICTTQRPGAILVYCTYTFMG  149 (455)
Q Consensus       126 -~lk~il~~~~~~~k~ilmSAT~~g  149 (455)
                       .++.+++..+++.|++++|||++.
T Consensus       162 ~~v~~I~~~l~~~~Q~il~SATl~~  186 (206)
T d1s2ma1         162 TIIEQILSFLPPTHQSLLFSATFPL  186 (206)
T ss_dssp             HHHHHHHTTSCSSCEEEEEESCCCH
T ss_pred             HHHHHHHHhCCCCCEEEEEEEeCCH
Confidence             477777677889999999999954

>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=99.01  E-value=4e-10  Score=102.14  Aligned_cols=113  Identities=13%  Similarity=0.128  Sum_probs=82.4

Q ss_pred             HHHHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcC-CeEEEEcCCCCCcccchh-hhhh--------------------
Q psy6094          37 MIRKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNN-QITVISGETGSGPPLHLD-FITL--------------------   94 (455)
Q Consensus        37 ~~~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~-~~vii~~~TGSGKTtqlp-~ll~--------------------   94 (455)
                      |++..+++...+.++..+.--..+.|.++++.+.++ ++++++++||||||..+. .+++                    
T Consensus         6 f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~   85 (208)
T d1hv8a1           6 FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELA   85 (208)
T ss_dssp             GGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHH
T ss_pred             HHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEEEeeccccc
Confidence            455568888888888888877889999999988776 599999999999996543 2222                    


Q ss_pred             --------h---------------------------hcCCCCChHHHHHhc--cCCCCcCcc------hHHHH-----HH
Q psy6094          95 --------K---------------------------RSETQQYPNDVLNML--KDPELEGVN------NDVIF-----SL  126 (455)
Q Consensus        95 --------e---------------------------~~~~vg~p~~ll~~l--~d~~L~~~~------~D~ll-----~~  126 (455)
                              .                           ...-||+|.++++.+  ....+.+..      +|.++     ..
T Consensus        86 ~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~~~~~  165 (208)
T d1hv8a1          86 IQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKD  165 (208)
T ss_dssp             HHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHH
T ss_pred             hhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcCCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCCChHH
Confidence                    0                           011233677788877  333456555      77765     44


Q ss_pred             HHHHHHhcCCCCeEEEEccCCCC
Q psy6094         127 LQHICTTQRPGAILVYCTYTFMG  149 (455)
Q Consensus       127 lk~il~~~~~~~k~ilmSAT~~g  149 (455)
                      ++.+++..+++.|++++|||++.
T Consensus       166 i~~I~~~~~~~~Q~i~~SAT~~~  188 (208)
T d1hv8a1         166 VEKILNACNKDKRILLFSATMPR  188 (208)
T ss_dssp             HHHHHHTSCSSCEEEEECSSCCH
T ss_pred             HHHHHHhCCCCCeEEEEEccCCH
Confidence            77777677889999999999954

>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=98.81  E-value=8.5e-10  Score=102.10  Aligned_cols=49  Identities=8%  Similarity=0.074  Sum_probs=42.2

Q ss_pred             HHhcCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc
Q psy6094          39 RKLQSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPL   87 (455)
Q Consensus        39 ~~~~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt   87 (455)
                      +..+++...+.+...+..-.++.|.+.++.+.+|++++++|+||||||.
T Consensus        25 ~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTl   73 (238)
T d1wrba1          25 ELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTA   73 (238)
T ss_dssp             GGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHH
T ss_pred             HCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcce
Confidence            4456666666677778888999999999999999999999999999994

>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=98.62  E-value=5.1e-09  Score=93.93  Aligned_cols=48  Identities=13%  Similarity=0.085  Sum_probs=39.6

Q ss_pred             cCHHHHHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccch
Q psy6094          42 QSRRYQEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLHL   89 (455)
Q Consensus        42 ~~~~~~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtql   89 (455)
                      .++.....++.|+.-..|++|.++++.+.+++++++.+|||||||+..
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a   57 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLA   57 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHH
Confidence            455667788888888899999999999999999999999999999653

>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=98.31  E-value=4.8e-07  Score=83.25  Aligned_cols=114  Identities=17%  Similarity=0.062  Sum_probs=76.0

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCC--ceEEEEeCCCCccCCCCCCe
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEG--VRKIVLATNIAETSITIDDI  261 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g--~~kVivaTniae~gitI~~V  261 (455)
                      ..+..+|||+.-...++.+...+....     +..+..+||+++..+|..+++.|.++  .+-++++|..+..|+++...
T Consensus        83 ~~g~kviIFs~~~~~~~~l~~~l~~~~-----~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a  157 (244)
T d1z5za1          83 DEGDKIAIFTQFVDMGKIIRNIIEKEL-----NTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSA  157 (244)
T ss_dssp             HTTCCEEEEESCHHHHHHHHHHHHHHH-----CSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTC
T ss_pred             ccccceEEEeeceehHHHHHHHHHhhc-----cceEEEEecccchhccchhhhhhhccccchhccccccccccccccchh
Confidence            457789999999999998888887642     24566789999999999999988544  34566778999999999999


Q ss_pred             eEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCCCeEEecCChhh
Q psy6094         262 VYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLKRSETQQYPNDV  317 (455)
Q Consensus       262 ~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~G~c~~L~t~~~  317 (455)
                      .+||.+..        .-+...       ..++.-|.-|.|+..+-.+|+|++...
T Consensus       158 ~~vi~~~~--------~wn~~~-------~~Qa~~R~~R~Gq~~~v~i~~l~~~~T  198 (244)
T d1z5za1         158 NRVIHFDR--------WWNPAV-------EDQATDRVYRIGQTRNVIVHKLISVGT  198 (244)
T ss_dssp             SEEEECSC--------CSCTTT-------C--------------CCEEEEEEETTS
T ss_pred             hhhhhcCc--------hhhhHH-------HhhhcceeeecCCCCceEEEEEeeCCC
Confidence            99997443        222111       123333444445555678888887553

>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=98.29  E-value=7e-07  Score=77.25  Aligned_cols=105  Identities=21%  Similarity=0.164  Sum_probs=73.9

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCccCCCCC----
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAETSITID----  259 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~gitI~----  259 (455)
                      ..+.+||||+.+.+..+.+.+.|.+.+      +....|++....++-..+-+.-.+|  .|.||||.|.||.||.    
T Consensus        32 ~~grPVLIgT~SIe~SE~ls~~L~~~g------i~h~vLnAk~~~~Ea~II~~Ag~~g--~VtIATNmAGRGtDikl~~~  103 (175)
T d1tf5a4          32 MTGQPVLVGTVAVETSELISKLLKNKG------IPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEG  103 (175)
T ss_dssp             HHTCCEEEEESCHHHHHHHHHHHHTTT------CCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTT
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHcC------CCceeehhhhHHHHHHHHHhccCCC--ceeehhhHHHcCCCccchHH
Confidence            567899999999999999999999875      4445566665444443333333333  6999999999999884    


Q ss_pred             ----CeeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC-CeEEecCC
Q psy6094         260 ----DIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK-RSETQQYP  314 (455)
Q Consensus       260 ----~V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~-G~c~~L~t  314 (455)
                          +=-|||-+-+                  +-|+---.|-.||+||.|. |.+-.+++
T Consensus       104 v~~~GGLhVI~t~~------------------~~s~Rid~Ql~GR~gRQGdpGs~~~~~s  145 (175)
T d1tf5a4         104 VKELGGLAVVGTER------------------HESRRIDNQLRGRSGRQGDPGITQFYLS  145 (175)
T ss_dssp             SGGGTSEEEEESSC------------------CSSHHHHHHHHTTSSGGGCCEEEEEEEE
T ss_pred             HHhCCCcEEEEecc------------------CcchhHHHHHhcchhhhCCCcccEEEEE
Confidence                2225554333                  3344556699999999887 87665555

>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=98.22  E-value=1.1e-06  Score=72.43  Aligned_cols=22  Identities=18%  Similarity=0.286  Sum_probs=19.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +++|+++++.++||||||++++
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~   25 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFL   25 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHH
T ss_pred             HHcCCcEEEEcCCCCChhHHHH
Confidence            5789999999999999997765

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.20  E-value=5.8e-07  Score=74.73  Aligned_cols=24  Identities=21%  Similarity=0.307  Sum_probs=20.6

Q ss_pred             HcCCeEEEEcCCCCCcccchh-hhh
Q psy6094          70 RNNQITVISGETGSGPPLHLD-FIT   93 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp-~ll   93 (455)
                      +++++.++.|+||||||++++ +++
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~   30 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYA   30 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHH
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHHH
Confidence            467899999999999999988 444

>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=98.16  E-value=1.4e-06  Score=84.26  Aligned_cols=109  Identities=11%  Similarity=0.062  Sum_probs=87.5

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCc---eEEEEeCCCCccCCCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGV---RKIVLATNIAETSITIDD  260 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~---~kVivaTniae~gitI~~  260 (455)
                      ..+..+|||......++.+.+.|...+      +.+..+||+++..+|..+++.|.++.   .-++++|..+..|+++..
T Consensus       116 ~~g~KvlIFs~~~~~ld~l~~~l~~~g------~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~  189 (346)
T d1z3ix1         116 TTSDKVVLVSNYTQTLDLFEKLCRNRR------YLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIG  189 (346)
T ss_dssp             HCCCEEEEEESCHHHHHHHHHHHHHHT------CCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTT
T ss_pred             hcCCceeEEeehhhhhHHHHHHHhhhh------ccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhcccccc
Confidence            556789999999999999999998875      77889999999999999988886553   247889999999999999


Q ss_pred             eeEEEeCCCCcccccccCCCcccccccccchhhHHhhhcccCCCCC---CeEEecCChh
Q psy6094         261 IVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRTLK---RSETQQYPND  316 (455)
Q Consensus       261 V~~VID~g~~k~~~yd~~~~~~~l~~~~iSka~~~QR~GRaGR~~~---G~c~~L~t~~  316 (455)
                      ..+||-        ||+.          -+-+...|+.||+-|.|.   =.+|+|++..
T Consensus       190 a~~vi~--------~d~~----------wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~  230 (346)
T d1z3ix1         190 ANRLVM--------FDPD----------WNPANDEQAMARVWRDGQKKTCYIYRLLSTG  230 (346)
T ss_dssp             EEEEEE--------CSCC----------SSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             ceEEEE--------ecCC----------CccchHhHhhhcccccCCCCceEEEEEEeCC
Confidence            999997        4432          234556688888866554   4778888754

>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=98.15  E-value=1.8e-07  Score=83.62  Aligned_cols=46  Identities=15%  Similarity=0.192  Sum_probs=36.1

Q ss_pred             CHHHHHHHHHH-ccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          43 SRRYQEMLEAR-KKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        43 ~~~~~~~l~~R-~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      ++..+++++.. +.-..+++|.++++++.+|+++++++|||||||..
T Consensus        10 ~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~   56 (206)
T d1oywa2          10 ESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLC   56 (206)
T ss_dssp             HHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHH
T ss_pred             CHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcch
Confidence            34445555554 55556778999999999999999999999999943

>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=98.09  E-value=5.4e-07  Score=82.32  Aligned_cols=41  Identities=10%  Similarity=0.056  Sum_probs=32.8

Q ss_pred             HHHHHHHccCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          47 QEMLEARKKLPSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        47 ~~~l~~R~~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      .++.+.. .-..|++|.+.++.+..|++++++||||||||+.
T Consensus        34 ~~~~~~~-~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~   74 (237)
T d1gkub1          34 VEFFRKC-VGEPRAIQKMWAKRILRKESFAATAPTGVGKTSF   74 (237)
T ss_dssp             HHHHHTT-TCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHH
T ss_pred             HHHHHhc-cCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHH
Confidence            3344433 3345899999999999999999999999999954

>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=97.62  E-value=3.3e-05  Score=67.70  Aligned_cols=31  Identities=16%  Similarity=0.229  Sum_probs=25.6

Q ss_pred             CCHHHHHHHHHHHHcCCeEEEEcCCCCCcccc
Q psy6094          57 PSYQMRDAVLDMVRNNQITVISGETGSGPPLH   88 (455)
Q Consensus        57 P~~~~q~~il~~i~~~~~vii~~~TGSGKTtq   88 (455)
                      -.+.+|.++++.+.+++ +++++|||||||+.
T Consensus         9 ~pr~~Q~~~~~~~~~~n-~lv~~pTGsGKT~i   39 (200)
T d1wp9a1           9 QPRIYQEVIYAKCKETN-CLIVLPTGLGKTLI   39 (200)
T ss_dssp             CCCHHHHHHHHHGGGSC-EEEECCTTSCHHHH
T ss_pred             CCCHHHHHHHHHHhcCC-eEEEeCCCCcHHHH
Confidence            45788999999887664 78899999999954

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.56  E-value=0.00023  Score=64.26  Aligned_cols=79  Identities=13%  Similarity=0.113  Sum_probs=61.2

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCc-cCCCCCCeeE
Q psy6094         185 LVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAE-TSITIDDIVY  263 (455)
Q Consensus       185 ~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae-~gitI~~V~~  263 (455)
                      .+.++++-+|+..-.....+.++....  .-+..+..+||.++..++..++....+|..+|||-|-.+- ..+..+++..
T Consensus       103 ~g~qv~~l~Pt~~La~Q~~~~~~~~~~--~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgL  180 (233)
T d2eyqa3         103 NHKQVAVLVPTTLLAQQHYDNFRDRFA--NWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGL  180 (233)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHST--TTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEE
T ss_pred             cCCceEEEccHHHhHHHHHHHHHHHHh--hCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccc
Confidence            355677777777777777777765421  2246899999999999999999999999999999997443 4678889987


Q ss_pred             EE
Q psy6094         264 VV  265 (455)
Q Consensus       264 VI  265 (455)
                      ||
T Consensus       181 iI  182 (233)
T d2eyqa3         181 LI  182 (233)
T ss_dssp             EE
T ss_pred             ee
Confidence            66

>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=97.36  E-value=0.00034  Score=61.33  Aligned_cols=66  Identities=18%  Similarity=0.209  Sum_probs=49.3

Q ss_pred             cCCCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCC-CCCceEEEEeCCCCccCCCC
Q psy6094         184 MLVVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTP-PEGVRKIVLATNIAETSITI  258 (455)
Q Consensus       184 ~~~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~-~~g~~kVivaTniae~gitI  258 (455)
                      ..+.+|||...+.+.-+.+.+.|.+.+      +..-.|++.-..+| ..|.... +.|  .|-||||.|-||.||
T Consensus        32 ~~GqPVLVGT~SVe~SE~lS~lL~~~g------i~h~vLNAK~herE-AeIIAqAG~~G--aVTIATNMAGRGTDI   98 (219)
T d1nkta4          32 AKGQPVLIGTTSVERSEYLSRQFTKRR------IPHNVLNAKYHEQE-ATIIAVAGRRG--GVTVATNMAGRGTDI   98 (219)
T ss_dssp             HTTCCEEEEESCHHHHHHHHHHHHHTT------CCCEEECSSCHHHH-HHHHHTTTSTT--CEEEEETTCSTTCCC
T ss_pred             hcCCCEEEeeCcHHHHHHHHHHHHHhc------cchhccchhhHHHH-HHHHHhcccCC--cEEeeccccCCCCce
Confidence            678899999999999999999999875      44445666533333 3344433 333  689999999999999

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.30  E-value=0.00046  Score=63.42  Aligned_cols=78  Identities=12%  Similarity=0.089  Sum_probs=56.2

Q ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCCCCCeEEEeecCCCChhhHhhhhcCCCCCceEEEEeCCCCcc-CCCCCCeeEE
Q psy6094         186 VVPILVFLPGWDTINSLHRSMCQSSFFNSSRFQIIPLHSMLPTVSQKSIFNTPPEGVRKIVLATNIAET-SITIDDIVYV  264 (455)
Q Consensus       186 ~g~iLVFlp~~~ei~~l~~~L~~~~~~~~~~~~v~~lhs~l~~~~r~~v~~~~~~g~~kVivaTniae~-gitI~~V~~V  264 (455)
                      +.++++-+|+.-=+....+.+....  ..-++.+..+||+++..+|.+++....+|..+|||.|-.+=. .+...++.+|
T Consensus       132 g~q~~~m~Pt~~La~Qh~~~~~~~f--~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglv  209 (264)
T d1gm5a3         132 GFQTAFMVPTSILAIQHYRRTVESF--SKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLV  209 (264)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHH--TCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEE
T ss_pred             ccceeEEeehHhhhHHHHHHHHHhh--hhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCcccccee
Confidence            4455666666555555555554432  112467999999999999999999999999999999976543 4677788876


Q ss_pred             E
Q psy6094         265 V  265 (455)
Q Consensus       265 I  265 (455)
                      |
T Consensus       210 i  210 (264)
T d1gm5a3         210 I  210 (264)
T ss_dssp             E
T ss_pred             e
Confidence            6

>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=95.66  E-value=0.0024  Score=56.04  Aligned_cols=33  Identities=18%  Similarity=0.173  Sum_probs=29.8

Q ss_pred             cCCCHHHHHHHHHHHHcCCeEEEEcCCCCCccc
Q psy6094          55 KLPSYQMRDAVLDMVRNNQITVISGETGSGPPL   87 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~~~~~vii~~~TGSGKTt   87 (455)
                      .+++.++|.++++.+.+++..++.++||+|||.
T Consensus        68 ~~~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~  100 (206)
T d2fz4a1          68 EISLRDYQEKALERWLVDKRGCIVLPTGSGKTH  100 (206)
T ss_dssp             CCCCCHHHHHHHHHHTTTSEEEEEESSSTTHHH
T ss_pred             CCCcCHHHHHHHHHHHhCCCcEEEeCCCCCcee
Confidence            467889999999999999989999999999993

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=95.32  E-value=0.0061  Score=53.58  Aligned_cols=32  Identities=13%  Similarity=0.214  Sum_probs=22.8

Q ss_pred             HcCCeEEEEcCCCCCcccchh---hhhhhhcCCCC
Q psy6094          70 RNNQITVISGETGSGPPLHLD---FITLKRSETQQ  101 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp---~ll~e~~~~vg  101 (455)
                      .+.++++++|+||+||||-+.   +.+...|..|+
T Consensus         8 ~~~~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~   42 (207)
T d1ls1a2           8 KDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPL   42 (207)
T ss_dssp             CSSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCcEE
Confidence            456677889999999998877   33334555555

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.06  E-value=0.005  Score=58.00  Aligned_cols=26  Identities=23%  Similarity=0.390  Sum_probs=21.7

Q ss_pred             HHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          65 VLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        65 il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..++..+++++|+|+|||||||.+-
T Consensus       159 l~~~v~~~~nili~G~tgSGKTT~l~  184 (323)
T d1g6oa_         159 IKDGIAIGKNVIVCGGTGSGKTTYIK  184 (323)
T ss_dssp             HHHHHHHTCCEEEEESTTSSHHHHHH
T ss_pred             HHHHHHhCCCEEEEeeccccchHHHH
Confidence            44567888999999999999997665

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=94.96  E-value=0.013  Score=51.46  Aligned_cols=20  Identities=15%  Similarity=0.459  Sum_probs=17.4

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..+++++.|+||+||||.+.
T Consensus         5 ~~~vi~lvGptGvGKTTTia   24 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIA   24 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            35788899999999999877

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.73  E-value=0.0041  Score=52.33  Aligned_cols=23  Identities=22%  Similarity=0.404  Sum_probs=19.7

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      |++++|.|++||||||++-.|.+
T Consensus         1 ~kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999875544

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=94.64  E-value=0.021  Score=46.36  Aligned_cols=22  Identities=23%  Similarity=0.258  Sum_probs=17.5

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+++++.|++||||||..-.|+
T Consensus         2 kklIii~G~pGsGKTTla~~L~   23 (152)
T d1ly1a_           2 KKIILTIGCPGSGKSTWAREFI   23 (152)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            3578999999999998765443

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=94.14  E-value=0.0094  Score=51.22  Aligned_cols=41  Identities=24%  Similarity=0.341  Sum_probs=28.8

Q ss_pred             HHHcCCeEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHH
Q psy6094          68 MVRNNQITVISGETGSGPPLHLDFITLKRSETQQYPNDVLN  108 (455)
Q Consensus        68 ~i~~~~~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~  108 (455)
                      -+.+.+++++.|++|||||||.-.|.+..|...=..+++++
T Consensus         4 ~~~~~~iI~l~G~pGSGKsT~a~~La~~~g~~~is~g~llr   44 (194)
T d3adka_           4 KLKKSKIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLR   44 (194)
T ss_dssp             HHHTSCEEEEEECTTSSHHHHHHHHHHHTCCEEEEHHHHHH
T ss_pred             cccCCcEEEEECCCCCCHHHHHHHHHHHhCCeeEeccHHHH
Confidence            46788999999999999999987776654433212344444

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.13  E-value=0.027  Score=49.38  Aligned_cols=29  Identities=14%  Similarity=0.263  Sum_probs=16.6

Q ss_pred             CeEEEEcCCCCCcccchh---hhhhhhcCCCC
Q psy6094          73 QITVISGETGSGPPLHLD---FITLKRSETQQ  101 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp---~ll~e~~~~vg  101 (455)
                      .++++.|+||+||||.+.   ..+...|..|+
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~   44 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAYFYKKKGFKVG   44 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHHHHHHTTCCEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceE
Confidence            467779999999999977   22234455555

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.76  E-value=0.0062  Score=50.83  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=19.7

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      .|+++++.|++||||||..-.+..+
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            5788999999999999865444433

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.49  E-value=0.0081  Score=49.93  Aligned_cols=24  Identities=25%  Similarity=0.375  Sum_probs=19.3

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +++++++.|++||||||+.-.|..
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            567899999999999988764443

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=93.44  E-value=0.038  Score=48.39  Aligned_cols=29  Identities=10%  Similarity=0.173  Sum_probs=20.2

Q ss_pred             CeEEEEcCCCCCcccchh---hhhhhhcCCCC
Q psy6094          73 QITVISGETGSGPPLHLD---FITLKRSETQQ  101 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp---~ll~e~~~~vg  101 (455)
                      .++++.|+||+||||.+.   ..+...|..|+
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~   41 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVM   41 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEE
Confidence            367789999999999988   22224445555

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=93.36  E-value=0.0072  Score=50.55  Aligned_cols=22  Identities=18%  Similarity=0.311  Sum_probs=17.7

Q ss_pred             CeEEEEcCCCCCcccchhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +.++|.|++||||||++-.|..
T Consensus         8 K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5689999999999988754443

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.36  E-value=0.0097  Score=49.63  Aligned_cols=18  Identities=17%  Similarity=0.401  Sum_probs=15.6

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ++++|+|++||||||.+-
T Consensus         2 k~v~ItG~~GtGKTtl~~   19 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH   19 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            569999999999997665

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=93.30  E-value=0.01  Score=49.24  Aligned_cols=26  Identities=8%  Similarity=0.224  Sum_probs=20.7

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      .++++++.|++||||||..-.|.+..
T Consensus         2 ~~kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            57899999999999998776555443

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=93.07  E-value=0.023  Score=54.85  Aligned_cols=36  Identities=22%  Similarity=0.259  Sum_probs=25.4

Q ss_pred             cCCCHHHHHHHHHHHH--cCCeEEEEcCCCCCcccchh
Q psy6094          55 KLPSYQMRDAVLDMVR--NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~--~~~~vii~~~TGSGKTtqlp   90 (455)
                      .|...+.|.+.+..+.  .+-.++++|+|||||||.+-
T Consensus       139 ~LG~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~  176 (401)
T d1p9ra_         139 SLGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY  176 (401)
T ss_dssp             GSCCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH
T ss_pred             hhcccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH
Confidence            3555556666565554  34479999999999997765

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=93.04  E-value=0.02  Score=54.50  Aligned_cols=31  Identities=23%  Similarity=0.402  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|.+.+..+.++++++|+|++||||||.+.
T Consensus       151 ~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~  181 (359)
T d1w36d1         151 NWQKVAAAVALTRRISVISGGPGTGKTTTVA  181 (359)
T ss_dssp             CHHHHHHHHHHTBSEEEEECCTTSTHHHHHH
T ss_pred             cHHHHHHHHHHcCCeEEEEcCCCCCceehHH
Confidence            3467777777788999999999999996654

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=92.92  E-value=0.011  Score=48.70  Aligned_cols=22  Identities=18%  Similarity=0.397  Sum_probs=17.4

Q ss_pred             CeEEEEcCCCCCcccchhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +.+++.|++||||||+.-.|..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999987654443

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=92.77  E-value=0.014  Score=47.51  Aligned_cols=23  Identities=13%  Similarity=0.167  Sum_probs=17.5

Q ss_pred             CCeEEEEcCCCCCcccchhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .++++++|+.||||||..-.|.+
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            45788999999999976544443

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.37  E-value=0.016  Score=48.48  Aligned_cols=20  Identities=30%  Similarity=0.451  Sum_probs=16.4

Q ss_pred             EEEEcCCCCCcccchhhhhh
Q psy6094          75 TVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~   94 (455)
                      ++|+|++||||||.+-.++.
T Consensus         3 i~I~G~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHh
Confidence            78999999999998764443

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.31  E-value=0.02  Score=48.85  Aligned_cols=36  Identities=19%  Similarity=0.225  Sum_probs=24.6

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHh
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNM  109 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~  109 (455)
                      +++|.|++|||||||.-.|.+..|...=.+++++|.
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~g~~~i~~g~llR~   38 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKYGYTHLSAGELLRD   38 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEEHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceEcHHHHHHH
Confidence            578999999999999877766554322124445543

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=92.24  E-value=0.016  Score=47.89  Aligned_cols=25  Identities=16%  Similarity=0.195  Sum_probs=19.4

Q ss_pred             CeEEEEcCCCCCcccchhhhhhhhc
Q psy6094          73 QITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      ..++++|++||||||+.-.|.++.|
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            3588999999999988766655444

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.15  E-value=0.021  Score=48.41  Aligned_cols=22  Identities=18%  Similarity=0.409  Sum_probs=18.4

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      |+.++++||+||||||+.-.+.
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~   23 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLR   23 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            6889999999999998765444

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=92.14  E-value=0.02  Score=48.77  Aligned_cols=36  Identities=17%  Similarity=0.184  Sum_probs=23.5

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHh
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNM  109 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~  109 (455)
                      -+|+.|++|||||||.-.|.+..|...-..++++|+
T Consensus         5 riil~G~pGSGKsT~a~~La~~~g~~~i~~gdllr~   40 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNFCVCHLATGDMLRA   40 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEEHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeHHHHHHH
Confidence            366789999999999877766554322124445543

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.88  E-value=0.02  Score=49.06  Aligned_cols=25  Identities=12%  Similarity=0.226  Sum_probs=19.6

Q ss_pred             CCeEEEEcCCCCCcccchhhhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      ..+++|.|++|||||||.-.|.+..
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578899999999999876555433

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=91.77  E-value=0.024  Score=46.92  Aligned_cols=24  Identities=21%  Similarity=0.383  Sum_probs=18.9

Q ss_pred             CCeEEEEcCCCCCcccchhhhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFITLK   95 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll~e   95 (455)
                      +-++++.|++||||||+...|.+.
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHH
Confidence            446899999999999887655543

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=91.49  E-value=0.021  Score=47.95  Aligned_cols=22  Identities=23%  Similarity=0.389  Sum_probs=17.8

Q ss_pred             CeEEEEcCCCCCcccchhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +++||.|..||||||++-.|.+
T Consensus         2 kiivi~G~~GsGKTT~~~~La~   23 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3678899999999999875544

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=91.45  E-value=0.021  Score=48.70  Aligned_cols=25  Identities=20%  Similarity=0.248  Sum_probs=19.6

Q ss_pred             CeEEEEcCCCCCcccchhhhhhhhc
Q psy6094          73 QITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      ++++|.|++||||||+.-.|.+..|
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~~g   31 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHC
Confidence            4788999999999998766655444

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=91.42  E-value=0.027  Score=48.68  Aligned_cols=36  Identities=11%  Similarity=0.123  Sum_probs=24.1

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHh
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNM  109 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~  109 (455)
                      ++.|.||+|||||||.-.|.++.|..-=..++|+|.
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~gl~~iStGdLlR~   40 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRV   40 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEEHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEECHHHHHHH
Confidence            677889999999999876665444322124455553

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.25  E-value=0.052  Score=47.50  Aligned_cols=17  Identities=18%  Similarity=0.292  Sum_probs=14.6

Q ss_pred             CeEEEEcCCCCCcccch
Q psy6094          73 QITVISGETGSGPPLHL   89 (455)
Q Consensus        73 ~~vii~~~TGSGKTtql   89 (455)
                      ..+++.||+||||||.+
T Consensus        46 ~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46899999999999655

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=91.18  E-value=0.027  Score=46.32  Aligned_cols=19  Identities=16%  Similarity=0.289  Sum_probs=16.1

Q ss_pred             eEEEEcCCCCCcccchhhh
Q psy6094          74 ITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~l   92 (455)
                      ++.|+|..||||||.+-.|
T Consensus         4 vi~itG~~GSGKTTL~~~L   22 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKL   22 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHH
Confidence            6889999999999877633

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=91.12  E-value=0.033  Score=46.62  Aligned_cols=24  Identities=21%  Similarity=0.223  Sum_probs=19.2

Q ss_pred             EEEEcCCCCCcccchhhhhhhhcC
Q psy6094          75 TVISGETGSGPPLHLDFITLKRSE   98 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~e~~~   98 (455)
                      ++|.|++||||||+.-.|.+..|.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~~   26 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYGI   26 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
Confidence            789999999999987666665443

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=91.08  E-value=0.025  Score=48.05  Aligned_cols=24  Identities=29%  Similarity=0.376  Sum_probs=18.7

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      .+++.|++||||||+.-.|.+..|
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            378999999999998766655444

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=91.06  E-value=0.032  Score=47.09  Aligned_cols=24  Identities=29%  Similarity=0.325  Sum_probs=19.1

Q ss_pred             EEEEcCCCCCcccchhhhhhhhcC
Q psy6094          75 TVISGETGSGPPLHLDFITLKRSE   98 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~e~~~   98 (455)
                      +++.|++|||||||.-.|.+..|.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g~   26 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYGT   26 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
Confidence            678999999999988766665543

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=91.06  E-value=0.043  Score=48.59  Aligned_cols=20  Identities=20%  Similarity=0.413  Sum_probs=16.2

Q ss_pred             CeEEEEcCCCCCcccchhhh
Q psy6094          73 QITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~l   92 (455)
                      ..+++.|++|+|||+.+-.+
T Consensus        44 ~~lll~GppGtGKT~l~~~l   63 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRKL   63 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHHH
T ss_pred             CceEEECCCCCCHHHHHHHH
Confidence            58999999999999655433

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=90.90  E-value=0.031  Score=47.11  Aligned_cols=20  Identities=20%  Similarity=0.353  Sum_probs=15.5

Q ss_pred             cCCeEE-EEcCCCCCcccchh
Q psy6094          71 NNQITV-ISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vi-i~~~TGSGKTtqlp   90 (455)
                      ++..+| |.|++||||||..-
T Consensus        20 ~~~~iIgI~G~~GSGKSTla~   40 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTLAN   40 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            455666 89999999997653

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=90.78  E-value=0.03  Score=49.11  Aligned_cols=29  Identities=10%  Similarity=0.231  Sum_probs=20.1

Q ss_pred             CeEEEEcCCCCCcccchh---hhhhhhcCCCC
Q psy6094          73 QITVISGETGSGPPLHLD---FITLKRSETQQ  101 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp---~ll~e~~~~vg  101 (455)
                      .+++++|+||+||||-+.   ..+-..+..|+
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~   43 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVV   43 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceE
Confidence            367789999999998877   21224455555

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=90.75  E-value=0.023  Score=50.86  Aligned_cols=22  Identities=23%  Similarity=0.463  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|+|++||||||.+-
T Consensus        26 i~~Ge~vaIvG~sGsGKSTLl~   47 (241)
T d2pmka1          26 IKQGEVIGIVGRSGSGKSTLTK   47 (241)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3568899999999999998765

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.73  E-value=0.031  Score=46.98  Aligned_cols=23  Identities=22%  Similarity=0.307  Sum_probs=18.6

Q ss_pred             EEEEcCCCCCcccchhhhhhhhc
Q psy6094          75 TVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      +++.|++|||||||.-.|.+..+
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            67899999999999876665544

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.73  E-value=0.024  Score=51.10  Aligned_cols=22  Identities=27%  Similarity=0.489  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|+|++||||||.+-
T Consensus        37 i~~Ge~vaivG~sGsGKSTLl~   58 (251)
T d1jj7a_          37 LRPGEVTALVGPNGSGKSTVAA   58 (251)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578999999999999998875

>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=90.64  E-value=0.046  Score=50.01  Aligned_cols=32  Identities=9%  Similarity=0.048  Sum_probs=27.1

Q ss_pred             cCCCHHHHHHHHHHHHcCCeEEEEcCCCCCcc
Q psy6094          55 KLPSYQMRDAVLDMVRNNQITVISGETGSGPP   86 (455)
Q Consensus        55 ~lP~~~~q~~il~~i~~~~~vii~~~TGSGKT   86 (455)
                      .+.+..+|.+++..+..++..++.++||+|||
T Consensus       111 ~~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT  142 (282)
T d1rifa_         111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRS  142 (282)
T ss_dssp             ECCCCHHHHHHHHHHHHHSEEEECCCTTSCHH
T ss_pred             ccccchHHHHHHHHHHhcCCceeEEEcccCcc
Confidence            35677788888888877778999999999999

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=90.63  E-value=0.025  Score=50.28  Aligned_cols=22  Identities=27%  Similarity=0.573  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|++||||||.+-
T Consensus        28 i~~Ge~~~iiG~sGsGKSTLl~   49 (230)
T d1l2ta_          28 IKEGEFVSIMGPSGSGKSTMLN   49 (230)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCcchhhH
Confidence            3578899999999999998876

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.51  E-value=0.034  Score=46.80  Aligned_cols=24  Identities=17%  Similarity=0.181  Sum_probs=18.8

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      .+++.|++|||||||.-.|.+..|
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            478899999999998766665443

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=90.51  E-value=0.023  Score=49.39  Aligned_cols=22  Identities=18%  Similarity=0.394  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++.+.|+.||||||.+-
T Consensus        24 i~~Gei~~l~G~NGsGKSTLl~   45 (200)
T d1sgwa_          24 IEKGNVVNFHGPNGIGKTTLLK   45 (200)
T ss_dssp             EETTCCEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCChHHHHHH
Confidence            3578899999999999998875

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=90.28  E-value=0.035  Score=45.87  Aligned_cols=22  Identities=14%  Similarity=0.131  Sum_probs=17.6

Q ss_pred             cCCeEEEEcCCCCCcccchhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFI   92 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~l   92 (455)
                      .|.++.++|..||||||..-.|
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~L   26 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARAL   26 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            5678889999999999765433

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.25  E-value=0.028  Score=50.75  Aligned_cols=22  Identities=14%  Similarity=0.413  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|+|++||||||.+-
T Consensus        41 i~~Ge~vaivG~sGsGKSTLl~   62 (255)
T d2hyda1          41 IEKGETVAFVGMSGGGKSTLIN   62 (255)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHT
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            4578999999999999998865

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=90.24  E-value=0.033  Score=51.20  Aligned_cols=31  Identities=16%  Similarity=0.156  Sum_probs=23.0

Q ss_pred             CHHHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          58 SYQMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        58 ~~~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.+-|.++++...  ..++|.|+.||||||.+.
T Consensus        12 L~~eQ~~~v~~~~--g~~lV~g~aGSGKTt~l~   42 (318)
T d1pjra1          12 LNKEQQEAVRTTE--GPLLIMAGAGSGKTRVLT   42 (318)
T ss_dssp             SCHHHHHHHHCCS--SCEEEEECTTSCHHHHHH
T ss_pred             CCHHHHHHHhCCC--CCEEEEecCCccHHHHHH
Confidence            4456777887643  348899999999997765

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=89.92  E-value=0.03  Score=50.51  Aligned_cols=22  Identities=18%  Similarity=0.374  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|+|++||||||.+-
T Consensus        38 i~~Ge~iaivG~sGsGKSTLl~   59 (253)
T d3b60a1          38 IPAGKTVALVGRSGSGKSTIAS   59 (253)
T ss_dssp             ECTTCEEEEEECTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCChHHHHHH
Confidence            3578899999999999998875

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.76  E-value=0.04  Score=46.44  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=18.2

Q ss_pred             EEEEcCCCCCcccchhhhhhhhc
Q psy6094          75 TVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      +++.|++|||||||.-.|.++.|
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            67789999999999876665443

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.71  E-value=0.045  Score=45.33  Aligned_cols=29  Identities=10%  Similarity=0.052  Sum_probs=20.4

Q ss_pred             CeEEEEcCCCCCcccchhhhhh---hhcCCCC
Q psy6094          73 QITVISGETGSGPPLHLDFITL---KRSETQQ  101 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~---e~~~~vg  101 (455)
                      +++-|+|..||||||.+-.++.   ++|..+|
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~g~~v~   33 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVG   33 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhCCCeEE
Confidence            4667999999999988863332   4455554

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=89.69  E-value=0.051  Score=49.31  Aligned_cols=29  Identities=10%  Similarity=0.180  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHcCCeEEEEcCCCCCcccchh
Q psy6094          60 QMRDAVLDMVRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        60 ~~q~~il~~i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +.|.++++.  ....++|.|+.||||||.+.
T Consensus         4 ~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1           4 PGQQQAVEF--VTGPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             HHHHHHHHC--CSSEEEECCCTTSCHHHHHH
T ss_pred             HHHHHHHhC--CCCCEEEEeeCCccHHHHHH
Confidence            456777764  24458899999999997754

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=89.58  E-value=0.033  Score=49.78  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.|.|++||||||.+-
T Consensus        28 i~~Ge~~~iiG~sGsGKSTLl~   49 (240)
T d3dhwc1          28 VPAGQIYGVIGASGAGKSTLIR   49 (240)
T ss_dssp             ECSSCEEEEEESTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578899999999999998876

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.55  E-value=0.034  Score=49.40  Aligned_cols=22  Identities=23%  Similarity=0.490  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.+.|++||||||.+-
T Consensus        23 i~~Gei~~liGpsGsGKSTLl~   44 (232)
T d2awna2          23 IHEGEFVVFVGPSGCGKSTLLR   44 (232)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCChHHHHHH
Confidence            3578899999999999998875

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.48  E-value=0.049  Score=45.82  Aligned_cols=19  Identities=21%  Similarity=0.434  Sum_probs=16.0

Q ss_pred             CCeEEEEcCCCCCcccchh
Q psy6094          72 NQITVISGETGSGPPLHLD   90 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp   90 (455)
                      -.++|++|.+||||||..-
T Consensus        14 p~liil~G~pGsGKST~a~   32 (172)
T d1yj5a2          14 PEVVVAVGFPGAGKSTFIQ   32 (172)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            4588999999999997654

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=89.43  E-value=0.03  Score=50.17  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=18.8

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+.+.|.|++||||||.+-
T Consensus        25 i~~Ge~vaivG~sGsGKSTLl~   46 (242)
T d1mv5a_          25 AQPNSIIAFAGPSGGGKSTIFS   46 (242)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3468889999999999998765

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.39  E-value=0.051  Score=46.92  Aligned_cols=22  Identities=23%  Similarity=0.415  Sum_probs=18.9

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      |+.+++.|.-|||||||+-.|.
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~   23 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVV   23 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            6789999999999999987444

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.25  E-value=0.062  Score=46.88  Aligned_cols=17  Identities=18%  Similarity=0.294  Sum_probs=14.5

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+++.||+||||||.+=
T Consensus        35 ~lll~Gp~G~GKTtl~~   51 (237)
T d1sxjd2          35 HMLFYGPPGTGKTSTIL   51 (237)
T ss_dssp             CEEEECSTTSSHHHHHH
T ss_pred             eEEEECCCCCChHHHHH
Confidence            48999999999997654

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=88.95  E-value=0.049  Score=46.48  Aligned_cols=24  Identities=29%  Similarity=0.206  Sum_probs=18.4

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRS   97 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~   97 (455)
                      -+++.|++||||||+.-.|.+..|
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHBC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHC
Confidence            367789999999998766665443

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.88  E-value=0.04  Score=50.45  Aligned_cols=21  Identities=33%  Similarity=0.498  Sum_probs=17.9

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|+.+.|.|++||||||.+-
T Consensus        60 ~~Ge~vaivG~nGsGKSTLl~   80 (281)
T d1r0wa_          60 EKGEMLAITGSTGSGKTSLLM   80 (281)
T ss_dssp             CTTCEEEEEESTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHHH
Confidence            467889999999999998765

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.83  E-value=0.1  Score=45.24  Aligned_cols=17  Identities=18%  Similarity=0.301  Sum_probs=14.4

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+++.|++|+||||.+-
T Consensus        37 ~lLl~Gp~G~GKttl~~   53 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTIV   53 (227)
T ss_dssp             CEEEECSSSSSHHHHHH
T ss_pred             eEEEECCCCCChhHHHH
Confidence            38899999999997654

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=88.59  E-value=0.063  Score=46.40  Aligned_cols=37  Identities=16%  Similarity=0.072  Sum_probs=23.9

Q ss_pred             eEEEEcCCCCCcccchhhhhhhhcCCCCChHHHHHhc
Q psy6094          74 ITVISGETGSGPPLHLDFITLKRSETQQYPNDVLNML  110 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~e~~~~vg~p~~ll~~l  110 (455)
                      ++.|.||.|||||||.-.|.++.|...=..+.|+|.+
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg~~~istGdl~R~~   41 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFGFTYLDTGAMYRAA   41 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHCCEEEEHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEECHHHHHHHH
Confidence            3457799999999998766655543322245555543

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.40  E-value=0.046  Score=48.74  Aligned_cols=22  Identities=23%  Similarity=0.552  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+.+.|+.||||||.+-
T Consensus        29 v~~Ge~~~liGpsGaGKSTLl~   50 (239)
T d1v43a3          29 IKDGEFLVLLGPSGCGKTTTLR   50 (239)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCChHHHHHH
Confidence            3578899999999999998875

>d2p6ra1 a.4.5.43 (A:404-488) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RecQ helicase DNA-binding domain-like
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=88.38  E-value=0.12  Score=38.05  Aligned_cols=37  Identities=3%  Similarity=-0.196  Sum_probs=32.1

Q ss_pred             hhhHHhHHhhhhhcccccCCCCCCcccCChHHHHHhhCCC
Q psy6094         347 PGAILVFLPGWDTINSLHRSMCQSSFFNSCLLYEFAMVDN  386 (455)
Q Consensus       347 ~~~i~~al~~L~~lgald~~~~l~~~~~T~lG~~l~~lp~  386 (455)
                      ...++.+++.|.+.|.++.++++   .+|++|+.+|.+.+
T Consensus        49 ~~~i~~~l~~L~~~~~I~~~~~l---~aT~lGri~S~~YI   85 (85)
T d2p6ra1          49 SYELERVVRQLENWGMVVEAAHL---APTKLGSLVSRLYI   85 (85)
T ss_dssp             HHHHHHHHHHHHHTTSEEESSSE---EECHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHCCCccccccc---ccCHHHHHHHHHhC
Confidence            57789999999999999887764   67999999998764

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=88.37  E-value=0.062  Score=44.70  Aligned_cols=22  Identities=14%  Similarity=0.105  Sum_probs=16.7

Q ss_pred             CeEEEEcCCCCCcccchhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +.+++.|..||||||+.-.+.+
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHH
Confidence            4577889999999987654443

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=88.33  E-value=0.046  Score=48.78  Aligned_cols=22  Identities=23%  Similarity=0.563  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+.+-+.|++||||||.+-
T Consensus        26 i~~Ge~~~liG~sGaGKSTll~   47 (240)
T d1g2912          26 VKDGEFMILLGPSGCGKTTTLR   47 (240)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCChHHHHHH
Confidence            3578899999999999998765

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=88.31  E-value=0.069  Score=46.30  Aligned_cols=19  Identities=16%  Similarity=0.436  Sum_probs=16.1

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .|+.+||+||+|+||||..
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3788999999999999544

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=88.22  E-value=0.061  Score=44.50  Aligned_cols=20  Identities=25%  Similarity=0.217  Sum_probs=15.4

Q ss_pred             eEEEEcCCCCCcccchhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll   93 (455)
                      +++++|..||||||..-.|.
T Consensus         2 ~I~liG~~GsGKsTi~k~La   21 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALA   21 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHH
Confidence            57888999999997654443

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.16  E-value=0.12  Score=44.76  Aligned_cols=17  Identities=29%  Similarity=0.448  Sum_probs=14.4

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+++.||+||||||.+-
T Consensus        38 ~~ll~Gp~G~GKTt~a~   54 (224)
T d1sxjb2          38 HMIISGMPGIGKTTSVH   54 (224)
T ss_dssp             CEEEECSTTSSHHHHHH
T ss_pred             eEEEECCCCCCchhhHH
Confidence            48999999999996653

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=88.12  E-value=0.063  Score=47.73  Aligned_cols=24  Identities=21%  Similarity=0.242  Sum_probs=18.1

Q ss_pred             CeEEEEcCCCCCcccchhhhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITLKR   96 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~e~   96 (455)
                      +.+++.||+||||||..-.+..+.
T Consensus        33 ~~ilL~GpPGtGKT~la~~la~~~   56 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLRSAIFEET   56 (273)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh
Confidence            458899999999997765554433

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.60  E-value=0.073  Score=45.10  Aligned_cols=21  Identities=29%  Similarity=0.455  Sum_probs=17.7

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +++|.|..||||||++-.|.+
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            688999999999998875554

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=87.54  E-value=0.074  Score=46.41  Aligned_cols=17  Identities=35%  Similarity=0.491  Sum_probs=14.8

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      +++|.|+.||||||.+-
T Consensus         2 vi~v~G~~GsGKTTLl~   18 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTG   18 (244)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHH
Confidence            68899999999997764

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=87.38  E-value=0.039  Score=48.93  Aligned_cols=22  Identities=41%  Similarity=0.640  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|.++.+.|++||||||.+-
T Consensus        23 i~~Ge~~~liGpsGaGKSTll~   44 (229)
T d3d31a2          23 VESGEYFVILGPTGAGKTLFLE   44 (229)
T ss_dssp             ECTTCEEEEECCCTHHHHHHHH
T ss_pred             ECCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998865

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.11  E-value=0.042  Score=46.30  Aligned_cols=22  Identities=14%  Similarity=0.157  Sum_probs=16.8

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      |.+++++|.+||||||..-.|.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La   40 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALE   40 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            4577789999999998654443

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=86.79  E-value=0.12  Score=45.29  Aligned_cols=17  Identities=18%  Similarity=0.245  Sum_probs=14.1

Q ss_pred             CeEEEEcCCCCCcccch
Q psy6094          73 QITVISGETGSGPPLHL   89 (455)
Q Consensus        73 ~~vii~~~TGSGKTtql   89 (455)
                      ..+++.||+|+||||.+
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            36899999999999543

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.78  E-value=0.097  Score=44.13  Aligned_cols=21  Identities=24%  Similarity=0.248  Sum_probs=17.3

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      ..|++++|.|++|||||+..-
T Consensus        21 ~~G~v~~i~G~~GsGKT~l~l   41 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQICH   41 (242)
T ss_dssp             ETTSEEEEECCTTSSHHHHHH
T ss_pred             cCCEEEEEEeCCCCCHHHHHH
Confidence            357899999999999996543

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=86.73  E-value=0.084  Score=46.24  Aligned_cols=16  Identities=19%  Similarity=0.333  Sum_probs=13.7

Q ss_pred             eEEEEcCCCCCcccch
Q psy6094          74 ITVISGETGSGPPLHL   89 (455)
Q Consensus        74 ~vii~~~TGSGKTtql   89 (455)
                      .+++.||+||||||.+
T Consensus        37 ~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          37 HVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CEEEESSTTSSHHHHH
T ss_pred             eEEEECCCCCcHHHHH
Confidence            5899999999999544

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.59  E-value=0.084  Score=44.70  Aligned_cols=21  Identities=33%  Similarity=0.455  Sum_probs=15.9

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +-+||+||+||||||..-.|+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~   22 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLF   22 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            347999999999997654443

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon 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: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=86.59  E-value=0.038  Score=49.42  Aligned_cols=22  Identities=23%  Similarity=0.394  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|..+.+.|++||||||.+-
T Consensus        28 i~~Ge~~~iiG~sGsGKSTll~   49 (242)
T d1oxxk2          28 IENGERFGILGPSGAGKTTFMR   49 (242)
T ss_dssp             ECTTCEEEEECSCHHHHHHHHH
T ss_pred             ECCCCEEEEECCCCCcHHHHHH
Confidence            3568899999999999998765

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=86.43  E-value=0.12  Score=47.68  Aligned_cols=15  Identities=27%  Similarity=0.445  Sum_probs=13.4

Q ss_pred             CCeEEEEcCCCCCcc
Q psy6094          72 NQITVISGETGSGPP   86 (455)
Q Consensus        72 ~~~vii~~~TGSGKT   86 (455)
                      ...+++.||||||||
T Consensus        49 ~~~iLl~GPpG~GKT   63 (309)
T d1ofha_          49 PKNILMIGPTGVGKT   63 (309)
T ss_dssp             CCCEEEECCTTSSHH
T ss_pred             CceEEEECCCCCCHH
Confidence            467889999999999

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=86.35  E-value=0.25  Score=43.81  Aligned_cols=16  Identities=19%  Similarity=0.248  Sum_probs=13.3

Q ss_pred             eEEEEcCCCCCcccch
Q psy6094          74 ITVISGETGSGPPLHL   89 (455)
Q Consensus        74 ~vii~~~TGSGKTtql   89 (455)
                      -+++.||+|||||+.+
T Consensus        42 ~vLL~GppGtGKT~la   57 (246)
T d1d2na_          42 SVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECcCCCCHHHHH
Confidence            4899999999999443

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=85.94  E-value=0.056  Score=47.93  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=19.3

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|+++-+.|+.||||||.+-
T Consensus        22 I~~Gei~~iiG~nGaGKSTLl~   43 (231)
T d1l7vc_          22 VRAGEILHLVGPNGAGKSTLLA   43 (231)
T ss_dssp             EETTCEEECBCCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            4578999999999999998765

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.87  E-value=0.11  Score=44.99  Aligned_cols=22  Identities=27%  Similarity=0.302  Sum_probs=17.9

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|++++|.|++||||||..-
T Consensus        31 i~~G~~~li~G~pGsGKT~l~l   52 (251)
T d1szpa2          31 VETGSITELFGEFRTGKSQLCH   52 (251)
T ss_dssp             EESSSEEEEEESTTSSHHHHHH
T ss_pred             CcCCeEEEEEcCCCCCHHHHHH
Confidence            3467899999999999996543

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.80  E-value=0.11  Score=44.89  Aligned_cols=24  Identities=13%  Similarity=0.203  Sum_probs=19.1

Q ss_pred             cCCeEEEEcCCCCCcccchhhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .|..++|.|.-|||||||+-.|.+
T Consensus         2 rG~lI~ieG~dGsGKsT~~~~L~~   25 (209)
T d1nn5a_           2 RGALIVLEGVDRAGKSTQSRKLVE   25 (209)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeeEEEEECCCCCCHHHHHHHHHH
Confidence            467788899999999999874433

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=85.71  E-value=0.079  Score=47.19  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=19.2

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|.++-+.|+.||||||.+-
T Consensus        29 i~~Gei~~liGpnGaGKSTl~~   50 (240)
T d1ji0a_          29 VPRGQIVTLIGANGAGKTTTLS   50 (240)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998876

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=85.62  E-value=0.1  Score=45.76  Aligned_cols=21  Identities=33%  Similarity=0.396  Sum_probs=17.4

Q ss_pred             HcCCeEEEEcCCCCCcccchh
Q psy6094          70 RNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        70 ~~~~~vii~~~TGSGKTtqlp   90 (455)
                      -.|++++|.|++||||||..-
T Consensus        34 p~G~~~li~G~pGsGKT~~~l   54 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAH   54 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHH
T ss_pred             cCCEEEEEEcCCCCCHHHHHH
Confidence            356899999999999996544

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.55  E-value=0.12  Score=44.89  Aligned_cols=23  Identities=13%  Similarity=0.339  Sum_probs=19.2

Q ss_pred             cCCeEEEEcCCCCCcccchhhhh
Q psy6094          71 NNQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .|..+++.|.-|||||||+-.|.
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~   24 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILY   24 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHH
T ss_pred             CeEEEEEECCCCCcHHHHHHHHH
Confidence            47789999999999999986443

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=85.48  E-value=0.084  Score=47.56  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      |..|.++-|.|+.||||||.+-
T Consensus        25 i~~GEi~~iiG~sGsGKSTLl~   46 (258)
T d1b0ua_          25 ARAGDVISIIGSSGSGKSTFLR   46 (258)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998765

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.47  E-value=0.12  Score=43.46  Aligned_cols=18  Identities=22%  Similarity=0.270  Sum_probs=14.8

Q ss_pred             CCeEEEEcCCCCCcccch
Q psy6094          72 NQITVISGETGSGPPLHL   89 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtql   89 (455)
                      .+.+|++||+|+||||.+
T Consensus         3 ~k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            467899999999999543

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.42  E-value=0.11  Score=45.37  Aligned_cols=22  Identities=14%  Similarity=0.314  Sum_probs=18.0

Q ss_pred             CCeEEEEcCCCCCcccchhhhh
Q psy6094          72 NQITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        72 ~~~vii~~~TGSGKTtqlp~ll   93 (455)
                      .+.++|.|..|||||||+-.|.
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~   23 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILK   23 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTG
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999999987443

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.18  E-value=0.12  Score=44.39  Aligned_cols=20  Identities=30%  Similarity=0.202  Sum_probs=14.8

Q ss_pred             EEEEcCCCCCcccchhhhhh
Q psy6094          75 TVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~ll~   94 (455)
                      +-|.|++||||||..-.|.+
T Consensus         5 IgI~G~~gSGKSTla~~L~~   24 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQ   24 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45899999999986543433

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.18  E-value=0.11  Score=44.19  Aligned_cols=21  Identities=29%  Similarity=0.390  Sum_probs=16.3

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      -+||+||+||||||+.-.|++
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            378999999999987554444

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.15  E-value=0.12  Score=45.46  Aligned_cols=21  Identities=14%  Similarity=0.377  Sum_probs=16.5

Q ss_pred             CeEEEEcCCCCCcccchhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFIT   93 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll   93 (455)
                      +.+++.||+||||||.+-.++
T Consensus        53 ~~lll~GPpG~GKTt~a~~la   73 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVA   73 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            579999999999996654333

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=84.94  E-value=0.16  Score=44.62  Aligned_cols=20  Identities=20%  Similarity=0.312  Sum_probs=16.9

Q ss_pred             cCCeEEEEcCCCCCcccchh
Q psy6094          71 NNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtqlp   90 (455)
                      .++.++|.|+.|+|||+.+-
T Consensus        28 ~~~~i~i~G~~G~GKTsLl~   47 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSIIK   47 (283)
T ss_dssp             CSSEEEEEESTTSSHHHHHH
T ss_pred             cCCEEEEEcCCCCcHHHHHH
Confidence            45689999999999997765

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=84.81  E-value=0.14  Score=47.45  Aligned_cols=19  Identities=16%  Similarity=0.309  Sum_probs=15.6

Q ss_pred             cCCeEEEEcCCCCCcccch
Q psy6094          71 NNQITVISGETGSGPPLHL   89 (455)
Q Consensus        71 ~~~~vii~~~TGSGKTtql   89 (455)
                      .+..+++.|++|+||||.+
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4456999999999999654

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=84.77  E-value=0.13  Score=50.12  Aligned_cols=15  Identities=27%  Similarity=0.445  Sum_probs=13.7

Q ss_pred             CCeEEEEcCCCCCcc
Q psy6094          72 NQITVISGETGSGPP   86 (455)
Q Consensus        72 ~~~vii~~~TGSGKT   86 (455)
                      .+++++.||||||||
T Consensus        49 ksNILliGPTGvGKT   63 (443)
T d1g41a_          49 PKNILMIGPTGVGKT   63 (443)
T ss_dssp             CCCEEEECCTTSSHH
T ss_pred             cccEEEECCCCCCHH
Confidence            457999999999999

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=84.70  E-value=0.16  Score=44.84  Aligned_cols=18  Identities=22%  Similarity=0.217  Sum_probs=13.6

Q ss_pred             EEEEcCCCCCcccchhhh
Q psy6094          75 TVISGETGSGPPLHLDFI   92 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~l   92 (455)
                      +++.|++|+|||+.+-.+
T Consensus        49 l~l~GppGtGKT~l~~~l   66 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKFT   66 (287)
T ss_dssp             EECTTCCSSSHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHH
Confidence            556799999999665433

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=84.64  E-value=0.13  Score=43.67  Aligned_cols=21  Identities=19%  Similarity=0.214  Sum_probs=16.9

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +++++|.+||||||..-.|..
T Consensus         4 li~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           4 LIVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578899999999988765544

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.58  E-value=0.14  Score=44.82  Aligned_cols=17  Identities=18%  Similarity=0.278  Sum_probs=14.6

Q ss_pred             eEEEEcCCCCCcccchh
Q psy6094          74 ITVISGETGSGPPLHLD   90 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp   90 (455)
                      .+++.|++|+||||.+-
T Consensus        35 ~lll~Gp~G~GKTt~~~   51 (252)
T d1sxje2          35 HLLLYGPNGTGKKTRCM   51 (252)
T ss_dssp             CEEEECSTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            48999999999997654

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {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: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=83.51  E-value=0.16  Score=44.98  Aligned_cols=18  Identities=33%  Similarity=0.647  Sum_probs=15.4

Q ss_pred             CeEEEEcCCCCCcccchh
Q psy6094          73 QITVISGETGSGPPLHLD   90 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp   90 (455)
                      ..+.+.||.||||||.+-
T Consensus        25 e~~~liGpnGaGKSTll~   42 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLE   42 (240)
T ss_dssp             SEEEEECCTTSSHHHHHH
T ss_pred             EEEEEECCCCChHHHHHH
Confidence            477789999999998765

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=83.42  E-value=0.12  Score=44.70  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=17.7

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..+++++|.|++|+|||+..-
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l   52 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMH   52 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHH
T ss_pred             ccCCeEEEEEeCCCCCHHHHHH
Confidence            3457899999999999995533

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.32  E-value=0.13  Score=44.89  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=17.9

Q ss_pred             CeEEEEcCCCCCcccchhhhhh
Q psy6094          73 QITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        73 ~~vii~~~TGSGKTtqlp~ll~   94 (455)
                      +.++|.|..|||||||+-.|.+
T Consensus         3 k~IviEG~~GsGKST~~~~L~~   24 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHH
Confidence            4688999999999999864443

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=82.98  E-value=0.12  Score=46.27  Aligned_cols=22  Identities=32%  Similarity=0.592  Sum_probs=19.1

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|.++-+.|+.||||||.+-
T Consensus        27 v~~Gei~~liG~nGaGKSTLl~   48 (254)
T d1g6ha_          27 VNKGDVTLIIGPNGSGKSTLIN   48 (254)
T ss_dssp             EETTCEEEEECSTTSSHHHHHH
T ss_pred             ECCCCEEEEECCCCCcHHHHHH
Confidence            3578899999999999998875

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.81  E-value=0.16  Score=41.79  Aligned_cols=18  Identities=28%  Similarity=0.303  Sum_probs=13.5

Q ss_pred             EEEEcCCCCCcccchhhh
Q psy6094          75 TVISGETGSGPPLHLDFI   92 (455)
Q Consensus        75 vii~~~TGSGKTtqlp~l   92 (455)
                      +|++|..||||||.--.+
T Consensus         4 IvliG~~G~GKSTig~~L   21 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRL   21 (165)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            667799999999764333

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.50  E-value=0.18  Score=42.88  Aligned_cols=21  Identities=19%  Similarity=0.349  Sum_probs=16.8

Q ss_pred             eEEEEcCCCCCcccchhhhhh
Q psy6094          74 ITVISGETGSGPPLHLDFITL   94 (455)
Q Consensus        74 ~vii~~~TGSGKTtqlp~ll~   94 (455)
                      .++|.|.-|||||||+-.|.+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~   22 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG   22 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999874443

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=80.98  E-value=0.16  Score=44.97  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.0

Q ss_pred             HHcCCeEEEEcCCCCCcccchh
Q psy6094          69 VRNNQITVISGETGSGPPLHLD   90 (455)
Q Consensus        69 i~~~~~vii~~~TGSGKTtqlp   90 (455)
                      +..|+++-+.|+.||||||.+-
T Consensus        25 v~~Gei~glvG~nGaGKSTLl~   46 (238)
T d1vpla_          25 IEEGEIFGLIGPNGAGKTTTLR   46 (238)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHH
Confidence            3578889999999999998876

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=80.69  E-value=0.31  Score=45.94  Aligned_cols=14  Identities=36%  Similarity=0.551  Sum_probs=12.8

Q ss_pred             CeEEEEcCCCCCcc
Q psy6094          73 QITVISGETGSGPP   86 (455)
Q Consensus        73 ~~vii~~~TGSGKT   86 (455)
                      .+++..||||+|||
T Consensus        69 ~niLfiGPTGvGKT   82 (364)
T d1um8a_          69 SNILLIGPTGSGKT   82 (364)
T ss_dssp             CCEEEECCTTSSHH
T ss_pred             cceeeeCCCCccHH
Confidence            46899999999999

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=80.08  E-value=0.43  Score=49.21  Aligned_cols=36  Identities=19%  Similarity=0.437  Sum_probs=26.5

Q ss_pred             HccCC--CHHHHHHHHHHHH---cCCeEEEEcCCCCCcccc
Q psy6094          53 RKKLP--SYQMRDAVLDMVR---NNQITVISGETGSGPPLH   88 (455)
Q Consensus        53 R~~lP--~~~~q~~il~~i~---~~~~vii~~~TGSGKTtq   88 (455)
                      ++.+|  +|..-+.++..+.   .+|.+||+|++|||||+.
T Consensus        70 ~~~~~PHif~vA~~Ay~~l~~~~~~Q~IiisGeSGsGKTe~  110 (730)
T d1w7ja2          70 MGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVS  110 (730)
T ss_dssp             GGGSCCCHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHH
T ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCeEEEEEeCCCCCHHHH
Confidence            44566  5666666666654   478899999999999954