Psyllid ID: psy1090

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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-------17
Protein Sequence
MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHHHccccccEEEEEccccHHHHHHHHHHHccccEEEEEEccHHHHHHHHHHHHccccccccccccccccccccccccEEEccHHHHHHHHHHHccccccEEEEEccccccccccHHHHHHcccccccEEEEEcccccccHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHHHHHcccHHHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHHHccccEEEEEcccHHHHHHHHHcccccccccccccccccccccccccccEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHccccHHcHHHHHHcc
Coil and Loop (DISEMBL)
mdtvipdptryrksgkVIAFFCKIIEEqalepnlivcplsvlnnWEAEFRKFAPFVRTVKYYGNAIERKALQsealslptikvpakkgktkkqislklplilvttpqiieNDFGFLKKITWnciivdeghsvknkkskLSIKLTALRATFKVLLTgwyypnkwskqctl
Flexible Loop (DISEMBL)
mdtvipdptryrksgkvIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERkalqsealslptikvpakkgktkkqislklplilvttpqIIENDFGFLKKITWNCIIvdeghsvknkksklsiKLTALRATFKvlltgwyypnkwskqctl
Low Complexity Region (SEG)
MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL
Disordered region (IsUnstruct)
*************SGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVP******KKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWS*****
Disordered Region (DISOPRED)
MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS**************KQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL
Disordered Region (DISEMBL)
MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVP********QISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL
Disordered Region (DISPRO)
MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSL***********TKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	169	2.2.26 [Sep-21-2011]
Q9S775	1384	CHD3-type chromatin-remod	yes	N/A	0.893	0.109	0.352	3e-19
Q8TDI0	1954	Chromodomain-helicase-DNA	yes	N/A	0.911	0.078	0.322	9e-17
Q6PDQ2	1915	Chromodomain-helicase-DNA	no	N/A	0.911	0.080	0.329	5e-16
Q14839	1912	Chromodomain-helicase-DNA	no	N/A	0.911	0.080	0.329	5e-16
Q86WJ1	897	Chromodomain-helicase-DNA	no	N/A	0.798	0.150	0.337	6e-16
P31380	1131	ATP-dependent helicase FU	yes	N/A	0.822	0.122	0.333	6e-16
Q9CXF7	900	Chromodomain-helicase-DNA	no	N/A	0.633	0.118	0.368	7e-16
Q3B7N1	897	Chromodomain-helicase-DNA	no	N/A	0.798	0.150	0.331	3e-15
O74842	1284	ATP-dependent helicase ff	yes	N/A	0.822	0.108	0.339	3e-15
Q12873	2000	Chromodomain-helicase-DNA	no	N/A	0.911	0.077	0.329	4e-15

>sp|Q9S775|PKL_ARATH CHD3-type chromatin-remodeling factor PICKLE OS=Arabidopsis thaliana GN=PKL PE=1 SV=1

 Score = 94.4 bits (233), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 56/159 (35%), Positives = 82/159 (51%), Gaps = 8/159 (5%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ + IA    + EE  L P+L++ PLS L NWE EF  +AP +  V Y+G
Sbjct: 295 ILADEMGLGKTIQSIALLASLFEEN-LIPHLVIAPLSTLRNWEREFATWAPQMNVVMYFG 353

Query: 64  NAIERKALQSEALSLPTIKV------PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLK 117
            A  R  ++     L   +         +     KQ  +K   +L+T+ ++I  D   LK
Sbjct: 354 TAQARAVIREHEFYLSKDQKKIKKKKSGQISSESKQKRIKFD-VLLTSYEMINLDSAVLK 412

Query: 118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
            I W C+IVDEGH +KNK SKL   LT   +  ++LLTG
Sbjct: 413 PIKWECMIVDEGHRLKNKDSKLFSSLTQYSSNHRILLTG 451

Chromatin remodeling factor that represses the expression of embryonic trait genes (such as NFYB9/LEC1) upon and after seed germination and thus enables the developmental switch to post-germinative growth. Silences some MADS-box proteins such as PHE1 and PHE2. Plays a role during carpel differentiation.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>sp|Q8TDI0|CHD5_HUMAN Chromodomain-helicase-DNA-binding protein 5 OS=Homo sapiens GN=CHD5 PE=2 SV=1

 Score = 86.3 bits (212), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 51/158 (32%), Positives = 82/158 (51%), Gaps = 4/158 (2%)

Query: 2   DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct: 720 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779

Query: 61  YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
           Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct: 780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 838

Query: 119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct: 839 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 876

May play a role in the development of the nervous system and the pathogenesis of neural tumors.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q6PDQ2|CHD4_MOUSE Chromodomain-helicase-DNA-binding protein 4 OS=Mus musculus GN=Chd4 PE=1 SV=1

 Score = 84.0 bits (206), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 52/158 (32%), Positives = 79/158 (50%), Gaps = 4/158 (2%)

Query: 2   DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           DT++ D     K+ +   F   + +E  +  P L+  PLS + NWE EF  +AP +  V 
Sbjct: 739 DTILADEMGLGKTVQTAVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDMYVVT 798

Query: 61  YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
           Y G+   R  ++    S     I+   K  + KK+ S+K   +L+T+ ++I  D   L  
Sbjct: 799 YVGDKDSRAIIRENEFSFEDNAIRGGKKASRMKKEASVKFH-VLLTSYELITIDMAILGS 857

Query: 119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           I W C+IVDE H +KN +SK    L       K+LLTG
Sbjct: 858 IDWACLIVDEAHRLKNNQSKFFRVLNGYSLQHKLLLTG 895

Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q14839|CHD4_HUMAN Chromodomain-helicase-DNA-binding protein 4 OS=Homo sapiens GN=CHD4 PE=1 SV=2

 Score = 83.6 bits (205), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 52/158 (32%), Positives = 79/158 (50%), Gaps = 4/158 (2%)

Query: 2   DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           DT++ D     K+ +   F   + +E  +  P L+  PLS + NWE EF  +AP +  V 
Sbjct: 746 DTILADEMGLGKTVQTAVFLYSLYKEGHSKGPFLVSAPLSTIINWEREFEMWAPDMYVVT 805

Query: 61  YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
           Y G+   R  ++    S     I+   K  + KK+ S+K   +L+T+ ++I  D   L  
Sbjct: 806 YVGDKDSRAIIRENEFSFEDNAIRGGKKASRMKKEASVKFH-VLLTSYELITIDMAILGS 864

Query: 119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           I W C+IVDE H +KN +SK    L       K+LLTG
Sbjct: 865 IDWACLIVDEAHRLKNNQSKFFRVLNGYSLQHKLLLTG 902

Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q86WJ1|CHD1L_HUMAN Chromodomain-helicase-DNA-binding protein 1-like OS=Homo sapiens GN=CHD1L PE=1 SV=2

 Score = 83.6 bits (205), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 52/154 (33%), Positives = 77/154 (50%), Gaps = 19/154 (12%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALE-PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYY 62
           ++ D     K+ + IA F  +      E P LI+CPLSVL+NW+ E ++FAP +  V Y 
Sbjct: 68  ILGDEMGLGKTCQTIALFIYLAGRLNDEGPFLILCPLSVLSNWKEEMQRFAPGLSCVTYA 127

Query: 63  GNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWN 122
           G+  ER  LQ +                K++       +L+TT +I   D  FLK   W+
Sbjct: 128 GDKEERACLQQD---------------LKQESRFH---VLLTTYEICLKDASFLKSFPWS 169

Query: 123 CIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
            ++VDE H +KN+ S L   L+     F +LLTG
Sbjct: 170 VLVVDEAHRLKNQSSLLHKTLSEFSVVFSLLLTG 203

DNA helicase which plays a role in chromatin-remodeling following DNA damage. Targeted to sites of DNA damage through interaction with poly(ADP-ribose) and functions to regulate chromatin during DNA repair. Able to catalyze nucleosome sliding in an ATP-dependent manner. Helicase activity is strongly stimulated upon poly(ADP-ribose)-binding.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P31380|FUN30_YEAST ATP-dependent helicase FUN30 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=FUN30 PE=1 SV=1

 Score = 83.6 bits (205), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 53/159 (33%), Positives = 80/159 (50%), Gaps = 20/159 (12%)

Query: 1   MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           M  ++ D     K+ +VI+FF  + +     P+L+V P S L NW  EF+KFAP ++   
Sbjct: 591 MSCILADDMGLGKTCQVISFFAYLKQINEPGPHLVVVPSSTLENWLREFQKFAPALKIEP 650

Query: 61  YYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN---DFGFLK 117
           YYG+  ER+ L+          +    GK           ++VTT  +      D  FLK
Sbjct: 651 YYGSLQEREELRD--------ILERNAGKYD---------VIVTTYNLAAGNKYDVSFLK 693

Query: 118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
              +N ++ DEGH +KN  S+   KL  +RA F++LLTG
Sbjct: 694 NRNFNVVVYDEGHMLKNSTSERFAKLMKIRANFRLLLTG 732

May function as a negative regulatory element in the process of UV damage repair.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q9CXF7|CHD1L_MOUSE Chromodomain-helicase-DNA-binding protein 1-like OS=Mus musculus GN=Chd1l PE=2 SV=1

 Score = 83.2 bits (204), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 46/125 (36%), Positives = 64/125 (51%), Gaps = 18/125 (14%)

Query: 32  PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTK 91
           P L++CPLSVL+NW+ E  +FAP +  V Y G+  ER  LQ +        V        
Sbjct: 91  PFLVLCPLSVLSNWKEEMERFAPGLSCVTYTGDKEERARLQQDLRQESGFHV-------- 142

Query: 92  KQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFK 151
                     L+TT +I   D  FLK  +W+ + VDE H +KN+ S L   L+   A F+
Sbjct: 143 ----------LLTTYEICLKDASFLKSFSWSVLAVDEAHRLKNQSSLLHRTLSEFSAVFR 192

Query: 152 VLLTG 156
           +LLTG
Sbjct: 193 LLLTG 197

DNA helicase which plays a role in chromatin-remodeling following DNA damage. Targeted to sites of DNA damage through interaction with poly(ADP-ribose) and functions to regulate chromatin during DNA repair. Able to catalyze nucleosome sliding in an ATP-dependent manner. Helicase activity is strongly stimulated upon poly(ADP-ribose)-binding.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q3B7N1|CHD1L_BOVIN Chromodomain-helicase-DNA-binding protein 1-like OS=Bos taurus GN=CHD1L PE=2 SV=1

 Score = 81.3 bits (199), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 51/154 (33%), Positives = 76/154 (49%), Gaps = 19/154 (12%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALE-PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYY 62
           ++ D     K+ + IA F  +      E P LI+CPLSVL+NW+ E  +FAP +  V Y 
Sbjct: 70  ILGDEMGLGKTCQTIALFIYLAGRLNDEGPFLILCPLSVLSNWKEEMERFAPGLSCVTYA 129

Query: 63  GNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWN 122
           G+  +R  LQ +                K++       +L+TT +I   D  FLK   W+
Sbjct: 130 GDKDKRACLQQD---------------LKQESRFH---VLLTTYEICLKDASFLKSFPWS 171

Query: 123 CIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
            ++VDE H +KN+ S L   L+     F +LLTG
Sbjct: 172 VLVVDEAHRLKNQSSLLHKTLSEFSVVFSLLLTG 205

DNA helicase which plays a role in chromatin-remodeling following DNA damage. Targeted to sites of DNA damage through interaction with poly(ADP-ribose) and functions to regulate chromatin during DNA repair. Able to catalyze nucleosome sliding in an ATP-dependent manner. Helicase activity is strongly stimulated upon poly(ADP-ribose)-binding.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O74842|FFT2_SCHPO ATP-dependent helicase fft2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=fft2 PE=1 SV=1

 Score = 80.9 bits (198), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 54/159 (33%), Positives = 80/159 (50%), Gaps = 20/159 (12%)

Query: 1   MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           +  ++ D     K+ +V+AFF  ++E+    P+L+V P S L NW  E  +F P +R   
Sbjct: 569 LSGILADEMGLGKTCQVVAFFALLLEQGHHGPHLVVVPSSTLENWLRELARFCPSLRVEP 628

Query: 61  YYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN---DFGFLK 117
           YYG+  ER  ++ EA+    IK                  ILVTT Q+  N   D  FLK
Sbjct: 629 YYGSQQERANIR-EAIEENEIKYD----------------ILVTTYQLATNNKEDRSFLK 671

Query: 118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
              ++  + DEGH +KN+ S+    L  L A F++LLTG
Sbjct: 672 HQNFDVCVYDEGHYLKNRMSERYKHLMNLNANFRLLLTG 710

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q12873|CHD3_HUMAN Chromodomain-helicase-DNA-binding protein 3 OS=Homo sapiens GN=CHD3 PE=1 SV=3

 Score = 80.9 bits (198), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 52/158 (32%), Positives = 80/158 (50%), Gaps = 4/158 (2%)

Query: 2   DTVIPDPTRYRKSGKVIAFFCKIIEEQALE-PNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           DT++ D     K+ + I F   + +E   + P L+  PLS + NWE EF+ +AP    V 
Sbjct: 756 DTILADEMGLGKTIQTIVFLYSLYKEGHTKGPFLVSAPLSTIINWEREFQMWAPKFYVVT 815

Query: 61  YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
           Y G+   R  ++    S     IK   K  K K++  +K   +L+T+ ++I  D   L  
Sbjct: 816 YTGDKDSRAIIRENEFSFEDNAIKGGKKAFKMKREAQVKFH-VLLTSYELITIDQAALGS 874

Query: 119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           I W C++VDE H +KN +SK    L   +   K+LLTG
Sbjct: 875 IRWACLVVDEAHRLKNNQSKFFRVLNGYKIDHKLLLTG 912

Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	169
302796603	1274	hypothetical protein SELMODRAFT_177985 [	0.976	0.129	0.365	2e-19
302811536	1292	hypothetical protein SELMODRAFT_158748 [	0.976	0.127	0.365	2e-19
302803789	1296	hypothetical protein SELMODRAFT_155996 [	0.976	0.127	0.364	8e-19
302817780	1296	hypothetical protein SELMODRAFT_185367 [	0.976	0.127	0.364	8e-19
393217224	1030	hypothetical protein FOMMEDRAFT_122741 [	0.863	0.141	0.346	2e-18
356562107	2586	PREDICTED: uncharacterized protein LOC10	0.893	0.058	0.383	2e-18
242094948	1147	hypothetical protein SORBIDRAFT_10g00563	0.893	0.131	0.356	5e-18
297802844	1221	hypothetical protein ARALYDRAFT_328538 [	0.834	0.115	0.367	6e-18
321263641	926	helicase [Cryptococcus gattii WM276] gi|	0.911	0.166	0.363	6e-18
405123404	926	helicase [Cryptococcus neoformans var. g	0.917	0.167	0.359	6e-18

>gi|302796603|ref|XP_002980063.1| hypothetical protein SELMODRAFT_177985 [Selaginella moellendorffii] gi|300152290|gb|EFJ18933.1| hypothetical protein SELMODRAFT_177985 [Selaginella moellendorffii]

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 61/167 (36%), Positives = 89/167 (53%), Gaps = 2/167 (1%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ + I+F   ++ E    P+LIV PLS L NWE EF  +AP +  V Y G
Sbjct: 291 ILADEMGLGKTIQTISFLTSLLHEGVSLPHLIVAPLSTLRNWEREFSIWAPQMSIVTYIG 350

Query: 64  NAIERKALQSEALSLPTIKVPAK-KGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWN 122
           +A  R+ ++ +   LP  + P K K    +Q  +K   +L+T+ +++  D   LK I W 
Sbjct: 351 SAQAREIIRQKEFFLPKERKPEKGKKNASRQRRVKFN-VLLTSYEMVNTDSAVLKPIKWE 409

Query: 123 CIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL 169
           C+IVDEGH +KNK SKL   L       +VLLTG    N   +  TL
Sbjct: 410 CLIVDEGHRLKNKDSKLFQTLHNYSTYSRVLLTGTPLQNNLDELFTL 456

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302811536|ref|XP_002987457.1| hypothetical protein SELMODRAFT_158748 [Selaginella moellendorffii] gi|300144863|gb|EFJ11544.1| hypothetical protein SELMODRAFT_158748 [Selaginella moellendorffii]

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 61/167 (36%), Positives = 89/167 (53%), Gaps = 2/167 (1%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ + I+F   ++ E    P+LIV PLS L NWE EF  +AP +  V Y G
Sbjct: 291 ILADEMGLGKTIQTISFLTSLLHEGVSLPHLIVAPLSTLRNWEREFSIWAPQMSIVTYIG 350

Query: 64  NAIERKALQSEALSLPTIKVPAK-KGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWN 122
           +A  R+ ++ +   LP  + P K K    +Q  +K   +L+T+ +++  D   LK I W 
Sbjct: 351 SAQAREIIRQKEFFLPKERKPEKGKKNASRQRRVKFN-VLLTSYEMVNTDSAVLKPIKWE 409

Query: 123 CIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL 169
           C+IVDEGH +KNK SKL   L       +VLLTG    N   +  TL
Sbjct: 410 CLIVDEGHRLKNKDSKLFQTLHNYSTYSRVLLTGTPLQNNLDELFTL 456

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302803789|ref|XP_002983647.1| hypothetical protein SELMODRAFT_155996 [Selaginella moellendorffii] gi|300148484|gb|EFJ15143.1| hypothetical protein SELMODRAFT_155996 [Selaginella moellendorffii]

 Score = 98.6 bits (244), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 62/170 (36%), Positives = 89/170 (52%), Gaps = 5/170 (2%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ + IAF   + +E+  +P+L+V PLS L NWE EF  +AP +  V Y G
Sbjct: 297 ILADEMGLGKTIQTIAFLASLKQEEVTDPHLVVAPLSTLRNWEREFATWAPDIHIVVYAG 356

Query: 64  NAIERKALQSEALSLP----TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKI 119
           NA  R  ++      P    T K    + K  KQ  +K   +L+T+ ++I  D   LK I
Sbjct: 357 NAKARSVIREFEFFYPKTDKTKKKYYSERKHSKQDRIKFD-VLLTSYEMITFDAAILKSI 415

Query: 120 TWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL 169
            W C+IVDEGH +K+K+SKL   L       +VLLTG    N   +  TL
Sbjct: 416 KWECLIVDEGHRLKSKESKLFQTLQNYTTYHRVLLTGTPLQNNLDELFTL 465

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302817780|ref|XP_002990565.1| hypothetical protein SELMODRAFT_185367 [Selaginella moellendorffii] gi|300141733|gb|EFJ08442.1| hypothetical protein SELMODRAFT_185367 [Selaginella moellendorffii]

 Score = 98.6 bits (244), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 62/170 (36%), Positives = 89/170 (52%), Gaps = 5/170 (2%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ + IAF   + +E+  +P+L+V PLS L NWE EF  +AP +  V Y G
Sbjct: 297 ILADEMGLGKTIQTIAFLASLKQEEVTDPHLVVAPLSTLRNWEREFATWAPDIHIVVYAG 356

Query: 64  NAIERKALQSEALSLP----TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKI 119
           NA  R  ++      P    T K    + K  KQ  +K   +L+T+ ++I  D   LK I
Sbjct: 357 NAKARSVIREFEFFYPKTDKTKKKYYSERKHSKQDRIKFD-VLLTSYEMITFDAAILKSI 415

Query: 120 TWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL 169
            W C+IVDEGH +K+K+SKL   L       +VLLTG    N   +  TL
Sbjct: 416 KWECLIVDEGHRLKSKESKLFQTLQNYTTYHRVLLTGTPLQNNLDELFTL 465

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|393217224|gb|EJD02713.1| hypothetical protein FOMMEDRAFT_122741 [Fomitiporia mediterranea MF3/22]

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 53/153 (34%), Positives = 83/153 (54%), Gaps = 7/153 (4%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ +VI+FF ++ EE  L P+LIV P S L NW  EF +FAP +    YYG
Sbjct: 421 ILADEMGLGKTVQVISFFAQLKEEGCLGPHLIVVPASTLENWCREFERFAPSISIEAYYG 480

Query: 64  NAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNC 123
              ER+A++ +           + G    ++  +  LI   +  + + D  FLKKI WN 
Sbjct: 481 KQDERRAIRGKLFR-------TQPGNNDMKVFTREVLITTYSLAVGKEDKAFLKKIPWNT 533

Query: 124 IIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
            + DEGH +KN ++     LT +++ +K+LLTG
Sbjct: 534 CVFDEGHVLKNFRAPRYSALTHIKSKWKLLLTG 566

Source: Fomitiporia mediterranea MF3/22

Species: Fomitiporia mediterranea

Genus: Fomitiporia

Family: Hymenochaetaceae

Order: Hymenochaetales

Class: Agaricomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

>gi|356562107|ref|XP_003549315.1| PREDICTED: uncharacterized protein LOC100779829 [Glycine max]

 Score = 97.1 bits (240), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 61/159 (38%), Positives = 88/159 (55%), Gaps = 8/159 (5%)

Query: 4    VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
            ++ D     K+ + IAF   + EE  + P+L+V PLS L NWE EF  +AP +  V Y+G
Sbjct: 1506 ILADEMGLGKTIQSIAFLASLFEEN-VSPHLVVAPLSTLRNWEREFATWAPQMNVVMYFG 1564

Query: 64   NAIERKALQSEALSLPTIKVPAKKGKTK------KQISLKLPLILVTTPQIIENDFGFLK 117
            +A  R  ++      P  +   KK K++      KQ  +K   +L+T+ +II +D   LK
Sbjct: 1565 SAKARAFIREYEFYFPKNQKRIKKKKSRQIVNESKQERIKFD-VLLTSYEIINSDTSSLK 1623

Query: 118  KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C+IVDEGH +KNK SKL   L    +  +VLLTG
Sbjct: 1624 HIKWECMIVDEGHRLKNKDSKLFSSLKQYSSKHRVLLTG 1662

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242094948|ref|XP_002437964.1| hypothetical protein SORBIDRAFT_10g005630 [Sorghum bicolor] gi|241916187|gb|EER89331.1| hypothetical protein SORBIDRAFT_10g005630 [Sorghum bicolor]

 Score = 95.9 bits (237), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 57/160 (35%), Positives = 85/160 (53%), Gaps = 9/160 (5%)

Query: 4   VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
           ++ D     K+ + IAF   + E++   P+L+V PLS L NWE EF  +AP +  V Y+G
Sbjct: 125 ILGDEMGLGKTIQSIAFLASLFEDK-FGPHLVVAPLSTLRNWEREFATWAPQMNVVMYFG 183

Query: 64  NAIERKALQSEALSLPTIKV-------PAKKGKTKKQISLKLPLILVTTPQIIENDFGFL 116
            A  R  ++      P  K+        +   + KKQ  ++   +L+T+ ++I  D   L
Sbjct: 184 AAASRDIIRKHEFYYPKEKLKKLKKKKSSPSNEEKKQSRIRFD-VLLTSYEMINMDSNVL 242

Query: 117 KKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           K I W C+IVDEGH +KNK SKL  +L       +VLLTG
Sbjct: 243 KNIEWECLIVDEGHRLKNKDSKLFGQLKDYNTKHRVLLTG 282

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297802844|ref|XP_002869306.1| hypothetical protein ARALYDRAFT_328538 [Arabidopsis lyrata subsp. lyrata] gi|297315142|gb|EFH45565.1| hypothetical protein ARALYDRAFT_328538 [Arabidopsis lyrata subsp. lyrata]

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 57/155 (36%), Positives = 79/155 (50%), Gaps = 14/155 (9%)

Query: 2   DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKY 61
           + ++ D     K+ + IAF   + EE  L P+L+V PLS L NWE EF  +AP +  V Y
Sbjct: 243 NVILADEMGLGKTIQSIAFLASLFEEN-LSPHLVVAPLSTLRNWEREFATWAPHMNVVMY 301

Query: 62  YGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITW 121
            G +  R  +       P       KG+  K        +L+T+ ++I  D   LK I W
Sbjct: 302 TGTSEARDVIWEHEFYFP-------KGRKIKFD------VLLTSYEMINQDTSVLKPIKW 348

Query: 122 NCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
            C+IVDEGH +KNK SKL   L    +  +VLLTG
Sbjct: 349 TCMIVDEGHRLKNKDSKLYSSLNQFTSKHRVLLTG 383

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|321263641|ref|XP_003196538.1| helicase [Cryptococcus gattii WM276] gi|317463015|gb|ADV24751.1| Helicase, putative [Cryptococcus gattii WM276]

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 60/165 (36%), Positives = 86/165 (52%), Gaps = 11/165 (6%)

Query: 1   MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           ++ ++ D     K+ + I+F   +  +    P LIVCPLSVLNNW  EF KF P V  + 
Sbjct: 244 LNGILADEMGLGKTLQTISFLSHLRSKGTWGPFLIVCPLSVLNNWIMEFEKFTPSVPVLM 303

Query: 61  YYGNAIERKALQSEALSLPTIKVPAKKGKTKKQIS---------LKLPLILVTTPQIIEN 111
           Y+GN   R  L++  L  PT    A   KTK++ S            P I++TT +I   
Sbjct: 304 YHGNPDHRAELRATRLQTPTAS-DAGSAKTKRRKSNGKVTGNDTSAFP-IVITTYEICMK 361

Query: 112 DFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           D  FL  I W  I+VDEGH +KN   KL  +L +  +  +++LTG
Sbjct: 362 DKQFLSGIRWKFIVVDEGHRLKNLDCKLIRELKSYTSANRMILTG 406

Source: Cryptococcus gattii WM276

Species: Cryptococcus gattii

Genus: Filobasidiella

Family: Tremellaceae

Order: Tremellales

Class: Tremellomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

>gi|405123404|gb|AFR98169.1| helicase [Cryptococcus neoformans var. grubii H99]

 Score = 95.5 bits (236), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 59/164 (35%), Positives = 85/164 (51%), Gaps = 9/164 (5%)

Query: 1   MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
           ++ ++ D     K+ + I+F   +  +    P LIVCPLSVLNNW  EF KF P V  + 
Sbjct: 244 LNGILADEMGLGKTLQTISFLSHLRSKGTWGPFLIVCPLSVLNNWIMEFEKFTPSVPVLM 303

Query: 61  YYGNAIERKALQSEALSLPT------IKVPAKK--GKTKKQISLKLPLILVTTPQIIEND 112
           Y+GN   R  L++  L  PT       K   +K  GK     +   P I++TT +I   D
Sbjct: 304 YHGNPDHRAELRATRLQTPTASDAGSTKTKGRKSNGKVTGNNTSTFP-IVITTYEICMKD 362

Query: 113 FGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             FL  I W  I+VDEGH +KN   KL  +L +  +  +++LTG
Sbjct: 363 KQFLSGIKWKFIVVDEGHRLKNLDCKLIRELKSYTSANRMILTG 406

Source: Cryptococcus neoformans var. grubii H99

Species: Cryptococcus neoformans

Genus: Filobasidiella

Family: Tremellaceae

Order: Tremellales

Class: Tremellomycetes

Phylum: Basidiomycota

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	169
TAIR|locus:2040184	1384	PKL "PICKLE" [Arabidopsis thal	0.893	0.109	0.371	1.2e-19
UNIPROTKB|K7EMY3	1060	CHD5 "Chromodomain-helicase-DN	0.911	0.145	0.322	8.2e-17
UNIPROTKB|J9NRN3	1195	CHD5 "Uncharacterized protein"	0.911	0.128	0.322	9.6e-17
UNIPROTKB|F2Z2R5	1225	CHD5 "Chromodomain-helicase-DN	0.911	0.125	0.322	1e-16
UNIPROTKB|F1SSZ2	1667	CHD5 "Uncharacterized protein"	0.911	0.092	0.322	1.5e-16
UNIPROTKB|F1RIM3	1723	CHD5 "Uncharacterized protein"	0.911	0.089	0.322	1.5e-16
UNIPROTKB|E2R1M3	1812	CHD5 "Uncharacterized protein"	0.911	0.084	0.322	1.6e-16
UNIPROTKB|F1MFF9	1852	Bt.62145 "Uncharacterized prot	0.911	0.083	0.322	1.7e-16
UNIPROTKB|Q8TDI0	1954	CHD5 "Chromodomain-helicase-DN	0.911	0.078	0.322	1.8e-16
RGD|1582725	1940	Chd5 "chromodomain helicase DN	0.911	0.079	0.322	2.3e-16

TAIR|locus:2040184 PKL "PICKLE" [Arabidopsis thaliana (taxid:3702)]

 Score = 248 (92.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 59/159 (37%), Positives = 85/159 (53%)

Query:     4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYG 63
             ++ D     K+ + IA    + EE  + P+L++ PLS L NWE EF  +AP +  V Y+G
Sbjct:   295 ILADEMGLGKTIQSIALLASLFEENLI-PHLVIAPLSTLRNWEREFATWAPQMNVVMYFG 353

Query:    64 NAIERKALQSEA--LSLPTIKVPAKKG----KTKKQISLKLPLILVTTPQIIENDFGFLK 117
              A  R  ++     LS    K+  KK        KQ  +K   +L+T+ ++I  D   LK
Sbjct:   354 TAQARAVIREHEFYLSKDQKKIKKKKSGQISSESKQKRIKFD-VLLTSYEMINLDSAVLK 412

Query:   118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
              I W C+IVDEGH +KNK SKL   LT   +  ++LLTG
Sbjct:   413 PIKWECMIVDEGHRLKNKDSKLFSSLTQYSSNHRILLTG 451

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=ISS

GO:0016568 "chromatin modification" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP

GO:0009736 "cytokinin mediated signaling pathway" evidence=IMP

GO:0009733 "response to auxin stimulus" evidence=IMP

GO:2000023 "regulation of lateral root development" evidence=IMP

GO:0009788 "negative regulation of abscisic acid mediated signaling pathway" evidence=IMP

GO:0006346 "methylation-dependent chromatin silencing" evidence=RCA

GO:0016246 "RNA interference" evidence=RCA

GO:0008283 "cell proliferation" evidence=IMP

GO:0009739 "response to gibberellin stimulus" evidence=IMP

GO:0048364 "root development" evidence=IMP

UNIPROTKB|K7EMY3 CHD5 "Chromodomain-helicase-DNA-binding protein 5" [Homo sapiens (taxid:9606)]

 Score = 220 (82.5 bits), Expect = 8.2e-17, P = 8.2e-17
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   103 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 162

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   163 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 221

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   222 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 259

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|J9NRN3 CHD5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 220 (82.5 bits), Expect = 9.6e-17, P = 9.6e-17
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   694 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 753

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   754 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 812

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   813 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 850

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F2Z2R5 CHD5 "Chromodomain-helicase-DNA-binding protein 5" [Homo sapiens (taxid:9606)]

 Score = 220 (82.5 bits), Expect = 1.0e-16, P = 1.0e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   720 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 838

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   839 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 876

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1SSZ2 CHD5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 220 (82.5 bits), Expect = 1.5e-16, P = 1.5e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   636 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 695

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   696 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 754

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   755 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 792

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1RIM3 CHD5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 220 (82.5 bits), Expect = 1.5e-16, P = 1.5e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   652 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 711

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   712 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 770

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   771 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 808

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2R1M3 CHD5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 220 (82.5 bits), Expect = 1.6e-16, P = 1.6e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   583 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 642

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   643 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 701

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   702 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 739

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1MFF9 Bt.62145 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 220 (82.5 bits), Expect = 1.7e-16, P = 1.7e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   666 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 725

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   726 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 784

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   785 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 822

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q8TDI0 CHD5 "Chromodomain-helicase-DNA-binding protein 5" [Homo sapiens (taxid:9606)]

 Score = 220 (82.5 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   720 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 779

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   780 YTGDKESRSVIRENEFSFEDNAIRSGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 838

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   839 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 876

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|1582725 Chd5 "chromodomain helicase DNA binding protein 5" [Rattus norvegicus (taxid:10116)]

 Score = 219 (82.2 bits), Expect = 2.3e-16, P = 2.3e-16
 Identities = 51/158 (32%), Positives = 82/158 (51%)

Query:     2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVK 60
             DT++ D     K+ + I F   + +E  +  P L+  PLS + NWE EF  +AP    V 
Sbjct:   718 DTILADEMGLGKTVQTIVFLYSLYKEGHSKGPYLVSAPLSTIINWEREFEMWAPDFYVVT 777

Query:    61 YYGNAIERKALQSEALSLP--TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK 118
             Y G+   R  ++    S     I+   K  + KK++ +K   +L+T+ ++I  D   L  
Sbjct:   778 YTGDKESRSVIRENEFSFEDNAIRGGKKVFRMKKEVQIKFH-VLLTSYELITIDQAILGS 836

Query:   119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
             I W C++VDE H +KN +SK    L + +  +K+LLTG
Sbjct:   837 IEWACLVVDEAHRLKNNQSKFFRVLNSYKIDYKLLLTG 874

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

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

---

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	169
pfam00176	301	pfam00176, SNF2_N, SNF2 family N-terminal domain	1e-22
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	9e-19
COG0553	866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	2e-17
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-10
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	5e-08
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	1e-04

>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain

 Score = 91.3 bits (227), Expect = 1e-22
 Identities = 49/150 (32%), Positives = 73/150 (48%), Gaps = 25/150 (16%)

Query: 15  GK---VIAFFCKIIEEQALE--PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERK 69
           GK    IA     ++E      P L+VCPLS L+NW  EF K+AP +R V Y+G+  ER 
Sbjct: 28  GKTLQTIALLATYLKEGKDRRGPTLVVCPLSTLHNWLNEFEKWAPALRVVVYHGDGRERS 87

Query: 70  ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF---GFLKKITWNCIIV 126
            L+         K                  +++TT +++  D      L K+ W+ +++
Sbjct: 88  KLRQS-----MAKRLDTYD------------VVITTYEVLRKDKKLLSLLNKVEWDRVVL 130

Query: 127 DEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
           DE H +KN KSKL   L  L+   ++LLTG
Sbjct: 131 DEAHRLKNSKSKLYKALKKLKTRNRLLLTG 160

This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA recombination (e.g. RAD54), and chromatin unwinding (e.g. ISWI) as well as a variety of other proteins with little functional information (e.g. lodestar, ETL1). Length = 301

>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 82.2 bits (203), Expect = 9e-19
 Identities = 40/125 (32%), Positives = 63/125 (50%), Gaps = 18/125 (14%)

Query: 32  PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTK 91
           P+++V P S L NW  E R+F P +R VK++GN  ER   + E L      V  K     
Sbjct: 221 PHMVVAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELL------VAGKFD--- 271

Query: 92  KQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFK 151
                    + VT+ ++   +   LK+ +W  II+DE H +KN+ S LS  +      ++
Sbjct: 272 ---------VCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYR 322

Query: 152 VLLTG 156
           +L+TG
Sbjct: 323 LLITG 327

Length = 1033

>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

 Score = 78.2 bits (192), Expect = 2e-17
 Identities = 47/145 (32%), Positives = 71/145 (48%), Gaps = 16/145 (11%)

Query: 17  VIAFFCKIIE--EQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTV-KYYGNAIERKALQS 73
            IA    ++E  +  L P LIV P S+L+NW+ EF KFAP +R V  Y+G          
Sbjct: 375 TIALLLSLLESIKVYLGPALIVVPASLLSNWKREFEKFAPDLRLVLVYHGEK-------- 426

Query: 74  EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN--DFGFLKKITWNCIIVDEGHS 131
              S    K  A +   K  + +   +++ T   +     D G LKKI W+ +++DE H 
Sbjct: 427 ---SELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHR 483

Query: 132 VKNKKSKLSIKLTALRATFKVLLTG 156
           +KN +S     L  L+A  ++ LTG
Sbjct: 484 IKNDQSSEGKALQFLKALNRLDLTG 508

Length = 866

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

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 37/164 (22%), Positives = 62/164 (37%), Gaps = 33/164 (20%)

Query: 1   MDTVIPDPTRYRKSGK---VIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAPF- 55
            D ++  PT    SGK    +    + ++       L++ P   L   W  E +K  P  
Sbjct: 25  RDVILAAPT---GSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL 81

Query: 56  -VRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF- 113
            ++ V  YG   +R+ L+             + GKT          ILVTTP  + +   
Sbjct: 82  GLKVVGLYGGDSKREQLRKL-----------ESGKTD---------ILVTTPGRLLDLLE 121

Query: 114 -GFLKKITWNCIIVDEGHSVKNK--KSKLSIKLTALRATFKVLL 154
              L     + +I+DE H + +     +L   L  L    ++LL
Sbjct: 122 NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165

Length = 201

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

 Score = 49.3 bits (118), Expect = 5e-08
 Identities = 30/141 (21%), Positives = 47/141 (33%), Gaps = 26/141 (18%)

Query: 14  SGKVIAFFCKIIEEQALEPN---LIVCPLSVLNNWEAE-FRKFAPFVRTVKYYGNAIERK 69
           SGK +A    I+E          L++ P   L N  AE  ++       V Y        
Sbjct: 11  SGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGT--- 67

Query: 70  ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVD 127
                     +IK   K    K  I       +V TP  + ++     L     + +I+D
Sbjct: 68  ----------SIKQQEKLLSGKTDI-------VVGTPGRLLDELERLKLSLKKLDLLILD 110

Query: 128 EGHSVKNKKSKLSIKLTALRA 148
           E H + N+   L      L+ 
Sbjct: 111 EAHRLLNQGFGLLGLKILLKL 131

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

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

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 51/160 (31%), Positives = 68/160 (42%), Gaps = 40/160 (25%)

Query: 14  SGKVIAFFCKII-------EEQALEPNLIVC----PLSVLNNWEAEFRK--FAPFVRTVK 60
           SGK +A F  II        E  LE + + C    PL  LNN   +  +    P      
Sbjct: 58  SGKTLAAFLAIIDELFRLGREGELE-DKVYCLYVSPLRALNN---DIHRNLEEPL----- 108

Query: 61  YYGNAIERKALQSEALSLPTIKVPAKKGKT---KKQISL-KLPLILVTTPQ---IIENDF 113
                I   A +     LP I+V  + G T   +KQ  L K P IL+TTP+   I+ N  
Sbjct: 109 ---TEIREIA-KERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSP 164

Query: 114 GF---LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALRA 148
            F   L+ + W  +IVDE HS+   K    LS+ L  L  
Sbjct: 165 KFREKLRTVKW--VIVDEIHSLAENKRGVHLSLSLERLEE 202

Length = 876

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	169
KOG0385|consensus	971		100.0
KOG0389|consensus	941		100.0
KOG0387|consensus	923		100.0
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG0391|consensus	1958		100.0
KOG0392|consensus	1549		100.0
KOG0388|consensus	1185		100.0
KOG0384|consensus	1373		100.0
KOG0386|consensus	1157		100.0
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	100.0
KOG0390|consensus	776		100.0
KOG1002|consensus	791		100.0
KOG4439|consensus	901		100.0
PRK04914	956	ATP-dependent helicase HepA; Validated	99.97
KOG1015|consensus	1567		99.96
KOG1000|consensus	689		99.95
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.95
KOG1016|consensus	1387		99.94
KOG1001|consensus	674		99.92
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.91
KOG0383|consensus	696		99.89
KOG0298|consensus	1394		99.88
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.84
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.8
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.77
PRK13766	773	Hef nuclease; Provisional	99.77
PHA02558	501	uvsW UvsW helicase; Provisional	99.75
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.75
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.72
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.67
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.65
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.65
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.64
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.63
KOG1123|consensus	776		99.61
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.59
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.57
COG4096	875	HsdR Type I site-specific restriction-modification	99.57
KOG0354|consensus	746		99.57
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.52
PRK10689	1147	transcription-repair coupling factor; Provisional	99.51
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.48
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.47
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.47
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.44
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.42
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.42
PTZ00424	401	helicase 45; Provisional	99.4
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.4
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.39
PRK02362	737	ski2-like helicase; Provisional	99.38
PRK00254	720	ski2-like helicase; Provisional	99.38
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.37
PTZ00110	545	helicase; Provisional	99.36
COG4889	1518	Predicted helicase [General function prediction on	99.36
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.36
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.36
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.36
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.35
COG1204	766	Superfamily II helicase [General function predicti	99.35
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.35
PRK09401	1176	reverse gyrase; Reviewed	99.32
PRK01172	674	ski2-like helicase; Provisional	99.32
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.3
PRK05580	679	primosome assembly protein PriA; Validated	99.29
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.26
PRK13767	876	ATP-dependent helicase; Provisional	99.23
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.21
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.19
COG1205	851	Distinct helicase family with a unique C-terminal	99.17
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.1
COG0610	962	Type I site-specific restriction-modification syst	99.09
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.08
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	99.07
KOG0330|consensus	476		99.04
PRK15483	986	type III restriction-modification system StyLTI en	99.02
KOG0331|consensus	519		98.98
PRK14701	1638	reverse gyrase; Provisional	98.95
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.92
PRK09694	878	helicase Cas3; Provisional	98.89
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.89
PHA02653	675	RNA helicase NPH-II; Provisional	98.88
KOG0952|consensus	1230		98.85
KOG0350|consensus	620		98.82
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.82
COG1201	814	Lhr Lhr-like helicases [General function predictio	98.81
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.8
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.75
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.75
KOG0338|consensus	691		98.73
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.68
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.66
KOG0345|consensus	567		98.64
KOG0335|consensus	482		98.62
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.6
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.59
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.56
KOG0342|consensus	543		98.47
PRK14873	665	primosome assembly protein PriA; Provisional	98.47
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.46
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.45
KOG0347|consensus	731		98.41
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.39
KOG0343|consensus	758		98.38
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.37
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.37
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.36
KOG0348|consensus	708		98.35
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.35
KOG4284|consensus	980		98.33
COG1202	830	Superfamily II helicase, archaea-specific [General	98.33
KOG0353|consensus	695		98.32
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.28
PRK10536	262	hypothetical protein; Provisional	98.24
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.23
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.22
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.22
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.19
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.19
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.17
KOG1802|consensus	935		98.15
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.15
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.15
KOG0346|consensus	569		98.14
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.14
KOG1803|consensus	649		98.13
KOG0951|consensus	1674		98.02
KOG0339|consensus	731		98.02
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.98
PRK13107	908	preprotein translocase subunit SecA; Reviewed	97.94
PRK04296	190	thymidine kinase; Provisional	97.93
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.91
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.9
KOG0352|consensus	641		97.85
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.84
KOG0328|consensus	400		97.8
KOG0949|consensus	1330		97.79
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.75
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.73
KOG0337|consensus	529		97.73
KOG1513|consensus	1300		97.71
KOG0340|consensus	442		97.71
KOG0947|consensus	1248		97.71
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.68
KOG0341|consensus	610		97.67
KOG1805|consensus	1100		97.59
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.58
KOG1131|consensus	755		97.56
KOG0922|consensus	674		97.55
KOG0336|consensus	629		97.54
KOG0329|consensus	387		97.53
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.52
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	97.49
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.47
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.46
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.46
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.46
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.43
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.29
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.27
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	97.27
smart00382	148	AAA ATPases associated with a variety of cellular	97.23
KOG0926|consensus	1172		97.22
PF13245	76	AAA_19: Part of AAA domain	97.18
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.16
KOG0351|consensus	941		97.14
KOG0948|consensus	1041		97.14
KOG0920|consensus	924		97.12
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.09
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.05
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.04
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.02
KOG0334|consensus	997		97.02
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.0
PRK06526	254	transposase; Provisional	96.98
KOG0344|consensus	593		96.96
KOG0333|consensus	673		96.95
KOG0332|consensus	477		96.94
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.91
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.88
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.85
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.8
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	96.8
KOG0951|consensus	1674		96.79
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.79
KOG0326|consensus	459		96.74
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.74
KOG1132|consensus	945		96.74
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	96.62
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.58
PRK08116	268	hypothetical protein; Validated	96.54
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.54
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.47
PRK14974	336	cell division protein FtsY; Provisional	96.44
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.44
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.4
PRK08727	233	hypothetical protein; Validated	96.36
KOG0924|consensus	1042		96.35
PLN03025	319	replication factor C subunit; Provisional	96.3
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.3
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.2
PRK11823	446	DNA repair protein RadA; Provisional	96.17
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.16
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.15
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.06
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.04
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.03
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.03
KOG0327|consensus	397		95.93
PTZ00293	211	thymidine kinase; Provisional	95.92
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	95.9
KOG0925|consensus	699		95.87
KOG0989|consensus	346		95.83
CHL00181	287	cbbX CbbX; Provisional	95.81
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.78
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	95.73
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.71
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	95.65
PRK12402	337	replication factor C small subunit 2; Reviewed	95.64
PRK08084	235	DNA replication initiation factor; Provisional	95.61
PRK12422	445	chromosomal replication initiation protein; Provis	95.61
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.6
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	95.58
PRK08181	269	transposase; Validated	95.57
KOG0923|consensus	902		95.56
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.55
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.55
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.54
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	95.54
PHA03372	668	DNA packaging terminase subunit 1; Provisional	95.48
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.45
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	95.37
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	95.37
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	95.34
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.3
KOG0952|consensus	1230		95.27
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.23
PF07015	231	VirC1: VirC1 protein; InterPro: IPR009744 This fam	95.22
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.21
COG3972	660	Superfamily I DNA and RNA helicases [General funct	95.2
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.19
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.14
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.11
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	95.01
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	94.99
KOG0780|consensus	483		94.92
PTZ00112	1164	origin recognition complex 1 protein; Provisional	94.9
PRK05642	234	DNA replication initiation factor; Validated	94.9
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	94.88
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	94.88
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.86
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	94.84
PHA03333	752	putative ATPase subunit of terminase; Provisional	94.81
PRK07940	394	DNA polymerase III subunit delta'; Validated	94.81
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.65
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	94.64
PRK06893	229	DNA replication initiation factor; Validated	94.6
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	94.57
KOG0950|consensus	1008		94.54
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.5
PHA02544	316	44 clamp loader, small subunit; Provisional	94.4
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.36
PRK05707	328	DNA polymerase III subunit delta'; Validated	94.33
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.24
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.21
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	94.2
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.18
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	94.11
KOG0991|consensus	333		94.11
PHA00012	361	I assembly protein	94.02
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	94.01
PRK05973	237	replicative DNA helicase; Provisional	94.0
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	94.0
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	93.97
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	93.97
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.96
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	93.94
PRK04195	482	replication factor C large subunit; Provisional	93.93
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.9
PRK10867	433	signal recognition particle protein; Provisional	93.78
PRK08058	329	DNA polymerase III subunit delta'; Validated	93.77
PHA02533	534	17 large terminase protein; Provisional	93.75
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	93.73
PRK00771	437	signal recognition particle protein Srp54; Provisi	93.72
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	93.71
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	93.69
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.66
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.62
PRK13889	988	conjugal transfer relaxase TraA; Provisional	93.47
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	93.44
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.43
CHL00095	821	clpC Clp protease ATP binding subunit	93.39
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	93.38
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	93.38
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.36
PRK00440	319	rfc replication factor C small subunit; Reviewed	93.35
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.33
PRK07952	244	DNA replication protein DnaC; Validated	93.29
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	93.27
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	93.26
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	93.19
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	93.09
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.05
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	93.0
PRK10416	318	signal recognition particle-docking protein FtsY;	92.96
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	92.9
COG2894	272	MinD Septum formation inhibitor-activating ATPase	92.88
PRK07471	365	DNA polymerase III subunit delta'; Validated	92.82
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	92.78
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	92.75
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	92.72
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	92.71
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	92.7
PRK08506	472	replicative DNA helicase; Provisional	92.57
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	92.43
PRK05298	652	excinuclease ABC subunit B; Provisional	92.4
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	92.25
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	92.24
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	92.17
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	92.16
PRK13826	1102	Dtr system oriT relaxase; Provisional	92.05
PHA00350	399	putative assembly protein	92.03
PRK13342	413	recombination factor protein RarA; Reviewed	92.01
PRK06067	234	flagellar accessory protein FlaH; Validated	91.99
PRK10865	857	protein disaggregation chaperone; Provisional	91.99
PRK12377	248	putative replication protein; Provisional	91.98
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	91.87
TIGR00064	272	ftsY signal recognition particle-docking protein F	91.85
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	91.83
PRK08760	476	replicative DNA helicase; Provisional	91.78
PRK04132	846	replication factor C small subunit; Provisional	91.77
KOG0739|consensus	439		91.69
PRK04328	249	hypothetical protein; Provisional	91.64
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	91.6
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	91.58
PHA00673	154	acetyltransferase domain containing protein	91.51
cd02034	116	CooC The accessory protein CooC, which contains a	91.47
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.43
PRK09376	416	rho transcription termination factor Rho; Provisio	91.42
COG3973	747	Superfamily I DNA and RNA helicases [General funct	91.39
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	91.37
PRK06871	325	DNA polymerase III subunit delta'; Validated	91.19
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	91.12
COG3265	161	GntK Gluconate kinase [Carbohydrate transport and	91.08
TIGR00347	166	bioD dethiobiotin synthase. Dethiobiotin synthase	91.07
PF12846	304	AAA_10: AAA-like domain	91.03
cd02037	169	MRP-like MRP (Multiple Resistance and pH adaptatio	90.96
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	90.94
TIGR01281	268	DPOR_bchL light-independent protochlorophyllide re	90.81
PRK08939	306	primosomal protein DnaI; Reviewed	90.77
PRK13235	274	nifH nitrogenase reductase; Reviewed	90.77
TIGR00682	311	lpxK tetraacyldisaccharide 4'-kinase. Also called	90.65
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	90.65
PF02606	326	LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPr	90.64
PRK13230	279	nitrogenase reductase-like protein; Reviewed	90.58
PRK05636	505	replicative DNA helicase; Provisional	90.53
PRK07993	334	DNA polymerase III subunit delta'; Validated	90.5
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	90.41
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	90.32
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	90.29
PRK10037	250	cell division protein; Provisional	90.29
PRK06921	266	hypothetical protein; Provisional	89.95
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	89.92
PRK13185	270	chlL protochlorophyllide reductase iron-sulfur ATP	89.87
PHA02518	211	ParA-like protein; Provisional	89.84
PRK06835	329	DNA replication protein DnaC; Validated	89.81
PRK07004	460	replicative DNA helicase; Provisional	89.73
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	89.53
cd02117	212	NifH_like This family contains the NifH (iron prot	89.51
TIGR00767	415	rho transcription termination factor Rho. Members	89.4
cd00983	325	recA RecA is a bacterial enzyme which has roles in	89.39
CHL00072	290	chlL photochlorophyllide reductase subunit L	89.39
PRK06321	472	replicative DNA helicase; Provisional	89.38
cd02032	267	Bchl_like This family of proteins contains bchL an	89.36
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	89.36
PRK09165	497	replicative DNA helicase; Provisional	89.11
PRK13849	231	putative crown gall tumor protein VirC1; Provision	89.02
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	88.98
cd02040	270	NifH NifH gene encodes component II (iron protein)	88.93
TIGR00665	434	DnaB replicative DNA helicase. This model describe	88.9
KOG1133|consensus	821		88.88
PF13500	199	AAA_26: AAA domain; PDB: 3OF5_A 2IOJ_A 4A0G_B 4A0R	88.81
TIGR01287	275	nifH nitrogenase iron protein. This model describe	88.76
PRK05748	448	replicative DNA helicase; Provisional	88.73
KOG1807|consensus	1025		88.72
KOG0738|consensus	491		88.68
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	88.68
PF13173	128	AAA_14: AAA domain	88.62
PRK00652	325	lpxK tetraacyldisaccharide 4'-kinase; Reviewed	88.61
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	88.58
COG2205	890	KdpD Osmosensitive K+ channel histidine kinase [Si	88.57
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	88.57
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	88.57
PRK10263	1355	DNA translocase FtsK; Provisional	88.51
PRK13232	273	nifH nitrogenase reductase; Reviewed	88.5
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	88.49
PF05729	166	NACHT: NACHT domain	88.33
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	88.24
PRK13833	323	conjugal transfer protein TrbB; Provisional	88.19
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	88.05
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	88.0
TIGR01969	251	minD_arch cell division ATPase MinD, archaeal. Thi	87.92
PRK13236	296	nitrogenase reductase; Reviewed	87.89
PF01656	195	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domai	87.88
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	87.78
PRK09354	349	recA recombinase A; Provisional	87.67
PRK09302	509	circadian clock protein KaiC; Reviewed	87.54
PRK06090	319	DNA polymerase III subunit delta'; Validated	87.28
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	87.21
PRK08769	319	DNA polymerase III subunit delta'; Validated	87.13
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	87.1
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	87.0
cd01394	218	radB RadB. The archaeal protein radB shares simila	86.93
PF00265	176	TK: Thymidine kinase; InterPro: IPR001267 Thymidin	86.77
COG1192	259	Soj ATPases involved in chromosome partitioning [C	86.73
PRK10689	1147	transcription-repair coupling factor; Provisional	86.61
PHA02542	473	41 41 helicase; Provisional	86.59
KOG2825|consensus	323		86.54
PRK13695	174	putative NTPase; Provisional	86.51
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	86.44
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	86.29
PHA02519	387	plasmid partition protein SopA; Reviewed	86.23
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	85.96
PRK13234	295	nifH nitrogenase reductase; Reviewed	85.82
PRK13233	275	nifH nitrogenase reductase; Reviewed	85.79
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	85.78
PRK10818	270	cell division inhibitor MinD; Provisional	85.72
PRK09302	509	circadian clock protein KaiC; Reviewed	85.7
TIGR02016	296	BchX chlorophyllide reductase iron protein subunit	85.68
PRK13705	388	plasmid-partitioning protein SopA; Provisional	85.6
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	85.53
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	85.44
PRK13869	405	plasmid-partitioning protein RepA; Provisional	85.37
cd01128	249	rho_factor Transcription termination factor rho is	85.34
PRK06964	342	DNA polymerase III subunit delta'; Validated	85.27
PRK00090	222	bioD dithiobiotin synthetase; Reviewed	85.22
TIGR02237	209	recomb_radB DNA repair and recombination protein R	85.2
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	85.19
PRK11054	684	helD DNA helicase IV; Provisional	85.11
PRK09435	332	membrane ATPase/protein kinase; Provisional	85.1
cd02036	179	MinD Bacterial cell division requires the formatio	85.1
TIGR01007	204	eps_fam capsular exopolysaccharide family. This mo	84.92
PRK01906	338	tetraacyldisaccharide 4'-kinase; Provisional	84.86
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	84.62
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	84.43
TIGR03371	246	cellulose_yhjQ cellulose synthase operon protein Y	84.41
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	84.33
TIGR01968	261	minD_bact septum site-determining protein MinD. Th	83.58
KOG2028|consensus	554		83.23
PF02702	211	KdpD: Osmosensitive K+ channel His kinase sensor d	83.18
PRK09183	259	transposase/IS protein; Provisional	83.03
PRK07773	886	replicative DNA helicase; Validated	82.96
PRK06904	472	replicative DNA helicase; Validated	82.89
PRK08903	227	DnaA regulatory inactivator Hda; Validated	82.89
cd02035	217	ArsA ArsA ATPase functionas as an efflux pump loca	82.85
COG1880	170	CdhB CO dehydrogenase/acetyl-CoA synthase epsilon	82.85
PF07726	131	AAA_3: ATPase family associated with various cellu	82.83
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	82.79
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	82.75
PRK05564	313	DNA polymerase III subunit delta'; Validated	82.75
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	82.7
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	82.57
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	82.47
TIGR00959	428	ffh signal recognition particle protein. This mode	82.45
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	82.38
cd00550	254	ArsA_ATPase Oxyanion-translocating ATPase (ArsA).	82.35
cd02042	104	ParA ParA and ParB of Caulobacter crescentus belon	82.3
KOG2543|consensus	438		82.11
PRK05595	444	replicative DNA helicase; Provisional	81.8
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	81.78
PRK13768	253	GTPase; Provisional	81.66
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	81.63
CHL00175	281	minD septum-site determining protein; Validated	81.14
PRK03992	389	proteasome-activating nucleotidase; Provisional	80.83
PTZ00301	210	uridine kinase; Provisional	80.53
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	80.47
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	80.29
cd03109	134	DTBS Dethiobiotin synthetase (DTBS) is the penulti	80.03

>KOG0385|consensus

Probab=100.00  E-value=1.7e-45  Score=286.24  Aligned_cols=151  Identities=30%  Similarity=0.514  Sum_probs=142.8

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      .|||||||||+|||+++|+++.++... +..+|.||+||.+++++|..||.+|+|+++++.|+|++.+|.......... 
T Consensus       187 ingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL~NW~~Ef~rf~P~l~~~~~~Gdk~eR~~~~r~~~~~-  265 (971)
T KOG0385|consen  187 INGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTLDNWMNEFKRFTPSLNVVVYHGDKEERAALRRDIMLP-  265 (971)
T ss_pred             cccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHHHhhcc-
Confidence            479999999999999999999999884 668999999999999999999999999999999999999998888766542 


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                                      +.+++ ++|||+.+.++...+.+++|.++|+||||++||.+|+.++.++.+++.+|+++||||+
T Consensus       266 ----------------~~fdV-~iTsYEi~i~dk~~lk~~~W~ylvIDEaHRiKN~~s~L~~~lr~f~~~nrLLlTGTPL  328 (971)
T KOG0385|consen  266 ----------------GRFDV-CITSYEIAIKDKSFLKKFNWRYLVIDEAHRIKNEKSKLSKILREFKTDNRLLLTGTPL  328 (971)
T ss_pred             ----------------CCCce-EeehHHHHHhhHHHHhcCCceEEEechhhhhcchhhHHHHHHHHhcccceeEeeCCcc
Confidence                            68888 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhhccC
Q psy1090         160 PNKWSKQCTL  169 (169)
Q Consensus       160 ~n~~~el~~l  169 (169)
                      ||++.|||+|
T Consensus       329 QNNL~ELWaL  338 (971)
T KOG0385|consen  329 QNNLHELWAL  338 (971)
T ss_pred             cccHHHHHHH
Confidence            9999999986

>KOG0389|consensus

Probab=100.00  E-value=5.8e-45  Score=283.90  Aligned_cols=152  Identities=32%  Similarity=0.512  Sum_probs=140.5

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      |+||||||||+|||.++|+|++++.+.+..+|.|||||++++.+|.+||++|||.+++..|+|++.+|..++.....-  
T Consensus       419 l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsSTleNWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~--  496 (941)
T KOG0389|consen  419 LNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSSTLENWLREFAKWCPSLKVEPYYGSQDERRELRERIKKN--  496 (941)
T ss_pred             ccceehhhccCcchhHHHHHHHHHHHcCCCCCcEEEecchhHHHHHHHHHHhCCceEEEeccCcHHHHHHHHHHHhcc--
Confidence            679999999999999999999999999999999999999999999999999999999999999999998877654321  


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHh---chhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEecc
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIEN---DFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGW  157 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~---~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~T  157 (169)
                                    ...+|+ ++|||+.+..   +..++++.+|+++|+||+|.+||..+.+++.+..+++++|++||||
T Consensus       497 --------------~~~ydV-llTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~LM~I~An~RlLLTGT  561 (941)
T KOG0389|consen  497 --------------KDDYDV-LLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHLMSINANFRLLLTGT  561 (941)
T ss_pred             --------------CCCccE-EEEEeecccCChHHHHHHHhccccEEEecchhhhhccchHHHHHhccccccceEEeeCC
Confidence                          157888 9999999864   5568889999999999999999999999999999999999999999


Q ss_pred             CCCCCchhhccC
Q psy1090         158 YYPNKWSKQCTL  169 (169)
Q Consensus       158 P~~n~~~el~~l  169 (169)
                      |+||++.||++|
T Consensus       562 PLQNNL~ELiSL  573 (941)
T KOG0389|consen  562 PLQNNLKELISL  573 (941)
T ss_pred             cccccHHHHHHH
Confidence            999999999986

>KOG0387|consensus

Probab=100.00  E-value=2.4e-41  Score=263.91  Aligned_cols=158  Identities=25%  Similarity=0.449  Sum_probs=132.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHH-HHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERK-ALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~-~~~~~~~~~~   79 (169)
                      ||||+||||+|||++.|+|+..+... ...+|+|||||.+++.||..||++|.|.+++.++++...... ......    
T Consensus       226 GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~Tii~qW~~E~~~w~p~~rv~ilh~t~s~~r~~~~~~~----  301 (923)
T KOG0387|consen  226 GGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPATIIHQWMKEFQTWWPPFRVFILHGTGSGARYDASHSS----  301 (923)
T ss_pred             CCeecccccCccchhHHHHHHHHhhcccccCceEEEccHHHHHHHHHHHHHhCcceEEEEEecCCcccccccchhh----
Confidence            89999999999999999999999988 667899999999999999999999999999999998765311 000000    


Q ss_pred             CcccccccCCc-cccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccC
Q psy1090          80 TIKVPAKKGKT-KKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWY  158 (169)
Q Consensus        80 ~~~~~~~~~~~-~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP  158 (169)
                           .+.... ..-......+ ++|||+.++...+.+....|+++|+||+|+++|++++.+.+++.+++.+|++|||||
T Consensus       302 -----~~~~~~L~r~~~~~~~i-litty~~~r~~~d~l~~~~W~y~ILDEGH~IrNpns~islackki~T~~RiILSGTP  375 (923)
T KOG0387|consen  302 -----HKKDKLLIRKVATDGGI-LITTYDGFRIQGDDLLGILWDYVILDEGHRIRNPNSKISLACKKIRTVHRIILSGTP  375 (923)
T ss_pred             -----hhhhhhheeeecccCcE-EEEehhhhcccCcccccccccEEEecCcccccCCccHHHHHHHhccccceEEeeCcc
Confidence                 000000 0000133445 999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCchhhccC
Q psy1090         159 YPNKWSKQCTL  169 (169)
Q Consensus       159 ~~n~~~el~~l  169 (169)
                      +||++.|||+|
T Consensus       376 iQNnL~ELwsL  386 (923)
T KOG0387|consen  376 IQNNLTELWSL  386 (923)
T ss_pred             ccchHHHHHHH
Confidence            99999999986

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=100.00  E-value=2.2e-40  Score=271.69  Aligned_cols=151  Identities=30%  Similarity=0.503  Sum_probs=136.5

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      .|||||||||+|||+++++++.++... +..+|+|||||.+++.||.+|+.+|+|.++++.++|....+.........  
T Consensus       189 ~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~SlL~nW~~Ei~kw~p~l~v~~~~G~~~eR~~~~~~~~~--  266 (1033)
T PLN03142        189 INGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELLV--  266 (1033)
T ss_pred             CCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeChHHHHHHHHHHHHHCCCCceEEEeCCHHHHHHHHHHHhc--
Confidence            479999999999999999999887654 55689999999999999999999999999999999998887665544332  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                                     ...+++ +++||+.+.++...+..+.|++||+||||++||+.++.+++++.+++++||+|||||+
T Consensus       267 ---------------~~~~dV-vITSYe~l~~e~~~L~k~~W~~VIvDEAHrIKN~~Sklskalr~L~a~~RLLLTGTPl  330 (1033)
T PLN03142        267 ---------------AGKFDV-CVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPL  330 (1033)
T ss_pred             ---------------ccCCCc-ceecHHHHHHHHHHhccCCCCEEEEcCccccCCHHHHHHHHHHHhhcCcEEEEecCCC
Confidence                           156778 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhhccC
Q psy1090         160 PNKWSKQCTL  169 (169)
Q Consensus       160 ~n~~~el~~l  169 (169)
                      +|++.|||+|
T Consensus       331 qNnl~ELwsL  340 (1033)
T PLN03142        331 QNNLHELWAL  340 (1033)
T ss_pred             CCCHHHHHHH
Confidence            9999999985

>KOG0391|consensus

Probab=100.00  E-value=7e-41  Score=268.97  Aligned_cols=151  Identities=26%  Similarity=0.449  Sum_probs=142.2

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      ++||||||||+|||+++|++++++..+ ++++|.|||+|.+++-+|.-||++|+|+++++-|+|+.++++..+..|..  
T Consensus       635 lNGILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviLnWEMElKRwcPglKILTYyGs~kErkeKRqgW~k--  712 (1958)
T KOG0391|consen  635 LNGILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVILNWEMELKRWCPGLKILTYYGSHKERKEKRQGWAK--  712 (1958)
T ss_pred             ccceehhhhcccchhHHHHHHHHHHhcccCCCCceEEeechhhhhhhHHHhhhCCcceEeeecCCHHHHHHHhhcccC--
Confidence            589999999999999999999988866 77899999999999999999999999999999999999999988887753  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                                     ...|.+ +|+||..+..+...|.+..|.++|+||+|++||..+++++++.++++.+|++|||||+
T Consensus       713 ---------------PnaFHV-CItSYklv~qd~~AFkrkrWqyLvLDEaqnIKnfksqrWQAllnfnsqrRLLLtgTPL  776 (1958)
T KOG0391|consen  713 ---------------PNAFHV-CITSYKLVFQDLTAFKRKRWQYLVLDEAQNIKNFKSQRWQALLNFNSQRRLLLTGTPL  776 (1958)
T ss_pred             ---------------CCeeEE-eehhhHHHHhHHHHHHhhccceeehhhhhhhcchhHHHHHHHhccchhheeeecCCch
Confidence                           256666 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhhccC
Q psy1090         160 PNKWSKQCTL  169 (169)
Q Consensus       160 ~n~~~el~~l  169 (169)
                      +|++.|||+|
T Consensus       777 qNslmELWSL  786 (1958)
T KOG0391|consen  777 QNSLMELWSL  786 (1958)
T ss_pred             hhHHHHHHHH
Confidence            9999999986

>KOG0392|consensus

Probab=100.00  E-value=1.3e-38  Score=257.11  Aligned_cols=148  Identities=30%  Similarity=0.576  Sum_probs=136.3

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhC-------CCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHH
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQ-------ALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~-------~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~   73 (169)
                      +.|||+|+||+|||++++++++.-....       ...|.|||||+++..+|..|+.+|+|.+++..|.|....|...+.
T Consensus       995 LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPsTLtGHW~~E~~kf~pfL~v~~yvg~p~~r~~lR~ 1074 (1549)
T KOG0392|consen  995 LHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPSTLTGHWKSEVKKFFPFLKVLQYVGPPAERRELRD 1074 (1549)
T ss_pred             ccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCchhhhHHHHHHHHhcchhhhhhhcCChHHHHHHHh
Confidence            4699999999999999999988655444       345899999999999999999999999999999999999988876


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEE
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVL  153 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~  153 (169)
                      ..                    .+.++ ++++|+.++++.+.+.+..|.++|+||.|.+||..++.+++++.+++.+|++
T Consensus      1075 q~--------------------~~~~i-iVtSYDv~RnD~d~l~~~~wNYcVLDEGHVikN~ktkl~kavkqL~a~hRLI 1133 (1549)
T KOG0392|consen 1075 QY--------------------KNANI-IVTSYDVVRNDVDYLIKIDWNYCVLDEGHVIKNSKTKLTKAVKQLRANHRLI 1133 (1549)
T ss_pred             hc--------------------cccce-EEeeHHHHHHHHHHHHhcccceEEecCcceecchHHHHHHHHHHHhhcceEE
Confidence            54                    55667 9999999999999999999999999999999999999999999999999999


Q ss_pred             EeccCCCCCchhhccC
Q psy1090         154 LTGWYYPNKWSKQCTL  169 (169)
Q Consensus       154 lT~TP~~n~~~el~~l  169 (169)
                      |||||+||++.|||+|
T Consensus      1134 LSGTPIQNnvleLWSL 1149 (1549)
T KOG0392|consen 1134 LSGTPIQNNVLELWSL 1149 (1549)
T ss_pred             eeCCCcccCHHHHHHH
Confidence            9999999999999986

>KOG0388|consensus

Probab=100.00  E-value=6.8e-39  Score=248.40  Aligned_cols=157  Identities=25%  Similarity=0.432  Sum_probs=143.7

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      ++||||||||+|||+++|++++++.+. +.++|.|||+|.+++++|.+|+.+|+|.++++.|-|+..+|..+++.+....
T Consensus       587 iNGILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaStL~NWaqEisrFlP~~k~lpywGs~~eRkiLrKfw~rKn  666 (1185)
T KOG0388|consen  587 INGILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPASTLHNWAQEISRFLPSFKVLPYWGSPSERKILRKFWNRKN  666 (1185)
T ss_pred             ccceehhhhccchhHHHHHHHHHHHHhccCCCceEEeehHHHHhHHHHHHHHhCccceeecCcCChhhhHHHHHhcchhh
Confidence            479999999999999999999999887 6688999999999999999999999999999999999999998887664321


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                                 .+.....+++ ++|||+.+..+...+..++|.+.|+||||.+|++.+.+++.+..++|+.|++|||||+
T Consensus       667 -----------mY~rna~fhV-viTSYQlvVtDeky~qkvKWQYMILDEAQAIKSSsS~RWKtLLsF~cRNRLLLTGTPI  734 (1185)
T KOG0388|consen  667 -----------MYRRNAPFHV-VITSYQLVVTDEKYLQKVKWQYMILDEAQAIKSSSSSRWKTLLSFKCRNRLLLTGTPI  734 (1185)
T ss_pred             -----------hhccCCCceE-EEEeeeeeechHHHHHhhhhhheehhHHHHhhhhhhhHHHHHhhhhccceeeecCCcc
Confidence                       1333467788 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhhccC
Q psy1090         160 PNKWSKQCTL  169 (169)
Q Consensus       160 ~n~~~el~~l  169 (169)
                      ||+..|||.|
T Consensus       735 QNsMqELWAL  744 (1185)
T KOG0388|consen  735 QNSMQELWAL  744 (1185)
T ss_pred             chHHHHHHHH
Confidence            9999999975

>KOG0384|consensus

Probab=100.00  E-value=3.5e-38  Score=254.80  Aligned_cols=155  Identities=28%  Similarity=0.462  Sum_probs=143.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC-CCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ-ALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~-~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +||||||||+|||++.++++.+++... ..+|+|||+|.+++.+|.+||..|. ++++++|+|+...|..++...+....
T Consensus       391 n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst~~~W~~ef~~w~-~mn~i~y~g~~~sr~~i~~ye~~~~~  469 (1373)
T KOG0384|consen  391 NCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITAWEREFETWT-DMNVIVYHGNLESRQLIRQYEFYHSS  469 (1373)
T ss_pred             cceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhhhHHHHHHHHHHh-hhceeeeecchhHHHHHHHHHheecC
Confidence            699999999999999999999999886 6789999999999999999999999 99999999999999999988876542


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCC
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                      .           .+.-++++ +||||+.+..+...+..++|.++++||||++||..++.+..+..++..+|+++||||+|
T Consensus       470 ~-----------~~~lkf~~-lltTye~~LkDk~~L~~i~w~~~~vDeahrLkN~~~~l~~~l~~f~~~~rllitgTPlQ  537 (1373)
T KOG0384|consen  470 N-----------TKKLKFNA-LLTTYEIVLKDKAELSKIPWRYLLVDEAHRLKNDESKLYESLNQFKMNHRLLITGTPLQ  537 (1373)
T ss_pred             C-----------ccccccce-eehhhHHHhccHhhhccCCcceeeecHHhhcCchHHHHHHHHHHhcccceeeecCCCcc
Confidence            1           11246888 99999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhhccC
Q psy1090         161 NKWSKQCTL  169 (169)
Q Consensus       161 n~~~el~~l  169 (169)
                      |++.|||+|
T Consensus       538 NsikEL~sL  546 (1373)
T KOG0384|consen  538 NSLKELWSL  546 (1373)
T ss_pred             ccHHHHHHH
Confidence            999999986

>KOG0386|consensus

Probab=100.00  E-value=6.6e-37  Score=243.72  Aligned_cols=150  Identities=35%  Similarity=0.552  Sum_probs=141.1

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      ++||||||||+|||+++|++|.++++. +..+|.||++|.+++.+|..||.+|.|++..+.|.|+...|..+......  
T Consensus       414 LNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~NW~~Ef~kWaPSv~~i~YkGtp~~R~~l~~qir~--  491 (1157)
T KOG0386|consen  414 LNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVNWSSEFPKWAPSVQKIQYKGTPQQRSGLTKQQRH--  491 (1157)
T ss_pred             cccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCCchhhccccccceeeeeeeCCHHHHhhHHHHHhc--
Confidence            479999999999999999999999987 55789999999999999999999999999999999999999888876654  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHh-ccccccEEEEeccC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLT-ALRATFKVLLTGWY  158 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~-~l~~~~~~~lT~TP  158 (169)
                                      ++|+| ++|||+.+.++...+..+.|.+.|+||.|++||..++....+. ...+++|++|||||
T Consensus       492 ----------------gKFnV-LlTtyEyiikdk~lLsKI~W~yMIIDEGHRmKNa~~KLt~~L~t~y~~q~RLLLTGTP  554 (1157)
T KOG0386|consen  492 ----------------GKFNV-LLTTYEYIIKDKALLSKISWKYMIIDEGHRMKNAICKLTDTLNTHYRAQRRLLLTGTP  554 (1157)
T ss_pred             ----------------cccee-eeeeHHHhcCCHHHHhccCCcceeecccccccchhhHHHHHhhccccchhhhhhcCCh
Confidence                            88999 9999999999999999999999999999999999999998887 67899999999999


Q ss_pred             CCCCchhhccC
Q psy1090         159 YPNKWSKQCTL  169 (169)
Q Consensus       159 ~~n~~~el~~l  169 (169)
                      +||++.|||+|
T Consensus       555 LQN~LpELWaL  565 (1157)
T KOG0386|consen  555 LQNNLPELWAL  565 (1157)
T ss_pred             hhhccHHHHHH
Confidence            99999999986

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

Probab=100.00  E-value=6.8e-36  Score=220.67  Aligned_cols=147  Identities=31%  Similarity=0.460  Sum_probs=117.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCC---ceEEEecCcchHHHHHHHHHhC-C-CceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALE---PNLIVCPLSVLNNWEAEFRKFA-P-FVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~---~~Liv~P~~~l~qW~~e~~~~~-~-~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ||+|+||||+|||+++++++..+.......   ++|||||.+++.||.+|+.+|+ | ..+++.+.|....+.....   
T Consensus        27 g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~~---  103 (299)
T PF00176_consen   27 GGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPSSLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSKN---  103 (299)
T ss_dssp             EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-TTTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTSS---
T ss_pred             CEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeeccchhhhhhhhhcccccccccccccccccccccccccc---
Confidence            799999999999999999999877665443   6999999999999999999999 4 6888888887722211111   


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHH-----hchhccccccccEEEEeCCcccCCcccHHHHHHhccccccE
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIE-----NDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFK  151 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~-----~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~  151 (169)
                                       .....++ +++||+.+.     ...+.+...+|+++|+||+|.+++..++.++++..+.++++
T Consensus       104 -----------------~~~~~~v-vi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~~s~~~~~l~~l~~~~~  165 (299)
T PF00176_consen  104 -----------------QLPKYDV-VITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNKDSKRYKALRKLRARYR  165 (299)
T ss_dssp             -----------------SCCCSSE-EEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTTTSHHHHHHHCCCECEE
T ss_pred             -----------------cccccee-eeccccccccccccccccccccccceeEEEecccccccccccccccccccccceE
Confidence                             1156677 999999999     66677778899999999999999999999999999999999


Q ss_pred             EEEeccCCCCCchhhccC
Q psy1090         152 VLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       152 ~~lT~TP~~n~~~el~~l  169 (169)
                      |+|||||++|++.|+|++
T Consensus       166 ~lLSgTP~~n~~~dl~~~  183 (299)
T PF00176_consen  166 WLLSGTPIQNSLEDLYSL  183 (299)
T ss_dssp             EEE-SS-SSSGSHHHHHH
T ss_pred             Eeeccccccccccccccc
Confidence            999999999999999863

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

>KOG0390|consensus

Probab=100.00  E-value=1e-34  Score=230.27  Aligned_cols=154  Identities=23%  Similarity=0.318  Sum_probs=129.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCC-----CceEEEecCcchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQAL-----EPNLIVCPLSVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSE   74 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~-----~~~Liv~P~~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~   74 (169)
                      |||+||+||+|||++.|+++..+.+..+.     .+.|||||++++.+|+.||.+|..  .+..+.+++..++.-.....
T Consensus       265 GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~sLv~nWkkEF~KWl~~~~i~~l~~~~~~~~~w~~~~s  344 (776)
T KOG0390|consen  265 GCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSSLVNNWKKEFGKWLGNHRINPLDFYSTKKSSWIKLKS  344 (776)
T ss_pred             ceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccHHHHHHHHHHHHHhccccccceeeeecccchhhhhhHH
Confidence            89999999999999999999999999888     899999999999999999999984  56777777776651000011


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEE
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLL  154 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~l  154 (169)
                      .....              .......|++.+|+.++++...+....++++|+||+|++||..+..++++..+++++|++|
T Consensus       345 il~~~--------------~~~~~~~vli~sye~~~~~~~~il~~~~glLVcDEGHrlkN~~s~~~kaL~~l~t~rRVLL  410 (776)
T KOG0390|consen  345 ILFLG--------------YKQFTTPVLIISYETASDYCRKILLIRPGLLVCDEGHRLKNSDSLTLKALSSLKTPRRVLL  410 (776)
T ss_pred             HHHhh--------------hhheeEEEEeccHHHHHHHHHHHhcCCCCeEEECCCCCccchhhHHHHHHHhcCCCceEEe
Confidence            11110              0122222599999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCCchhhccC
Q psy1090         155 TGWYYPNKWSKQCTL  169 (169)
Q Consensus       155 T~TP~~n~~~el~~l  169 (169)
                      ||||+||++.|+|||
T Consensus       411 SGTp~QNdl~EyFnl  425 (776)
T KOG0390|consen  411 TGTPIQNDLKEYFNL  425 (776)
T ss_pred             eCCcccccHHHHHHH
Confidence            999999999999986

>KOG1002|consensus

Probab=100.00  E-value=2.4e-34  Score=216.13  Aligned_cols=142  Identities=23%  Similarity=0.414  Sum_probs=122.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      |||||||||+|||+++|+++..   +-...|+|||||.-.+.||.+|+.++. ..++++.|+|.++......-       
T Consensus       206 GGiLADEMGMGKTIQtIaLlla---e~~ra~tLVvaP~VAlmQW~nEI~~~T~gslkv~~YhG~~R~~nikel-------  275 (791)
T KOG1002|consen  206 GGILADEMGMGKTIQTIALLLA---EVDRAPTLVVAPTVALMQWKNEIERHTSGSLKVYIYHGAKRDKNIKEL-------  275 (791)
T ss_pred             cceehhhhccchHHHHHHHHHh---ccccCCeeEEccHHHHHHHHHHHHHhccCceEEEEEecccccCCHHHh-------
Confidence            8999999999999999999876   333468999999999999999999998 46899999998876543222       


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhch-----------------hccccccccEEEEeCCcccCCcccHHHHHH
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDF-----------------GFLKKITWNCIIVDEGHSVKNKKSKLSIKL  143 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~-----------------~~~~~~~~~~vi~DEah~~k~~~~~~~~~~  143 (169)
                                     ...|+ ++|||..+...+                 ..+++++|-.+|+||||.+|+..+...+++
T Consensus       276 ---------------~~YDv-VLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~snTArAV  339 (791)
T KOG1002|consen  276 ---------------MNYDV-VLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQSNTARAV  339 (791)
T ss_pred             ---------------hcCcE-EEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhcccccccccHHHHH
Confidence                           66677 999999886432                 235678999999999999999999999999


Q ss_pred             hccccccEEEEeccCCCCCchhhccC
Q psy1090         144 TALRATFKVLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       144 ~~l~~~~~~~lT~TP~~n~~~el~~l  169 (169)
                      -.+.+.+||.|||||+||++.|||+|
T Consensus       340 ~~L~tt~rw~LSGTPLQNrigElySL  365 (791)
T KOG1002|consen  340 FALETTYRWCLSGTPLQNRIGELYSL  365 (791)
T ss_pred             HhhHhhhhhhccCCcchhhHHHHHHH
Confidence            99999999999999999999999986

>KOG4439|consensus

Probab=100.00  E-value=7.1e-35  Score=225.59  Aligned_cols=146  Identities=24%  Similarity=0.402  Sum_probs=122.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC--------CCceEEEecCcchHHHHHHHHHhC--CCceEEEEeCCHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA--------LEPNLIVCPLSVLNNWEAEFRKFA--PFVRTVKYYGNAIERKAL   71 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~--------~~~~Liv~P~~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~   71 (169)
                      ||||+|+||+|||.++|++|........        ..++|||||.+++.||..|+.+-.  ..+.++.|+|+.+  ..+
T Consensus       347 GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaSli~qW~~Ev~~rl~~n~LsV~~~HG~n~--r~i  424 (901)
T KOG4439|consen  347 GGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPASLIHQWEAEVARRLEQNALSVYLYHGPNK--REI  424 (901)
T ss_pred             CcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcHHHHHHHHHHHHHHHhhcceEEEEecCCcc--ccC
Confidence            8999999999999999999987664311        126999999999999999998665  4678999999875  222


Q ss_pred             HHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHh----------chhccccccccEEEEeCCcccCCcccHHHH
Q psy1090          72 QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN----------DFGFLKKITWNCIIVDEGHSVKNKKSKLSI  141 (169)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~----------~~~~~~~~~~~~vi~DEah~~k~~~~~~~~  141 (169)
                      ....+                   ..+|+ |||||..+.+          +...+.++.|..||+||||.+||+.++.+.
T Consensus       425 ~~~~L-------------------~~YDv-ViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~~tq~S~  484 (901)
T KOG4439|consen  425 SAKEL-------------------RKYDV-VITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNSNTQCSK  484 (901)
T ss_pred             CHHHH-------------------hhcce-EEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhcccchhHHH
Confidence            22222                   66777 9999999876          223566789999999999999999999999


Q ss_pred             HHhccccccEEEEeccCCCCCchhhccC
Q psy1090         142 KLTALRATFKVLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       142 ~~~~l~~~~~~~lT~TP~~n~~~el~~l  169 (169)
                      ++-.+++..||+|||||++|+..|+|+|
T Consensus       485 AVC~L~a~~RWclTGTPiqNn~~DvysL  512 (901)
T KOG4439|consen  485 AVCKLSAKSRWCLTGTPIQNNLWDVYSL  512 (901)
T ss_pred             HHHHHhhcceeecccCccccchhHHHHH
Confidence            9999999999999999999999999986

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.97  E-value=4.7e-31  Score=216.25  Aligned_cols=148  Identities=14%  Similarity=0.110  Sum_probs=114.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      .++||||||+|||+++++++..+...+..+|+|||||.+++.||..|+.+++ ++.+.++.+..-.... ....      
T Consensus       171 R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~sL~~QW~~El~~kF-~l~~~i~~~~~~~~~~-~~~~------  242 (956)
T PRK04914        171 RVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRF-NLRFSLFDEERYAEAQ-HDAD------  242 (956)
T ss_pred             CEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCHHHHHHHHHHHHHHh-CCCeEEEcCcchhhhc-cccc------
Confidence            3789999999999999999998888888889999999999999999997765 4555555544321110 0000      


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhch---hccccccccEEEEeCCcccCCc---ccHHHHHHhcc--ccccEEE
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDF---GFLKKITWNCIIVDEGHSVKNK---KSKLSIKLTAL--RATFKVL  153 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~---~~~~~~~~~~vi~DEah~~k~~---~~~~~~~~~~l--~~~~~~~  153 (169)
                             .    .-...++ +|+||+.+.++.   +.+....||++|+||||++++.   .++.++.+..+  +++++++
T Consensus       243 -------~----pf~~~~~-vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~~~~LL  310 (956)
T PRK04914        243 -------N----PFETEQL-VICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIPGVLL  310 (956)
T ss_pred             -------C----ccccCcE-EEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhccCCEEE
Confidence                   0    0024566 999999998754   4456679999999999999853   45668888777  6789999


Q ss_pred             EeccCCCCCchhhccC
Q psy1090         154 LTGWYYPNKWSKQCTL  169 (169)
Q Consensus       154 lT~TP~~n~~~el~~l  169 (169)
                      |||||.+|+..|+|++
T Consensus       311 LTATP~q~~~~e~fal  326 (956)
T PRK04914        311 LTATPEQLGQESHFAR  326 (956)
T ss_pred             EEcCcccCCcHHHHHh
Confidence            9999999999999975

>KOG1015|consensus

Probab=99.96  E-value=1.1e-29  Score=202.06  Aligned_cols=148  Identities=21%  Similarity=0.291  Sum_probs=116.2

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh--CCCCceEEEecCcchHHHHHHHHHhCCCce------EEEEeC--CHHHHHH
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE--QALEPNLIVCPLSVLNNWEAEFRKFAPFVR------TVKYYG--NAIERKA   70 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~--~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~------~~~~~g--~~~~~~~   70 (169)
                      .|||||+-||+|||+++++|+...+..  -..+++|||||.+++.+|..||.+|.+++.      +.....  ....|..
T Consensus       697 sGcILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~PlNt~~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R~~  776 (1567)
T KOG1015|consen  697 SGCILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPLNTALNWMNEFEKWMEGLEDDEKLEVSELATVKRPEERSY  776 (1567)
T ss_pred             cchHHHHhhcccceehhhHHHHHHHHhhccCCceEEEEcchHHHHHHHHHHHHhcccccccccceeehhhhccChHHHHH
Confidence            389999999999999999998876654  234689999999999999999999997532      222222  2233444


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh---------------ccccccccEEEEeCCcccCCc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---------------FLKKITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---------------~~~~~~~~~vi~DEah~~k~~  135 (169)
                      .-+.++                   ...-+ +|..|+.++....               .+..-..|+|||||+|.+||.
T Consensus       777 ~L~~W~-------------------~~ggV-mIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNe  836 (1567)
T KOG1015|consen  777 MLQRWQ-------------------EDGGV-MIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNE  836 (1567)
T ss_pred             HHHHHH-------------------hcCCE-EEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccc
Confidence            444444                   33344 9999999875321               223346899999999999999


Q ss_pred             ccHHHHHHhccccccEEEEeccCCCCCchhhcc
Q psy1090         136 KSKLSIKLTALRATFKVLLTGWYYPNKWSKQCT  168 (169)
Q Consensus       136 ~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el~~  168 (169)
                      .+..++++..+++++|++|||||+||++.|+|-
T Consensus       837 ksa~Skam~~irtkRRI~LTGTPLQNNLmEY~C  869 (1567)
T KOG1015|consen  837 KSAVSKAMNSIRTKRRIILTGTPLQNNLMEYHC  869 (1567)
T ss_pred             hHHHHHHHHHHHhheeEEeecCchhhhhHHHHH
Confidence            999999999999999999999999999999873

>KOG1000|consensus

Probab=99.95  E-value=1.1e-28  Score=185.62  Aligned_cols=139  Identities=23%  Similarity=0.256  Sum_probs=115.8

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceE-EEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRT-VKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~-~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      ++||||||+|||++||+++.++..   .+|.|||||.++...|.+++++|.|..-. .+..+.++.-..           
T Consensus       217 ~llADeMGLGKTiQAlaIA~yyra---EwplliVcPAsvrftWa~al~r~lps~~pi~vv~~~~D~~~~-----------  282 (689)
T KOG1000|consen  217 ILLADEMGLGKTIQALAIARYYRA---EWPLLIVCPASVRFTWAKALNRFLPSIHPIFVVDKSSDPLPD-----------  282 (689)
T ss_pred             EEEecccccchHHHHHHHHHHHhh---cCcEEEEecHHHhHHHHHHHHHhcccccceEEEecccCCccc-----------
Confidence            789999999999999999877654   45999999999999999999999986544 233333221100           


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc--ccccEEEEeccCC
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL--RATFKVLLTGWYY  159 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l--~~~~~~~lT~TP~  159 (169)
                                   -+..+-|.+.||+.+....+.+..-+|.++|+||+|++|+..+++.+++..+  .+++.++|||||-
T Consensus       283 -------------~~t~~~v~ivSye~ls~l~~~l~~~~~~vvI~DEsH~Lk~sktkr~Ka~~dllk~akhvILLSGTPa  349 (689)
T KOG1000|consen  283 -------------VCTSNTVAIVSYEQLSLLHDILKKEKYRVVIFDESHMLKDSKTKRTKAATDLLKVAKHVILLSGTPA  349 (689)
T ss_pred             -------------cccCCeEEEEEHHHHHHHHHHHhcccceEEEEechhhhhccchhhhhhhhhHHHHhhheEEecCCcc
Confidence                         0233335999999999988888888999999999999999999999999877  6889999999999


Q ss_pred             CCCchhhcc
Q psy1090         160 PNKWSKQCT  168 (169)
Q Consensus       160 ~n~~~el~~  168 (169)
                      -.++.|||+
T Consensus       350 vSRP~elyt  358 (689)
T KOG1000|consen  350 VSRPSELYT  358 (689)
T ss_pred             cCCchhhhh
Confidence            999999996

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=99.95  E-value=1.7e-28  Score=203.39  Aligned_cols=153  Identities=33%  Similarity=0.526  Sum_probs=130.9

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCC--CCceEEEecCcchHHHHHHHHHhCCCce-EEEEeCCHHH----HHHHHH
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQA--LEPNLIVCPLSVLNNWEAEFRKFAPFVR-TVKYYGNAIE----RKALQS   73 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~--~~~~Liv~P~~~l~qW~~e~~~~~~~~~-~~~~~g~~~~----~~~~~~   73 (169)
                      .||+|+||||+|||+++++++.+......  .+|.||+||.+++.+|.+|+.+|.|..+ +..++|....    +.....
T Consensus       359 ~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~~~nw~~e~~k~~~~~~~~~~~~g~~~~~~~~~~~~~~  438 (866)
T COG0553         359 LGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLLSNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRD  438 (866)
T ss_pred             CCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHHHHHHHHHHHhhhCccccceeeeeCCcccccHHHHHHHH
Confidence            48999999999999999999987555544  4699999999999999999999999999 9999998753    333332


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHh---chhccccccccEEEEeCCcccCCcccHHHHHHhcccccc
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN---DFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATF  150 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~---~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~  150 (169)
                      ......               ...+++ +++||+.+.+   +...+....|+.+|+||+|++||..++.++++..+++.+
T Consensus       439 ~~~~~~---------------~~~~~v-~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~~s~~~~~l~~~~~~~  502 (866)
T COG0553         439 LLKLHL---------------VIIFDV-VITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQFLKALN  502 (866)
T ss_pred             Hhhhcc---------------cceeeE-EechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhhhhHHHHHHHHHhhcc
Confidence            211000               023666 9999999999   899999999999999999999999999999999999999


Q ss_pred             EEEEeccCCCCCchhhccC
Q psy1090         151 KVLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       151 ~~~lT~TP~~n~~~el~~l  169 (169)
                      ++.|||||++|++.|||+|
T Consensus       503 ~~~LtgTPlen~l~eL~sl  521 (866)
T COG0553         503 RLDLTGTPLENRLGELWSL  521 (866)
T ss_pred             eeeCCCChHhhhHHHHHHH
Confidence            9999999999999999975

>KOG1016|consensus

Probab=99.94  E-value=2.2e-26  Score=180.67  Aligned_cols=149  Identities=20%  Similarity=0.329  Sum_probs=117.2

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCC-----------ceEEEEeCCHH---
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPF-----------VRTVKYYGNAI---   66 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~-----------~~~~~~~g~~~---   66 (169)
                      +|||||+.||+|||+++|+|+...++....+.+|+|+|-.++++|..||.+|.|.           +++.+.....+   
T Consensus       283 FGCILAHSMGLGKTlQVisF~diflRhT~AKtVL~ivPiNTlQNWlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~KT~~  362 (1387)
T KOG1016|consen  283 FGCILAHSMGLGKTLQVISFSDIFLRHTKAKTVLVIVPINTLQNWLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFD  362 (1387)
T ss_pred             cceeeeeccccCceeEEeehhHHHhhcCccceEEEEEehHHHHHHHHHhhhhcCCCcccCCCccceeEEEEecCchhhHH
Confidence            6999999999999999999998888888788999999999999999999999864           33444433322   


Q ss_pred             HHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhch---------------------------------
Q psy1090          67 ERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF---------------------------------  113 (169)
Q Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~---------------------------------  113 (169)
                      .|..+-..+.                   ...-+ ++..|++++-..                                 
T Consensus       363 ~Rakvi~~Wv-------------------~~GGV-lLvGYemfRLL~lk~~~~~grpkkt~kr~~~~~i~~d~eD~~qe~  422 (1387)
T KOG1016|consen  363 QRAKVIEQWV-------------------QTGGV-LLVGYEMFRLLILKTLPKKGRPKKTLKRISSGFIKDDSEDQRQEA  422 (1387)
T ss_pred             HHHHHHHHHh-------------------ccCCE-EEehHHHHHHHHHhcccccCCccccccccCCcccCCchhhhHHHH
Confidence            2343333332                   33333 777887765311                                 


Q ss_pred             -----hccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCchhhccC
Q psy1090         114 -----GFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       114 -----~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el~~l  169 (169)
                           ..+.+-..|+|||||.|++||..+..+.+++.+++++|++|||=|+||++-|.|-|
T Consensus       423 ~~li~~AL~~PGPDlVICDEGHrIKN~~A~iS~aLk~IrtrRRiVLTGYPLQNNLlEYwCM  483 (1387)
T KOG1016|consen  423 YSLIRSALLEPGPDLVICDEGHRIKNITAEISMALKAIRTRRRIVLTGYPLQNNLLEYWCM  483 (1387)
T ss_pred             HHHHHHHhcCCCCCeEEecCCceeccchHHHHHHHHHhhhceeEEEeccccccchHHHhhh
Confidence                 11223468899999999999999999999999999999999999999999998843

>KOG1001|consensus

Probab=99.92  E-value=1.1e-25  Score=179.21  Aligned_cols=141  Identities=29%  Similarity=0.448  Sum_probs=118.1

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhC-------CCCceEEEecCcchHHHHHHHHHhC--CCceEEEEeC-CHHHHHH
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQ-------ALEPNLIVCPLSVLNNWEAEFRKFA--PFVRTVKYYG-NAIERKA   70 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~-------~~~~~Liv~P~~~l~qW~~e~~~~~--~~~~~~~~~g-~~~~~~~   70 (169)
                      .|||++|+||+|||+++++++.......       ..+.+|||||.+++.||..|+.+..  ..+.+.+|+| .+.... 
T Consensus       153 ~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~s~~~qW~~elek~~~~~~l~v~v~~gr~kd~~e-  231 (674)
T KOG1001|consen  153 RGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTSLLTQWKTELEKVTEEDKLSIYVYHGRTKDKSE-  231 (674)
T ss_pred             ccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecchHHHHHHHHHHhccCCccceEEEEecccccccch-
Confidence            4899999999999999999987655433       2457899999999999999995554  3577788888 211111 


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcccccc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATF  150 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~  150 (169)
                           .                   ...|+ |++||+.+..  ..+.++.|-++|+||||.++|.+++.++++..+.+.+
T Consensus       232 -----l-------------------~~~dV-VltTy~il~~--~~l~~i~w~Riildea~~ikn~~tq~~~a~~~L~a~~  284 (674)
T KOG1001|consen  232 -----L-------------------NSYDV-VLTTYDILKN--SPLVKIKWLRIVLDEAHTIKNKDTQIFKAVCQLDAKY  284 (674)
T ss_pred             -----h-------------------cCCce-EEeeHHHhhc--ccccceeEEEEEeccccccCCcchHhhhhheeeccce
Confidence                 0                   55666 9999999976  5666799999999999999999999999999999999


Q ss_pred             EEEEeccCCCCCchhhccC
Q psy1090         151 KVLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       151 ~~~lT~TP~~n~~~el~~l  169 (169)
                      ||.|||||.+|+..|+|++
T Consensus       285 RWcLtgtPiqn~~~~lysl  303 (674)
T KOG1001|consen  285 RWCLTGTPIQNNLDELYSL  303 (674)
T ss_pred             eeeecCChhhhhHHHHHHH
Confidence            9999999999999999974

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.91  E-value=4.8e-24  Score=170.57  Aligned_cols=128  Identities=21%  Similarity=0.346  Sum_probs=98.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +|++..+||+|||++++++++.+     .+++|||||.. ++.||.++|.+|.  +...+..++|..+.+.         
T Consensus       275 ~GIIvLPtGaGKTlvai~aa~~l-----~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~I~~~tg~~k~~~---------  340 (732)
T TIGR00603       275 SGIIVLPCGAGKSLVGVTAACTV-----KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQICRFTSDAKERF---------  340 (732)
T ss_pred             CcEEEeCCCCChHHHHHHHHHHh-----CCCEEEEeCcHHHHHHHHHHHHHhcCCCCceEEEEecCccccc---------
Confidence            58999999999999999887654     36899999985 5789999999996  3456666777543321         


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc----------hhccccccccEEEEeCCcccCCcccHHHHHHhcccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND----------FGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRA  148 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~----------~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~  148 (169)
                                      ....++ +++||+++...          .+.+....|+++|+||||++.  .....+.+..+++
T Consensus       341 ----------------~~~~~V-vVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lp--A~~fr~il~~l~a  401 (732)
T TIGR00603       341 ----------------HGEAGV-VVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVP--AAMFRRVLTIVQA  401 (732)
T ss_pred             ----------------ccCCcE-EEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEcccccc--HHHHHHHHHhcCc
Confidence                            023455 99999998643          234555689999999999995  3445556778899


Q ss_pred             ccEEEEeccCCCCC
Q psy1090         149 TFKVLLTGWYYPNK  162 (169)
Q Consensus       149 ~~~~~lT~TP~~n~  162 (169)
                      .+|++|||||.+++
T Consensus       402 ~~RLGLTATP~ReD  415 (732)
T TIGR00603       402 HCKLGLTATLVRED  415 (732)
T ss_pred             CcEEEEeecCcccC
Confidence            99999999999875

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).

>KOG0383|consensus

Probab=99.89  E-value=3.1e-25  Score=175.15  Aligned_cols=167  Identities=33%  Similarity=0.470  Sum_probs=144.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC-CCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ-ALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~-~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .+|||||||+|||++++.++..+.... ..+|.|+++|.+++.+|..++..|.|+..+..|.|..+.+..++...+....
T Consensus       316 ~~ilADEmgLgktVqsi~fl~sl~~~~~~~~P~Lv~ap~sT~~nwe~e~~~wap~~~vv~~~G~~k~r~iirepe~s~ed  395 (696)
T KOG0383|consen  316 DAILADEMGLGKTVQSIVFLYSLPKEIHSPGPPLVVAPLSTIVNWEREFELWAPSFYVVPYPGTAKSRAIIREPEFSFED  395 (696)
T ss_pred             CcccchhhcCCceeeEEEEEeecccccCCCCCceeeccCccccCCCCchhccCCCcccccCCCCccchhhhhcccccccc
Confidence            479999999999999999988777664 4579999999999999999999999999999999999999888877766554


Q ss_pred             ccc--ccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccC
Q psy1090          81 IKV--PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWY  158 (169)
Q Consensus        81 ~~~--~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP  158 (169)
                      ...  ..+-+....+....+.+ .+++|+....+...+..+.|.++|+||+|+++|..+++.+.+......+++++||||
T Consensus       396 ~~~~~~~~i~~~~~~s~~k~~v-l~~s~~~~~~~~~il~~v~w~~livde~~rlkn~~s~~f~~l~~~~~~~~~lltgtP  474 (696)
T KOG0383|consen  396 SSIKSSPKISEMKTESSAKFHV-LLPSYETIEIDQSILFSVQWGLLIVDEAHRLKNKQSKRFRVLTAYPIDSKLLLTGTP  474 (696)
T ss_pred             cccccCCccccccchhhccccc-CCCchhhcccCHHHHhhhhcceeEeechhhcccchhhhhhhccccccchhhhccCCc
Confidence            432  11122223445577788 999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCchhhccC
Q psy1090         159 YPNKWSKQCTL  169 (169)
Q Consensus       159 ~~n~~~el~~l  169 (169)
                      .+|++.+||+|
T Consensus       475 lqnn~~el~~l  485 (696)
T KOG0383|consen  475 LQNNLEELFNL  485 (696)
T ss_pred             chhhhHHhhhc
Confidence            99999999986

>KOG0298|consensus

Probab=99.88  E-value=8e-24  Score=172.87  Aligned_cols=145  Identities=21%  Similarity=0.278  Sum_probs=116.0

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH------------Hh----CCCCceEEEecCcchHHHHHHHHHhCCCc-eEEEEeCCH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII------------EE----QALEPNLIVCPLSVLNNWEAEFRKFAPFV-RTVKYYGNA   65 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~------------~~----~~~~~~Liv~P~~~l~qW~~e~~~~~~~~-~~~~~~g~~   65 (169)
                      ++++||||+|||...++....-.            ..    ...+++|||||++++.||.+|+.++++.. +++.|.|-.
T Consensus       377 ~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~aIl~QW~~EI~kH~~~~lKv~~Y~Gir  456 (1394)
T KOG0298|consen  377 VQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPNAILMQWFEEIHKHISSLLKVLLYFGIR  456 (1394)
T ss_pred             eeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcHHHHHHHHHHHHHhccccceEEEEechh
Confidence            48999999999998887753221            11    12378999999999999999999999766 999999865


Q ss_pred             HHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh----------------------ccccccccE
Q psy1090          66 IERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG----------------------FLKKITWNC  123 (169)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~----------------------~~~~~~~~~  123 (169)
                      +.--... ..                   -...|| |+|||+.++.+..                      .+..+.|..
T Consensus       457 k~~~~~~-~e-------------------l~~yDI-VlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWR  515 (1394)
T KOG0298|consen  457 KTFWLSP-FE-------------------LLQYDI-VLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWR  515 (1394)
T ss_pred             hhcccCc-hh-------------------hhccCE-EEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHH
Confidence            4421111 11                   167788 9999999987542                      233468999


Q ss_pred             EEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCchhhccC
Q psy1090         124 IIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL  169 (169)
Q Consensus       124 vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el~~l  169 (169)
                      +++||||.+....+...+++..+.+.++|..||||+++ +.|||.|
T Consensus       516 IclDEaQMvesssS~~a~M~~rL~~in~W~VTGTPiq~-Iddl~~L  560 (1394)
T KOG0298|consen  516 ICLDEAQMVESSSSAAAEMVRRLHAINRWCVTGTPIQK-IDDLFPL  560 (1394)
T ss_pred             HhhhHHHhhcchHHHHHHHHHHhhhhceeeecCCchhh-hhhhHHH
Confidence            99999999999888899999999999999999999999 9999864

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.84  E-value=1e-19  Score=119.65  Aligned_cols=136  Identities=18%  Similarity=0.191  Sum_probs=98.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      ++++..++|+|||.+++.++.........++++|++|...+ .||.+.+.++.. ...+..+.+............    
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----   77 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQEKLLS----   77 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHHHHHhc----
Confidence            57899999999999999998887766567899999998655 567777777764 455666666544433321111    


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhcc--ccccccEEEEeCCcccCCcccHHH---HHHhccccccEEEE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL--KKITWNCIIVDEGHSVKNKKSKLS---IKLTALRATFKVLL  154 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~--~~~~~~~vi~DEah~~k~~~~~~~---~~~~~l~~~~~~~l  154 (169)
                                      ...++ ++.|++.+.+.....  ....++++|+||+|.+.+......   ......+...++++
T Consensus        78 ----------------~~~~i-~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~  140 (144)
T cd00046          78 ----------------GKTDI-VVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLL  140 (144)
T ss_pred             ----------------CCCCE-EEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEE
Confidence                            45556 999999887654432  345789999999999987655443   23344577889999


Q ss_pred             eccC
Q psy1090         155 TGWY  158 (169)
Q Consensus       155 T~TP  158 (169)
                      ||||
T Consensus       141 saTp  144 (144)
T cd00046         141 SATP  144 (144)
T ss_pred             eccC
Confidence            9998

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

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

Probab=99.80  E-value=2.4e-19  Score=123.47  Aligned_cols=143  Identities=20%  Similarity=0.256  Sum_probs=88.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      +++..++|+|||.++++++..+..     +++++||. .++.||.+++..+.+................ .  ....   
T Consensus        28 ~ll~~~tGsGKT~~~~~~~~~l~~-----~~l~~~p~~~l~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~-~--~~~~---   96 (184)
T PF04851_consen   28 VLLNAPTGSGKTIIALALILELAR-----KVLIVAPNISLLEQWYDEFDDFGSEKYNFFEKSIKPAYDS-K--EFIS---   96 (184)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHC-----EEEEEESSHHHHHHHHHHHHHHSTTSEEEEE--GGGCCE--S--EEET---
T ss_pred             EEEEECCCCCcChhhhhhhhcccc-----ceeEecCHHHHHHHHHHHHHHhhhhhhhhccccccccccc-c--cccc---
Confidence            678899999999999988877664     89999998 7788999999887754443322211000000 0  0000   


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhc-------------cccccccEEEEeCCcccCCcccHHHHHHhcccc
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-------------LKKITWNCIIVDEGHSVKNKKSKLSIKLTALRA  148 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-------------~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~  148 (169)
                       ................++ ++++++.+......             .....++++|+||||+..+...  ++.+.....
T Consensus        97 -~~~~~~~~~~~~~~~~~i-~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~~--~~~i~~~~~  172 (184)
T PF04851_consen   97 -IQDDISDKSESDNNDKDI-ILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSDSS--YREIIEFKA  172 (184)
T ss_dssp             -TTTEEEHHHHHCBSS-SE-EEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHHHH--HHHHHHSSC
T ss_pred             -cccccccccccccccccc-hhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCHHH--HHHHHcCCC
Confidence             000000000011255666 99999998765332             2234689999999999854322  555555888


Q ss_pred             ccEEEEeccCCC
Q psy1090         149 TFKVLLTGWYYP  160 (169)
Q Consensus       149 ~~~~~lT~TP~~  160 (169)
                      .++++|||||.+
T Consensus       173 ~~~l~lTATp~r  184 (184)
T PF04851_consen  173 AFILGLTATPFR  184 (184)
T ss_dssp             CEEEEEESS-S-
T ss_pred             CeEEEEEeCccC
Confidence            999999999974

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 ....

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

Probab=99.77  E-value=1.4e-18  Score=134.51  Aligned_cols=126  Identities=21%  Similarity=0.247  Sum_probs=90.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCc-eEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFV-RTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      .|++...+|.|||+.++..+..+.     .++|||||. .++.||.+.+.++.... .+..+.|..++-.          
T Consensus        57 ~gvivlpTGaGKT~va~~~~~~~~-----~~~Lvlv~~~~L~~Qw~~~~~~~~~~~~~~g~~~~~~~~~~----------  121 (442)
T COG1061          57 RGVIVLPTGAGKTVVAAEAIAELK-----RSTLVLVPTKELLDQWAEALKKFLLLNDEIGIYGGGEKELE----------  121 (442)
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHhc-----CCEEEEECcHHHHHHHHHHHHHhcCCccccceecCceeccC----------
Confidence            378899999999999988887654     349999998 77889998888877332 3444444433211          


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcccHHHHHHhcccccc-EEEEec
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATF-KVLLTG  156 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~-~~~lT~  156 (169)
                                      . ..+ .++||+++.+.  ...+..-.|+++|+||||++..+  ........+...+ +++|||
T Consensus       122 ----------------~-~~i-~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~--~~~~~~~~~~~~~~~LGLTA  181 (442)
T COG1061         122 ----------------P-AKV-TVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAP--SYRRILELLSAAYPRLGLTA  181 (442)
T ss_pred             ----------------C-CcE-EEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcH--HHHHHHHhhhcccceeeecc
Confidence                            1 234 99999999885  23444447999999999998543  3334445556666 999999


Q ss_pred             cCCCCC
Q psy1090         157 WYYPNK  162 (169)
Q Consensus       157 TP~~n~  162 (169)
                      ||.+.+
T Consensus       182 Tp~R~D  187 (442)
T COG1061         182 TPERED  187 (442)
T ss_pred             Cceeec
Confidence            998665

>PRK13766 Hef nuclease; Provisional

Probab=99.77  E-value=1.1e-17  Score=137.84  Aligned_cols=137  Identities=23%  Similarity=0.291  Sum_probs=97.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      ++++++++|+|||++++.++.... ....+++||+||. .+..||.+++.++..  ..++..++|......  +...+  
T Consensus        31 n~lv~~ptG~GKT~~a~~~i~~~l-~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~--r~~~~--  105 (773)
T PRK13766         31 NTLVVLPTGLGKTAIALLVIAERL-HKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEK--RAELW--  105 (773)
T ss_pred             CeEEEcCCCccHHHHHHHHHHHHH-HhCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHH--HHHHH--
Confidence            578999999999999887777655 3456799999998 788899999998863  347777887543321  11111  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCcccHHHHHHhc---cccccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA---LRATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~---l~~~~~~~  153 (169)
                                       ...++ +++|++.+..+.  ..+.-..|+++|+||||++.+..+....+-..   .+.+++++
T Consensus       106 -----------------~~~~i-iv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~il~  167 (773)
T PRK13766        106 -----------------EKAKV-IVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLG  167 (773)
T ss_pred             -----------------hCCCE-EEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEEEE
Confidence                             33456 999999887653  23334478999999999998655443322222   24567999


Q ss_pred             EeccCCCC
Q psy1090         154 LTGWYYPN  161 (169)
Q Consensus       154 lT~TP~~n  161 (169)
                      |||||..+
T Consensus       168 lTaTP~~~  175 (773)
T PRK13766        168 LTASPGSD  175 (773)
T ss_pred             EEcCCCCC
Confidence            99999654

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.75  E-value=1.8e-17  Score=130.41  Aligned_cols=127  Identities=25%  Similarity=0.236  Sum_probs=88.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC--CCceE-EEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRT-VKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~-~~~~g~~~~~~~~~~~~~~   77 (169)
                      .+++..++|+|||+++..++..... ....++||+||. .++.||.+++.+|.  +.... ..+.|....          
T Consensus       131 ~~il~apTGsGKT~i~~~l~~~~~~-~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~~i~~g~~~~----------  199 (501)
T PHA02558        131 RRLLNLPTSAGKSLIQYLLSRYYLE-NYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKIYSGTAKD----------  199 (501)
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHHHh-cCCCeEEEEECcHHHHHHHHHHHHHhccccccceeEEecCcccC----------
Confidence            3688999999999987765544333 333489999998 78899999999886  22222 223332211          


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEec
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLTG  156 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT~  156 (169)
                                        ...++ +++|++.+.+..... -.+++++|+||||++...  .....+..+ +++++++|||
T Consensus       200 ------------------~~~~I-~VaT~qsl~~~~~~~-~~~~~~iIvDEaH~~~~~--~~~~il~~~~~~~~~lGLTA  257 (501)
T PHA02558        200 ------------------TDAPI-VVSTWQSAVKQPKEW-FDQFGMVIVDECHLFTGK--SLTSIITKLDNCKFKFGLTG  257 (501)
T ss_pred             ------------------CCCCE-EEeeHHHHhhchhhh-ccccCEEEEEchhcccch--hHHHHHHhhhccceEEEEec
Confidence                              23455 999999987643221 137899999999998643  344555666 6788999999


Q ss_pred             cCCCC
Q psy1090         157 WYYPN  161 (169)
Q Consensus       157 TP~~n  161 (169)
                      ||...
T Consensus       258 Tp~~~  262 (501)
T PHA02558        258 SLRDG  262 (501)
T ss_pred             cCCCc
Confidence            99654

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.75  E-value=2.1e-17  Score=114.49  Aligned_cols=138  Identities=20%  Similarity=0.233  Sum_probs=94.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCC---ceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPF---VRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||.+++.++.........+++|+++|. .+..||..++..+.+.   .....+.+.... ........ 
T Consensus        26 ~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~-  103 (201)
T smart00487       26 DVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKR-EQLRKLES-  103 (201)
T ss_pred             cEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHhccCCeEEEEEeCCcchH-HHHHHHhc-
Confidence            46889999999999888777766655546789999996 6778999999988754   333344443322 11111110 


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCC-cccHHH-HHHhcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKN-KKSKLS-IKLTAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~-~~~~~~-~~~~~l-~~~~~~  152 (169)
                                        ...++ +++|++.+.+....  .....++++|+||+|.+.. ...... ..+..+ +..+++
T Consensus       104 ------------------~~~~v-~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~~v  164 (201)
T smart00487      104 ------------------GKTDI-LVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLL  164 (201)
T ss_pred             ------------------CCCCE-EEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccceEE
Confidence                              22256 99999988876654  3455788999999999885 222223 333444 578899


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++||||..
T Consensus       165 ~~saT~~~  172 (201)
T smart00487      165 LLSATPPE  172 (201)
T ss_pred             EEecCCch
Confidence            99999953

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

Probab=99.72  E-value=7.1e-17  Score=122.65  Aligned_cols=133  Identities=22%  Similarity=0.212  Sum_probs=99.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCH--HHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNA--IERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~--~~~~~~~~~~~   76 (169)
                      +++++..+|+|||+.|+.++...+..... ++|+++|. .++.|-..-+.++.  |...+..++|.-  .+|...+    
T Consensus        31 NtLvvlPTGLGKT~IA~~V~~~~l~~~~~-kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w----  105 (542)
T COG1111          31 NTLVVLPTGLGKTFIAAMVIANRLRWFGG-KVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELW----  105 (542)
T ss_pred             CeEEEecCCccHHHHHHHHHHHHHHhcCC-eEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHH----
Confidence            47889999999999999998877665533 89999997 78888888888876  678888999953  4455444    


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCcccHHHHHHh-cc---cccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSKLSIKLT-AL---RATF  150 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~-~l---~~~~  150 (169)
                                         ...++ +++|++.+.+|.  ..+..-++.++|+||||+.-+..+ +...++ .+   +.++
T Consensus       106 -------------------~~~kV-fvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyA-Yv~Va~~y~~~~k~~~  164 (542)
T COG1111         106 -------------------AKKKV-FVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYA-YVFVAKEYLRSAKNPL  164 (542)
T ss_pred             -------------------hhCCE-EEeccHHHHhHHhcCccChHHceEEEechhhhccCcch-HHHHHHHHHHhccCce
Confidence                               33445 999999999875  345556788999999999876544 333333 22   4457


Q ss_pred             EEEEeccCCC
Q psy1090         151 KVLLTGWYYP  160 (169)
Q Consensus       151 ~~~lT~TP~~  160 (169)
                      .++|||||=.
T Consensus       165 ilgLTASPGs  174 (542)
T COG1111         165 ILGLTASPGS  174 (542)
T ss_pred             EEEEecCCCC
Confidence            8999999953

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

Probab=99.67  E-value=5.9e-16  Score=125.30  Aligned_cols=134  Identities=16%  Similarity=0.055  Sum_probs=89.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +|++.+.+|+|||++++.++..+.......++|||+|. .+..||.++|..+.++..  ...++   ...+......   
T Consensus       265 ~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~~~~--~~~~s---~~~L~~~l~~---  336 (667)
T TIGR00348       265 GGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQKDCA--ERIES---IAELKRLLEK---  336 (667)
T ss_pred             eeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCCCCC--cccCC---HHHHHHHHhC---
Confidence            58899999999999999888777665556789999998 677899999998874211  01111   1111111100   


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchh-cccccc----ccEEEEeCCcccCCcccHHHHHH-hccccccEEEE
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG-FLKKIT----WNCIIVDEGHSVKNKKSKLSIKL-TALRATFKVLL  154 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~-~~~~~~----~~~vi~DEah~~k~~~~~~~~~~-~~l~~~~~~~l  154 (169)
                                     ...++ +++|.+.+.+... .+....    ..++|+||||+...  ....+.+ ..++...++++
T Consensus       337 ---------------~~~~i-ivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~--~~~~~~l~~~~p~a~~lGf  398 (667)
T TIGR00348       337 ---------------DDGGI-IITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQY--GELAKNLKKALKNASFFGF  398 (667)
T ss_pred             ---------------CCCCE-EEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccc--hHHHHHHHhhCCCCcEEEE
Confidence                           23455 9999999975322 122211    23899999999753  3334445 35677899999


Q ss_pred             eccCCCC
Q psy1090         155 TGWYYPN  161 (169)
Q Consensus       155 T~TP~~n  161 (169)
                      ||||...
T Consensus       399 TaTP~~~  405 (667)
T TIGR00348       399 TGTPIFK  405 (667)
T ss_pred             eCCCccc
Confidence            9999853

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

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

Probab=99.65  E-value=1.3e-15  Score=128.36  Aligned_cols=137  Identities=18%  Similarity=0.146  Sum_probs=89.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCce--EEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVR--TVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~--~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      ++++.+.+|+|||+++++++..+...+..+++||++|. .++.||.++|..+.+...  +....+...    +.....  
T Consensus       435 ~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~~~~~~i~~i~~----L~~~~~--  508 (1123)
T PRK11448        435 EILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGDQTFASIYDIKG----LEDKFP--  508 (1123)
T ss_pred             CeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccccchhhhhchhh----hhhhcc--
Confidence            47899999999999999988777766667899999997 677899999988742111  100111000    000000  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhc-------cccccccEEEEeCCcccCCc----------------
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-------LKKITWNCIIVDEGHSVKNK----------------  135 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-------~~~~~~~~vi~DEah~~k~~----------------  135 (169)
                                      .....+ +++|++.+.+....       +.--.|+++|+||||+....                
T Consensus       509 ----------------~~~~~I-~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~~~  571 (1123)
T PRK11448        509 ----------------EDETKV-HVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQLD  571 (1123)
T ss_pred             ----------------cCCCCE-EEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchhhh
Confidence                            034556 99999988654211       22346889999999985310                


Q ss_pred             -ccHHHHHHhccccccEEEEeccCCCCC
Q psy1090         136 -KSKLSIKLTALRATFKVLLTGWYYPNK  162 (169)
Q Consensus       136 -~~~~~~~~~~l~~~~~~~lT~TP~~n~  162 (169)
                       .+++.+.+..++ ..+++|||||..+.
T Consensus       572 ~~~~yr~iL~yFd-A~~IGLTATP~r~t  598 (1123)
T PRK11448        572 YVSKYRRVLDYFD-AVKIGLTATPALHT  598 (1123)
T ss_pred             HHHHHHHHHhhcC-ccEEEEecCCccch
Confidence             123333344445 58999999998764

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.65  E-value=3.1e-15  Score=120.66  Aligned_cols=136  Identities=13%  Similarity=0.115  Sum_probs=92.2

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHH--HHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERK--ALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~--~~~~~~   75 (169)
                      |+.++.-++|+|||..++..+......  ...++|++|. .+..|+.+++.++++  +.++..++|......  ......
T Consensus       257 ~~~Ll~g~TGSGKT~va~l~il~~~~~--g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i  334 (630)
T TIGR00643       257 MNRLLQGDVGSGKTLVAALAMLAAIEA--GYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETI  334 (630)
T ss_pred             ccEEEECCCCCcHHHHHHHHHHHHHHc--CCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHH
Confidence            456889999999998876544443333  3589999998 556799999999885  578888888643322  222111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccc---cccEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALR---ATFKV  152 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~---~~~~~  152 (169)
                      .                  .+..++ ++.|+..+.+...   -.+.+++|+||+|++..  .++........   .++.+
T Consensus       335 ~------------------~g~~~I-iVgT~~ll~~~~~---~~~l~lvVIDEaH~fg~--~qr~~l~~~~~~~~~~~~l  390 (630)
T TIGR00643       335 A------------------SGQIHL-VVGTHALIQEKVE---FKRLALVIIDEQHRFGV--EQRKKLREKGQGGFTPHVL  390 (630)
T ss_pred             h------------------CCCCCE-EEecHHHHhcccc---ccccceEEEechhhccH--HHHHHHHHhcccCCCCCEE
Confidence            1                  156677 9999988865432   23578999999999742  22233322333   57899


Q ss_pred             EEeccCCCCC
Q psy1090         153 LLTGWYYPNK  162 (169)
Q Consensus       153 ~lT~TP~~n~  162 (169)
                      +|||||.+..
T Consensus       391 ~~SATp~prt  400 (630)
T TIGR00643       391 VMSATPIPRT  400 (630)
T ss_pred             EEeCCCCcHH
Confidence            9999997653

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

Probab=99.64  E-value=2.7e-15  Score=102.10  Aligned_cols=142  Identities=23%  Similarity=0.229  Sum_probs=94.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      .++..++|+|||..++..+.....++....+++++|. .++.|-.+++.++..  ..++..+++............ .  
T Consensus        17 ~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~--   93 (169)
T PF00270_consen   17 VLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL-S--   93 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH-H--
T ss_pred             EEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccccccccccccccccccccccccc-c--
Confidence            4788899999999888666555544445689999997 677888899988874  467777776544221111111 1  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc-cH-HHHHHhcc---ccccEE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK-SK-LSIKLTAL---RATFKV  152 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~-~~-~~~~~~~l---~~~~~~  152 (169)
                                      ...++ +++|++.+......  ..-...+++|+||+|.+.... .. ....+..+   .....+
T Consensus        94 ----------------~~~~i-lv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i  156 (169)
T PF00270_consen   94 ----------------NQADI-LVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFKNIQII  156 (169)
T ss_dssp             ----------------TTSSE-EEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTTTSEEE
T ss_pred             ----------------ccccc-cccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCCCCCcEE
Confidence                            56677 99999998765543  122347999999999886531 11 22222333   346699


Q ss_pred             EEeccCCCCCchh
Q psy1090         153 LLTGWYYPNKWSK  165 (169)
Q Consensus       153 ~lT~TP~~n~~~e  165 (169)
                      ++||||- .++.+
T Consensus       157 ~~SAT~~-~~~~~  168 (169)
T PF00270_consen  157 LLSATLP-SNVEK  168 (169)
T ss_dssp             EEESSST-HHHHH
T ss_pred             EEeeCCC-hhHhh
Confidence            9999998 65544

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 ....

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

Probab=99.63  E-value=4.4e-15  Score=116.89  Aligned_cols=137  Identities=17%  Similarity=0.204  Sum_probs=99.7

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH-HHHHHHHHhCC--CceEEEEeCCHHH--HHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN-NWEAEFRKFAP--FVRTVKYYGNAIE--RKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~-qW~~e~~~~~~--~~~~~~~~g~~~~--~~~~~~~~   75 (169)
                      |+.+|..|+|+|||+.|+..+......+  ..+.+.+|..++. |=++.+.+|++  ++++...+|+-+-  +.......
T Consensus       284 M~RLlQGDVGSGKTvVA~laml~ai~~G--~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l  361 (677)
T COG1200         284 MNRLLQGDVGSGKTVVALLAMLAAIEAG--YQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQL  361 (677)
T ss_pred             hHHHhccCcCCCHHHHHHHHHHHHHHcC--CeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHH
Confidence            5678999999999988765554444444  6789999998775 78888999985  6778888886443  33333332


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccc-cccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALR-ATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~-~~~~~~l  154 (169)
                      ..                  +..++ ++-|+..+++..++   .+.+++|+||-|++.  -.++.+....=. .++.+.|
T Consensus       362 ~~------------------G~~~i-vVGTHALiQd~V~F---~~LgLVIiDEQHRFG--V~QR~~L~~KG~~~Ph~LvM  417 (677)
T COG1200         362 AS------------------GEIDI-VVGTHALIQDKVEF---HNLGLVIIDEQHRFG--VHQRLALREKGEQNPHVLVM  417 (677)
T ss_pred             hC------------------CCCCE-EEEcchhhhcceee---cceeEEEEecccccc--HHHHHHHHHhCCCCCcEEEE
Confidence            22                  77888 99999999887664   467899999999985  233333333334 6899999


Q ss_pred             eccCCCCCc
Q psy1090         155 TGWYYPNKW  163 (169)
Q Consensus       155 T~TP~~n~~  163 (169)
                      ||||++.++
T Consensus       418 TATPIPRTL  426 (677)
T COG1200         418 TATPIPRTL  426 (677)
T ss_pred             eCCCchHHH
Confidence            999998754

>KOG1123|consensus

Probab=99.61  E-value=1e-16  Score=121.85  Aligned_cols=128  Identities=22%  Similarity=0.348  Sum_probs=101.0

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++||+.-.+|.|||+..+..++.+.     +..||+|.+++ +.||.++|..|.  .+..+++++...+++..       
T Consensus       321 RSGiIVLPCGAGKtLVGvTAa~tik-----K~clvLcts~VSVeQWkqQfk~wsti~d~~i~rFTsd~Ke~~~-------  388 (776)
T KOG1123|consen  321 RSGIIVLPCGAGKTLVGVTAACTIK-----KSCLVLCTSAVSVEQWKQQFKQWSTIQDDQICRFTSDAKERFP-------  388 (776)
T ss_pred             cCceEEEecCCCCceeeeeeeeeec-----ccEEEEecCccCHHHHHHHHHhhcccCccceEEeeccccccCC-------
Confidence            3689999999999998887766543     57899999865 789999999997  46677888877665432       


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHh----------chhccccccccEEEEeCCcccCCcccHHHHHHhccc
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN----------DFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALR  147 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~----------~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~  147 (169)
                                        ....+ +++||+++..          -.+++...+|+++++||+|.+  +.....+.+.-+.
T Consensus       389 ------------------~~~gv-vvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvv--PA~MFRRVlsiv~  447 (776)
T KOG1123|consen  389 ------------------SGAGV-VVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVV--PAKMFRRVLSIVQ  447 (776)
T ss_pred             ------------------CCCcE-EEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccc--hHHHHHHHHHHHH
Confidence                              55556 9999999853          235777889999999999987  4455555556668


Q ss_pred             cccEEEEeccCCCC
Q psy1090         148 ATFKVLLTGWYYPN  161 (169)
Q Consensus       148 ~~~~~~lT~TP~~n  161 (169)
                      +-++++||||.++.
T Consensus       448 aHcKLGLTATLvRE  461 (776)
T KOG1123|consen  448 AHCKLGLTATLVRE  461 (776)
T ss_pred             HHhhccceeEEeec
Confidence            88999999999965

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.59  E-value=1.7e-14  Score=117.27  Aligned_cols=134  Identities=15%  Similarity=0.176  Sum_probs=90.8

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCHHH--HHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNAIE--RKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~~~--~~~~~~~~   75 (169)
                      |+.+|.-++|+|||..++..+......  ..+++|++|. .+..|..+.++++++.  .++..++|....  +.......
T Consensus       283 ~~~Ll~~~TGSGKT~va~~~il~~~~~--g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l  360 (681)
T PRK10917        283 MNRLLQGDVGSGKTVVAALAALAAIEA--GYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAI  360 (681)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHHHHc--CCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHH
Confidence            456889999999998877555443332  3579999998 5567999999988754  677888886543  22222221


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~l  154 (169)
                      ..                  +..++ ++.|+..+.....   -.+.+++|+||+|++.-  .. ...+... ..+..++|
T Consensus       361 ~~------------------g~~~I-vVgT~~ll~~~v~---~~~l~lvVIDE~Hrfg~--~q-r~~l~~~~~~~~iL~~  415 (681)
T PRK10917        361 AS------------------GEADI-VIGTHALIQDDVE---FHNLGLVIIDEQHRFGV--EQ-RLALREKGENPHVLVM  415 (681)
T ss_pred             hC------------------CCCCE-EEchHHHhcccch---hcccceEEEechhhhhH--HH-HHHHHhcCCCCCEEEE
Confidence            11                  56777 9999988765322   23678999999999732  22 2233322 35789999


Q ss_pred             eccCCCC
Q psy1090         155 TGWYYPN  161 (169)
Q Consensus       155 T~TP~~n  161 (169)
                      ||||.+.
T Consensus       416 SATp~pr  422 (681)
T PRK10917        416 TATPIPR  422 (681)
T ss_pred             eCCCCHH
Confidence            9999754

>cd00268 DEADc DEAD-box helicases

Probab=99.57  E-value=8e-14  Score=97.73  Aligned_cols=138  Identities=16%  Similarity=0.133  Sum_probs=88.4

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHh--CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEE--QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~--~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      +.++..++|+|||...+.. +..+...  ....+++|++|. .++.|+.+.+..+..  +..+..++|............
T Consensus        38 ~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (203)
T cd00268          38 DVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK  117 (203)
T ss_pred             cEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc
Confidence            4678899999999885444 4444333  234579999997 677899999888863  566677777554433221111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc-cHHH-HHHhccc-ccc
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK-SKLS-IKLTALR-ATF  150 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~-~~~~-~~~~~l~-~~~  150 (169)
                                          ...++ +++|.+.+.....  .+.-...+++|+||+|.+.+.. .... ..+..++ ...
T Consensus       118 --------------------~~~~i-iv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~~~~~~~~~~~l~~~~~  176 (203)
T cd00268         118 --------------------RGPHI-VVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQ  176 (203)
T ss_pred             --------------------CCCCE-EEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccChHHHHHHHHHhCCcccE
Confidence                                35566 8999876654221  1222357899999999876433 1112 2233343 567


Q ss_pred             EEEEeccCCC
Q psy1090         151 KVLLTGWYYP  160 (169)
Q Consensus       151 ~~~lT~TP~~  160 (169)
                      .+++||||-.
T Consensus       177 ~~~~SAT~~~  186 (203)
T cd00268         177 TLLFSATMPK  186 (203)
T ss_pred             EEEEeccCCH
Confidence            8999999984

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.

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

Probab=99.57  E-value=1.8e-15  Score=120.85  Aligned_cols=127  Identities=14%  Similarity=0.116  Sum_probs=94.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      ++|++.+|+|||.+|++++-.+...+..+++|+++-. +++.|-+..+..|.|....+........              
T Consensus       188 aLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~~~n~i~~~~~--------------  253 (875)
T COG4096         188 ALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGTKMNKIEDKKG--------------  253 (875)
T ss_pred             EEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCccceeeeecccC--------------
Confidence            5789999999999999999999999999999999986 6778999999999987665544322111              


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhc-------cccccccEEEEeCCcccCCcccHHHHHHhccccccEEEE
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-------LKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLL  154 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-------~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~l  154 (169)
                                   ...+++ +++||+.+......       +..-.||++|+||||+.   ..+-++.+...-...+++|
T Consensus       254 -------------~~s~~i-~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRg---i~~~~~~I~dYFdA~~~gL  316 (875)
T COG4096         254 -------------DTSSEI-YLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRG---IYSEWSSILDYFDAATQGL  316 (875)
T ss_pred             -------------CcceeE-EEeehHHHHhhhhccccccccCCCCceeEEEechhhhh---HHhhhHHHHHHHHHHHHhh
Confidence                         023455 99999999764432       22335899999999983   3333444444444577778


Q ss_pred             eccCCC
Q psy1090         155 TGWYYP  160 (169)
Q Consensus       155 T~TP~~  160 (169)
                      ||||-.
T Consensus       317 TATP~~  322 (875)
T COG4096         317 TATPKE  322 (875)
T ss_pred             ccCccc
Confidence            999986

>KOG0354|consensus

Probab=99.57  E-value=1.6e-14  Score=115.16  Aligned_cols=136  Identities=19%  Similarity=0.163  Sum_probs=93.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +++++-.+|+|||+.|.-++...++..+.+++++.+|. .++.|....+..+.-.-......|....+......+     
T Consensus        78 Ntii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~~~~T~~l~~~~~~~~r~~i~-----  152 (746)
T KOG0354|consen   78 NTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIPYSVTGQLGDTVPRSNRGEIV-----  152 (746)
T ss_pred             CeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCcccceeeccCccCCCchhhhh-----
Confidence            47899999999999998887777777777899999998 677777788887763233333333322211111111     


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhcccccc---ccEEEEeCCcccCCcccHHHHHHh---cc--ccccEE
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKIT---WNCIIVDEGHSVKNKKSKLSIKLT---AL--RATFKV  152 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~---~~~vi~DEah~~k~~~~~~~~~~~---~l--~~~~~~  152 (169)
                                     ...++ ++.|.+.+.++........   |.++|+||||+.... +.+....+   .+  .....+
T Consensus       153 ---------------~s~~v-ff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn-~~Y~~Vmr~~l~~k~~~~qIL  215 (746)
T KOG0354|consen  153 ---------------ASKRV-FFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKN-HPYNNIMREYLDLKNQGNQIL  215 (746)
T ss_pred             ---------------cccce-EEeChHhhhhhcccccccccceEEEEEEccccccccc-ccHHHHHHHHHHhhhccccEE
Confidence                           45566 9999999998876555444   889999999987643 33443332   22  233789


Q ss_pred             EEeccCC
Q psy1090         153 LLTGWYY  159 (169)
Q Consensus       153 ~lT~TP~  159 (169)
                      +|||||=
T Consensus       216 gLTASpG  222 (746)
T KOG0354|consen  216 GLTASPG  222 (746)
T ss_pred             EEecCCC
Confidence            9999996

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.52  E-value=3.1e-13  Score=112.33  Aligned_cols=135  Identities=17%  Similarity=0.170  Sum_probs=88.2

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCH--HHHHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNA--IERKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~--~~~~~~~~~~   75 (169)
                      |+.+++-++|+|||..++..+......+  ..++|++|. .+..|..+.+.+++..  .++..++|..  +++.......
T Consensus       473 ~d~Ll~adTGsGKT~val~a~l~al~~g--~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l  550 (926)
T TIGR00580       473 MDRLVCGDVGFGKTEVAMRAAFKAVLDG--KQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKEL  550 (926)
T ss_pred             CCEEEECCCCccHHHHHHHHHHHHHHhC--CeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHH
Confidence            4678999999999988765444333333  679999998 5567899999887643  4555555532  2222222211


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~l  154 (169)
                      ..                  +..++ ++.|+..+.+...   -.+.+++|+||+|++..   .....++.+ .....++|
T Consensus       551 ~~------------------g~~dI-VIGTp~ll~~~v~---f~~L~llVIDEahrfgv---~~~~~L~~~~~~~~vL~~  605 (926)
T TIGR00580       551 AS------------------GKIDI-LIGTHKLLQKDVK---FKDLGLLIIDEEQRFGV---KQKEKLKELRTSVDVLTL  605 (926)
T ss_pred             Hc------------------CCceE-EEchHHHhhCCCC---cccCCEEEeecccccch---hHHHHHHhcCCCCCEEEE
Confidence            11                  45677 9999977654322   23568999999999742   233444444 35679999


Q ss_pred             eccCCCCC
Q psy1090         155 TGWYYPNK  162 (169)
Q Consensus       155 T~TP~~n~  162 (169)
                      ||||.+..
T Consensus       606 SATpiprt  613 (926)
T TIGR00580       606 SATPIPRT  613 (926)
T ss_pred             ecCCCHHH
Confidence            99997643

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=99.51  E-value=2.6e-13  Score=114.96  Aligned_cols=136  Identities=19%  Similarity=0.217  Sum_probs=87.7

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCC--ceEEEEeC--CHHHHHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPF--VRTVKYYG--NAIERKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~--~~~~~~~g--~~~~~~~~~~~~   75 (169)
                      |+.+++.++|+|||..++-.+.....  ...+++|++|.. +..|..+.+.+++..  .++..+.|  +.+++.......
T Consensus       622 ~d~Ll~a~TGsGKT~val~aa~~~~~--~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l  699 (1147)
T PRK10689        622 MDRLVCGDVGFGKTEVAMRAAFLAVE--NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEA  699 (1147)
T ss_pred             CCEEEEcCCCcCHHHHHHHHHHHHHH--cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHH
Confidence            46789999999999877633322222  246899999985 557888888876533  45545554  333333222211


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~l  154 (169)
                      ..                  +..++ ++.|++.+.....   -.+.+++|+||+|++..   +....++.+ .....+++
T Consensus       700 ~~------------------g~~dI-VVgTp~lL~~~v~---~~~L~lLVIDEahrfG~---~~~e~lk~l~~~~qvLl~  754 (1147)
T PRK10689        700 AE------------------GKIDI-LIGTHKLLQSDVK---WKDLGLLIVDEEHRFGV---RHKERIKAMRADVDILTL  754 (1147)
T ss_pred             Hh------------------CCCCE-EEECHHHHhCCCC---HhhCCEEEEechhhcch---hHHHHHHhcCCCCcEEEE
Confidence            11                  45677 9999987754322   23678999999999842   223445555 35678999


Q ss_pred             eccCCCCCc
Q psy1090         155 TGWYYPNKW  163 (169)
Q Consensus       155 T~TP~~n~~  163 (169)
                      ||||.+...
T Consensus       755 SATpiprtl  763 (1147)
T PRK10689        755 TATPIPRTL  763 (1147)
T ss_pred             cCCCCHHHH
Confidence            999987543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.48  E-value=9.2e-13  Score=103.12  Aligned_cols=138  Identities=16%  Similarity=0.217  Sum_probs=89.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC-CCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ-ALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~-~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.++..++|+|||...+..+....... ....+||++|. .+..||.++++++.   ++.++..++|......+..... 
T Consensus        43 dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~-  121 (460)
T PRK11776         43 DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE-  121 (460)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc-
Confidence            467888999999977544443333332 23368999998 67789999998775   4677777777654433332221 


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCccc--HHHHHHhccc-cccE
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKKS--KLSIKLTALR-ATFK  151 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l~-~~~~  151 (169)
                                         ...++ +++|++.+......  +.-..++++|+||||++-...-  .....+..++ ....
T Consensus       122 -------------------~~~~I-vV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g~~~~l~~i~~~~~~~~q~  181 (460)
T PRK11776        122 -------------------HGAHI-IVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQT  181 (460)
T ss_pred             -------------------CCCCE-EEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcCcHHHHHHHHHhCCcccEE
Confidence                               45567 99999888654321  2223678999999998764331  1223334443 4457


Q ss_pred             EEEeccCCC
Q psy1090         152 VLLTGWYYP  160 (169)
Q Consensus       152 ~~lT~TP~~  160 (169)
                      +++|||+..
T Consensus       182 ll~SAT~~~  190 (460)
T PRK11776        182 LLFSATYPE  190 (460)
T ss_pred             EEEEecCcH
Confidence            999999853

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.47  E-value=6.8e-13  Score=104.03  Aligned_cols=138  Identities=17%  Similarity=0.088  Sum_probs=87.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHH--HHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIER--KALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~--~~~~~~~~~~   78 (169)
                      ++++..++|+|||+..+.-+.  .   ..+.+|||+|. .++.|+.+.+..+  +.......+.....  ..+.....  
T Consensus        28 dvlv~apTGsGKTl~y~lp~l--~---~~~~~lVi~P~~~L~~dq~~~l~~~--gi~~~~l~~~~~~~~~~~i~~~~~--   98 (470)
T TIGR00614        28 DCFVVMPTGGGKSLCYQLPAL--C---SDGITLVISPLISLMEDQVLQLKAS--GIPATFLNSSQSKEQQKNVLTDLK--   98 (470)
T ss_pred             CEEEEcCCCCcHhHHHHHHHH--H---cCCcEEEEecHHHHHHHHHHHHHHc--CCcEEEEeCCCCHHHHHHHHHHHh--
Confidence            367889999999976533222  1   23579999997 7778899998866  34555555543322  22221111  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhch---hcc-ccccccEEEEeCCcccCCcccH---HHH----HHhccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF---GFL-KKITWNCIIVDEGHSVKNKKSK---LSI----KLTALR  147 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~---~~~-~~~~~~~vi~DEah~~k~~~~~---~~~----~~~~l~  147 (169)
                                      .+..++ +++|++.+....   ..+ .....+++|+||||++...+..   .+.    ....+.
T Consensus        99 ----------------~~~~~i-l~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~~~~  161 (470)
T TIGR00614        99 ----------------DGKIKL-LYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFP  161 (470)
T ss_pred             ----------------cCCCCE-EEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHHHHHHcC
Confidence                            155677 999999876543   222 3457889999999998654321   111    122345


Q ss_pred             cccEEEEeccCCCCCchh
Q psy1090         148 ATFKVLLTGWYYPNKWSK  165 (169)
Q Consensus       148 ~~~~~~lT~TP~~n~~~e  165 (169)
                      ....+++||||......|
T Consensus       162 ~~~~l~lTAT~~~~~~~d  179 (470)
T TIGR00614       162 NVPIMALTATASPSVRED  179 (470)
T ss_pred             CCceEEEecCCCHHHHHH
Confidence            567899999998754444

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

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.47  E-value=1.4e-12  Score=101.95  Aligned_cols=138  Identities=15%  Similarity=0.168  Sum_probs=86.5

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHhCC------CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEEQA------LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKAL   71 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~~~------~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~   71 (169)
                      +.++..++|+|||+..+..+. .+.....      ...+||++|. .+..||.+++..+..  +++.....|........
T Consensus        40 dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~  119 (456)
T PRK10590         40 DLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQM  119 (456)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHH
Confidence            467888999999988654433 3322211      1258999997 777899999988763  45555566554333222


Q ss_pred             HHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhccc
Q psy1090          72 QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTALR  147 (169)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l~  147 (169)
                      ....                    ...+| +++|++.+.....  .+.-...+++|+||||++-....  .....+..+.
T Consensus       120 ~~l~--------------------~~~~I-iV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~~~~~i~~il~~l~  178 (456)
T PRK10590        120 MKLR--------------------GGVDV-LVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLP  178 (456)
T ss_pred             HHHc--------------------CCCcE-EEEChHHHHHHHHcCCcccccceEEEeecHHHHhccccHHHHHHHHHhCC
Confidence            2111                    45677 9999988754322  22234678999999998765332  1122333443


Q ss_pred             -cccEEEEeccCCC
Q psy1090         148 -ATFKVLLTGWYYP  160 (169)
Q Consensus       148 -~~~~~~lT~TP~~  160 (169)
                       ....+++|||+..
T Consensus       179 ~~~q~l~~SAT~~~  192 (456)
T PRK10590        179 AKRQNLLFSATFSD  192 (456)
T ss_pred             ccCeEEEEeCCCcH
Confidence             3457999999754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.44  E-value=2.2e-12  Score=100.01  Aligned_cols=138  Identities=12%  Similarity=0.090  Sum_probs=86.0

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHhC-------CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEEQ-------ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKA   70 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~~-------~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~   70 (169)
                      +.++..++|+|||+..+..+. .+....       ....+||++|. .+..|+.+++..+..  ++++..+.|.......
T Consensus        47 dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~  126 (423)
T PRK04837         47 DVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQ  126 (423)
T ss_pred             cEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHH
Confidence            357788999999988654433 332211       12368999998 677899988887763  5667666765433322


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhcc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL  146 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l  146 (169)
                      .....                    ...++ +++|++.+.....  .+.-..++++|+||||++-...-  .....+..+
T Consensus       127 ~~~l~--------------------~~~~I-lV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~~f~~~i~~i~~~~  185 (423)
T PRK04837        127 LKVLE--------------------SGVDI-LIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRM  185 (423)
T ss_pred             HHHhc--------------------CCCCE-EEECHHHHHHHHHcCCcccccccEEEEecHHHHhhcccHHHHHHHHHhC
Confidence            22111                    44577 9999988865432  22334678999999998765331  112223333


Q ss_pred             c---cccEEEEeccCCC
Q psy1090         147 R---ATFKVLLTGWYYP  160 (169)
Q Consensus       147 ~---~~~~~~lT~TP~~  160 (169)
                      .   ....+++|||+..
T Consensus       186 ~~~~~~~~~l~SAT~~~  202 (423)
T PRK04837        186 PPANQRLNMLFSATLSY  202 (423)
T ss_pred             CCccceeEEEEeccCCH
Confidence            2   2345889999753

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.42  E-value=4.2e-12  Score=102.34  Aligned_cols=137  Identities=13%  Similarity=0.130  Sum_probs=87.8

Q ss_pred             ccccCCCCCcHHHHHH-HHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      .++.-++|+|||...+ .++..+........+||+||. .+..|+.+++.++.   ++..+..++|............  
T Consensus        46 vl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~--  123 (629)
T PRK11634         46 VLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALR--  123 (629)
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhc--
Confidence            5677899999998754 333333333333468999998 67789999987764   5677777777654433332221  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhccc-cccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTALR-ATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l~-~~~~~  152 (169)
                                        ...++ +++|++.+.....  .+.-....++|+||||.+-....  .....+..++ ....+
T Consensus       124 ------------------~~~~I-VVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~gf~~di~~Il~~lp~~~q~l  184 (629)
T PRK11634        124 ------------------QGPQI-VVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTA  184 (629)
T ss_pred             ------------------CCCCE-EEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcccHHHHHHHHHhCCCCCeEE
Confidence                              44667 9999888765432  12223567899999998654332  2233344453 34578


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||+..
T Consensus       185 lfSAT~p~  192 (629)
T PRK11634        185 LFSATMPE  192 (629)
T ss_pred             EEEccCCh
Confidence            99999743

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.42  E-value=4.2e-12  Score=98.73  Aligned_cols=143  Identities=13%  Similarity=0.108  Sum_probs=87.7

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHh----CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEE----QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~----~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~   73 (169)
                      +.++...+|+|||...+..+. .+...    ....++||++|. .+..|+.+.+..+..  +..+..++|..........
T Consensus        40 d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~  119 (434)
T PRK11192         40 DVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEV  119 (434)
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHH
Confidence            457888999999988654433 33221    122479999997 677898888887753  5677777775433222111


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc-cHHH-HHHhccc-c
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK-SKLS-IKLTALR-A  148 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~-~~~~-~~~~~l~-~  148 (169)
                        ..                  ...++ +++|++.+.....  .+....++++|+||||++-... .... .....+. .
T Consensus       120 --l~------------------~~~~I-lV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~~~~~~~~i~~~~~~~  178 (434)
T PRK11192        120 --FS------------------ENQDI-VVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWR  178 (434)
T ss_pred             --hc------------------CCCCE-EEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCCcHHHHHHHHHhCccc
Confidence              11                  45567 9999988765432  2233467899999999876433 1111 2222232 3


Q ss_pred             ccEEEEeccCCCCCchh
Q psy1090         149 TFKVLLTGWYYPNKWSK  165 (169)
Q Consensus       149 ~~~~~lT~TP~~n~~~e  165 (169)
                      ...+++|||+....+.+
T Consensus       179 ~q~~~~SAT~~~~~~~~  195 (434)
T PRK11192        179 KQTLLFSATLEGDAVQD  195 (434)
T ss_pred             cEEEEEEeecCHHHHHH
Confidence            45689999986543333

>PTZ00424 helicase 45; Provisional

Probab=99.40  E-value=5.7e-12  Score=97.00  Aligned_cols=138  Identities=14%  Similarity=0.158  Sum_probs=85.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.++..++|+|||..++..+...... ....++||++|. .+..|+.+.+..+..  ........|....+.......  
T Consensus        67 d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--  144 (401)
T PTZ00424         67 DTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLK--  144 (401)
T ss_pred             CEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHc--
Confidence            35778899999998765444333322 234579999997 667788888777653  334444455443332222111  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~~  152 (169)
                                        ...++ +++|++.+.....  .+.-..++++|+||+|++....  ......++.+ .....+
T Consensus       145 ------------------~~~~I-vv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~~~~~~~~i~~~~~~~~~~i  205 (401)
T PTZ00424        145 ------------------AGVHM-VVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVA  205 (401)
T ss_pred             ------------------CCCCE-EEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcchHHHHHHHHhhCCCCcEEE
Confidence                              33466 9999887654322  2233467899999999875432  2233444555 345689


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||+..
T Consensus       206 ~~SAT~~~  213 (401)
T PTZ00424        206 LFSATMPN  213 (401)
T ss_pred             EEEecCCH
Confidence            99999753

>TIGR00595 priA primosomal protein N'

Probab=99.40  E-value=1.7e-11  Score=96.66  Aligned_cols=132  Identities=12%  Similarity=-0.006  Sum_probs=84.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCH--HHHHHHHHhhhcCCC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNA--IERKALQSEALSLPT   80 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~--~~~~~~~~~~~~~~~   80 (169)
                      +|.-.+|+|||...+.++......+  +.+||++|. .+..|+.+.+++.+ +..+..+++..  .++...+.....   
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g--~~vLvlvP~i~L~~Q~~~~l~~~f-~~~v~vlhs~~~~~er~~~~~~~~~---   74 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALG--KSVLVLVPEIALTPQMIQRFKYRF-GSQVAVLHSGLSDSEKLQAWRKVKN---   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCcHHHHHHHHHHHHHHh-CCcEEEEECCCCHHHHHHHHHHHHc---
Confidence            3566899999999887776655443  679999998 67789999998876 34566677643  233222222111   


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCC--cccHHH-----HHH-hccccccEE
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKN--KKSKLS-----IKL-TALRATFKV  152 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~--~~~~~~-----~~~-~~l~~~~~~  152 (169)
                                     +..++ ++.|++.+..   .  -.+.+++|+||.|...-  ...-.+     ... ........+
T Consensus        75 ---------------g~~~I-VVGTrsalf~---p--~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vi  133 (505)
T TIGR00595        75 ---------------GEILV-VIGTRSALFL---P--FKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVV  133 (505)
T ss_pred             ---------------CCCCE-EECChHHHcC---c--ccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEE
Confidence                           55667 9999887632   1  23569999999997542  111111     111 123445688


Q ss_pred             EEeccCCCCC
Q psy1090         153 LLTGWYYPNK  162 (169)
Q Consensus       153 ~lT~TP~~n~  162 (169)
                      ++||||...+
T Consensus       134 l~SATPsles  143 (505)
T TIGR00595       134 LGSATPSLES  143 (505)
T ss_pred             EEeCCCCHHH
Confidence            8999998543

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).

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.39  E-value=7.8e-12  Score=98.28  Aligned_cols=138  Identities=12%  Similarity=0.097  Sum_probs=86.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC--------CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA--------LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKA   70 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~--------~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~   70 (169)
                      +.++.-.+|+|||+..+--+........        ...+||++|. .+..|+.+++..+..  +.++..++|..+....
T Consensus       126 dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~  205 (475)
T PRK01297        126 DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQ  205 (475)
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHH
Confidence            3577889999999876544333222221        2468999997 777899998887763  4566667775433222


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhcc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL  146 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l  146 (169)
                      ......                   ...++ +++|++.+.....  ...-...+++|+||+|++.+..-  ...+.+..+
T Consensus       206 ~~~~~~-------------------~~~~I-iv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~~~~~~l~~i~~~~  265 (475)
T PRK01297        206 LKQLEA-------------------RFCDI-LVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQT  265 (475)
T ss_pred             HHHHhC-------------------CCCCE-EEECHHHHHHHHHcCCcccccCceEEechHHHHHhcccHHHHHHHHHhC
Confidence            222111                   45677 9999999864322  11223567999999999865432  122233333


Q ss_pred             c---cccEEEEeccCC
Q psy1090         147 R---ATFKVLLTGWYY  159 (169)
Q Consensus       147 ~---~~~~~~lT~TP~  159 (169)
                      .   ....+++|||..
T Consensus       266 ~~~~~~q~i~~SAT~~  281 (475)
T PRK01297        266 PRKEERQTLLFSATFT  281 (475)
T ss_pred             CCCCCceEEEEEeecC
Confidence            2   346899999964

>PRK02362 ski2-like helicase; Provisional

Probab=99.38  E-value=5.6e-12  Score=103.72  Aligned_cols=132  Identities=20%  Similarity=0.120  Sum_probs=85.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.+++-++|+|||+.+...+.....  ..+++|+++|. .+..|+.+++.++.+ +.++..++|.......    .    
T Consensus        41 nvlv~APTGSGKTlia~lail~~l~--~~~kal~i~P~raLa~q~~~~~~~~~~~g~~v~~~tGd~~~~~~----~----  110 (737)
T PRK02362         41 NLLAAIPTASGKTLIAELAMLKAIA--RGGKALYIVPLRALASEKFEEFERFEELGVRVGISTGDYDSRDE----W----  110 (737)
T ss_pred             cEEEECCCcchHHHHHHHHHHHHHh--cCCcEEEEeChHHHHHHHHHHHHHhhcCCCEEEEEeCCcCcccc----c----
Confidence            4678899999999887544333322  34689999997 788899999998753 6778888876432210    0    


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc-cHHHHH-H---hcc-ccccE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK-SKLSIK-L---TAL-RATFK  151 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~-~~~~~~-~---~~l-~~~~~  151 (169)
                                     ....++ +++|++.+......  ..-...+++|+||+|.+.+.. ...... +   +.+ .....
T Consensus       111 ---------------l~~~~I-iV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~le~il~rl~~~~~~~qi  174 (737)
T PRK02362        111 ---------------LGDNDI-IVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTLEVTLAKLRRLNPDLQV  174 (737)
T ss_pred             ---------------cCCCCE-EEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHHHHHHHHHHhcCCCCcE
Confidence                           044567 99998876443221  001256899999999986432 111221 2   222 34568


Q ss_pred             EEEeccCC
Q psy1090         152 VLLTGWYY  159 (169)
Q Consensus       152 ~~lT~TP~  159 (169)
                      ++||||+.
T Consensus       175 i~lSATl~  182 (737)
T PRK02362        175 VALSATIG  182 (737)
T ss_pred             EEEcccCC
Confidence            99999974

>PRK00254 ski2-like helicase; Provisional

Probab=99.38  E-value=7.3e-12  Score=102.85  Aligned_cols=130  Identities=15%  Similarity=0.165  Sum_probs=86.0

Q ss_pred             CccccCCCCCcHHHHHH-HHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +.+++..+|+|||..+. +++..+..  ..+++|+++|. .+..|+.+++.+|.. +.++..++|........       
T Consensus        41 nvlv~apTGsGKT~~~~l~il~~l~~--~~~~~l~l~P~~aLa~q~~~~~~~~~~~g~~v~~~~Gd~~~~~~~-------  111 (720)
T PRK00254         41 NLVLAIPTASGKTLVAEIVMVNKLLR--EGGKAVYLVPLKALAEEKYREFKDWEKLGLRVAMTTGDYDSTDEW-------  111 (720)
T ss_pred             cEEEECCCCcHHHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHHHHHHHHHhhcCCEEEEEeCCCCCchhh-------
Confidence            46788999999999884 44433332  24689999997 677899998887642 56777777764322110       


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchh----ccccccccEEEEeCCcccCCc--ccHHHHHHhcc-ccccE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG----FLKKITWNCIIVDEGHSVKNK--KSKLSIKLTAL-RATFK  151 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~----~~~~~~~~~vi~DEah~~k~~--~~~~~~~~~~l-~~~~~  151 (169)
                                      ....++ +++|++.+.....    ++  .+.+++|+||+|.+...  .......+..+ .....
T Consensus       112 ----------------~~~~~I-iV~Tpe~~~~ll~~~~~~l--~~l~lvViDE~H~l~~~~rg~~le~il~~l~~~~qi  172 (720)
T PRK00254        112 ----------------LGKYDI-IIATAEKFDSLLRHGSSWI--KDVKLVVADEIHLIGSYDRGATLEMILTHMLGRAQI  172 (720)
T ss_pred             ----------------hccCCE-EEEcHHHHHHHHhCCchhh--hcCCEEEEcCcCccCCccchHHHHHHHHhcCcCCcE
Confidence                            144567 9999887654322    22  25789999999998542  22223333333 45678


Q ss_pred             EEEeccCC
Q psy1090         152 VLLTGWYY  159 (169)
Q Consensus       152 ~~lT~TP~  159 (169)
                      ++||||+-
T Consensus       173 I~lSATl~  180 (720)
T PRK00254        173 LGLSATVG  180 (720)
T ss_pred             EEEEccCC
Confidence            99999974

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.37  E-value=1.1e-11  Score=99.28  Aligned_cols=138  Identities=13%  Similarity=0.102  Sum_probs=86.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC--------CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ--------ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKA   70 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~--------~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~   70 (169)
                      +.++.-++|+|||+..+..+.......        ....+||++|. .+..|+.+++.+|..  ++++...+|.......
T Consensus        48 Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q  127 (572)
T PRK04537         48 DVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQ  127 (572)
T ss_pred             CEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHH
Confidence            357788999999988765544322211        12479999998 777899999998874  4556666665433222


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCccc--HHHHHHhc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTA  145 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~  145 (169)
                      .....                    ...++ +++|++.+.+...   .+.-...+++|+||||++-...-  .....+..
T Consensus       128 ~~~l~--------------------~~~dI-iV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~gf~~~i~~il~~  186 (572)
T PRK04537        128 RELLQ--------------------QGVDV-IIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRR  186 (572)
T ss_pred             HHHHh--------------------CCCCE-EEECHHHHHHHHHhccccchhheeeeEecCHHHHhhcchHHHHHHHHHh
Confidence            11111                    44677 9999988765432   22233567899999998754221  11222333


Q ss_pred             cc---cccEEEEeccCCC
Q psy1090         146 LR---ATFKVLLTGWYYP  160 (169)
Q Consensus       146 l~---~~~~~~lT~TP~~  160 (169)
                      +.   ....+++|||...
T Consensus       187 lp~~~~~q~ll~SATl~~  204 (572)
T PRK04537        187 MPERGTRQTLLFSATLSH  204 (572)
T ss_pred             cccccCceEEEEeCCccH
Confidence            33   3457899999754

>PTZ00110 helicase; Provisional

Probab=99.36  E-value=1.2e-11  Score=98.52  Aligned_cols=137  Identities=12%  Similarity=0.139  Sum_probs=84.5

Q ss_pred             CccccCCCCCcHHHHHHH-HHHHHHHhC-----CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIA-FFCKIIEEQ-----ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQ   72 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~-~i~~~~~~~-----~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~   72 (169)
                      +.|+..++|+|||+..+. .+..+....     ....+||++|. .+..|+.+++.+|..  ..+....+|......+..
T Consensus       169 dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~  248 (545)
T PTZ00110        169 DMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIY  248 (545)
T ss_pred             CEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHH
Confidence            357788999999987543 333333221     12248999997 777899999999874  345555555433333222


Q ss_pred             HhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCccc--HHHHHHhcc-c
Q psy1090          73 SEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL-R  147 (169)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l-~  147 (169)
                      ...                    ...++ +++|++.+.+....  ..-...+++|+||||++-....  ...+.+..+ .
T Consensus       249 ~l~--------------------~~~~I-lVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~  307 (545)
T PTZ00110        249 ALR--------------------RGVEI-LIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRP  307 (545)
T ss_pred             HHH--------------------cCCCE-EEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCC
Confidence            221                    44567 99999877543321  1223578999999998765331  122333344 3


Q ss_pred             cccEEEEeccCC
Q psy1090         148 ATFKVLLTGWYY  159 (169)
Q Consensus       148 ~~~~~~lT~TP~  159 (169)
                      ....+++|||..
T Consensus       308 ~~q~l~~SAT~p  319 (545)
T PTZ00110        308 DRQTLMWSATWP  319 (545)
T ss_pred             CCeEEEEEeCCC
Confidence            455789999964

>COG4889 Predicted helicase [General function prediction only]

Probab=99.36  E-value=2.3e-13  Score=109.73  Aligned_cols=150  Identities=13%  Similarity=0.104  Sum_probs=87.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      |=|.+.+|+|||++++-+...+..    .++|+++|+ +++.|-.+|+..-. -+++........+..+  .++....+.
T Consensus       183 GkLIMAcGTGKTfTsLkisEala~----~~iL~LvPSIsLLsQTlrew~~~~~l~~~a~aVcSD~kvsr--s~eDik~sd  256 (1518)
T COG4889         183 GKLIMACGTGKTFTSLKISEALAA----ARILFLVPSISLLSQTLREWTAQKELDFRASAVCSDDKVSR--SAEDIKASD  256 (1518)
T ss_pred             CcEEEecCCCccchHHHHHHHHhh----hheEeecchHHHHHHHHHHHhhccCccceeEEEecCccccc--ccccccccc
Confidence            446778999999999988777664    569999998 67777666654221 1333333333222211  122222222


Q ss_pred             cccccc-------cCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCC-----cccHHHHHH---
Q psy1090          81 IKVPAK-------KGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKN-----KKSKLSIKL---  143 (169)
Q Consensus        81 ~~~~~~-------~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~-----~~~~~~~~~---  143 (169)
                      ...+.+       +.....++....-+ +++||+++.+-  .+..---+||++||||||+-.+     .+...+-.+   
T Consensus       257 l~~p~sT~~~~il~~~~~~~k~~~~~v-vFsTYQSl~~i~eAQe~G~~~fDliicDEAHRTtGa~~a~dd~saFt~vHs~  335 (1518)
T COG4889         257 LPIPVSTDLEDILSEMEHRQKANGLTV-VFSTYQSLPRIKEAQEAGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSD  335 (1518)
T ss_pred             CCCCCcccHHHHHHHHHHhhccCCcEE-EEEcccchHHHHHHHHcCCCCccEEEecchhccccceecccCcccceeecCc
Confidence            211111       11112223344444 99999998753  3333445899999999998544     112122222   


Q ss_pred             hccccccEEEEeccCC
Q psy1090         144 TALRATFKVLLTGWYY  159 (169)
Q Consensus       144 ~~l~~~~~~~lT~TP~  159 (169)
                      ..+++.+|+.|||||-
T Consensus       336 ~niKa~kRlYmTATPk  351 (1518)
T COG4889         336 QNIKAAKRLYMTATPK  351 (1518)
T ss_pred             chhHHHHhhhcccCch
Confidence            2457888999999995

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.36  E-value=1.3e-11  Score=93.64  Aligned_cols=151  Identities=15%  Similarity=0.080  Sum_probs=85.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      .++..++|+|||..++..+......+...++++++|. .++.|+.+.+..++.. ++..+++............    ..
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~~-~~~~~~~~~~~~~~~~~~~----~~   76 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGS-NLGLLHSSSSFKRIKEMGD----SE   76 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhCc-ccEEeeccHHHHHHhccCC----ch
Confidence            4678899999999988887766555666789999997 7788999999887633 4444555432111000000    00


Q ss_pred             cccccc--CCccccccCCCCeEEEecHHHHHhchhc-c-------ccccccEEEEeCCcccCCcccH-HHHHHhccc--c
Q psy1090          82 KVPAKK--GKTKKQISLKLPLILVTTPQIIENDFGF-L-------KKITWNCIIVDEGHSVKNKKSK-LSIKLTALR--A  148 (169)
Q Consensus        82 ~~~~~~--~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~-------~~~~~~~vi~DEah~~k~~~~~-~~~~~~~l~--~  148 (169)
                      ......  ...........++ +++|++.+...... +       ......++|+||+|.+...... ....+..+.  .
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~I-~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~l~~~l~~l~~~~  155 (358)
T TIGR01587        77 EFEHLFPLYIHSNDKLFLDPI-TVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLALILAVLEVLKDND  155 (358)
T ss_pred             hHHHHHHHHhhchhhhhhCCe-eeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHHHHHHHHHHHHcC
Confidence            000000  0000000133456 89999887654322 1       1223478999999998643211 122222222  3


Q ss_pred             ccEEEEeccCC
Q psy1090         149 TFKVLLTGWYY  159 (169)
Q Consensus       149 ~~~~~lT~TP~  159 (169)
                      ...+++|||+.
T Consensus       156 ~~~i~~SATlp  166 (358)
T TIGR01587       156 VPILLMSATLP  166 (358)
T ss_pred             CCEEEEecCch
Confidence            45799999975

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.

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

Probab=99.36  E-value=1.2e-11  Score=102.75  Aligned_cols=135  Identities=20%  Similarity=0.239  Sum_probs=89.4

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHH-HHHHHH-HhCCCceEE--E--EeCCHHHHHHHHHh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNN-WEAEFR-KFAPFVRTV--K--YYGNAIERKALQSE   74 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~q-W~~e~~-~~~~~~~~~--~--~~g~~~~~~~~~~~   74 (169)
                      |..++|.|+|.|||=.|+=.+-.  .-...+.+.|+||..++.| =++.|. +|. ++.+-  .  -.-+.++.+.....
T Consensus       616 MDRLiCGDVGFGKTEVAmRAAFk--AV~~GKQVAvLVPTTlLA~QHy~tFkeRF~-~fPV~I~~LSRF~s~kE~~~il~~  692 (1139)
T COG1197         616 MDRLICGDVGFGKTEVAMRAAFK--AVMDGKQVAVLVPTTLLAQQHYETFKERFA-GFPVRIEVLSRFRSAKEQKEILKG  692 (1139)
T ss_pred             chheeecCcCCcHHHHHHHHHHH--HhcCCCeEEEEcccHHhHHHHHHHHHHHhc-CCCeeEEEecccCCHHHHHHHHHH
Confidence            67899999999999776632221  1233478999999998864 334443 444 33222  2  22233333333333


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccc-cccEEE
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALR-ATFKVL  153 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~-~~~~~~  153 (169)
                      -..                  +..|| +|-|+..+.+++.+   .+.+++|+||-|++.-.   --..++.++ ....+-
T Consensus       693 la~------------------G~vDI-vIGTHrLL~kdv~F---kdLGLlIIDEEqRFGVk---~KEkLK~Lr~~VDvLT  747 (1139)
T COG1197         693 LAE------------------GKVDI-VIGTHRLLSKDVKF---KDLGLLIIDEEQRFGVK---HKEKLKELRANVDVLT  747 (1139)
T ss_pred             Hhc------------------CCccE-EEechHhhCCCcEE---ecCCeEEEechhhcCcc---HHHHHHHHhccCcEEE
Confidence            222                  88888 99999999887765   46789999999998643   345556663 567899


Q ss_pred             EeccCCCCCc
Q psy1090         154 LTGWYYPNKW  163 (169)
Q Consensus       154 lT~TP~~n~~  163 (169)
                      |||||++..+
T Consensus       748 LSATPIPRTL  757 (1139)
T COG1197         748 LSATPIPRTL  757 (1139)
T ss_pred             eeCCCCcchH
Confidence            9999997654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.36  E-value=1.7e-11  Score=98.72  Aligned_cols=139  Identities=19%  Similarity=0.199  Sum_probs=88.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHH--HHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIE--RKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~   78 (169)
                      +.++..++|.|||+.....+.  .   ..+.++||+|. +++.|+.+.++..  +..+..+++....  .........  
T Consensus        30 dvlv~~PTG~GKTl~y~lpal--~---~~g~~lVisPl~sL~~dq~~~l~~~--gi~~~~~~s~~~~~~~~~~~~~l~--  100 (591)
T TIGR01389        30 DVLVVMPTGGGKSLCYQVPAL--L---LKGLTVVISPLISLMKDQVDQLRAA--GVAAAYLNSTLSAKEQQDIEKALV--  100 (591)
T ss_pred             CEEEEcCCCccHhHHHHHHHH--H---cCCcEEEEcCCHHHHHHHHHHHHHc--CCcEEEEeCCCCHHHHHHHHHHHh--
Confidence            467889999999987643322  2   23578999997 6778899888876  4555556654322  222221111  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcccH-------HHHHHhccccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKKSK-------LSIKLTALRAT  149 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~~~-------~~~~~~~l~~~  149 (169)
                                      .+..++ ++.|++.+...  ...+.....+++|+||||++...+..       .......+...
T Consensus       101 ----------------~~~~~i-l~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~l~~~~~~~  163 (591)
T TIGR01389       101 ----------------NGELKL-LYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQV  163 (591)
T ss_pred             ----------------CCCCCE-EEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHHHHHhCCCC
Confidence                            155667 88888887532  23445568899999999998653321       11222334445


Q ss_pred             cEEEEeccCCCCCchhh
Q psy1090         150 FKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       150 ~~~~lT~TP~~n~~~el  166 (169)
                      ..+++|||+......|+
T Consensus       164 ~vi~lTAT~~~~~~~~i  180 (591)
T TIGR01389       164 PRIALTATADAETRQDI  180 (591)
T ss_pred             CEEEEEeCCCHHHHHHH
Confidence            58999999976654443

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.

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

Probab=99.35  E-value=1.7e-11  Score=97.22  Aligned_cols=138  Identities=13%  Similarity=0.128  Sum_probs=85.9

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHh-------CCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEE-------QALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNAIERKA   70 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~-------~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~~~~~~   70 (169)
                      +.++..++|+|||+..+.- +..+...       +....+||++|. .+..|+.+++..+...  .+.....|.......
T Consensus       160 dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q  239 (518)
T PLN00206        160 SLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQ  239 (518)
T ss_pred             CEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHH
Confidence            4678889999999876543 3333221       123469999997 6778998888877643  344444443322222


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL  146 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l  146 (169)
                      .....                    ...++ +++|++.+.....  .+.-....++|+||||++...+  ....+.+..+
T Consensus       240 ~~~l~--------------------~~~~I-iV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l  298 (518)
T PLN00206        240 LYRIQ--------------------QGVEL-IVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQAL  298 (518)
T ss_pred             HHHhc--------------------CCCCE-EEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcchHHHHHHHHHhC
Confidence            22111                    44567 9999987754322  2222356799999999886532  2223444556


Q ss_pred             ccccEEEEeccCCC
Q psy1090         147 RATFKVLLTGWYYP  160 (169)
Q Consensus       147 ~~~~~~~lT~TP~~  160 (169)
                      .....+++|||...
T Consensus       299 ~~~q~l~~SATl~~  312 (518)
T PLN00206        299 SQPQVLLFSATVSP  312 (518)
T ss_pred             CCCcEEEEEeeCCH
Confidence            67788999999854

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.35  E-value=1.2e-11  Score=101.06  Aligned_cols=133  Identities=15%  Similarity=0.081  Sum_probs=91.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.+++-.+|+|||+.++..+..-..++ .++++.|||. ++..+=.++|.+|. -+.++..++|+.......        
T Consensus        49 N~li~aPTgsGKTlIA~lai~~~l~~~-~~k~vYivPlkALa~Ek~~~~~~~~~~GirV~~~TgD~~~~~~~--------  119 (766)
T COG1204          49 NVLISAPTGSGKTLIALLAILSTLLEG-GGKVVYIVPLKALAEEKYEEFSRLEELGIRVGISTGDYDLDDER--------  119 (766)
T ss_pred             cEEEEcCCCCchHHHHHHHHHHHHHhc-CCcEEEEeChHHHHHHHHHHhhhHHhcCCEEEEecCCcccchhh--------
Confidence            478899999999999887766554443 5799999996 77778888888443 278999999986643311        


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCc-ccHHH-----HHHhccccccE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNK-KSKLS-----IKLTALRATFK  151 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~-~~~~~-----~~~~~l~~~~~  151 (169)
                                     ..+.+| +++||+.+...-..  .-....+++|+||+|.+..+ -....     +........+.
T Consensus       120 ---------------l~~~~V-iVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~iv~r~~~~~~~~ri  183 (766)
T COG1204         120 ---------------LARYDV-IVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRRLNELIRI  183 (766)
T ss_pred             ---------------hccCCE-EEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehhHHHHHHhhCcceEE
Confidence                           167777 99999987532111  02236789999999998765 22222     22222223578


Q ss_pred             EEEeccCC
Q psy1090         152 VLLTGWYY  159 (169)
Q Consensus       152 ~~lT~TP~  159 (169)
                      ++||||--
T Consensus       184 vgLSATlp  191 (766)
T COG1204         184 VGLSATLP  191 (766)
T ss_pred             EEEeeecC
Confidence            99999964

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.35  E-value=1.5e-11  Score=99.12  Aligned_cols=138  Identities=17%  Similarity=0.075  Sum_probs=84.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHH--HHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIER--KALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~--~~~~~~~~~~   78 (169)
                      ++++..++|+|||+.....+.  ..   .+.+|||+|. +++.|+.+.+...  +.......+.....  ........  
T Consensus        42 dvlv~apTGsGKTl~y~lpal--~~---~g~tlVisPl~sL~~dqv~~l~~~--gi~~~~~~s~~~~~~~~~~~~~~~--  112 (607)
T PRK11057         42 DCLVVMPTGGGKSLCYQIPAL--VL---DGLTLVVSPLISLMKDQVDQLLAN--GVAAACLNSTQTREQQLEVMAGCR--  112 (607)
T ss_pred             CEEEEcCCCchHHHHHHHHHH--Hc---CCCEEEEecHHHHHHHHHHHHHHc--CCcEEEEcCCCCHHHHHHHHHHHh--
Confidence            467889999999976543322  11   3579999997 6778899888866  34444444433222  11111111  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcccH---HHHHH----hccccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKKSK---LSIKL----TALRAT  149 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~~~---~~~~~----~~l~~~  149 (169)
                                      .+..++ ++.|++.+...  .+.+...+++++|+||||++...+..   .++.+    ..+...
T Consensus       113 ----------------~g~~~i-l~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~p~~  175 (607)
T PRK11057        113 ----------------TGQIKL-LYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL  175 (607)
T ss_pred             ----------------CCCCcE-EEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHHHHHhCCCC
Confidence                            145566 77888877532  23344557899999999988653321   12222    233455


Q ss_pred             cEEEEeccCCCCCchh
Q psy1090         150 FKVLLTGWYYPNKWSK  165 (169)
Q Consensus       150 ~~~~lT~TP~~n~~~e  165 (169)
                      ..+++|||+....-.|
T Consensus       176 ~~v~lTAT~~~~~~~d  191 (607)
T PRK11057        176 PFMALTATADDTTRQD  191 (607)
T ss_pred             cEEEEecCCChhHHHH
Confidence            6899999998664443

>PRK09401 reverse gyrase; Reviewed

Probab=99.32  E-value=4.8e-11  Score=101.64  Aligned_cols=110  Identities=19%  Similarity=0.234  Sum_probs=73.0

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCC----HHHHHHHHHhh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGN----AIERKALQSEA   75 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~----~~~~~~~~~~~   75 (169)
                      .++..++|+|||..++..+..+  .....++||++|. .++.|+.+.++++...  ..+....|.    .+++.......
T Consensus        98 v~i~ApTGsGKT~f~l~~~~~l--~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l  175 (1176)
T PRK09401         98 FAIIAPTGVGKTTFGLVMSLYL--AKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERL  175 (1176)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH--HhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHH
Confidence            4677899999996444333332  2234689999998 6778999999998743  333333322    12222111111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccC
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k  133 (169)
                      .                  .+.+++ +++|++.+.+..+.+....++++|+||||++-
T Consensus       176 ~------------------~~~~~I-lV~Tp~rL~~~~~~l~~~~~~~lVvDEaD~~L  214 (1176)
T PRK09401        176 K------------------EGDFDI-LVTTSQFLSKNFDELPKKKFDFVFVDDVDAVL  214 (1176)
T ss_pred             h------------------cCCCCE-EEECHHHHHHHHHhccccccCEEEEEChHHhh
Confidence            1                  045677 99999999887776666679999999999865

>PRK01172 ski2-like helicase; Provisional

Probab=99.32  E-value=2.3e-11  Score=99.29  Aligned_cols=132  Identities=11%  Similarity=0.071  Sum_probs=83.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.+++.++|+|||+.+...+......  .+++++++|. .+..|+.+++.++.. +.++...+|........        
T Consensus        39 nvlv~apTGSGKTl~a~lail~~l~~--~~k~v~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~~~~~~~~--------  108 (674)
T PRK01172         39 NVIVSVPTAAGKTLIAYSAIYETFLA--GLKSIYIVPLRSLAMEKYEELSRLRSLGMRVKISIGDYDDPPDF--------  108 (674)
T ss_pred             cEEEECCCCchHHHHHHHHHHHHHHh--CCcEEEEechHHHHHHHHHHHHHHhhcCCeEEEEeCCCCCChhh--------
Confidence            46888999999998876554443333  3679999997 677899999987642 45666666653321110        


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc-cHHHHHH----hcc-ccccE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK-SKLSIKL----TAL-RATFK  151 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~-~~~~~~~----~~l-~~~~~  151 (169)
                                     ....++ +++|++.+......  ..-.+++++|+||+|.+.... ......+    +.+ ...+.
T Consensus       109 ---------------~~~~dI-iv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le~ll~~~~~~~~~~ri  172 (674)
T PRK01172        109 ---------------IKRYDV-VILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPDARI  172 (674)
T ss_pred             ---------------hccCCE-EEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHHHHHHHHHhcCcCCcE
Confidence                           034567 89998765432211  111357899999999986432 1122222    222 24567


Q ss_pred             EEEeccCC
Q psy1090         152 VLLTGWYY  159 (169)
Q Consensus       152 ~~lT~TP~  159 (169)
                      ++||||+-
T Consensus       173 I~lSATl~  180 (674)
T PRK01172        173 LALSATVS  180 (674)
T ss_pred             EEEeCccC
Confidence            99999973

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.30  E-value=7.1e-11  Score=89.66  Aligned_cols=150  Identities=13%  Similarity=0.086  Sum_probs=82.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC------CCceEEEEeCCHHHH-HHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA------PFVRTVKYYGNAIER-KALQSE   74 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~------~~~~~~~~~g~~~~~-~~~~~~   74 (169)
                      .++.-.+|+|||..++..+..     ...++++++|. .+.+||.+.+.+++      .+..+..++|..... ......
T Consensus        17 ~~i~apTGsGKT~~~~~~~l~-----~~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v~~~~g~~~~d~~~~~~~   91 (357)
T TIGR03158        17 IFNTAPTGAGKTLAWLTPLLH-----GENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNLLHVSKATLKDIKEYAND   91 (357)
T ss_pred             EEEECCCCCCHHHHHHHHHHH-----cCCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceEEEecCCchHHHHHhhhh
Confidence            466889999999877544331     23578999997 67788888888775      245666677752221 111111


Q ss_pred             hhcCCCcccccccCC-ccccccCCCCeEEEecHHHHHhchhc---c-------ccccccEEEEeCCcccCCccc------
Q psy1090          75 ALSLPTIKVPAKKGK-TKKQISLKLPLILVTTPQIIENDFGF---L-------KKITWNCIIVDEGHSVKNKKS------  137 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~-~~~~~~~~~~ii~i~ty~~~~~~~~~---~-------~~~~~~~vi~DEah~~k~~~~------  137 (169)
                      .......  ...... .........++ ++|+++.+......   .       ....++++|+||+|.+.....      
T Consensus        92 ~~~~~~g--~~~~~~~r~~~~~~~p~i-llT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~H~~~~~~~~~~~~~  168 (357)
T TIGR03158        92 KVGSSKG--EKLYNLLRNPIGTSTPII-LLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFHLYDAKQLVGMLFL  168 (357)
T ss_pred             hcccCcc--chhhhhHHHHHhcCCCCE-EEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecccccCcccchhhhhh
Confidence            1000000  000000 00011134555 99999887632110   0       113678999999999874221      


Q ss_pred             -HHHHHHhcc-ccccEEEEeccCCC
Q psy1090         138 -KLSIKLTAL-RATFKVLLTGWYYP  160 (169)
Q Consensus       138 -~~~~~~~~l-~~~~~~~lT~TP~~  160 (169)
                       .....++.. ...+.++|||||-.
T Consensus       169 l~~~~~~~~~~~~~~~i~lSAT~~~  193 (357)
T TIGR03158       169 LAYMQLIRFFECRRKFVFLSATPDP  193 (357)
T ss_pred             hHHHHHHHhhhcCCcEEEEecCCCH
Confidence             112222222 23588999999954

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.29  E-value=9.1e-11  Score=95.57  Aligned_cols=134  Identities=15%  Similarity=0.051  Sum_probs=85.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCH--HHHHHHHHhhhcCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNA--IERKALQSEALSLP   79 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~--~~~~~~~~~~~~~~   79 (169)
                      .+|...+|+|||...+..+......+  +.+||++|. .+..|+.+.+++.+ +..+..++|..  .++...+.....  
T Consensus       165 ~Ll~~~TGSGKT~v~l~~i~~~l~~g--~~vLvLvPt~~L~~Q~~~~l~~~f-g~~v~~~~s~~s~~~r~~~~~~~~~--  239 (679)
T PRK05580        165 FLLDGVTGSGKTEVYLQAIAEVLAQG--KQALVLVPEIALTPQMLARFRARF-GAPVAVLHSGLSDGERLDEWRKAKR--  239 (679)
T ss_pred             EEEECCCCChHHHHHHHHHHHHHHcC--CeEEEEeCcHHHHHHHHHHHHHHh-CCCEEEEECCCCHHHHHHHHHHHHc--
Confidence            56778899999988877665555443  689999998 67789999998876 45677777643  233222221111  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCc--ccHHH-----HHHh-ccccccE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNK--KSKLS-----IKLT-ALRATFK  151 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~--~~~~~-----~~~~-~l~~~~~  151 (169)
                                      +..++ ++.|++.+-.     .-.+.+++|+||+|...-.  ..-.+     ...+ .......
T Consensus       240 ----------------g~~~I-VVgTrsal~~-----p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra~~~~~~~  297 (679)
T PRK05580        240 ----------------GEAKV-VIGARSALFL-----PFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPV  297 (679)
T ss_pred             ----------------CCCCE-EEeccHHhcc-----cccCCCEEEEECCCccccccCcCCCCcHHHHHHHHhhccCCCE
Confidence                            45677 8888876532     1236789999999975321  11111     1111 1234567


Q ss_pred             EEEeccCCCCCc
Q psy1090         152 VLLTGWYYPNKW  163 (169)
Q Consensus       152 ~~lT~TP~~n~~  163 (169)
                      +++||||...+.
T Consensus       298 il~SATps~~s~  309 (679)
T PRK05580        298 VLGSATPSLESL  309 (679)
T ss_pred             EEEcCCCCHHHH
Confidence            888999975443

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

Probab=99.26  E-value=1.2e-10  Score=95.60  Aligned_cols=134  Identities=18%  Similarity=0.204  Sum_probs=85.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.++.-.+|+|||+..+.-+......+....+|+++|. .+..|-.++++++. .+.++..+.|........   ...  
T Consensus        53 nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~---~i~--  127 (742)
T TIGR03817        53 HVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERR---WAR--  127 (742)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHH---HHh--
Confidence            46788899999998765443333333444579999997 66678888888875 356777788865432211   110  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchh--------ccccccccEEEEeCCcccCCc-ccHHHHHHhcc----
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--------FLKKITWNCIIVDEGHSVKNK-KSKLSIKLTAL----  146 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--------~~~~~~~~~vi~DEah~~k~~-~~~~~~~~~~l----  146 (169)
                                      ...++ +++|++.+....-        .+  .+.+++|+||+|.+.+. .+.....++.+    
T Consensus       128 ----------------~~~~I-ivtTPd~L~~~~L~~~~~~~~~l--~~l~~vViDEah~~~g~fg~~~~~il~rL~ri~  188 (742)
T TIGR03817       128 ----------------EHARY-VLTNPDMLHRGILPSHARWARFL--RRLRYVVIDECHSYRGVFGSHVALVLRRLRRLC  188 (742)
T ss_pred             ----------------cCCCE-EEEChHHHHHhhccchhHHHHHH--hcCCEEEEeChhhccCccHHHHHHHHHHHHHHH
Confidence                            34566 9999998863211        12  25689999999998652 22222223322    


Q ss_pred             ----ccccEEEEeccCC
Q psy1090         147 ----RATFKVLLTGWYY  159 (169)
Q Consensus       147 ----~~~~~~~lT~TP~  159 (169)
                          ..+..+++|||.-
T Consensus       189 ~~~g~~~q~i~~SATi~  205 (742)
T TIGR03817       189 ARYGASPVFVLASATTA  205 (742)
T ss_pred             HhcCCCCEEEEEecCCC
Confidence                2345789999964

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.

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.23  E-value=1.4e-10  Score=96.98  Aligned_cols=137  Identities=23%  Similarity=0.228  Sum_probs=81.2

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhC------CCCceEEEecC-cchHHHHHHHH-------HhC-------CCceEE
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQ------ALEPNLIVCPL-SVLNNWEAEFR-------KFA-------PFVRTV   59 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~------~~~~~Liv~P~-~~l~qW~~e~~-------~~~-------~~~~~~   59 (169)
                      ++++.-++|+|||..++.. +..+....      ....+|+|+|. .+..|+.+.+.       ++.       ++.++.
T Consensus        49 nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~  128 (876)
T PRK13767         49 NVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVA  128 (876)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEE
Confidence            4788999999999886544 33333221      12358999997 66667765433       222       356777


Q ss_pred             EEeCCHHHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--c--ccccccEEEEeCCcccCCc
Q psy1090          60 KYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--L--KKITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        60 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~--~~~~~~~vi~DEah~~k~~  135 (169)
                      ..+|............                    ...++ +++|++.+......  +  .-...+++|+||+|.+.+.
T Consensus       129 v~~Gdt~~~~r~~~l~--------------------~~p~I-lVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~  187 (876)
T PRK13767        129 IRTGDTSSYEKQKMLK--------------------KPPHI-LITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAEN  187 (876)
T ss_pred             EEcCCCCHHHHHHHHh--------------------CCCCE-EEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccC
Confidence            7887654332211111                    34566 99999988532211  1  0125689999999998643


Q ss_pred             c--cHHH---HHHhcc--ccccEEEEeccCC
Q psy1090         136 K--SKLS---IKLTAL--RATFKVLLTGWYY  159 (169)
Q Consensus       136 ~--~~~~---~~~~~l--~~~~~~~lT~TP~  159 (169)
                      .  ....   ..+..+  +...++++|||+-
T Consensus       188 ~RG~~l~~~L~rL~~l~~~~~q~IglSATl~  218 (876)
T PRK13767        188 KRGVHLSLSLERLEELAGGEFVRIGLSATIE  218 (876)
T ss_pred             ccHHHHHHHHHHHHHhcCCCCeEEEEecccC
Confidence            2  1111   112222  3456899999974

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

Probab=99.21  E-value=1.6e-10  Score=75.52  Aligned_cols=126  Identities=17%  Similarity=0.079  Sum_probs=64.3

Q ss_pred             cccCCCCCcHHHHHHHHH-HHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcc
Q psy1090           4 VIPDPTRYRKSGKVIAFF-CKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIK   82 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i-~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   82 (169)
                      +|..-+|.|||...+--+ ....  +...++||+.|.-++.   +|..+...+..+. +......+.     .       
T Consensus         8 ~~d~hpGaGKTr~vlp~~~~~~i--~~~~rvLvL~PTRvva---~em~~aL~~~~~~-~~t~~~~~~-----~-------   69 (148)
T PF07652_consen    8 VLDLHPGAGKTRRVLPEIVREAI--KRRLRVLVLAPTRVVA---EEMYEALKGLPVR-FHTNARMRT-----H-------   69 (148)
T ss_dssp             EEE--TTSSTTTTHHHHHHHHHH--HTT--EEEEESSHHHH---HHHHHHTTTSSEE-EESTTSS---------------
T ss_pred             EEecCCCCCCcccccHHHHHHHH--HccCeEEEecccHHHH---HHHHHHHhcCCcc-cCceeeecc-----c-------
Confidence            456679999998766433 2222  2347899999997665   3444444444433 332211110     0       


Q ss_pred             cccccCCccccccCCCCeEEEecHHHHHh-chhccccccccEEEEeCCcccCCcccHHHHH-Hhcc---ccccEEEEecc
Q psy1090          83 VPAKKGKTKKQISLKLPLILVTTPQIIEN-DFGFLKKITWNCIIVDEGHSVKNKKSKLSIK-LTAL---RATFKVLLTGW  157 (169)
Q Consensus        83 ~~~~~~~~~~~~~~~~~ii~i~ty~~~~~-~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~-~~~l---~~~~~~~lT~T  157 (169)
                                  .+...+ -+.+|..+.. ..+.....+|+++|+||||.. ++.+...+- +..+   .....++||||
T Consensus        70 ------------~g~~~i-~vMc~at~~~~~~~p~~~~~yd~II~DEcH~~-Dp~sIA~rg~l~~~~~~g~~~~i~mTAT  135 (148)
T PF07652_consen   70 ------------FGSSII-DVMCHATYGHFLLNPCRLKNYDVIIMDECHFT-DPTSIAARGYLRELAESGEAKVIFMTAT  135 (148)
T ss_dssp             -------------SSSSE-EEEEHHHHHHHHHTSSCTTS-SEEEECTTT---SHHHHHHHHHHHHHHHTTS-EEEEEESS
T ss_pred             ------------cCCCcc-cccccHHHHHHhcCcccccCccEEEEeccccC-CHHHHhhheeHHHhhhccCeeEEEEeCC
Confidence                        033333 6677766644 233444568999999999974 233322222 1222   22357999999


Q ss_pred             CCCC
Q psy1090         158 YYPN  161 (169)
Q Consensus       158 P~~n  161 (169)
                      |.-.
T Consensus       136 PPG~  139 (148)
T PF07652_consen  136 PPGS  139 (148)
T ss_dssp             -TT-
T ss_pred             CCCC
Confidence            9743

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 ....

>TIGR01054 rgy reverse gyrase

Probab=99.19  E-value=2.8e-10  Score=97.09  Aligned_cols=110  Identities=15%  Similarity=0.160  Sum_probs=73.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCc--e---EEEEeCCHHHHH--HHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFV--R---TVKYYGNAIERK--ALQSE   74 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~--~---~~~~~g~~~~~~--~~~~~   74 (169)
                      .++..++|+|||..++.++..+..  ...++||++|. .+..|+.+++.++.+..  .   +..++|......  .....
T Consensus        96 ~vi~ApTGsGKT~f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~  173 (1171)
T TIGR01054        96 FAIIAPTGVGKTTFGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMER  173 (1171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHH
Confidence            466789999999755544433322  24679999997 67789999999887532  2   223555432221  11111


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCC
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~  134 (169)
                      ..                  .+.+++ +++|+..+.+....+.. .++++|+||||++-.
T Consensus       174 l~------------------~~~~dI-lV~Tp~rL~~~~~~l~~-~~~~iVvDEaD~~L~  213 (1171)
T TIGR01054       174 IE------------------NGDFDI-LITTTMFLSKNYDELGP-KFDFIFVDDVDALLK  213 (1171)
T ss_pred             Hh------------------cCCCCE-EEECHHHHHHHHHHhcC-CCCEEEEeChHhhhh
Confidence            10                  045777 99999999877666554 799999999998754

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.

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

Probab=99.17  E-value=3.2e-10  Score=94.00  Aligned_cols=136  Identities=15%  Similarity=0.209  Sum_probs=90.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC---C-CceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA---P-FVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~---~-~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.++...||+|||.+-+--|..........++|++-|. .+.+...+.+.++.   | ..++..|+|+.......  ...
T Consensus        87 ~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~--~~~  164 (851)
T COG1205          87 NVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERR--AII  164 (851)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHH--HHH
Confidence            46788999999998876666555555666789999997 56667888888876   3 56788899865443221  111


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhch------hccccccccEEEEeCCcccCCcc-cHHHHHHhccc--
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF------GFLKKITWNCIIVDEGHSVKNKK-SKLSIKLTALR--  147 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~------~~~~~~~~~~vi~DEah~~k~~~-~~~~~~~~~l~--  147 (169)
                                        ...++| ++|+|+++.-..      -.....++.++|+||+|..++.- +.....++++.  
T Consensus       165 ------------------~~pp~I-llTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~vA~llRRL~~~  225 (851)
T COG1205         165 ------------------RNPPDI-LLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRR  225 (851)
T ss_pred             ------------------hCCCCE-EEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhHHHHHHHHHHHH
Confidence                              166777 999999986411      11111248899999999887633 33344444441  


Q ss_pred             ------cccEEEEeccC
Q psy1090         148 ------ATFKVLLTGWY  158 (169)
Q Consensus       148 ------~~~~~~lT~TP  158 (169)
                            ....+..|||-
T Consensus       226 ~~~~~~~~q~i~~SAT~  242 (851)
T COG1205         226 LRRYGSPLQIICTSATL  242 (851)
T ss_pred             HhccCCCceEEEEeccc
Confidence                  34568888884

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.10  E-value=1.9e-09  Score=93.20  Aligned_cols=134  Identities=17%  Similarity=0.168  Sum_probs=80.6

Q ss_pred             ccCCCCCcHHHHHHH-HHHHHHHhC----------CCCceEEEecC-cchHHHHHHHHH-----------h---CCCceE
Q psy1090           5 IPDPTRYRKSGKVIA-FFCKIIEEQ----------ALEPNLIVCPL-SVLNNWEAEFRK-----------F---APFVRT   58 (169)
Q Consensus         5 L~de~G~GKT~~~i~-~i~~~~~~~----------~~~~~Liv~P~-~~l~qW~~e~~~-----------~---~~~~~~   58 (169)
                      ++-.+|+|||..+.- .+..+....          ...++|+|+|. .+..|-.++++.           +   .+++++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            356899999998765 444444321          12468999997 555555555542           1   136778


Q ss_pred             EEEeCCHHHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCc
Q psy1090          59 VKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        59 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~  135 (169)
                      ...+|............                    ...+| +++|++.+.....   ...-.+.++||+||+|.+.+.
T Consensus        81 ~vrtGDt~~~eR~rll~--------------------~ppdI-LVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~  139 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTR--------------------NPPDI-LITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGS  139 (1490)
T ss_pred             EEEECCCCHHHHHHHhc--------------------CCCCE-EEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhccc
Confidence            88888644332221111                    34566 9999998864321   111135679999999998753


Q ss_pred             c--cHHHHHH---hcc--ccccEEEEeccCC
Q psy1090         136 K--SKLSIKL---TAL--RATFKVLLTGWYY  159 (169)
Q Consensus       136 ~--~~~~~~~---~~l--~~~~~~~lT~TP~  159 (169)
                      +  +.....+   ..+  +...++++|||--
T Consensus       140 kRG~~Lel~LeRL~~l~~~~~QrIgLSATI~  170 (1490)
T PRK09751        140 KRGAHLALSLERLDALLHTSAQRIGLSATVR  170 (1490)
T ss_pred             ccccHHHHHHHHHHHhCCCCCeEEEEEeeCC
Confidence            2  2222222   222  2356899999974

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.09  E-value=6.7e-10  Score=93.34  Aligned_cols=136  Identities=21%  Similarity=0.110  Sum_probs=87.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      ||++=+-+|+|||++++-+...+.+......++||+-.. +-.|-.++|..+........   .......+...-..   
T Consensus       275 ~G~IWHtqGSGKTlTm~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~---~~~s~~~Lk~~l~~---  348 (962)
T COG0610         275 GGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP---KAESTSELKELLED---  348 (962)
T ss_pred             ceEEEeecCCchHHHHHHHHHHHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc---cccCHHHHHHHHhc---
Confidence            688899999999999988877776665555677777764 45599999998874333222   22222222222211   


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhc----cccccccEEEEeCCcccCCcccHHHHHH-hccccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF----LKKITWNCIIVDEGHSVKNKKSKLSIKL-TALRATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~----~~~~~~~~vi~DEah~~k~~~~~~~~~~-~~l~~~~~~~lT  155 (169)
                                     .... |++||-+.+......    ...-+.-++|+||||+.....  ..+.+ ..++...-+++|
T Consensus       349 ---------------~~~~-ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~G~--~~~~~~~~~~~a~~~gFT  410 (962)
T COG0610         349 ---------------GKGK-IIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQYGE--LAKLLKKALKKAIFIGFT  410 (962)
T ss_pred             ---------------CCCc-EEEEEecccchhhhcccccccCCCcEEEEEechhhccccH--HHHHHHHHhccceEEEee
Confidence                           2223 499998887655432    123345589999999976433  23333 345557889999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||+..
T Consensus       411 GTPi~~  416 (962)
T COG0610         411 GTPIFK  416 (962)
T ss_pred             CCcccc
Confidence            999964

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

Probab=99.08  E-value=1.2e-09  Score=91.57  Aligned_cols=141  Identities=16%  Similarity=0.065  Sum_probs=82.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHH--HHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIE--RKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~   78 (169)
                      ++++...+|.|||+...--+..     ..+.+|||+|. +++.++...+...  ++......+....  .......... 
T Consensus       477 DVLVimPTGSGKSLcYQLPAL~-----~~GiTLVISPLiSLmqDQV~~L~~~--GI~Aa~L~s~~s~~eq~~ilr~l~s-  548 (1195)
T PLN03137        477 DVFVLMPTGGGKSLTYQLPALI-----CPGITLVISPLVSLIQDQIMNLLQA--NIPAASLSAGMEWAEQLEILQELSS-  548 (1195)
T ss_pred             CEEEEcCCCccHHHHHHHHHHH-----cCCcEEEEeCHHHHHHHHHHHHHhC--CCeEEEEECCCCHHHHHHHHHHHHh-
Confidence            3677889999999875433221     13679999997 6766566666543  4555555554322  2111111100 


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc---hhccc----cccccEEEEeCCcccCCcccH---HHHH----Hh
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND---FGFLK----KITWNCIIVDEGHSVKNKKSK---LSIK----LT  144 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~---~~~~~----~~~~~~vi~DEah~~k~~~~~---~~~~----~~  144 (169)
                                     ..+..++ +++|++.+...   ...+.    .....++|+||||++...+..   .++.    ..
T Consensus       549 ---------------~~g~~~I-LyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~  612 (1195)
T PLN03137        549 ---------------EYSKYKL-LYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQ  612 (1195)
T ss_pred             ---------------cCCCCCE-EEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHHHHHHHHHHHH
Confidence                           0145677 99999887532   11111    123688999999998654322   1222    22


Q ss_pred             ccccccEEEEeccCCCCCchhh
Q psy1090         145 ALRATFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       145 ~l~~~~~~~lT~TP~~n~~~el  166 (169)
                      .+.....++||||...+.-.|+
T Consensus       613 ~fp~vPilALTATAT~~V~eDI  634 (1195)
T PLN03137        613 KFPNIPVLALTATATASVKEDV  634 (1195)
T ss_pred             hCCCCCeEEEEecCCHHHHHHH
Confidence            3455668999999887654443

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=99.07  E-value=8.7e-10  Score=80.39  Aligned_cols=133  Identities=17%  Similarity=0.137  Sum_probs=81.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe-cCcchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC-PLSVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~-P~~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      |-+|+|.+|.||-.+..++|.....+++.+ .++|. +..+...-.+++....- ...+.....       ......   
T Consensus        64 Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~r-~vwvS~s~dL~~Da~RDl~DIG~~~i~v~~l~~-------~~~~~~---  132 (303)
T PF13872_consen   64 GFFLGDGTGVGKGRQIAGIILENWLRGRKR-AVWVSVSNDLKYDAERDLRDIGADNIPVHPLNK-------FKYGDI---  132 (303)
T ss_pred             EEEeccCCCcCccchhHHHHHHHHHcCCCc-eEEEECChhhhhHHHHHHHHhCCCcccceechh-------hccCcC---
Confidence            568999999999999999998877776544 55555 45666666666664431 111111111       000000   


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchh-------cccc------ccc-cEEEEeCCcccCCccc------HH
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG-------FLKK------ITW-NCIIVDEGHSVKNKKS------KL  139 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~-------~~~~------~~~-~~vi~DEah~~k~~~~------~~  139 (169)
                                    ..-...+ +++||+.+.....       .+.+      ..| +++|+||||..+|..+      +.
T Consensus       133 --------------~~~~~Gv-lF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~sk~  197 (303)
T PF13872_consen  133 --------------IRLKEGV-LFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGSKKPSKT  197 (303)
T ss_pred             --------------CCCCCCc-cchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccCccccHH
Confidence                          0122334 9999999876532       1111      122 4999999999999654      44


Q ss_pred             HHHHhc----cccccEEEEeccCCC
Q psy1090         140 SIKLTA----LRATFKVLLTGWYYP  160 (169)
Q Consensus       140 ~~~~~~----l~~~~~~~lT~TP~~  160 (169)
                      ..+...    ++..+.+..|||...
T Consensus       198 g~avl~LQ~~LP~ARvvY~SATgas  222 (303)
T PF13872_consen  198 GIAVLELQNRLPNARVVYASATGAS  222 (303)
T ss_pred             HHHHHHHHHhCCCCcEEEecccccC
Confidence            455443    445568889999874

>KOG0330|consensus

Probab=99.04  E-value=1.7e-09  Score=80.59  Aligned_cols=139  Identities=15%  Similarity=0.188  Sum_probs=96.1

Q ss_pred             CccccCCCCCcHHHH-HHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGK-VIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~-~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      .+|.+-|+|+|||.. ++-++..+.........||++|. .+-.|-.+.|+.+..  ++++.+.-|.-....+-....  
T Consensus       100 dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~--  177 (476)
T KOG0330|consen  100 DVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLS--  177 (476)
T ss_pred             cEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhh--
Confidence            367889999999977 44556666665555678999998 566688888888863  566666666554443333222  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCcc--cHHHHHHhcccc-ccE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALRA-TFK  151 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~~-~~~  151 (169)
                                        .++++ ++.|+..+.+...   -++-....++|+|||.++-+.+  ....+.++.++. +..
T Consensus       178 ------------------kkPhi-lVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~erqt  238 (476)
T KOG0330|consen  178 ------------------KKPHI-LVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPRERQT  238 (476)
T ss_pred             ------------------cCCCE-EEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcCccceE
Confidence                              66666 9999999887655   2333456789999999998744  334555666654 445


Q ss_pred             EEEeccCCCC
Q psy1090         152 VLLTGWYYPN  161 (169)
Q Consensus       152 ~~lT~TP~~n  161 (169)
                      ++.|||...+
T Consensus       239 ~LfsATMt~k  248 (476)
T KOG0330|consen  239 FLFSATMTKK  248 (476)
T ss_pred             EEEEeecchh
Confidence            7889998754

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

Probab=99.02  E-value=5.5e-09  Score=86.71  Aligned_cols=143  Identities=14%  Similarity=0.154  Sum_probs=89.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHH---------HHHHhCC--CceEEEEeCCHHHH--
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEA---------EFRKFAP--FVRTVKYYGNAIER--   68 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~---------e~~~~~~--~~~~~~~~g~~~~~--   68 (169)
                      .-+.+++|+|||.+++..+..+.......++|||||...+ .....         .|...++  ..+..+|.+.++.+  
T Consensus        62 ~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~k~g  141 (986)
T PRK15483         62 IDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKKKSG  141 (986)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCcccccc
Confidence            3467899999999999999888877777899999998543 33332         2332222  24455555443111  


Q ss_pred             -----HHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh------cc----cccccc-------EEEE
Q psy1090          69 -----KALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG------FL----KKITWN-------CIIV  126 (169)
Q Consensus        69 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~------~~----~~~~~~-------~vi~  126 (169)
                           ..+++  |....           ........| ++++-+++..+..      .+    ...+|+       ++|+
T Consensus       142 r~~~~~~i~~--Fa~~~-----------~~~~~~I~I-lv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIi  207 (986)
T PRK15483        142 RKNFPAQLSN--FVKAS-----------RQNSNTIHV-LLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVII  207 (986)
T ss_pred             cccChHHHHH--HHhcc-----------ccCCCceEE-EEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEE
Confidence                 11111  11000           000023455 8999888865321      11    113444       8999


Q ss_pred             eCCcccCCcccHHHHHHhccccccEEEEeccCCC
Q psy1090         127 DEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus       127 DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                      ||+|++.. ..+.++++..++..+.+..|||--.
T Consensus       208 DEPh~~~~-~~k~~~~i~~lnpl~~lrysAT~~~  240 (986)
T PRK15483        208 DEPHRFPR-DNKFYQAIEALKPQMIIRFGATFPD  240 (986)
T ss_pred             ECCCCCCc-chHHHHHHHhcCcccEEEEeeecCC
Confidence            99999965 3557888999999999999999865

>KOG0331|consensus

Probab=98.98  E-value=7.5e-09  Score=80.68  Aligned_cols=137  Identities=17%  Similarity=0.204  Sum_probs=90.9

Q ss_pred             CccccCCCCCcHHHHHH-HHHHHHHHh-----CCCC-ceEEEecC-cchHHHHHHHHHhCCCce--EEEEeCCHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVI-AFFCKIIEE-----QALE-PNLIVCPL-SVLNNWEAEFRKFAPFVR--TVKYYGNAIERKAL   71 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i-~~i~~~~~~-----~~~~-~~Liv~P~-~~l~qW~~e~~~~~~~~~--~~~~~g~~~~~~~~   71 (169)
                      +++...++|+|||+.-+ -.|.++...     ...+ .+||++|. .+..|-.+++.+|...+.  ....+|......+.
T Consensus       130 D~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~  209 (519)
T KOG0331|consen  130 DLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQL  209 (519)
T ss_pred             ceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHH
Confidence            46778899999997643 334444431     2223 48999998 777899999999985544  55555544444444


Q ss_pred             HHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-
Q psy1090          72 QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-  146 (169)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-  146 (169)
                      ++..                    ...++ +++|+..+....+  .+.-....++|+|||.++-...  .+.-+.+..+ 
T Consensus       210 ~~l~--------------------~gvdi-viaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~  268 (519)
T KOG0331|consen  210 RDLE--------------------RGVDV-VIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEPQIRKILSQIP  268 (519)
T ss_pred             HHHh--------------------cCCcE-EEeCChHHHHHHHcCCccccceeEEEeccHHhhhccccHHHHHHHHHhcC
Confidence            4433                    55677 9999998876543  2333467899999999876543  4455666677 


Q ss_pred             cccc-EEEEeccCC
Q psy1090         147 RATF-KVLLTGWYY  159 (169)
Q Consensus       147 ~~~~-~~~lT~TP~  159 (169)
                      +... .++.|||=.
T Consensus       269 ~~~rQtlm~saTwp  282 (519)
T KOG0331|consen  269 RPDRQTLMFSATWP  282 (519)
T ss_pred             CCcccEEEEeeecc
Confidence            4443 688888854

>PRK14701 reverse gyrase; Provisional

Probab=98.95  E-value=4.5e-09  Score=92.03  Aligned_cols=111  Identities=22%  Similarity=0.216  Sum_probs=72.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC----CceEEEEeCCHHHHHHHHH-hhh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP----FVRTVKYYGNAIERKALQS-EAL   76 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~----~~~~~~~~g~~~~~~~~~~-~~~   76 (169)
                      .++..++|+|||...+-....  .......+|||+|. .++.|..+.++.+..    +.++..++|.......... ...
T Consensus        97 ~li~APTGsGKTl~~~~~al~--~~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l  174 (1638)
T PRK14701         97 FSIVAPTGMGKSTFGAFIALF--LALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERI  174 (1638)
T ss_pred             EEEEEcCCCCHHHHHHHHHHH--HHhcCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHH
Confidence            467789999999843322222  22223579999998 677899999988763    3455667765433222111 111


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccC
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k  133 (169)
                      .                 .+.+++ +++|++.+......+....++++|+||||++-
T Consensus       175 ~-----------------~g~~dI-LV~TPgrL~~~~~~l~~~~i~~iVVDEAD~ml  213 (1638)
T PRK14701        175 E-----------------NGDFDI-LVTTAQFLARNFPEMKHLKFDFIFVDDVDAFL  213 (1638)
T ss_pred             h-----------------cCCCCE-EEECCchhHHhHHHHhhCCCCEEEEECceecc
Confidence            0                 145777 89999888765554444678999999999874

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

Probab=98.92  E-value=1.1e-08  Score=84.25  Aligned_cols=135  Identities=16%  Similarity=0.123  Sum_probs=76.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC-CCCceEEEecC-cchHHHHHHHHHhCC-------------------------Cc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ-ALEPNLIVCPL-SVLNNWEAEFRKFAP-------------------------FV   56 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~-~~~~~Liv~P~-~~l~qW~~e~~~~~~-------------------------~~   56 (169)
                      ++.-.+|+|||....+++..+.... ...+.++++|. .+..|-.+++.++..                         .+
T Consensus        35 ~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l  114 (844)
T TIGR02621        35 SCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPL  114 (844)
T ss_pred             eEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCe
Confidence            3457999999975544443332222 22344557797 677888888887763                         24


Q ss_pred             eEEEEeCCHHHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc------cc--------ccccc
Q psy1090          57 RTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF------LK--------KITWN  122 (169)
Q Consensus        57 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~------~~--------~~~~~  122 (169)
                      ++...+|......++....                    ...+| ++.|.+.+.+..-.      +.        -.+..
T Consensus       115 ~v~~l~GG~~~~~q~~~l~--------------------~~p~I-IVgT~D~i~sr~L~~gYg~~~~~~pi~ag~L~~v~  173 (844)
T TIGR02621       115 AISTLRGQFADNDEWMLDP--------------------HRPAV-IVGTVDMIGSRLLFSGYGCGFKSRPLHAGFLGQDA  173 (844)
T ss_pred             EEEEEECCCChHHHHHhcC--------------------CCCcE-EEECHHHHcCCccccccccccccccchhhhhccce
Confidence            4455555543333333221                    45566 99998877653210      00        12356


Q ss_pred             EEEEeCCcccCCcccHHHHHHhc-c--cc----ccEEEEeccCCC
Q psy1090         123 CIIVDEGHSVKNKKSKLSIKLTA-L--RA----TFKVLLTGWYYP  160 (169)
Q Consensus       123 ~vi~DEah~~k~~~~~~~~~~~~-l--~~----~~~~~lT~TP~~  160 (169)
                      ++|+|||| +...-......+.. +  ..    ...++||||+..
T Consensus       174 ~LVLDEAD-Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~  217 (844)
T TIGR02621       174 LIVHDEAH-LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRT  217 (844)
T ss_pred             EEEEehhh-hccccHHHHHHHHHhcccCcccccceEEEEecCCCc
Confidence            99999999 43333333333332 2  11    368999999853

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.

>PRK09694 helicase Cas3; Provisional

Probab=98.89  E-value=1.5e-08  Score=84.25  Aligned_cols=157  Identities=18%  Similarity=0.143  Sum_probs=84.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHh----CCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKF----APFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~----~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      .+|-..||+|||-.++.++..+...+....+++..|. .+.++-.+.+.+|    ++...+...+|..............
T Consensus       304 ~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~v~L~Hg~a~l~~~~~~~~~~  383 (878)
T PRK09694        304 TIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLKSR  383 (878)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCceEeecCcchhhhhhhhhhcc
Confidence            3677899999999999887776666656789999997 5667777776543    3445667777754322111110000


Q ss_pred             CCCcccccccC----Ccc---ccccCCCCeEEEecHHHHHhch-----hccc--cccccEEEEeCCcccCCcccHHH-HH
Q psy1090          78 LPTIKVPAKKG----KTK---KQISLKLPLILVTTPQIIENDF-----GFLK--KITWNCIIVDEGHSVKNKKSKLS-IK  142 (169)
Q Consensus        78 ~~~~~~~~~~~----~~~---~~~~~~~~ii~i~ty~~~~~~~-----~~~~--~~~~~~vi~DEah~~k~~~~~~~-~~  142 (169)
                      ...........    ...   ..+.-..++ +++|.+.+....     ..++  .+.-.+||+||+|.+-....... ..
T Consensus       384 ~~~~~~~~~~~~~~~~w~~~~~kr~llapi-~V~TiDQlL~a~l~~kh~~lR~~~La~svvIiDEVHAyD~ym~~lL~~~  462 (878)
T PRK09694        384 AATEQGQEEAWVQCCEWLSQSNKRVFLGQI-GVCTIDQVLISVLPVKHRFIRGFGLGRSVLIVDEVHAYDAYMYGLLEAV  462 (878)
T ss_pred             cccccccchhhhHHHHHHhhhhhhhhcCCE-EEcCHHHHHHHHHccchHHHHHHhhccCeEEEechhhCCHHHHHHHHHH
Confidence            00000000000    000   011122566 888876654221     1111  12234899999998732111111 22


Q ss_pred             Hhcc--ccccEEEEeccCCC
Q psy1090         143 LTAL--RATFKVLLTGWYYP  160 (169)
Q Consensus       143 ~~~l--~~~~~~~lT~TP~~  160 (169)
                      ++.+  .....++||||+..
T Consensus       463 L~~l~~~g~~vIllSATLP~  482 (878)
T PRK09694        463 LKAQAQAGGSVILLSATLPA  482 (878)
T ss_pred             HHHHHhcCCcEEEEeCCCCH
Confidence            2222  22458999999874

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

Probab=98.89  E-value=3.9e-08  Score=78.06  Aligned_cols=142  Identities=18%  Similarity=0.201  Sum_probs=92.6

Q ss_pred             ccccCCCCCcHHHHH-HHHHHHHHH-hCCCCc-eEEEecC-cchHHHHHHHHHhCC---CceEEEEeCCHHHHHHHHHhh
Q psy1090           3 TVIPDPTRYRKSGKV-IAFFCKIIE-EQALEP-NLIVCPL-SVLNNWEAEFRKFAP---FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         3 ~iL~de~G~GKT~~~-i~~i~~~~~-~~~~~~-~Liv~P~-~~l~qW~~e~~~~~~---~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      .+....+|+|||..- +-.+..+.. ...... +||++|. .+..|-.+++.++..   .+++...+|......+.....
T Consensus        69 vi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~  148 (513)
T COG0513          69 VLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK  148 (513)
T ss_pred             EEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh
Confidence            456778999999663 334444332 222222 9999998 677799999888873   566777777655444443322


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhccc-ccc
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-ATF  150 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~~~  150 (169)
                                          ...++ ++.|+..+.....  .+.-....++|+|||.++-+.+  ......+..++ .+.
T Consensus       149 --------------------~~~~i-vVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~Gf~~~i~~I~~~~p~~~q  207 (513)
T COG0513         149 --------------------RGVDI-VVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQ  207 (513)
T ss_pred             --------------------cCCCE-EEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcCCCHHHHHHHHHhCCcccE
Confidence                                33677 9999988775443  3344567899999999887653  22334445554 366


Q ss_pred             EEEEeccCCCCCchhh
Q psy1090         151 KVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       151 ~~~lT~TP~~n~~~el  166 (169)
                      .++.|||... .+.++
T Consensus       208 tllfSAT~~~-~i~~l  222 (513)
T COG0513         208 TLLFSATMPD-DIREL  222 (513)
T ss_pred             EEEEecCCCH-HHHHH
Confidence            7899999887 44443

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.88  E-value=1e-08  Score=83.26  Aligned_cols=131  Identities=14%  Similarity=0.101  Sum_probs=72.7

Q ss_pred             ccccCCCCCcHHHHHHHHH----------HHHH--H-hCCCCceEEEecC-cchHHHHHHHHHhC-----CCceEEEEeC
Q psy1090           3 TVIPDPTRYRKSGKVIAFF----------CKII--E-EQALEPNLIVCPL-SVLNNWEAEFRKFA-----PFVRTVKYYG   63 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i----------~~~~--~-~~~~~~~Liv~P~-~~l~qW~~e~~~~~-----~~~~~~~~~g   63 (169)
                      .++.-++|+|||.+.-.++          ..+.  . .....+++|++|. .+..|...++.+..     ++..+....|
T Consensus       182 vIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg~~~~~g~~v~v~~G  261 (675)
T PHA02653        182 VVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLGFDEIDGSPISLKYG  261 (675)
T ss_pred             EEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhCccccCCceEEEEEC
Confidence            5778899999997742222          1111  1 2234589999997 55667777776533     2344555555


Q ss_pred             CHHHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHH
Q psy1090          64 NAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKL  143 (169)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~  143 (169)
                      .....  ......                   ...++ ++.|.....   ..  -..++++|+||||............+
T Consensus       262 g~~~~--~~~t~~-------------------k~~~I-lv~T~~L~l---~~--L~~v~~VVIDEaHEr~~~~DllL~ll  314 (675)
T PHA02653        262 SIPDE--LINTNP-------------------KPYGL-VFSTHKLTL---NK--LFDYGTVIIDEVHEHDQIGDIIIAVA  314 (675)
T ss_pred             CcchH--Hhhccc-------------------CCCCE-EEEeCcccc---cc--cccCCEEEccccccCccchhHHHHHH
Confidence            43321  000000                   22345 777643211   11  23678999999998654433333333


Q ss_pred             hcc--ccccEEEEeccCCC
Q psy1090         144 TAL--RATFKVLLTGWYYP  160 (169)
Q Consensus       144 ~~l--~~~~~~~lT~TP~~  160 (169)
                      +.+  +.+..++||||+-.
T Consensus       315 k~~~~~~rq~ILmSATl~~  333 (675)
T PHA02653        315 RKHIDKIRSLFLMTATLED  333 (675)
T ss_pred             HHhhhhcCEEEEEccCCcH
Confidence            333  12367999999853

>KOG0952|consensus

Probab=98.85  E-value=2.4e-08  Score=82.49  Aligned_cols=134  Identities=17%  Similarity=0.144  Sum_probs=84.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh--------CCCCceEEEecC-cchHHHHHHHHH-hCC-CceEEEEeCCHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE--------QALEPNLIVCPL-SVLNNWEAEFRK-FAP-FVRTVKYYGNAIERKA   70 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~--------~~~~~~Liv~P~-~~l~qW~~e~~~-~~~-~~~~~~~~g~~~~~~~   70 (169)
                      +++++-.+|+|||..++..|.....+        +..-+++-|+|. ++...-.+.+.+ +.| ++.+..++|+-.-.+.
T Consensus       128 NMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kkl~~~gi~v~ELTGD~ql~~t  207 (1230)
T KOG0952|consen  128 NMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLAPLGISVRELTGDTQLTKT  207 (1230)
T ss_pred             CEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhhhcccccceEEEecCcchhhHH
Confidence            57899999999998776555444432        233589999996 555444444432 222 6788888987544322


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHH---hchh--ccccccccEEEEeCCcccCCcccHHHHHHh-
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIE---NDFG--FLKKITWNCIIVDEGHSVKNKKSKLSIKLT-  144 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~---~~~~--~~~~~~~~~vi~DEah~~k~~~~~~~~~~~-  144 (169)
                      .-                       .+.|+ ++||++...   +...  .-......+||+||.|.+..+..-....+- 
T Consensus       208 ei-----------------------~~tqi-iVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~RGpvlEtiVa  263 (1230)
T KOG0952|consen  208 EI-----------------------ADTQI-IVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDDRGPVLETIVA  263 (1230)
T ss_pred             HH-----------------------HhcCE-EEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCcccchHHHHHH
Confidence            11                       56677 999987753   2111  111125679999999999876655444331 


Q ss_pred             --------ccccccEEEEeccCC
Q psy1090         145 --------ALRATFKVLLTGWYY  159 (169)
Q Consensus       145 --------~l~~~~~~~lT~TP~  159 (169)
                              ....-+.++||||..
T Consensus       264 Rtlr~vessqs~IRivgLSATlP  286 (1230)
T KOG0952|consen  264 RTLRLVESSQSMIRIVGLSATLP  286 (1230)
T ss_pred             HHHHHHHhhhhheEEEEeeccCC
Confidence                    114556799999965

>KOG0350|consensus

Probab=98.82  E-value=1.4e-08  Score=77.98  Aligned_cols=116  Identities=12%  Similarity=0.221  Sum_probs=76.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCC--CceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQAL--EPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~--~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      .+++-.+|+|||+...--|......++.  -+.+||+|. .+..|-++.|.+|.++  +-++...|..+-+.........
T Consensus       186 IcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~  265 (620)
T KOG0350|consen  186 ICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASD  265 (620)
T ss_pred             eEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcC
Confidence            4567889999997643333333333322  378999997 5667999999999964  5556666655444333322211


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhc---cccccccEEEEeCCcccCC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF---LKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~---~~~~~~~~vi~DEah~~k~  134 (169)
                      .+               -++.|| +++|+..+......   +.-....++|+|||.++.+
T Consensus       266 ~~---------------~~~~DI-lVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~  309 (620)
T KOG0350|consen  266 PP---------------ECRIDI-LVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLD  309 (620)
T ss_pred             CC---------------ccccce-EEcCchHHHHhccCCCCcchhhceEEEechHHHHHH
Confidence            11               146688 99999999876653   2223567999999999865

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

Probab=98.82  E-value=1.1e-07  Score=70.36  Aligned_cols=118  Identities=15%  Similarity=0.146  Sum_probs=82.5

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcccccc
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAK   86 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~   86 (169)
                      -+|+|||-+....+......+  +.+.|..|. .++..-...++.-+++..+...+|.++...                 
T Consensus       124 V~GaGKTEMif~~i~~al~~G--~~vciASPRvDVclEl~~Rlk~aF~~~~I~~Lyg~S~~~f-----------------  184 (441)
T COG4098         124 VTGAGKTEMIFQGIEQALNQG--GRVCIASPRVDVCLELYPRLKQAFSNCDIDLLYGDSDSYF-----------------  184 (441)
T ss_pred             ecCCCchhhhHHHHHHHHhcC--CeEEEecCcccchHHHHHHHHHhhccCCeeeEecCCchhc-----------------
Confidence            479999988887777766555  789999997 677777777877777888988888876542                 


Q ss_pred             cCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccH-HHHHHhcc--ccccEEEEeccCCC
Q psy1090          87 KGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSK-LSIKLTAL--RATFKVLLTGWYYP  160 (169)
Q Consensus        87 ~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~-~~~~~~~l--~~~~~~~lT~TP~~  160 (169)
                                ..+.|+.||++.++- .     .-||++|+||+..+--.... ..-+++.-  ....++.|||||..
T Consensus       185 ----------r~plvVaTtHQLlrF-k-----~aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~IylTATp~k  245 (441)
T COG4098         185 ----------RAPLVVATTHQLLRF-K-----QAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATIYLTATPTK  245 (441)
T ss_pred             ----------cccEEEEehHHHHHH-H-----hhccEEEEeccccccccCCHHHHHHHHHhhcccCceEEEecCChH
Confidence                      234446666666543 2     25899999999975433332 23333332  34568999999984

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

Probab=98.81  E-value=4.7e-08  Score=80.23  Aligned_cols=134  Identities=18%  Similarity=0.201  Sum_probs=81.2

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCC-----ceEEEecCc-chHHHHHHHHHhC--CCceEEEEeCCHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALE-----PNLIVCPLS-VLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQ   72 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~-----~~Liv~P~~-~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~   72 (169)
                      +.++.-.+|+|||..|+.- +..+.......     .+|-|.|.- +...-...+..|.  -++.+-+-+|+.......+
T Consensus        39 nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r  118 (814)
T COG1201          39 NVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQK  118 (814)
T ss_pred             ceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHcCCccceecCCCChHHhhh
Confidence            4678889999999988754 44555442111     479999974 4444555555554  2566666666433322111


Q ss_pred             HhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhch------hccccccccEEEEeCCcccCCcc--cHHHHHHh
Q psy1090          73 SEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF------GFLKKITWNCIIVDEGHSVKNKK--SKLSIKLT  144 (169)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~------~~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~  144 (169)
                      ..                    ...++| ++||++++.-..      ..+.  +..++|+||.|.+.+.+  ++.+-.+.
T Consensus       119 ~~--------------------~~PPdI-LiTTPEsL~lll~~~~~r~~l~--~vr~VIVDEiHel~~sKRG~~Lsl~Le  175 (814)
T COG1201         119 ML--------------------KNPPHI-LITTPESLAILLNSPKFRELLR--DVRYVIVDEIHALAESKRGVQLALSLE  175 (814)
T ss_pred             cc--------------------CCCCcE-EEeChhHHHHHhcCHHHHHHhc--CCcEEEeehhhhhhccccchhhhhhHH
Confidence            11                    155566 999999986422      2222  56789999999987522  22233333


Q ss_pred             c---cc-cccEEEEeccC
Q psy1090         145 A---LR-ATFKVLLTGWY  158 (169)
Q Consensus       145 ~---l~-~~~~~~lT~TP  158 (169)
                      +   +. .-.|++||||=
T Consensus       176 RL~~l~~~~qRIGLSATV  193 (814)
T COG1201         176 RLRELAGDFQRIGLSATV  193 (814)
T ss_pred             HHHhhCcccEEEeehhcc
Confidence            2   22 45699999994

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

Probab=98.80  E-value=2.6e-08  Score=78.98  Aligned_cols=138  Identities=21%  Similarity=0.233  Sum_probs=90.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeC--CHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYG--NAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g--~~~~~~~~~~~~~~~   78 (169)
                      .++....+|.||+++.  -|-.+..   .+.+|||.|. +++...++.++...  ......++  +.+++..+...... 
T Consensus        34 d~lvvmPTGgGKSlCy--QiPAll~---~G~TLVVSPLiSLM~DQV~~l~~~G--i~A~~lnS~l~~~e~~~v~~~l~~-  105 (590)
T COG0514          34 DTLVVMPTGGGKSLCY--QIPALLL---EGLTLVVSPLISLMKDQVDQLEAAG--IRAAYLNSTLSREERQQVLNQLKS-  105 (590)
T ss_pred             cEEEEccCCCCcchHh--hhHHHhc---CCCEEEECchHHHHHHHHHHHHHcC--ceeehhhcccCHHHHHHHHHHHhc-
Confidence            3567789999999653  2222222   4699999997 78888888888664  44444444  44555444443332 


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcccH-------HHHHHhccccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKKSK-------LSIKLTALRAT  149 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~~~-------~~~~~~~l~~~  149 (169)
                                       +..++ +..+++.+...  .+.+...+..++++||||++...+..       .......+...
T Consensus       106 -----------------g~~kl-LyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~~~~  167 (590)
T COG0514         106 -----------------GQLKL-LYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNP  167 (590)
T ss_pred             -----------------CceeE-EEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHhhCCCC
Confidence                             55677 88888888654  34556788999999999998775422       22333344556


Q ss_pred             cEEEEeccCCCCCchh
Q psy1090         150 FKVLLTGWYYPNKWSK  165 (169)
Q Consensus       150 ~~~~lT~TP~~n~~~e  165 (169)
                      -++++|||--+.--.|
T Consensus       168 p~~AlTATA~~~v~~D  183 (590)
T COG0514         168 PVLALTATATPRVRDD  183 (590)
T ss_pred             CEEEEeCCCChHHHHH
Confidence            7999988876544333

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.75  E-value=9.4e-08  Score=78.07  Aligned_cols=111  Identities=14%  Similarity=-0.037  Sum_probs=66.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCC-HHH--HHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGN-AIE--RKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~-~~~--~~~~~~~~   75 (169)
                      |.|....+|.|||+++...+......  ...++||+|+ .+..||.+++..++.  ++.+....+. ..+  ....+.. 
T Consensus        85 G~Iaem~TGeGKTLta~Lpa~l~aL~--g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~~~~s~~~~~~~~~rr~-  161 (762)
T TIGR03714        85 GNIAEMKTGEGKTLTATMPLYLNALT--GKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLGVVDDPDEEYDANEKRK-  161 (762)
T ss_pred             CceeEecCCcchHHHHHHHHHHHhhc--CCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEEECCCCccccCHHHHHH-
Confidence            57888999999999876543322222  3468999998 566788877765542  4455443332 110  1111111 


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhch---------hccccccccEEEEeCCcccCCc
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF---------GFLKKITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~---------~~~~~~~~~~vi~DEah~~k~~  135 (169)
                                         ...++| +++|++.+..+.         ......++.++|+||||.+--+
T Consensus       162 -------------------~y~~dI-vygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiD  210 (762)
T TIGR03714       162 -------------------IYNSDI-VYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLD  210 (762)
T ss_pred             -------------------hCCCCE-EEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhc
Confidence                               145677 888888874321         1122346789999999987543

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.

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

Probab=98.75  E-value=7.7e-08  Score=79.53  Aligned_cols=106  Identities=22%  Similarity=0.302  Sum_probs=75.4

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-----CceEEEEeCCHHHHHHHH-HhhhcC
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-----FVRTVKYYGNAIERKALQ-SEALSL   78 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-----~~~~~~~~g~~~~~~~~~-~~~~~~   78 (169)
                      .-++|+|||.-.+.+..++...+  ++.++|+|. .++.|-.+.+.++.+     ...+. |++.-..+.... .+.+. 
T Consensus       103 iAPTGvGKTTfg~~~sl~~a~kg--kr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~-yh~~l~~~ekee~le~i~-  178 (1187)
T COG1110         103 IAPTGVGKTTFGLLMSLYLAKKG--KRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVV-YHSALPTKEKEEALERIE-  178 (1187)
T ss_pred             EcCCCCchhHHHHHHHHHHHhcC--CeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeee-eccccchHHHHHHHHHHh-
Confidence            35799999966655544444333  899999998 456789999999873     22333 777522222111 11111 


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSV  132 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~  132 (169)
                                      .+++|+ +++|-+.+.++.+.+.+.+||++++|.+..+
T Consensus       179 ----------------~gdfdI-litTs~FL~k~~e~L~~~kFdfifVDDVDA~  215 (1187)
T COG1110         179 ----------------SGDFDI-LITTSQFLSKRFEELSKLKFDFIFVDDVDAI  215 (1187)
T ss_pred             ----------------cCCccE-EEEeHHHHHhhHHHhcccCCCEEEEccHHHH
Confidence                            178999 9999999999999999999999999999853

>KOG0338|consensus

Probab=98.73  E-value=8.6e-08  Score=74.08  Aligned_cols=132  Identities=8%  Similarity=0.070  Sum_probs=83.1

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCC----CCceEEEecCc-ch---HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQA----LEPNLIVCPLS-VL---NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~----~~~~Liv~P~~-~l---~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +--+|+|||..-+--+...+..++    .-++||+||.- +-   ++-...+..|+ ++.++..-|.-+-+.+-....  
T Consensus       224 ~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LR--  300 (691)
T KOG0338|consen  224 CAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLR--  300 (691)
T ss_pred             eecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHh--
Confidence            456899999653322332222222    23799999984 32   34556677787 688888777655544333222  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHh---chhccccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN---DFGFLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFK  151 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~---~~~~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~  151 (169)
                                        ..+|| +|.|+..+..   +...|.--...++|+|||.++-...  ......++.. +.+..
T Consensus       301 ------------------s~PDI-VIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeegFademnEii~lcpk~RQT  361 (691)
T KOG0338|consen  301 ------------------SRPDI-VIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKNRQT  361 (691)
T ss_pred             ------------------hCCCE-EEecchhHHHHhccCCCccccceeEEEechHHHHHHHHHHHHHHHHHHhccccccc
Confidence                              77888 9999988864   3444555567799999999876432  2223333333 45557


Q ss_pred             EEEeccCC
Q psy1090         152 VLLTGWYY  159 (169)
Q Consensus       152 ~~lT~TP~  159 (169)
                      +++|||+.
T Consensus       362 mLFSATMt  369 (691)
T KOG0338|consen  362 MLFSATMT  369 (691)
T ss_pred             eeehhhhH
Confidence            99999975

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

Probab=98.68  E-value=4.6e-07  Score=73.10  Aligned_cols=61  Identities=15%  Similarity=0.181  Sum_probs=41.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC-----CCceEEEEeC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-----PFVRTVKYYG   63 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-----~~~~~~~~~g   63 (169)
                      .++.-.+|+|||+..+.-+..........++||.+|. .+..|+.+++..+.     ..++.....|
T Consensus        19 lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~lkG   85 (636)
T TIGR03117        19 GMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPG   85 (636)
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEEEC
Confidence            3456789999998876655433333335789999998 56678888877554     2455555555

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.66  E-value=3.5e-08  Score=80.18  Aligned_cols=136  Identities=9%  Similarity=0.009  Sum_probs=77.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HH---HHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NN---WEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~q---W~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|....+|.|||+.+...+......  ...++||+|+..+ .|   |...+.++. ++.+....|..........    
T Consensus        71 G~Iaem~TGeGKTLva~lpa~l~aL~--G~~V~VvTpt~~LA~qdae~~~~l~~~L-GLsv~~i~g~~~~~~r~~~----  143 (745)
T TIGR00963        71 GKIAEMKTGEGKTLTATLPAYLNALT--GKGVHVVTVNDYLAQRDAEWMGQVYRFL-GLSVGLILSGMSPEERREA----  143 (745)
T ss_pred             CceeeecCCCccHHHHHHHHHHHHHh--CCCEEEEcCCHHHHHHHHHHHHHHhccC-CCeEEEEeCCCCHHHHHHh----
Confidence            55667899999998754332212222  2469999999655 34   444444444 5777777765433221111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhch----hccccccccEEEEeCCcccCCcccHHHHHHhcc--
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDF----GFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL--  146 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~----~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l--  146 (169)
                                        ..++| ++.|+..+     +...    +.+...+++++|+||+|++--+.. +...+.+-  
T Consensus       144 ------------------y~~dI-vyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDea-RtpLiisg~~  203 (745)
T TIGR00963       144 ------------------YACDI-TYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEA-RTPLIISGPA  203 (745)
T ss_pred             ------------------cCCCE-EEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhh-hhHHhhcCCC
Confidence                              33566 88777654     2221    122335688999999998765333 33333222  


Q ss_pred             ccccEEEEeccCCCCCch
Q psy1090         147 RATFKVLLTGWYYPNKWS  164 (169)
Q Consensus       147 ~~~~~~~lT~TP~~n~~~  164 (169)
                      .....+.+++||+...+.
T Consensus       204 ~~~~~ly~~a~~i~r~L~  221 (745)
T TIGR00963       204 EKSTELYLQANRFAKALE  221 (745)
T ss_pred             CCchHHHHHHHHHHHhhc
Confidence            233456677777765543

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.

>KOG0345|consensus

Probab=98.64  E-value=3.5e-07  Score=70.08  Aligned_cols=136  Identities=15%  Similarity=0.128  Sum_probs=85.9

Q ss_pred             ccCCCCCcHHHHHHHHHHHHH--HhCCC--C--ceEEEecC-cchHHHHH---HHHHhCCCceEEEEeCCHHHHHHHHHh
Q psy1090           5 IPDPTRYRKSGKVIAFFCKII--EEQAL--E--PNLIVCPL-SVLNNWEA---EFRKFAPFVRTVKYYGNAIERKALQSE   74 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~--~~~~~--~--~~Liv~P~-~~l~qW~~---e~~~~~~~~~~~~~~g~~~~~~~~~~~   74 (169)
                      ....+|+|||+.-+.-+..+.  +....  +  -.||+.|. .+-.|-.+   .|..+.+.++...+.|.......+...
T Consensus        48 veavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~f  127 (567)
T KOG0345|consen   48 VEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTF  127 (567)
T ss_pred             EEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHH
Confidence            345689999977655544444  22222  2  36999998 44445443   344445788888888876666655554


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhc----hhccccccccEEEEeCCcccCCcc--cHHHHHHhcccc
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND----FGFLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALRA  148 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~----~~~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~~  148 (169)
                      ..                   ...+| ++.|+..+..-    ...+.-....++|+|||.++-.-+  ......+..++.
T Consensus       128 ke-------------------e~~nI-lVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgFe~~~n~ILs~LPK  187 (567)
T KOG0345|consen  128 KE-------------------EGPNI-LVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGFEASVNTILSFLPK  187 (567)
T ss_pred             HH-------------------hCCcE-EEeCchhHHHHHhchhhhccccccceEEecchHhHhcccHHHHHHHHHHhccc
Confidence            43                   55566 99998776543    333444456799999999986543  334555666765


Q ss_pred             ccE-EEEeccCCC
Q psy1090         149 TFK-VLLTGWYYP  160 (169)
Q Consensus       149 ~~~-~~lT~TP~~  160 (169)
                      .+| =+.|||..+
T Consensus       188 QRRTGLFSATq~~  200 (567)
T KOG0345|consen  188 QRRTGLFSATQTQ  200 (567)
T ss_pred             ccccccccchhhH
Confidence            555 445888643

>KOG0335|consensus

Probab=98.62  E-value=5.6e-07  Score=69.53  Aligned_cols=139  Identities=17%  Similarity=0.233  Sum_probs=90.7

Q ss_pred             CccccCCCCCcHHHHHH-HHHHHHHHhCC----------CCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHH
Q psy1090           2 DTVIPDPTRYRKSGKVI-AFFCKIIEEQA----------LEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIE   67 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i-~~i~~~~~~~~----------~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~   67 (169)
                      +.+.+-++|+|||..-+ -++.++++++.          ....||++|. .+..|-+.|-++|.  ..++....+|....
T Consensus       113 dl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~  192 (482)
T KOG0335|consen  113 DLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDL  192 (482)
T ss_pred             ceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcch
Confidence            35567899999997643 33455554433          2358999997 78889999999987  45666776666444


Q ss_pred             HHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCC---cccHHHHH
Q psy1090          68 RKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKN---KKSKLSIK  142 (169)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~---~~~~~~~~  142 (169)
                      ..+.+...                    ..+++ +++|...+..-.+  .+.--+..++|+|||.++-.   ......+.
T Consensus       193 ~~q~~~~~--------------------~gcdI-lvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~i  251 (482)
T KOG0335|consen  193 GAQLRFIK--------------------RGCDI-LVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKI  251 (482)
T ss_pred             hhhhhhhc--------------------cCccE-EEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHH
Confidence            44333322                    77888 9999988876443  22233455999999998754   12233333


Q ss_pred             Hhcc-----ccccEEEEeccCCCC
Q psy1090         143 LTAL-----RATFKVLLTGWYYPN  161 (169)
Q Consensus       143 ~~~l-----~~~~~~~lT~TP~~n  161 (169)
                      +...     +.+..++.|||-..+
T Consensus       252 v~~~~~~~~~~~qt~mFSAtfp~~  275 (482)
T KOG0335|consen  252 VEQLGMPPKNNRQTLLFSATFPKE  275 (482)
T ss_pred             hcccCCCCccceeEEEEeccCChh
Confidence            3322     356678999996543

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.60  E-value=4.2e-07  Score=75.65  Aligned_cols=136  Identities=13%  Similarity=0.014  Sum_probs=74.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      .++.-++|+|||.+..-.+...  ....++++|++|.-.+ .|-.+.+.+..   .+..+....+... ..         
T Consensus        23 vvv~A~TGSGKTt~~pl~lL~~--~~~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~-~~---------   90 (812)
T PRK11664         23 VLLKAPTGAGKSTWLPLQLLQH--GGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAES-KV---------   90 (812)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHc--CCcCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCcc-cc---------
Confidence            5788899999998876444321  1223589999998554 46555554332   1222222111110 00         


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhc-cccccccEEEEeCCccc-CCcccH---HHHHHhccc-cccEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGHSV-KNKKSK---LSIKLTALR-ATFKV  152 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah~~-k~~~~~---~~~~~~~l~-~~~~~  152 (169)
                                      ....++ ++.|...+.+.... ..-..++++|+||+|.- -+.+-.   ..+....++ ....+
T Consensus        91 ----------------~~~t~I-~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqli  153 (812)
T PRK11664         91 ----------------GPNTRL-EVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLL  153 (812)
T ss_pred             ----------------CCCCcE-EEEChhHHHHHHhhCCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEE
Confidence                            023345 78888877654321 12247889999999962 221111   111223332 34579


Q ss_pred             EEeccCCCCCchhhc
Q psy1090         153 LLTGWYYPNKWSKQC  167 (169)
Q Consensus       153 ~lT~TP~~n~~~el~  167 (169)
                      +||||+-...+.+++
T Consensus       154 lmSATl~~~~l~~~~  168 (812)
T PRK11664        154 IMSATLDNDRLQQLL  168 (812)
T ss_pred             EEecCCCHHHHHHhc
Confidence            999998655444443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.59  E-value=6.9e-07  Score=74.33  Aligned_cols=135  Identities=14%  Similarity=0.037  Sum_probs=75.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhC-C--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFA-P--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~-~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      .++.-++|+|||.+..-.+....  ...++++|+.|.-.+ .|-.+.+.+.. .  +..+....+. +..          
T Consensus        20 vIi~a~TGSGKTT~vpl~lL~~~--~~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~-~~~----------   86 (819)
T TIGR01970        20 VVLEAPPGAGKSTAVPLALLDAP--GIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRG-ENK----------   86 (819)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh--ccCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEcc-ccc----------
Confidence            57889999999988776654332  234589999998654 45555554332 1  1222211111 000          


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhc-cccccccEEEEeCCcc-cCCcccH--HHHHH-hccc-cccEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGHS-VKNKKSK--LSIKL-TALR-ATFKV  152 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah~-~k~~~~~--~~~~~-~~l~-~~~~~  152 (169)
                                     .....++ ++.|...+.+.... ..-..++++|+||+|. .-+.+-.  ..+.+ ..++ ....+
T Consensus        87 ---------------~s~~t~I-~v~T~G~Llr~l~~d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlI  150 (819)
T TIGR01970        87 ---------------VSRRTRL-EVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKIL  150 (819)
T ss_pred             ---------------cCCCCcE-EEECCcHHHHHHhhCcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEE
Confidence                           0033456 77888777654321 2224688999999994 4332211  11222 2233 34578


Q ss_pred             EEeccCCCCCchhh
Q psy1090         153 LLTGWYYPNKWSKQ  166 (169)
Q Consensus       153 ~lT~TP~~n~~~el  166 (169)
                      +||||+-...+.++
T Consensus       151 lmSATl~~~~l~~~  164 (819)
T TIGR01970       151 AMSATLDGERLSSL  164 (819)
T ss_pred             EEeCCCCHHHHHHH
Confidence            99999876544444

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.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.56  E-value=5.9e-07  Score=73.23  Aligned_cols=131  Identities=16%  Similarity=0.142  Sum_probs=81.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH-H-------HHHHH-HHhCC--CceEEEEeCCHHHHHHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN-N-------WEAEF-RKFAP--FVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~-q-------W~~e~-~~~~~--~~~~~~~~g~~~~~~~~~~   73 (169)
                      +-+|+|+|||.+.+-.+..+.......+.+||||+..+. -       -.++| ..++.  .++.+.+... ..+.....
T Consensus        79 I~METGTGKTy~YlrtmfeLhk~YG~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~-~~~~~~~~  157 (985)
T COG3587          79 ILMETGTGKTYTYLRTMFELHKKYGLFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDED-IEKFKFKS  157 (985)
T ss_pred             EEEecCCCceeeHHHHHHHHHHHhCceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechH-HHHHhhcc
Confidence            468999999999988888777777677999999985442 1       11233 33332  3344444311 11111110


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhc---hhcccc-------------ccc-------cEEEEeCCc
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND---FGFLKK-------------ITW-------NCIIVDEGH  130 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~---~~~~~~-------------~~~-------~~vi~DEah  130 (169)
                                           ...+.+ ++.+.+...++   .+.+.+             .++       -++|+||-|
T Consensus       158 ---------------------~~~~~v-Ll~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh  215 (985)
T COG3587         158 ---------------------NNKPCV-LLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPH  215 (985)
T ss_pred             ---------------------CCCceE-EEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChh
Confidence                                 033344 77777776655   322211             112       289999999


Q ss_pred             ccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090         131 SVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus       131 ~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                      ++..+ .+.+.++..++..+.+=.+||--
T Consensus       216 ~f~~~-~k~~~~i~~l~pl~ilRfgATfk  243 (985)
T COG3587         216 RFLGD-DKTYGAIKQLNPLLILRFGATFK  243 (985)
T ss_pred             hcccc-hHHHHHHHhhCceEEEEecccch
Confidence            99865 78899999998888887788753

>KOG0342|consensus

Probab=98.47  E-value=1.6e-06  Score=66.72  Aligned_cols=135  Identities=14%  Similarity=0.135  Sum_probs=79.3

Q ss_pred             cccCCCCCcHHHHHH----HHHHHHHHhCCCC-ceEEEecCc-chHHHHHHH---HHhCCCceEEEEeCCHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVI----AFFCKIIEEQALE-PNLIVCPLS-VLNNWEAEF---RKFAPFVRTVKYYGNAIERKALQSE   74 (169)
Q Consensus         4 iL~de~G~GKT~~~i----~~i~~~~~~~~~~-~~Liv~P~~-~l~qW~~e~---~~~~~~~~~~~~~g~~~~~~~~~~~   74 (169)
                      +-+--+|+|||+.-+    ..+.......+.+ .++||||.- +--|-..|.   .++.+...+....|....+...+..
T Consensus       123 l~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl  202 (543)
T KOG0342|consen  123 LAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKL  202 (543)
T ss_pred             eeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHh
Confidence            345568999996533    2222222222222 589999984 445766554   4555677777666654443332222


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhcccc---ccccEEEEeCCcccCCcccH--HHHHHhcc-cc
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK---ITWNCIIVDEGHSVKNKKSK--LSIKLTAL-RA  148 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~---~~~~~vi~DEah~~k~~~~~--~~~~~~~l-~~  148 (169)
                      .                    ...++ +++|+..+....+--..   ...+++|+|||.++-.-+-.  .-+.+..+ +.
T Consensus       203 ~--------------------k~~ni-liATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~  261 (543)
T KOG0342|consen  203 V--------------------KGCNI-LIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQ  261 (543)
T ss_pred             h--------------------ccccE-EEeCCchHHhHhhcCCcchhhccceeEeecchhhhhcccHHHHHHHHHhcccc
Confidence            1                    45666 99999887665442221   23378999999997653321  23334444 45


Q ss_pred             ccEEEEeccCC
Q psy1090         149 TFKVLLTGWYY  159 (169)
Q Consensus       149 ~~~~~lT~TP~  159 (169)
                      +..++.|||-.
T Consensus       262 rqt~LFSAT~~  272 (543)
T KOG0342|consen  262 RQTLLFSATQP  272 (543)
T ss_pred             ceeeEeeCCCc
Confidence            56799999965

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.47  E-value=1.6e-06  Score=70.63  Aligned_cols=128  Identities=10%  Similarity=0.002  Sum_probs=82.3

Q ss_pred             CCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHH--HHHHHHhhhcCCCccccc
Q psy1090           9 TRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIE--RKALQSEALSLPTIKVPA   85 (169)
Q Consensus         9 ~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~~~~~~~~   85 (169)
                      .|+|||-..+.++......+  +.+||++|. .+..|+.+.|+..++...+..+++....  |...+.....        
T Consensus       169 ~GSGKTevyl~~i~~~l~~G--k~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~--------  238 (665)
T PRK14873        169 PGEDWARRLAAAAAATLRAG--RGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLR--------  238 (665)
T ss_pred             CCCcHHHHHHHHHHHHHHcC--CeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhC--------
Confidence            49999999988888777655  679999998 6778999999988865667777774333  3222222211        


Q ss_pred             ccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcc--cCCcccHHH----HHHh-c-cccccEEEEecc
Q psy1090          86 KKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHS--VKNKKSKLS----IKLT-A-LRATFKVLLTGW  157 (169)
Q Consensus        86 ~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~--~k~~~~~~~----~~~~-~-l~~~~~~~lT~T  157 (169)
                                +...| ++-|.+.+---     -.+.+++|+||-|.  +|....-++    -++. . ......++-|+|
T Consensus       239 ----------G~~~I-ViGtRSAvFaP-----~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaT  302 (665)
T PRK14873        239 ----------GQARV-VVGTRSAVFAP-----VEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHA  302 (665)
T ss_pred             ----------CCCcE-EEEcceeEEec-----cCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCC
Confidence                      56667 88887764221     12568999999984  444322221    1111 1 123345666999


Q ss_pred             CCCCC
Q psy1090         158 YYPNK  162 (169)
Q Consensus       158 P~~n~  162 (169)
                      |--.+
T Consensus       303 PSles  307 (665)
T PRK14873        303 RTAEA  307 (665)
T ss_pred             CCHHH
Confidence            97443

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

Probab=98.46  E-value=1.9e-06  Score=70.36  Aligned_cols=132  Identities=16%  Similarity=0.101  Sum_probs=86.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeC--CHHHHHHHHHhhhcCCC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYG--NAIERKALQSEALSLPT   80 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g--~~~~~~~~~~~~~~~~~   80 (169)
                      +|.--+|+|||-..+.+|......+  +.+||++|. ++..|-.+.|+..+ +.++.++++  +..+|...+.....   
T Consensus       221 Ll~GvTGSGKTEvYl~~i~~~L~~G--kqvLvLVPEI~Ltpq~~~rf~~rF-g~~v~vlHS~Ls~~er~~~W~~~~~---  294 (730)
T COG1198         221 LLDGVTGSGKTEVYLEAIAKVLAQG--KQVLVLVPEIALTPQLLARFKARF-GAKVAVLHSGLSPGERYRVWRRARR---  294 (730)
T ss_pred             eEeCCCCCcHHHHHHHHHHHHHHcC--CEEEEEeccccchHHHHHHHHHHh-CCChhhhcccCChHHHHHHHHHHhc---
Confidence            5667899999988888888777666  789999998 77888888887666 366666665  34444444433332   


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcc--cCCcccHHHHH----H-h-ccccccEE
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHS--VKNKKSKLSIK----L-T-ALRATFKV  152 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~--~k~~~~~~~~~----~-~-~l~~~~~~  152 (169)
                                     +...+ ++-|.+.+-.-.     .+.+++|+||=|.  +|..+.-++-+    + + .....-.+
T Consensus       295 ---------------G~~~v-VIGtRSAlF~Pf-----~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~Ra~~~~~pvv  353 (730)
T COG1198         295 ---------------GEARV-VIGTRSALFLPF-----KNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRAKKENAPVV  353 (730)
T ss_pred             ---------------CCceE-EEEechhhcCch-----hhccEEEEeccccccccCCcCCCcCHHHHHHHHHHHhCCCEE
Confidence                           66666 888877753322     2568999999994  44443222211    1 1 11233456


Q ss_pred             EEeccCCCCC
Q psy1090         153 LLTGWYYPNK  162 (169)
Q Consensus       153 ~lT~TP~~n~  162 (169)
                      +=||||--.+
T Consensus       354 LgSATPSLES  363 (730)
T COG1198         354 LGSATPSLES  363 (730)
T ss_pred             EecCCCCHHH
Confidence            7799997443

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.45  E-value=2.4e-06  Score=70.52  Aligned_cols=109  Identities=11%  Similarity=-0.001  Sum_probs=66.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-H---HHHHHHHHhCCCceEEEEeCCHH-HHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-N---NWEAEFRKFAPFVRTVKYYGNAI-ERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~---qW~~e~~~~~~~~~~~~~~g~~~-~~~~~~~~~~   76 (169)
                      |.|....+|.|||+++...+......  ...++||+|+..+ .   +|...+.++. ++.+....|... .....  .. 
T Consensus        93 G~Iaem~TGeGKTL~a~lp~~l~al~--G~~v~VvTpt~~LA~qd~e~~~~l~~~l-Gl~v~~i~g~~~~~~~r~--~~-  166 (790)
T PRK09200         93 GNIAEMQTGEGKTLTATMPLYLNALE--GKGVHLITVNDYLAKRDAEEMGQVYEFL-GLTVGLNFSDIDDASEKK--AI-  166 (790)
T ss_pred             CceeeecCCCcchHHHHHHHHHHHHc--CCCeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCcHHHHH--Hh-
Confidence            56778899999998765443322222  3579999999655 3   3555555565 677777776543 21111  11 


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHH-----Hhchh----ccccccccEEEEeCCcccCCcc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDFG----FLKKITWNCIIVDEGHSVKNKK  136 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~~----~~~~~~~~~vi~DEah~~k~~~  136 (169)
                                         ...|| ++.|+..+     .....    ....-++.++|+||++.+--+.
T Consensus       167 -------------------y~~dI-vygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDe  215 (790)
T PRK09200        167 -------------------YEADI-IYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDE  215 (790)
T ss_pred             -------------------cCCCE-EEECCccccchhHHhccccchhhhcccccceEEEeccccceecc
Confidence                               34667 88885544     33221    1223467899999999865433

>KOG0347|consensus

Probab=98.41  E-value=2.6e-06  Score=66.72  Aligned_cols=133  Identities=17%  Similarity=0.232  Sum_probs=80.8

Q ss_pred             cCCCCCcHHHH-HHHHHHHHHH------------hCCCC-ceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHHH
Q psy1090           6 PDPTRYRKSGK-VIAFFCKIIE------------EQALE-PNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIER   68 (169)
Q Consensus         6 ~de~G~GKT~~-~i~~i~~~~~------------~~~~~-~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~   68 (169)
                      +-|+|+|||+. +|-++..+.+            ....+ -.|||+|. .+..|-.+.+...+  +..++....|.-...
T Consensus       225 aAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavq  304 (731)
T KOG0347|consen  225 AAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQ  304 (731)
T ss_pred             ccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHH
Confidence            57999999964 3333332111            11112 27999997 77788888887666  467777788865544


Q ss_pred             HHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhch----hccccc-cccEEEEeCCcccCCccc--HHHH
Q psy1090          69 KALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF----GFLKKI-TWNCIIVDEGHSVKNKKS--KLSI  141 (169)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~----~~~~~~-~~~~vi~DEah~~k~~~~--~~~~  141 (169)
                      .+.+-..                    ..++| |++|+..+-..+    -.+.++ +..++|+||+.++-..+.  ...+
T Consensus       305 KQqRlL~--------------------~~p~I-VVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmvekghF~Els~  363 (731)
T KOG0347|consen  305 KQQRLLN--------------------QRPDI-VVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSK  363 (731)
T ss_pred             HHHHHHh--------------------cCCCE-EEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHhhhccHHHHHH
Confidence            4333322                    55666 899877654322    223322 567999999999865442  2233


Q ss_pred             HHhccc------cccEEEEeccCC
Q psy1090         142 KLTALR------ATFKVLLTGWYY  159 (169)
Q Consensus       142 ~~~~l~------~~~~~~lT~TP~  159 (169)
                      .+..++      -+-.++.|||..
T Consensus       364 lL~~L~e~~~~~qrQTlVFSATlt  387 (731)
T KOG0347|consen  364 LLKHLNEEQKNRQRQTLVFSATLT  387 (731)
T ss_pred             HHHHhhhhhcccccceEEEEEEee
Confidence            333332      234688999864

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

Probab=98.39  E-value=5.9e-06  Score=69.58  Aligned_cols=60  Identities=12%  Similarity=0.056  Sum_probs=38.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHH-HHH---HhCC-CceEEEEeCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEA-EFR---KFAP-FVRTVKYYGN   64 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~-e~~---~~~~-~~~~~~~~g~   64 (169)
                      +++.-.+|+|||...+.-+.....  ..++++|.+|.. +..|+.. ++.   +..+ .+++....|.
T Consensus       267 ~~~eA~TG~GKT~ayLlp~~~~~~--~~~~vvi~t~t~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~  332 (850)
T TIGR01407       267 SLIEAPTGTGKTLGYLLPALYYAI--TEKPVVISTNTKVLQSQLLEKDIPLLNEILNFKINAALIKGK  332 (850)
T ss_pred             EEEECCCCCchhHHHHHHHHHHhc--CCCeEEEEeCcHHHHHHHHHHHHHHHHHHcCCCceEEEEEcc
Confidence            455679999999887655443332  346899999985 4568754 444   3332 3666666653

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.

>KOG0343|consensus

Probab=98.38  E-value=2.6e-06  Score=66.74  Aligned_cols=134  Identities=13%  Similarity=0.101  Sum_probs=82.5

Q ss_pred             cCCCCCcHHHHHH-HHHHHHHHhCCC---C-ceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           6 PDPTRYRKSGKVI-AFFCKIIEEQAL---E-PNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         6 ~de~G~GKT~~~i-~~i~~~~~~~~~---~-~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |--+|+|||+.-+ -++..+.+.+..   + -+||+.|. .+.-|-.+-+.+...  ++-.....|..+-......    
T Consensus       112 AAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eR----  187 (758)
T KOG0343|consen  112 AAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELER----  187 (758)
T ss_pred             ccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHh----
Confidence            5679999997533 334444443322   2 48999998 555577666665431  3444444554443222221    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCccc--HHHHHHhcc-ccccE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL-RATFK  151 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l-~~~~~  151 (169)
                                       ....+| +++|+..+....+   .++..+..++|+|||.++-..+-  .....+..+ ..+-.
T Consensus       188 -----------------i~~mNI-LVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQT  249 (758)
T KOG0343|consen  188 -----------------ISQMNI-LVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKRQT  249 (758)
T ss_pred             -----------------hhcCCe-EEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhhee
Confidence                             156677 9999998876554   34455678999999998754332  223334556 45667


Q ss_pred             EEEeccCCCC
Q psy1090         152 VLLTGWYYPN  161 (169)
Q Consensus       152 ~~lT~TP~~n  161 (169)
                      +++|||+..+
T Consensus       250 LLFSATqt~s  259 (758)
T KOG0343|consen  250 LLFSATQTKS  259 (758)
T ss_pred             eeeecccchh
Confidence            9999999754

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.37  E-value=2.8e-06  Score=73.17  Aligned_cols=68  Identities=18%  Similarity=0.157  Sum_probs=41.1

Q ss_pred             CCCCeEEEecHHHHHhchhc-cccccccEEEEeCCc-ccCCcccHHHHHHhcc----ccccEEEEeccCCCCCchh
Q psy1090          96 LKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGH-SVKNKKSKLSIKLTAL----RATFKVLLTGWYYPNKWSK  165 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah-~~k~~~~~~~~~~~~l----~~~~~~~lT~TP~~n~~~e  165 (169)
                      ....+ ++.|...+.+.... ..-..++.+|+|||| +.-+.+-. ...++.+    +....+++|||.-.+.+.+
T Consensus       162 ~~t~I-~v~TpG~LL~~l~~d~~Ls~~~~IIIDEAHERsLn~DfL-Lg~Lk~lL~~rpdlKvILmSATid~e~fs~  235 (1294)
T PRK11131        162 DNTMV-KLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFI-LGYLKELLPRRPDLKVIITSATIDPERFSR  235 (1294)
T ss_pred             CCCCE-EEEChHHHHHHHhcCCccccCcEEEecCccccccccchH-HHHHHHhhhcCCCceEEEeeCCCCHHHHHH
Confidence            44566 88898888765431 112478999999999 45443322 2223322    2346799999985444333

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.37  E-value=8.3e-06  Score=66.10  Aligned_cols=61  Identities=7%  Similarity=-0.180  Sum_probs=39.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HH---HHHHHHHhCCCceEEEEeCCH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NN---WEAEFRKFAPFVRTVKYYGNA   65 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~q---W~~e~~~~~~~~~~~~~~g~~   65 (169)
                      |.|....+|.|||+++...+......  ...++||+|+.-+ .|   |...+.++. ++.+....|..
T Consensus       118 G~Iae~~TGeGKTla~~lp~~~~al~--G~~v~VvTptreLA~qdae~~~~l~~~l-Glsv~~i~gg~  182 (656)
T PRK12898        118 GRLAEMQTGEGKTLTATLPAGTAALA--GLPVHVITVNDYLAERDAELMRPLYEAL-GLTVGCVVEDQ  182 (656)
T ss_pred             CCeeeeeCCCCcHHHHHHHHHHHhhc--CCeEEEEcCcHHHHHHHHHHHHHHHhhc-CCEEEEEeCCC
Confidence            55677899999998865444333322  3579999998544 44   444454554 67777776653

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

Probab=98.36  E-value=1.6e-06  Score=61.61  Aligned_cols=49  Identities=18%  Similarity=0.342  Sum_probs=34.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH------HhCCCCceEEEecC-cchHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII------EEQALEPNLIVCPL-SVLNNWEAEFRK   51 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~------~~~~~~~~Liv~P~-~~l~qW~~e~~~   51 (169)
                      .++...+|+|||.+..+++..+.      .....+++||++|+ ..+++-.+.+.+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            45677899999988888777762      24556799999998 456677767665

>KOG0348|consensus

Probab=98.35  E-value=3.3e-06  Score=65.90  Aligned_cols=133  Identities=11%  Similarity=0.136  Sum_probs=81.8

Q ss_pred             ccccCCCCCcHHHHHHHHHH-HHHHh-----CCCC-ceEEEecC-cchHHHHHHHHHhCCCceEEE----EeCCHHH--H
Q psy1090           3 TVIPDPTRYRKSGKVIAFFC-KIIEE-----QALE-PNLIVCPL-SVLNNWEAEFRKFAPFVRTVK----YYGNAIE--R   68 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~-~~~~~-----~~~~-~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~----~~g~~~~--~   68 (169)
                      +++-..+|+|||+..+.-+. .+...     +..+ -+||++|. .+..|-++-+++....+..++    ..|.++.  +
T Consensus       177 ~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEK  256 (708)
T KOG0348|consen  177 ALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEK  256 (708)
T ss_pred             eEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHH
Confidence            45667899999987665443 33321     1123 36999997 777888888887763333222    3343332  2


Q ss_pred             HHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhcccc---ccccEEEEeCCcccCC-----cccHHH
Q psy1090          69 KALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK---ITWNCIIVDEGHSVKN-----KKSKLS  140 (169)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~---~~~~~vi~DEah~~k~-----~~~~~~  140 (169)
                      ..++                       ...+| +|.|+..+......-..   ....++|+||+.++-.     .-++..
T Consensus       257 ARLR-----------------------KGiNI-LIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLGfekdit~Il  312 (708)
T KOG0348|consen  257 ARLR-----------------------KGINI-LIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFEKDITQIL  312 (708)
T ss_pred             HHHh-----------------------cCceE-EEcCchHHHHHHhccchheeeeeeEEEecchhHHHhccchhhHHHHH
Confidence            2222                       66677 99999998876543333   3456899999998654     224444


Q ss_pred             HHHhcc---cc--------ccEEEEeccCC
Q psy1090         141 IKLTAL---RA--------TFKVLLTGWYY  159 (169)
Q Consensus       141 ~~~~~l---~~--------~~~~~lT~TP~  159 (169)
                      +++...   .+        .-++++|||..
T Consensus       313 ~~v~~~~~~e~~~~~lp~q~q~mLlSATLt  342 (708)
T KOG0348|consen  313 KAVHSIQNAECKDPKLPHQLQNMLLSATLT  342 (708)
T ss_pred             HHHhhccchhcccccccHHHHhHhhhhhhH
Confidence            455332   11        33688999975

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.35  E-value=4e-06  Score=69.61  Aligned_cols=107  Identities=15%  Similarity=0.071  Sum_probs=63.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHH---HHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNN---WEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~q---W~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |-|-...+|.|||+++..-+......+  ..++||+|+. +..|   |...+-++. ++.+....|..........    
T Consensus        97 G~Iaem~TGeGKTL~a~Lpa~~~al~G--~~V~VvTpn~yLA~qd~e~m~~l~~~l-GLtv~~i~gg~~~~~r~~~----  169 (896)
T PRK13104         97 GNIAEMRTGEGKTLVATLPAYLNAISG--RGVHIVTVNDYLAKRDSQWMKPIYEFL-GLTVGVIYPDMSHKEKQEA----  169 (896)
T ss_pred             CccccccCCCCchHHHHHHHHHHHhcC--CCEEEEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCCCHHHHHHH----
Confidence            456678899999987654433222223  4699999985 4434   555555555 5777777665332222111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhchhc----cccccccEEEEeCCcccCC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDFGF----LKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~~~----~~~~~~~~vi~DEah~~k~  134 (169)
                                        ...|| ++.|...+     +.....    .-.-++.++|+||++.+--
T Consensus       170 ------------------y~~dI-vygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLI  216 (896)
T PRK13104        170 ------------------YKADI-VYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILI  216 (896)
T ss_pred             ------------------hCCCE-EEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhh
Confidence                              33566 88887765     222111    1124788999999997644

>KOG4284|consensus

Probab=98.33  E-value=8.1e-07  Score=70.74  Aligned_cols=138  Identities=17%  Similarity=0.210  Sum_probs=90.3

Q ss_pred             CccccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC---CceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP---FVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~---~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      .-|+..-.|+|||+.- +..+..+..+...-..+||+|. .+--|-.+-+...+|   ++++.+|.|.......+...  
T Consensus        64 DliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rl--  141 (980)
T KOG4284|consen   64 DLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRL--  141 (980)
T ss_pred             ceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhh--
Confidence            4466778899999642 1222233223333358999997 455577777776664   78888888865544333322  


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCcccH---HHHHHhcc-cccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSK---LSIKLTAL-RATF  150 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~~~~---~~~~~~~l-~~~~  150 (169)
                                         ....| +|-|+..+...+  +.+.-...+++|+|||..+-...+.   ....+..+ ..+-
T Consensus       142 -------------------k~~rI-vIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~slP~~rQ  201 (980)
T KOG4284|consen  142 -------------------KQTRI-VIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIRQ  201 (980)
T ss_pred             -------------------hhceE-EecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHhcchhhe
Confidence                               34445 999998887644  3455567889999999988653332   34555666 4566


Q ss_pred             EEEEeccCCCC
Q psy1090         151 KVLLTGWYYPN  161 (169)
Q Consensus       151 ~~~lT~TP~~n  161 (169)
                      .++.|||-.+|
T Consensus       202 v~a~SATYp~n  212 (980)
T KOG4284|consen  202 VAAFSATYPRN  212 (980)
T ss_pred             eeEEeccCchh
Confidence            88999998766

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

Probab=98.33  E-value=2e-06  Score=67.81  Aligned_cols=136  Identities=14%  Similarity=0.103  Sum_probs=80.2

Q ss_pred             cccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           4 VIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         4 iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +....+++|||+.+ +|=+....  +..+++|+++|. .+.+|=+++|.+-+.  ++++.+--|....+..-.       
T Consensus       236 lVVSaTasGKTLIgElAGi~~~l--~~g~KmlfLvPLVALANQKy~dF~~rYs~LglkvairVG~srIk~~~~-------  306 (830)
T COG1202         236 LVVSATASGKTLIGELAGIPRLL--SGGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREE-------  306 (830)
T ss_pred             EEEeccCCCcchHHHhhCcHHHH--hCCCeEEEEehhHHhhcchHHHHHHHhhcccceEEEEechhhhcccCC-------
Confidence            34567899999764 22233322  334799999997 666787888865443  445555556554432211       


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhc-cccccccEEEEeCCcccCCc--ccHHHHHH---hcc-ccccEE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGHSVKNK--KSKLSIKL---TAL-RATFKV  152 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah~~k~~--~~~~~~~~---~~l-~~~~~~  152 (169)
                               +.........|| ++-||+-+.-.... -.--+.+.||+||.|.+...  +...--.+   +.+ .....+
T Consensus       307 ---------pv~~~t~~dADI-IVGTYEGiD~lLRtg~~lgdiGtVVIDEiHtL~deERG~RLdGLI~RLr~l~~~AQ~i  376 (830)
T COG1202         307 ---------PVVVDTSPDADI-IVGTYEGIDYLLRTGKDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFI  376 (830)
T ss_pred             ---------ccccCCCCCCcE-EEeechhHHHHHHcCCcccccceEEeeeeeeccchhcccchhhHHHHHHHhCCCCeEE
Confidence                     111222377788 99999876422211 11236789999999998752  22222222   333 345678


Q ss_pred             EEeccC
Q psy1090         153 LLTGWY  158 (169)
Q Consensus       153 ~lT~TP  158 (169)
                      .||||-
T Consensus       377 ~LSATV  382 (830)
T COG1202         377 YLSATV  382 (830)
T ss_pred             EEEeec
Confidence            999994

>KOG0353|consensus

Probab=98.32  E-value=3.3e-06  Score=63.57  Aligned_cols=142  Identities=18%  Similarity=0.156  Sum_probs=85.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      ++|...+|-||++..-     +..-...+-+|||||. ++++...-.++...-+...+.-..++++........-+.   
T Consensus       112 ~~lil~tgggkslcyq-----lpal~adg~alvi~plislmedqil~lkqlgi~as~lnansske~~k~v~~~i~nk---  183 (695)
T KOG0353|consen  112 AFLILPTGGGKSLCYQ-----LPALCADGFALVICPLISLMEDQILQLKQLGIDASMLNANSSKEEAKRVEAAITNK---  183 (695)
T ss_pred             eEEEEeCCCccchhhh-----hhHHhcCCceEeechhHHHHHHHHHHHHHhCcchhhccCcccHHHHHHHHHHHcCC---
Confidence            5678899999996431     1111234679999997 666655555665543333333334444444444333322   


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccc-------cccccEEEEeCCcccCCcc-------cHHHHHHhccc
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLK-------KITWNCIIVDEGHSVKNKK-------SKLSIKLTALR  147 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~-------~~~~~~vi~DEah~~k~~~-------~~~~~~~~~l~  147 (169)
                                   ...+.. +-.|++.+.+...++.       .--|.++-+||+|+-....       ......-+.++
T Consensus       184 -------------dse~kl-iyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~  249 (695)
T KOG0353|consen  184 -------------DSEFKL-IYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFK  249 (695)
T ss_pred             -------------CceeEE-EEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhCC
Confidence                         156666 6677777765443332       3356789999999754422       22223334667


Q ss_pred             cccEEEEeccCCCCCchhh
Q psy1090         148 ATFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       148 ~~~~~~lT~TP~~n~~~el  166 (169)
                      ..-.++||||...+-+.|.
T Consensus       250 ~~~iigltatatn~vl~d~  268 (695)
T KOG0353|consen  250 GAPIIGLTATATNHVLDDA  268 (695)
T ss_pred             CCceeeeehhhhcchhhHH
Confidence            7889999999988877664

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

Probab=98.28  E-value=4.2e-06  Score=63.65  Aligned_cols=43  Identities=14%  Similarity=0.084  Sum_probs=31.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      ++.-..|+|||+.++.++..+.........+++|++..+.+..
T Consensus         5 ~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l   47 (352)
T PF09848_consen    5 LITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKL   47 (352)
T ss_pred             EEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHH
Confidence            4566799999999999887773344456788888887665433

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

>PRK10536 hypothetical protein; Provisional

Probab=98.24  E-value=8.4e-06  Score=58.84  Aligned_cols=55  Identities=16%  Similarity=0.237  Sum_probs=39.6

Q ss_pred             EEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCc
Q psy1090         102 LVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKW  163 (169)
Q Consensus       102 ~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~  163 (169)
                      -+.+...++..     .++-+++|+||||++.-  ......+.++....+++++|=|-|.+.
T Consensus       163 ei~~l~ymRGr-----tl~~~~vIvDEaqn~~~--~~~k~~ltR~g~~sk~v~~GD~~QiD~  217 (262)
T PRK10536        163 EIAPFAYMRGR-----TFENAVVILDEAQNVTA--AQMKMFLTRLGENVTVIVNGDITQCDL  217 (262)
T ss_pred             EEecHHHhcCC-----cccCCEEEEechhcCCH--HHHHHHHhhcCCCCEEEEeCChhhccC
Confidence            56665555432     23557999999999853  455566678888999999999887654

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.23  E-value=8.3e-06  Score=67.76  Aligned_cols=107  Identities=11%  Similarity=-0.044  Sum_probs=64.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH----HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN----NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~----qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|.-+.+|.|||+++...+....  -..+.+-||+|+..+.    +|...+-+|. ++.+....+..........    
T Consensus        97 G~iaEM~TGEGKTLvA~l~a~l~a--l~G~~VhvvT~ndyLA~RD~e~m~~l~~~l-Gl~v~~i~~~~~~~err~~----  169 (913)
T PRK13103         97 GKIAEMRTGEGKTLVGTLAVYLNA--LSGKGVHVVTVNDYLARRDANWMRPLYEFL-GLSVGIVTPFQPPEEKRAA----  169 (913)
T ss_pred             CccccccCCCCChHHHHHHHHHHH--HcCCCEEEEeCCHHHHHHHHHHHHHHhccc-CCEEEEECCCCCHHHHHHH----
Confidence            567778899999987543322222  2236788999987663    4555555555 6777777665333221111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhchh----ccccccccEEEEeCCcccCC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDFG----FLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~~----~~~~~~~~~vi~DEah~~k~  134 (169)
                                        -..|| +..|...+     +.+..    ..-..+++++|+||+|.+--
T Consensus       170 ------------------Y~~dI-~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLI  216 (913)
T PRK13103        170 ------------------YAADI-TYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILI  216 (913)
T ss_pred             ------------------hcCCE-EEEcccccccchhhccceechhhhcccccceeEechhhheec
Confidence                              33566 66666554     33322    12235788999999998644

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.22  E-value=1.2e-05  Score=59.47  Aligned_cols=50  Identities=12%  Similarity=0.133  Sum_probs=31.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCC----CceEEEecCc-chHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQAL----EPNLIVCPLS-VLNNWEAEFRKF   52 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~----~~~Liv~P~~-~l~qW~~e~~~~   52 (169)
                      +++...+|+|||+..+..+.........    .+++++++.. .+.|-..++++.
T Consensus        30 ~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488       30 GILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             EEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            5677889999999887665433333222    2677777764 334555556543

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.22  E-value=1.2e-05  Score=59.47  Aligned_cols=50  Identities=12%  Similarity=0.133  Sum_probs=31.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCC----CceEEEecCc-chHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQAL----EPNLIVCPLS-VLNNWEAEFRKF   52 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~----~~~Liv~P~~-~l~qW~~e~~~~   52 (169)
                      +++...+|+|||+..+..+.........    .+++++++.. .+.|-..++++.
T Consensus        30 ~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489       30 GILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             EEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            5677889999999887665433333222    2677777764 334555556543

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

Probab=98.19  E-value=2.2e-06  Score=60.02  Aligned_cols=138  Identities=16%  Similarity=0.145  Sum_probs=56.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      ++.-..|+|||+.+++.......++...+++++-|.--..+   + .-|.|+-.--.+..-  .....+.......    
T Consensus        23 ~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~---~-lGflpG~~~eK~~p~--~~p~~d~l~~~~~----   92 (205)
T PF02562_consen   23 IVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGE---D-LGFLPGDLEEKMEPY--LRPIYDALEELFG----   92 (205)
T ss_dssp             EEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT--------SS---------TT--THHHHHHHTTTS-----
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCcc---c-cccCCCCHHHHHHHH--HHHHHHHHHHHhC----
Confidence            34567899999999999888777777778888877643221   1 112221100000000  0000111000000    


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCc
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKW  163 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~  163 (169)
                          ............+ -+.+.+.++.     +.++..++|+||||.+.  ....-..+.++....+++++|=|.|.+.
T Consensus        93 ----~~~~~~~~~~~~I-e~~~~~~iRG-----rt~~~~~iIvDEaQN~t--~~~~k~ilTR~g~~skii~~GD~~Q~D~  160 (205)
T PF02562_consen   93 ----KEKLEELIQNGKI-EIEPLAFIRG-----RTFDNAFIIVDEAQNLT--PEELKMILTRIGEGSKIIITGDPSQIDL  160 (205)
T ss_dssp             ----TTCHHHHHHTTSE-EEEEGGGGTT-------B-SEEEEE-SGGG----HHHHHHHHTTB-TT-EEEEEE-------
T ss_pred             ----hHhHHHHhhcCeE-EEEehhhhcC-----ccccceEEEEecccCCC--HHHHHHHHcccCCCcEEEEecCceeecC
Confidence                0000000012222 4444433332     12455799999999974  2344455667788899999998887654

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

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

Probab=98.19  E-value=1.9e-06  Score=55.95  Aligned_cols=35  Identities=23%  Similarity=0.314  Sum_probs=26.2

Q ss_pred             cEEEEeCCcccCCcccHHHHHHhcc--ccccEEEEeccC
Q psy1090         122 NCIIVDEGHSVKNKKSKLSIKLTAL--RATFKVLLTGWY  158 (169)
Q Consensus       122 ~~vi~DEah~~k~~~~~~~~~~~~l--~~~~~~~lT~TP  158 (169)
                      .++|+||+|++.  +......++.+  .....+++.|||
T Consensus        89 ~~lviDe~~~l~--~~~~l~~l~~l~~~~~~~vvl~G~~  125 (131)
T PF13401_consen   89 VLLVIDEADHLF--SDEFLEFLRSLLNESNIKVVLVGTP  125 (131)
T ss_dssp             EEEEEETTHHHH--THHHHHHHHHHTCSCBEEEEEEESS
T ss_pred             eEEEEeChHhcC--CHHHHHHHHHHHhCCCCeEEEEECh
Confidence            789999999983  23344455444  677899999999

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

Probab=98.17  E-value=1.2e-05  Score=67.77  Aligned_cols=127  Identities=16%  Similarity=0.104  Sum_probs=76.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCc--eEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFV--RTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +.+.+-.+|+|||+.+--++......+  .+++-..|- .+-+|=+++|..-+.+.  -+..++|+...           
T Consensus       136 sVlV~ApTssGKTvVaeyAi~~al~~~--qrviYTsPIKALsNQKyrdl~~~fgdv~~~vGL~TGDv~I-----------  202 (1041)
T COG4581         136 SVLVCAPTSSGKTVVAEYAIALALRDG--QRVIYTSPIKALSNQKYRDLLAKFGDVADMVGLMTGDVSI-----------  202 (1041)
T ss_pred             cEEEEccCCCCcchHHHHHHHHHHHcC--CceEeccchhhhhhhHHHHHHHHhhhhhhhccceecceee-----------
Confidence            356788899999988866665544444  458888896 66667666664332221  23445554332           


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcc-cHHH-HHHhcc-ccccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKK-SKLS-IKLTAL-RATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~-~~~~-~~~~~l-~~~~~~~  153 (169)
                                      .....+ ++.|-+.+++-  .+.....+...||+||.|++.... .-.+ ..+..+ +...-++
T Consensus       203 ----------------N~~A~c-lvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v~~v~  265 (1041)
T COG4581         203 ----------------NPDAPC-LVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVF  265 (1041)
T ss_pred             ----------------CCCCce-EEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCCcEEE
Confidence                            155555 55554777642  111222356789999999987633 2223 334444 3447899


Q ss_pred             EeccC
Q psy1090         154 LTGWY  158 (169)
Q Consensus       154 lT~TP  158 (169)
                      ||||=
T Consensus       266 LSATv  270 (1041)
T COG4581         266 LSATV  270 (1041)
T ss_pred             EeCCC
Confidence            99994

>KOG1802|consensus

Probab=98.15  E-value=3.6e-06  Score=67.28  Aligned_cols=60  Identities=13%  Similarity=0.266  Sum_probs=45.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhCCCceEEEEeCCHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFAPFVRTVKYYGNAI   66 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~~~~~~~~~~g~~~   66 (169)
                      +|...+|+|||++.-+++-.+.+. ..+|+|+++|+.+ ++|-.+.+.+-  +++++.....++
T Consensus       429 LIQGPPGTGKTvtsa~IVyhl~~~-~~~~VLvcApSNiAVDqLaeKIh~t--gLKVvRl~aksR  489 (935)
T KOG1802|consen  429 LIQGPPGTGKTVTSATIVYHLARQ-HAGPVLVCAPSNIAVDQLAEKIHKT--GLKVVRLCAKSR  489 (935)
T ss_pred             eeecCCCCCceehhHHHHHHHHHh-cCCceEEEcccchhHHHHHHHHHhc--CceEeeeehhhh
Confidence            678899999999987776665554 5789999999865 67888878765  578877665433

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.15  E-value=2.4e-05  Score=65.30  Aligned_cols=107  Identities=11%  Similarity=0.012  Sum_probs=62.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chH---HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLN---NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~---qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.+....+|+|||+.++.-+......+  .+++||+|+. +..   +|...+.++. ++.+....|..........    
T Consensus       109 gvIAeaqTGeGKTLAf~LP~l~~aL~g--~~v~IVTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~----  181 (970)
T PRK12899        109 GFITEMQTGEGKTLTAVMPLYLNALTG--KPVHLVTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEI----  181 (970)
T ss_pred             CeEEEeCCCCChHHHHHHHHHHHHhhc--CCeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHH----
Confidence            456678999999988654433222222  3588889974 443   4666666665 5777666654333322211    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-H----hchhccc-----cccccEEEEeCCcccCC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-E----NDFGFLK-----KITWNCIIVDEGHSVKN  134 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-~----~~~~~~~-----~~~~~~vi~DEah~~k~  134 (169)
                                        -.+|| ++.|+..+ -    +..-.+.     .-.+.++|+|||..+--
T Consensus       182 ------------------y~~DI-VygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEADsmLi  229 (970)
T PRK12899        182 ------------------YQCDV-VYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEVDSILI  229 (970)
T ss_pred             ------------------cCCCE-EEECCChhHHHHhhCCCCCcCHHHhhcccccEEEEechhhhhh
Confidence                              23566 88887666 2    1111111     23577999999987543

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.15  E-value=2e-06  Score=71.18  Aligned_cols=151  Identities=21%  Similarity=0.271  Sum_probs=78.0

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC--CCCceEEEecC-cchHHHHHHHHHhCCCceEEEE--eCCHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ--ALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKY--YGNAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~--~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~--~g~~~~~~~~~~~~~~   77 (169)
                      .+|..++|.|||..++....+.....  ...+.+.+.|- +++++-.+.+.++.....+...  ++.....-........
T Consensus       217 ~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~  296 (733)
T COG1203         217 VVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQDI  296 (733)
T ss_pred             EEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccccccccccccccchhhhcccccc
Confidence            46889999999998888877766653  45678888886 5566778888877643333322  4443332211111100


Q ss_pred             -CCCcccccccCCccccccCCCCeEEEecHHHHHhc-----hhccccccccEEEEeCCcccCCcc-cHHHHHH-hcc--c
Q psy1090          78 -LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND-----FGFLKKITWNCIIVDEGHSVKNKK-SKLSIKL-TAL--R  147 (169)
Q Consensus        78 -~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~-----~~~~~~~~~~~vi~DEah~~k~~~-~~~~~~~-~~l--~  147 (169)
                       ......++..       ......++.++.+.+...     ...+..+....+|+||+|.+.... .....++ ..+  .
T Consensus       297 ~~~~~~~ds~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~~~~~l~~~i~~l~~~  369 (733)
T COG1203         297 LLTLTTNDSYK-------KLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEA  369 (733)
T ss_pred             ceeEEeccccc-------ceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccchHHHHHHHHHHHHhC
Confidence             0000000000       011111122333332210     111223456799999999887552 2222222 222  3


Q ss_pred             cccEEEEeccCCC
Q psy1090         148 ATFKVLLTGWYYP  160 (169)
Q Consensus       148 ~~~~~~lT~TP~~  160 (169)
                      -...++||||+.+
T Consensus       370 g~~ill~SATlP~  382 (733)
T COG1203         370 GVPVLLMSATLPP  382 (733)
T ss_pred             CCCEEEEecCCCH
Confidence            4668999999974

>KOG0346|consensus

Probab=98.14  E-value=1.3e-05  Score=61.34  Aligned_cols=131  Identities=15%  Similarity=0.099  Sum_probs=74.6

Q ss_pred             CCCCcHHHHH-HHHHHHHHHhCCC-----C-ceEEEecC-cchHHHHHHHHHhC---C-CceEEEEeCCHHHHHHHHHhh
Q psy1090           8 PTRYRKSGKV-IAFFCKIIEEQAL-----E-PNLIVCPL-SVLNNWEAEFRKFA---P-FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         8 e~G~GKT~~~-i~~i~~~~~~~~~-----~-~~Liv~P~-~~l~qW~~e~~~~~---~-~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      -+|+|||... |-++..+......     + ..+|++|. .+.+|-+..+.+..   + .++++-...+..+....  ..
T Consensus        64 rTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~--~~  141 (569)
T KOG0346|consen   64 RTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNS--VA  141 (569)
T ss_pred             ccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHH--HH
Confidence            4899999764 3445555443221     2 57999997 78888887776543   2 34444333222221111  11


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc---cccccccEEEEeCCcccCCcccH-H-HHHHhccc-cc
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF---LKKITWNCIIVDEGHSVKNKKSK-L-SIKLTALR-AT  149 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~---~~~~~~~~vi~DEah~~k~~~~~-~-~~~~~~l~-~~  149 (169)
                      ..                  ..++| +++|+..+.+....   ...-...++|+|||.-+-..+-. - .+....++ .-
T Consensus       142 L~------------------d~pdI-vV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLllsfGYeedlk~l~~~LPr~~  202 (569)
T KOG0346|consen  142 LM------------------DLPDI-VVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFGYEEDLKKLRSHLPRIY  202 (569)
T ss_pred             Hc------------------cCCCe-EEeChHHHHHHHhhccchhhhheeeEEechhhhhhhcccHHHHHHHHHhCCchh
Confidence            11                  66777 99999988765432   11224578999999976543321 1 22223343 23


Q ss_pred             cEEEEeccCC
Q psy1090         150 FKVLLTGWYY  159 (169)
Q Consensus       150 ~~~~lT~TP~  159 (169)
                      -.++||||.-
T Consensus       203 Q~~LmSATl~  212 (569)
T KOG0346|consen  203 QCFLMSATLS  212 (569)
T ss_pred             hheeehhhhh
Confidence            3688899864

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.14  E-value=2.1e-05  Score=65.25  Aligned_cols=107  Identities=12%  Similarity=-0.030  Sum_probs=63.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HH---HHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NN---WEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~q---W~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|....+|.|||+++...+......+  +.+-||+|+..+ .|   |...+-++. ++.+....|..........    
T Consensus        96 G~Iaem~TGeGKTLva~lpa~l~aL~G--~~V~IvTpn~yLA~rd~e~~~~l~~~L-Glsv~~i~~~~~~~er~~~----  168 (830)
T PRK12904         96 GKIAEMKTGEGKTLVATLPAYLNALTG--KGVHVVTVNDYLAKRDAEWMGPLYEFL-GLSVGVILSGMSPEERREA----  168 (830)
T ss_pred             CchhhhhcCCCcHHHHHHHHHHHHHcC--CCEEEEecCHHHHHHHHHHHHHHHhhc-CCeEEEEcCCCCHHHHHHh----
Confidence            667788999999987654332222223  357799998655 33   555555554 6777777764333322221    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHh-----ch----hccccccccEEEEeCCcccCC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN-----DF----GFLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~-----~~----~~~~~~~~~~vi~DEah~~k~  134 (169)
                                        -..|| ++.|...+.-     ..    +.....++.++|+||+..+--
T Consensus       169 ------------------y~~dI-~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLI  215 (830)
T PRK12904        169 ------------------YAADI-TYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILI  215 (830)
T ss_pred             ------------------cCCCe-EEECCcchhhhhhhcccccchhhhcccccceEEEechhhhee
Confidence                              22566 7777666522     11    112234678999999987544

>KOG1803|consensus

Probab=98.13  E-value=6.3e-06  Score=65.17  Aligned_cols=44  Identities=16%  Similarity=0.414  Sum_probs=35.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~   49 (169)
                      ++-..+|+|||.+...+|+.+...+  +++||++|+++ +++-.+.+
T Consensus       205 ~I~GPPGTGKT~TlvEiI~qlvk~~--k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  205 IIHGPPGTGKTRTLVEIISQLVKQK--KRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             EeeCCCCCCceeeHHHHHHHHHHcC--CeEEEEcCchHHHHHHHHHh
Confidence            4567899999999999988877666  88999999864 66766643

>KOG0951|consensus

Probab=98.02  E-value=1.4e-05  Score=67.93  Aligned_cols=132  Identities=14%  Similarity=0.129  Sum_probs=78.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCC---------CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQA---------LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKAL   71 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~---------~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~   71 (169)
                      .|+-.+|+|||-.|+..+......+.         ..+..-++|. .+++.|...|.++..  +..+.-.+|...-....
T Consensus       329 LlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~q  408 (1674)
T KOG0951|consen  329 LLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQ  408 (1674)
T ss_pred             EEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEecccccchhhh
Confidence            57778999999877655443333221         1267888995 788899999988875  44555566664422211


Q ss_pred             HHhhhcCCCcccccccCCccccccCCCCeEEEecHHHH---Hhchhc-cccccccEEEEeCCccc---CCcccH--HHHH
Q psy1090          72 QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQII---ENDFGF-LKKITWNCIIVDEGHSV---KNKKSK--LSIK  142 (169)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~---~~~~~~-~~~~~~~~vi~DEah~~---k~~~~~--~~~~  142 (169)
                      .                       ...++ +++|++..   .+.... --..-++++|+||.|.+   +++.-.  ..+.
T Consensus       409 i-----------------------eeTqV-IV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDdRGpvLESIVaRt  464 (1674)
T KOG0951|consen  409 I-----------------------EETQV-IVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDDRGPVLESIVART  464 (1674)
T ss_pred             h-----------------------hccee-EEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccccchHHHHHHHHH
Confidence            1                       44555 77776553   332211 11224678999999988   433221  1122


Q ss_pred             Hhcc----ccccEEEEeccCC
Q psy1090         143 LTAL----RATFKVLLTGWYY  159 (169)
Q Consensus       143 ~~~l----~~~~~~~lT~TP~  159 (169)
                      ++..    ...+.++||||..
T Consensus       465 ~r~ses~~e~~RlVGLSATLP  485 (1674)
T KOG0951|consen  465 FRRSESTEEGSRLVGLSATLP  485 (1674)
T ss_pred             HHHhhhcccCceeeeecccCC
Confidence            2222    2456799999975

>KOG0339|consensus

Probab=98.02  E-value=9.3e-05  Score=57.84  Aligned_cols=131  Identities=16%  Similarity=0.215  Sum_probs=75.5

Q ss_pred             CCCCcHHHHHH-HHHHHHHHh----CCCCce-EEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           8 PTRYRKSGKVI-AFFCKIIEE----QALEPN-LIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         8 e~G~GKT~~~i-~~i~~~~~~----~~~~~~-Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      -+|+|||-..+ -.+..++++    ...+|+ ||+||. .+..|-..|..+|..  +++++..+|....-.+.....   
T Consensus       268 ktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk---  344 (731)
T KOG0339|consen  268 KTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK---  344 (731)
T ss_pred             eccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh---
Confidence            46889984322 223333332    134565 777897 677799999999863  677766665433322222211   


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhcccc-ccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTALRA-TFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l~~-~~~~~  153 (169)
                                       ....+ +++|++.+..-..  ...-....++|+||+.++-...-  +.-.....++. +..++
T Consensus       345 -----------------~g~Ei-vVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtll  406 (731)
T KOG0339|consen  345 -----------------EGAEI-VVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLL  406 (731)
T ss_pred             -----------------cCCeE-EEechHHHHHHHHhhcccceeeeEEEEechhhhhccccHHHHHHHHhhcCCcceEEE
Confidence                             34455 9999988765332  22234567999999998754321  11112223443 44688


Q ss_pred             EeccCC
Q psy1090         154 LTGWYY  159 (169)
Q Consensus       154 lT~TP~  159 (169)
                      +|||.-
T Consensus       407 FsaTf~  412 (731)
T KOG0339|consen  407 FSATFK  412 (731)
T ss_pred             eeccch
Confidence            888864

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.98  E-value=5.4e-05  Score=61.81  Aligned_cols=62  Identities=10%  Similarity=-0.089  Sum_probs=41.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH----HHHHHHHHhCCCceEEEEeCCHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN----NWEAEFRKFAPFVRTVKYYGNAI   66 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~----qW~~e~~~~~~~~~~~~~~g~~~   66 (169)
                      |.|.-+.+|.|||+++...+......  .+.+-||+|+..+.    +|...+-+|. ++.+....+...
T Consensus        93 G~VaEM~TGEGKTLvA~l~a~l~AL~--G~~VhvvT~NdyLA~RDae~m~~ly~~L-GLsvg~i~~~~~  158 (764)
T PRK12326         93 GDVIEMATGEGKTLAGAIAAAGYALQ--GRRVHVITVNDYLARRDAEWMGPLYEAL-GLTVGWITEEST  158 (764)
T ss_pred             CCcccccCCCCHHHHHHHHHHHHHHc--CCCeEEEcCCHHHHHHHHHHHHHHHHhc-CCEEEEECCCCC
Confidence            56677888999998876544333333  36789999987663    4666666666 677777766443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=97.94  E-value=6e-05  Score=62.80  Aligned_cols=109  Identities=7%  Similarity=-0.075  Sum_probs=65.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch----HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL----NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l----~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|....+|.|||+++...+.....  ....+.||+|+.-+    .+|...+-+|. ++.+....+.........     
T Consensus        97 G~IaEm~TGEGKTL~a~lp~~l~al--~g~~VhIvT~ndyLA~RD~e~m~~l~~~l-Glsv~~i~~~~~~~~r~~-----  168 (908)
T PRK13107         97 NRIAEMRTGEGKTLTATLPAYLNAL--TGKGVHVITVNDYLARRDAENNRPLFEFL-GLTVGINVAGLGQQEKKA-----  168 (908)
T ss_pred             CccccccCCCCchHHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHHHHHHHHhc-CCeEEEecCCCCHHHHHh-----
Confidence            5567788999999876433322222  23458999998544    26888888887 777776655433211111     


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhch----hccccccccEEEEeCCcccCCcc
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDF----GFLKKITWNCIIVDEGHSVKNKK  136 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~----~~~~~~~~~~vi~DEah~~k~~~  136 (169)
                                       .-.+|| +..|...+     +...    +..-..++.++|+||+..+-.+.
T Consensus       169 -----------------~Y~~dI-~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDE  218 (908)
T PRK13107        169 -----------------AYNADI-TYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDE  218 (908)
T ss_pred             -----------------cCCCCe-EEeCCCcccchhhhccCccchhhhhccccceeeecchhhhcccc
Confidence                             135677 66664443     2221    11223578899999999765543

>PRK04296 thymidine kinase; Provisional

Probab=97.93  E-value=3.6e-05  Score=53.55  Aligned_cols=33  Identities=18%  Similarity=0.066  Sum_probs=24.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      ++.-+||.|||..++.++......  ..+++++-|
T Consensus         6 litG~~GsGKTT~~l~~~~~~~~~--g~~v~i~k~   38 (190)
T PRK04296          6 FIYGAMNSGKSTELLQRAYNYEER--GMKVLVFKP   38 (190)
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHc--CCeEEEEec
Confidence            566789999999998887765543  356777755

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.91  E-value=7.3e-05  Score=61.84  Aligned_cols=61  Identities=8%  Similarity=-0.147  Sum_probs=41.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH----HHHHHHHHhCCCceEEEEeCCH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN----NWEAEFRKFAPFVRTVKYYGNA   65 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~----qW~~e~~~~~~~~~~~~~~g~~   65 (169)
                      |.|.-..+|.|||+++...+......  ...+-||+|+..+.    +|...+-++. ++.+....+..
T Consensus        95 G~iaEm~TGEGKTLvA~l~a~l~al~--G~~v~vvT~neyLA~Rd~e~~~~~~~~L-Gl~vg~i~~~~  159 (796)
T PRK12906         95 GNIAEMKTGEGKTLTATLPVYLNALT--GKGVHVVTVNEYLSSRDATEMGELYRWL-GLTVGLNLNSM  159 (796)
T ss_pred             CCcccccCCCCCcHHHHHHHHHHHHc--CCCeEEEeccHHHHHhhHHHHHHHHHhc-CCeEEEeCCCC
Confidence            66778899999998865443333333  36788999987663    4666666665 67777777643

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.90  E-value=5.7e-05  Score=65.49  Aligned_cols=71  Identities=17%  Similarity=0.127  Sum_probs=40.3

Q ss_pred             CCCCeEEEecHHHHHhchhc-cccccccEEEEeCCc-ccCCcccHH--HHHHh-ccccccEEEEeccCCCCCchhhc
Q psy1090          96 LKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGH-SVKNKKSKL--SIKLT-ALRATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah-~~k~~~~~~--~~~~~-~l~~~~~~~lT~TP~~n~~~el~  167 (169)
                      ....+ .+.|...+.+.... -.-..++++|+||+| +.-+.+-..  .+.+. .......++||||.-...+.+.|
T Consensus       155 ~~T~I-~~~TdGiLLr~l~~d~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~rpdLKlIlmSATld~~~fa~~F  230 (1283)
T TIGR01967       155 SNTLV-KLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHF  230 (1283)
T ss_pred             CCcee-eeccccHHHHHhhhCcccccCcEEEEcCcchhhccchhHHHHHHHHHhhCCCCeEEEEeCCcCHHHHHHHh
Confidence            33445 78888877654321 112368999999999 454433221  12221 11334579999998654444443

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.

>KOG0352|consensus

Probab=97.85  E-value=7.9e-05  Score=57.11  Aligned_cols=143  Identities=17%  Similarity=0.202  Sum_probs=74.8

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      .+.++.+|.||++..-  +-.++..   +-++||.|. .++....+.+.+.--...-+.-.-+..+|..+-..-...   
T Consensus        39 VyVsMPTGaGKSLCyQ--LPaL~~~---gITIV~SPLiALIkDQiDHL~~LKVp~~SLNSKlSt~ER~ri~~DL~~e---  110 (641)
T KOG0352|consen   39 VYVSMPTGAGKSLCYQ--LPALVHG---GITIVISPLIALIKDQIDHLKRLKVPCESLNSKLSTVERSRIMGDLAKE---  110 (641)
T ss_pred             EEEeccCCCchhhhhh--chHHHhC---CeEEEehHHHHHHHHHHHHHHhcCCchhHhcchhhHHHHHHHHHHHHhc---
Confidence            4678999999996431  1112222   357888886 667777788876531111111111223332222211110   


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhc-h----hcc-ccccccEEEEeCCcccCCcccHH---HHHHhcc----cc
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIEND-F----GFL-KKITWNCIIVDEGHSVKNKKSKL---SIKLTAL----RA  148 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~-~----~~~-~~~~~~~vi~DEah~~k~~~~~~---~~~~~~l----~~  148 (169)
                                   .....+ +-+|++..... .    +.+ ++-...++++||||+....+...   +-.+..+    .-
T Consensus       111 -------------kp~~K~-LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~  176 (641)
T KOG0352|consen  111 -------------KPTIKM-LYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPG  176 (641)
T ss_pred             -------------CCceeE-EEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcchhhhhhHHhhCCC
Confidence                         033334 55666655432 2    222 23456799999999876543221   2222333    34


Q ss_pred             ccEEEEeccCCCCCchhhc
Q psy1090         149 TFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       149 ~~~~~lT~TP~~n~~~el~  167 (169)
                      .-.++||||--..--+|+|
T Consensus       177 vpwvALTATA~~~VqEDi~  195 (641)
T KOG0352|consen  177 VPWVALTATANAKVQEDIA  195 (641)
T ss_pred             CceEEeecccChhHHHHHH
Confidence            4578999998776666654

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

Probab=97.84  E-value=0.00023  Score=59.82  Aligned_cols=38  Identities=16%  Similarity=0.096  Sum_probs=26.9

Q ss_pred             cCCCCeEEEecHHHHHhchhccc-cccccEEEEeCCcccC
Q psy1090          95 SLKLPLILVTTPQIIENDFGFLK-KITWNCIIVDEGHSVK  133 (169)
Q Consensus        95 ~~~~~ii~i~ty~~~~~~~~~~~-~~~~~~vi~DEah~~k  133 (169)
                      ....|+ +|++++.+..+...-. --.++.+|+||||++-
T Consensus       411 a~~Adi-vItNHall~~~~~~~~~~p~~~~lIiDEAH~l~  449 (820)
T PRK07246        411 AKTARL-LITNHAYFLTRVQDDKDFARNKVLVFDEAQKLM  449 (820)
T ss_pred             HHhCCE-EEEchHHHHHHHhhccCCCCCCEEEEECcchhH
Confidence            355666 9999998776542211 1358999999999985

>KOG0328|consensus

Probab=97.80  E-value=1.8e-05  Score=57.49  Aligned_cols=138  Identities=13%  Similarity=0.101  Sum_probs=84.8

Q ss_pred             ccccCCCCCcHHHH-HHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           3 TVIPDPTRYRKSGK-VIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         3 ~iL~de~G~GKT~~-~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      .|-....|+|||.+ +++++....-..+.-.+||+.|.. +-.|-.+-+.-...  +..+....|.+.-...+....   
T Consensus        67 ViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld---  143 (400)
T KOG0328|consen   67 VIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLD---  143 (400)
T ss_pred             eEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhc---
Confidence            45567889999965 556655544444445799999984 44566655655543  344444555444433333332   


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCc--ccHHHHHHhccc-cccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNK--KSKLSIKLTALR-ATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~--~~~~~~~~~~l~-~~~~~~  153 (169)
                                       ....+ +.-|+..+-.-.  ..+.-....++|+|||..+-+.  ..+.+...+.++ ....++
T Consensus       144 -----------------~G~hv-VsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~  205 (400)
T KOG0328|consen  144 -----------------YGQHV-VSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVL  205 (400)
T ss_pred             -----------------ccceE-eeCCCchHHHHHHhccccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCceEEE
Confidence                             22223 666665543321  2333446789999999976553  456777888885 667889


Q ss_pred             EeccCCCC
Q psy1090         154 LTGWYYPN  161 (169)
Q Consensus       154 lT~TP~~n  161 (169)
                      +|||..+.
T Consensus       206 ~SATlp~e  213 (400)
T KOG0328|consen  206 VSATLPHE  213 (400)
T ss_pred             EeccCcHH
Confidence            99998643

>KOG0949|consensus

Probab=97.79  E-value=0.00014  Score=60.82  Aligned_cols=134  Identities=21%  Similarity=0.182  Sum_probs=86.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHH-Hh-CCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFR-KF-APFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~-~~-~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +++.-.+-+|||....-++....+....+-++.|+|. .++.|-..+.. +| .+.+.    .|...-....+....+  
T Consensus       529 avIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~----rg~sl~g~ltqEYsin--  602 (1330)
T KOG0949|consen  529 AVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFL----RGVSLLGDLTQEYSIN--  602 (1330)
T ss_pred             eEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccc----cchhhHhhhhHHhcCC--
Confidence            5777889999999988888888888888899999997 67777665553 33 22221    2222222222222111  


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhc-----cccccccEEEEeCCcccCCcc-cHHHHHHhccccccEEE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-----LKKITWNCIIVDEGHSVKNKK-SKLSIKLTALRATFKVL  153 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-----~~~~~~~~vi~DEah~~k~~~-~~~~~~~~~l~~~~~~~  153 (169)
                                     ...+++ +||-++.+..-...     ..-....++|+||+|.+.+.. +..+..+..+-..--++
T Consensus       603 ---------------p~nCQV-LITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li~CP~L~  666 (1330)
T KOG0949|consen  603 ---------------PWNCQV-LITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLIPCPFLV  666 (1330)
T ss_pred             ---------------chhceE-EEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhcCCCeeE
Confidence                           156777 99999988653221     011256799999999998854 44555555554445678


Q ss_pred             EeccC
Q psy1090         154 LTGWY  158 (169)
Q Consensus       154 lT~TP  158 (169)
                      ||||-
T Consensus       667 LSATi  671 (1330)
T KOG0949|consen  667 LSATI  671 (1330)
T ss_pred             Eeccc
Confidence            99983

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.75  E-value=0.00041  Score=57.57  Aligned_cols=49  Identities=14%  Similarity=0.212  Sum_probs=34.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcc-hHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSV-LNNWEAEFRK   51 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~-l~qW~~e~~~   51 (169)
                      +++-..+|+|||+..|......... +...++++++..+. +.|-.+|+++
T Consensus        32 ~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~   82 (705)
T TIGR00604        32 AILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRK   82 (705)
T ss_pred             eEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHh
Confidence            6788899999999888665544443 32345555555544 5689999988

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).

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

Probab=97.73  E-value=0.00044  Score=50.47  Aligned_cols=106  Identities=12%  Similarity=-0.030  Sum_probs=60.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH----HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN----NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~----qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.+....+|=|||+++...+......  .+++=||+.+.-+.    +|...+-+++ ++.+....+..........    
T Consensus        92 G~laEm~TGEGKTli~~l~a~~~AL~--G~~V~vvT~NdyLA~RD~~~~~~~y~~L-Glsv~~~~~~~~~~~r~~~----  164 (266)
T PF07517_consen   92 GRLAEMKTGEGKTLIAALPAALNALQ--GKGVHVVTSNDYLAKRDAEEMRPFYEFL-GLSVGIITSDMSSEERREA----  164 (266)
T ss_dssp             TSEEEESTTSHHHHHHHHHHHHHHTT--SS-EEEEESSHHHHHHHHHHHHHHHHHT-T--EEEEETTTEHHHHHHH----
T ss_pred             ceeEEecCCCCcHHHHHHHHHHHHHh--cCCcEEEeccHHHhhccHHHHHHHHHHh-hhccccCccccCHHHHHHH----
Confidence            56777899999998875443333222  35677777775552    5777777777 6777776664432211111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhch---------hccccccccEEEEeCCcccC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF---------GFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~---------~~~~~~~~~~vi~DEah~~k  133 (169)
                                        -..|| +-.|...+..++         ......+++++|+||+..+-
T Consensus       165 ------------------Y~~dI-~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  165 ------------------YAADI-VYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             ------------------HHSSE-EEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             ------------------HhCcc-cccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence                              23455 555554443321         11123578899999988643

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

>KOG0337|consensus

Probab=97.73  E-value=0.00019  Score=54.93  Aligned_cols=129  Identities=15%  Similarity=0.111  Sum_probs=76.4

Q ss_pred             CCCcHHHHHH-HHHHHHHHhC-CCCceEEEecCc-chHHHHH---HHHHhCCCceEE-EEeCCHHHHHHHHHhhhcCCCc
Q psy1090           9 TRYRKSGKVI-AFFCKIIEEQ-ALEPNLIVCPLS-VLNNWEA---EFRKFAPFVRTV-KYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         9 ~G~GKT~~~i-~~i~~~~~~~-~~~~~Liv~P~~-~l~qW~~---e~~~~~~~~~~~-~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      +|.|||..-+ -.++.+.... ..-+.||+.|+. +..|-.+   ++-++. +++.. .+.|++.+..... ..      
T Consensus        67 tgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~-l~------  138 (529)
T KOG0337|consen   67 TGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFIL-LN------  138 (529)
T ss_pred             cCCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHH-hc------
Confidence            7899996532 2233333222 223899999984 4445444   444444 45555 4555554433222 11      


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCc--ccHHHHHHhccc-cccEEEEec
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNK--KSKLSIKLTALR-ATFKVLLTG  156 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~--~~~~~~~~~~l~-~~~~~~lT~  156 (169)
                                    ...|+ +++|+..+......  +.-....+||+||+.++-..  ..+..+.+.+++ ..-.+++||
T Consensus       139 --------------~npDi-i~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemgfqeql~e~l~rl~~~~QTllfSa  203 (529)
T KOG0337|consen  139 --------------ENPDI-IIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPESRQTLLFSA  203 (529)
T ss_pred             --------------cCCCE-EEecCceeeeeehheeccccceeeeeehhhhHHHhhhhHHHHHHHHHhCCCcceEEEEec
Confidence                          56777 88888776543222  22335678999999987543  345566677774 457899999


Q ss_pred             cCCC
Q psy1090         157 WYYP  160 (169)
Q Consensus       157 TP~~  160 (169)
                      |...
T Consensus       204 tlp~  207 (529)
T KOG0337|consen  204 TLPR  207 (529)
T ss_pred             cCch
Confidence            9763

>KOG1513|consensus

Probab=97.71  E-value=1.1e-05  Score=65.88  Aligned_cols=137  Identities=15%  Similarity=0.114  Sum_probs=76.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe-cCcchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC-PLSVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~-P~~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      |-+++|.-|.||-.+..++|-....+++ +++|.+. .+.+.-.-.+++.... +...+  +.-++.+..++....    
T Consensus       291 GfLiGDGAGVGKGRTvAgiIfeNyLkGR-KrAlW~SVSsDLKfDAERDL~DigA~~I~V--~alnK~KYakIss~e----  363 (1300)
T KOG1513|consen  291 GFLIGDGAGVGKGRTVAGIIFENYLKGR-KRALWFSVSSDLKFDAERDLRDIGATGIAV--HALNKFKYAKISSKE----  363 (1300)
T ss_pred             eeeeccCcccCCCceeEEEEehhhhccc-ceeEEEEeccccccchhhchhhcCCCCccc--eehhhcccccccccc----
Confidence            4578899999998887777654444443 4566555 4455445556665443 22222  221221111111110    


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchh--------cccc------ccc-cEEEEeCCcccCC-------ccc
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--------FLKK------ITW-NCIIVDEGHSVKN-------KKS  137 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--------~~~~------~~~-~~vi~DEah~~k~-------~~~  137 (169)
                                   ....+.- |+++||..+..+..        .+++      ..| +++|+||||..||       ..+
T Consensus       364 -------------n~n~krG-ViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkAKNL~p~~~~k~T  429 (1300)
T KOG1513|consen  364 -------------NTNTKRG-VIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKAKNLVPTAGAKST  429 (1300)
T ss_pred             -------------cCCccce-eEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhhcccccccCCCcC
Confidence                         1113333 49999999875433        1211      123 4999999999998       445


Q ss_pred             HHHHHHhc----cccccEEEEeccCC
Q psy1090         138 KLSIKLTA----LRATFKVLLTGWYY  159 (169)
Q Consensus       138 ~~~~~~~~----l~~~~~~~lT~TP~  159 (169)
                      |..+.+..    +...+.+..|||--
T Consensus       430 KtG~tVLdLQk~LP~ARVVYASATGA  455 (1300)
T KOG1513|consen  430 KTGKTVLDLQKKLPNARVVYASATGA  455 (1300)
T ss_pred             cccHhHHHHHHhCCCceEEEeeccCC
Confidence            66666543    45667777787743

>KOG0340|consensus

Probab=97.71  E-value=0.00053  Score=51.44  Aligned_cols=138  Identities=12%  Similarity=0.083  Sum_probs=79.1

Q ss_pred             CccccCCCCCcHHHH-HHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGK-VIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~-~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +||=+--+|+|||.. ++-.+..+.+....-=.||+.|.. +.-|-.++|.-..  -.+++.++.|..+.-.+-....  
T Consensus        46 dcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~--  123 (442)
T KOG0340|consen   46 DCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILS--  123 (442)
T ss_pred             ccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcc--
Confidence            466678899999965 223333332222222479999984 4446666665333  2567777777554432221111  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh------ccccccccEEEEeCCcccCCcc-cHHHHHH-hcccc-
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG------FLKKITWNCIIVDEGHSVKNKK-SKLSIKL-TALRA-  148 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~------~~~~~~~~~vi~DEah~~k~~~-~~~~~~~-~~l~~-  148 (169)
                                        .+.++ ++++++.+.....      .....+..++++|||.++.+.. ......+ ..++. 
T Consensus       124 ------------------~rPHv-VvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~f~d~L~~i~e~lP~~  184 (442)
T KOG0340|consen  124 ------------------DRPHV-VVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGCFPDILEGIEECLPKP  184 (442)
T ss_pred             ------------------cCCCe-EecCccccccccccCCccchhhhhceeeEEecchhhhhccchhhHHhhhhccCCCc
Confidence                              55555 9999888764332      1112355689999999987542 1112222 23333 


Q ss_pred             ccEEEEeccCCC
Q psy1090         149 TFKVLLTGWYYP  160 (169)
Q Consensus       149 ~~~~~lT~TP~~  160 (169)
                      +-.+++|||--.
T Consensus       185 RQtLlfSATitd  196 (442)
T KOG0340|consen  185 RQTLLFSATITD  196 (442)
T ss_pred             cceEEEEeehhh
Confidence            467999999653

>KOG0947|consensus

Probab=97.71  E-value=0.00011  Score=61.17  Aligned_cols=122  Identities=15%  Similarity=0.166  Sum_probs=74.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH-HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN-NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~-qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      .+.+--+.+|||+.|=..|...  ....-+++.-.|--.+. |=.++|+.-+.+..  ..+|+....             
T Consensus       315 VFVAAHTSAGKTvVAEYAiala--q~h~TR~iYTSPIKALSNQKfRDFk~tF~Dvg--LlTGDvqin-------------  377 (1248)
T KOG0947|consen  315 VFVAAHTSAGKTVVAEYAIALA--QKHMTRTIYTSPIKALSNQKFRDFKETFGDVG--LLTGDVQIN-------------  377 (1248)
T ss_pred             EEEEecCCCCcchHHHHHHHHH--HhhccceEecchhhhhccchHHHHHHhccccc--eeecceeeC-------------
Confidence            4567778899998764443332  23345788888975554 55567765554444  567653321             


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHh----chhccccccccEEEEeCCcccCCcc-cHHHHHH-hcc-ccccEEEE
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIEN----DFGFLKKITWNCIIVDEGHSVKNKK-SKLSIKL-TAL-RATFKVLL  154 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~----~~~~~~~~~~~~vi~DEah~~k~~~-~~~~~~~-~~l-~~~~~~~l  154 (169)
                                    ....+ +|.|-+.+++    ..+.++  ..++||+||+|++.+.. .-.+..+ ..+ +-..-++|
T Consensus       378 --------------PeAsC-LIMTTEILRsMLYrgadliR--DvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~~IlL  440 (1248)
T KOG0947|consen  378 --------------PEASC-LIMTTEILRSMLYRGADLIR--DVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVNFILL  440 (1248)
T ss_pred             --------------CCcce-EeehHHHHHHHHhcccchhh--ccceEEEeeeeecccccccccceeeeeeccccceEEEE
Confidence                          44455 8888777764    344444  36779999999986522 2223333 344 33446788


Q ss_pred             eccC
Q psy1090         155 TGWY  158 (169)
Q Consensus       155 T~TP  158 (169)
                      |||=
T Consensus       441 SATV  444 (1248)
T KOG0947|consen  441 SATV  444 (1248)
T ss_pred             eccC
Confidence            8884

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

Probab=97.68  E-value=0.00066  Score=57.98  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=26.7

Q ss_pred             CCCCeEEEecHHHHHhchhcccc--ccccEEEEeCCcccC
Q psy1090          96 LKLPLILVTTPQIIENDFGFLKK--ITWNCIIVDEGHSVK  133 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~~~~--~~~~~vi~DEah~~k  133 (169)
                      ...|+ +|++++.+..+...-..  -+++.+|+||||++-
T Consensus       430 ~~Adi-vItNHalLl~dl~~~~~ilp~~~~lViDEAH~l~  468 (928)
T PRK08074        430 KFADL-VITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFE  468 (928)
T ss_pred             hcCCE-EEECHHHHHHHHhhhcccCCCCCeEEEECCchHH
Confidence            55666 99999988776521111  257999999999985

>KOG0341|consensus

Probab=97.67  E-value=6.7e-05  Score=56.85  Aligned_cols=132  Identities=16%  Similarity=0.224  Sum_probs=72.0

Q ss_pred             CCCCcHHHH----HHHHHHHHHH----hCCCCc-eEEEecC-cchHHHHHHHHHhC--------CCceEEEEeCCHHHHH
Q psy1090           8 PTRYRKSGK----VIAFFCKIIE----EQALEP-NLIVCPL-SVLNNWEAEFRKFA--------PFVRTVKYYGNAIERK   69 (169)
Q Consensus         8 e~G~GKT~~----~i~~i~~~~~----~~~~~~-~Liv~P~-~~l~qW~~e~~~~~--------~~~~~~~~~g~~~~~~   69 (169)
                      -+|+|||+.    .+.++...-.    ....+| -||+||+ .+..|-.+-+..|+        |.++.....|.-.-+.
T Consensus       215 fTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~e  294 (610)
T KOG0341|consen  215 FTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVRE  294 (610)
T ss_pred             eecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHH
Confidence            379999953    3333322111    123355 4999998 45556666665553        5556555555444444


Q ss_pred             HHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhc
Q psy1090          70 ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTA  145 (169)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~  145 (169)
                      +...-.                    ....+ ++.|+..+..-..  .++----.++.+|||.++-.-.  ......+..
T Consensus       295 ql~~v~--------------------~GvHi-vVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~  353 (610)
T KOG0341|consen  295 QLDVVR--------------------RGVHI-VVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSF  353 (610)
T ss_pred             HHHHHh--------------------cCeeE-EEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHH
Confidence            333322                    34445 8899877754221  1111123478999999875422  111222233


Q ss_pred             ccc-ccEEEEeccCCC
Q psy1090         146 LRA-TFKVLLTGWYYP  160 (169)
Q Consensus       146 l~~-~~~~~lT~TP~~  160 (169)
                      ++. +..+++|||...
T Consensus       354 FK~QRQTLLFSATMP~  369 (610)
T KOG0341|consen  354 FKGQRQTLLFSATMPK  369 (610)
T ss_pred             HhhhhheeeeeccccH
Confidence            333 457899999763

>KOG1805|consensus

Probab=97.59  E-value=0.00044  Score=57.80  Aligned_cols=139  Identities=14%  Similarity=0.113  Sum_probs=72.5

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccccc
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPA   85 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   85 (169)
                      .=+|+|||.+...++..+...+  +++|+.+=. +.++|-.-.+..+  +..++......+....+.......   ..+.
T Consensus       692 GMPGTGKTTtI~~LIkiL~~~g--kkVLLtsyThsAVDNILiKL~~~--~i~~lRLG~~~kih~~v~e~~~~~---~~s~  764 (1100)
T KOG1805|consen  692 GMPGTGKTTTISLLIKILVALG--KKVLLTSYTHSAVDNILIKLKGF--GIYILRLGSEEKIHPDVEEFTLTN---ETSE  764 (1100)
T ss_pred             cCCCCCchhhHHHHHHHHHHcC--CeEEEEehhhHHHHHHHHHHhcc--CcceeecCCccccchHHHHHhccc---ccch
Confidence            3479999999888887776655  778888876 4566766566544  333333333222222222221100   0000


Q ss_pred             ccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCC
Q psy1090          86 KKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus        86 ~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                      +....-+..-....+ |.+|=-.+  .-..|...+||++|+|||..+.-+-+     +.-+....+.+|-|-+.|
T Consensus       765 ks~~~l~~~~~~~~I-Va~TClgi--~~plf~~R~FD~cIiDEASQI~lP~~-----LgPL~~s~kFVLVGDh~Q  831 (1100)
T KOG1805|consen  765 KSYADLKKFLDQTSI-VACTCLGI--NHPLFVNRQFDYCIIDEASQILLPLC-----LGPLSFSNKFVLVGDHYQ  831 (1100)
T ss_pred             hhHHHHHHHhCCCcE-EEEEccCC--CchhhhccccCEEEEccccccccchh-----hhhhhhcceEEEeccccc
Confidence            011111111144445 44432111  12344556799999999988755433     344555566666665554

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

Probab=97.58  E-value=0.00014  Score=57.13  Aligned_cols=48  Identities=19%  Similarity=0.255  Sum_probs=38.5

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCce
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVR   57 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~   57 (169)
                      |-.-+|+|||+++.-+|...     ..|+||++|+- +..|-+.||+.|+|+-.
T Consensus        37 LLGvTGSGKTfT~AnVI~~~-----~rPtLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          37 LLGVTGSGKTFTMANVIAKV-----QRPTLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             EeeeccCCchhHHHHHHHHh-----CCCeEEEecchhHHHHHHHHHHHhCcCcc
Confidence            45568999999987777543     47999999984 55699999999998643

>KOG1131|consensus

Probab=97.56  E-value=0.00017  Score=56.65  Aligned_cols=49  Identities=14%  Similarity=0.248  Sum_probs=36.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCC-CCceEEEecCcc--hHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQA-LEPNLIVCPLSV--LNNWEAEFRK   51 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~-~~~~Liv~P~~~--l~qW~~e~~~   51 (169)
                      |+|-+..|+|||+..++++..+....+ .-.-||-|...+  ++.-..|+++
T Consensus        38 ~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   38 CLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             EEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHH
Confidence            899999999999999999877666654 446788888754  4455556543

>KOG0922|consensus

Probab=97.55  E-value=0.00038  Score=55.96  Aligned_cols=66  Identities=17%  Similarity=0.181  Sum_probs=40.9

Q ss_pred             EEecHHHHHhchh-ccccccccEEEEeCCcccCCcccH-HHHHHhcc---ccc-cEEEEeccCCCCCchhhcc
Q psy1090         102 LVTTPQIIENDFG-FLKKITWNCIIVDEGHSVKNKKSK-LSIKLTAL---RAT-FKVLLTGWYYPNKWSKQCT  168 (169)
Q Consensus       102 ~i~ty~~~~~~~~-~~~~~~~~~vi~DEah~~k~~~~~-~~~~~~~l---~~~-~~~~lT~TP~~n~~~el~~  168 (169)
                      ...|-..+.++.- .-.-.+|+++|+||||. ++-.+. ..-.++.+   +.. +.+++|||.=...+++.|+
T Consensus       144 kymTDG~LLRE~l~Dp~LskYsvIIlDEAHE-Rsl~TDiLlGlLKki~~~R~~LklIimSATlda~kfS~yF~  215 (674)
T KOG0922|consen  144 KYMTDGMLLREILKDPLLSKYSVIILDEAHE-RSLHTDILLGLLKKILKKRPDLKLIIMSATLDAEKFSEYFN  215 (674)
T ss_pred             EEecchHHHHHHhcCCccccccEEEEechhh-hhhHHHHHHHHHHHHHhcCCCceEEEEeeeecHHHHHHHhc
Confidence            7778778776542 11234899999999996 222222 22223333   333 5688999987777777664

>KOG0336|consensus

Probab=97.54  E-value=0.00061  Score=52.16  Aligned_cols=134  Identities=13%  Similarity=0.210  Sum_probs=77.8

Q ss_pred             ccccCCCCCcHHHHHH--HHHHH-----HHHhCCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVI--AFFCK-----IIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i--~~i~~-----~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~   73 (169)
                      ++-...+|+|||+.-+  +++..     ..+....-.+|++.|. .+-.|-.-|..++- .+.+.+.++|......+...
T Consensus       260 liGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~ygggnR~eqie~  339 (629)
T KOG0336|consen  260 LIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQIED  339 (629)
T ss_pred             eEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhhcCcceEEEecCCCchhHHHH
Confidence            3445679999997654  22211     1122223357888897 45556666666554 34555554444333222332


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCC--cccHHHHHHhccccc
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKN--KKSKLSIKLTALRAT  149 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~--~~~~~~~~~~~l~~~  149 (169)
                      ..                    ...++ ++.|+..+.+..  +.+.-....++|+|||.++-.  ...+.-+.+..++..
T Consensus       340 lk--------------------rgvei-iiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiRPD  398 (629)
T KOG0336|consen  340 LK--------------------RGVEI-IIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPD  398 (629)
T ss_pred             Hh--------------------cCceE-EeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccccHHHHHHhhhcCCc
Confidence            22                    55566 899988876532  233334567999999998765  335556666677766


Q ss_pred             cEEEE-ecc
Q psy1090         150 FKVLL-TGW  157 (169)
Q Consensus       150 ~~~~l-T~T  157 (169)
                      +-.+| |||
T Consensus       399 RqtvmTSAT  407 (629)
T KOG0336|consen  399 RQTVMTSAT  407 (629)
T ss_pred             ceeeeeccc
Confidence            65555 454

>KOG0329|consensus

Probab=97.53  E-value=0.00016  Score=51.98  Aligned_cols=136  Identities=17%  Similarity=0.222  Sum_probs=75.7

Q ss_pred             CccccCCCCCcHHHH-HHHHHHHHHHhCCCCceEEEecC-cchHHHHHH---HHHhCCCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGK-VIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAE---FRKFAPFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~-~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e---~~~~~~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ..++.-..|+|||.. .++.+..+-.....-.+|++|-. .+.-|-..|   |.++.|+.++.++.|.-..+......  
T Consensus        81 dvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~l--  158 (387)
T KOG0329|consen   81 DVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELL--  158 (387)
T ss_pred             hhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHH--
Confidence            355667789999943 33333322211222267888876 454466555   45566999999999854332211111  


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCcccHHH---HHHhcc--ccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSKLS---IKLTAL--RAT  149 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~~~~~~---~~~~~l--~~~  149 (169)
                                         ..++.|++.|+..+....  ..+.-....-+|+|||..+-.. ....   +.+.++  .-+
T Consensus       159 -------------------k~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~-lDMrRDvQEifr~tp~~K  218 (387)
T KOG0329|consen  159 -------------------KNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQ-LDMRRDVQEIFRMTPHEK  218 (387)
T ss_pred             -------------------hCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHH-HHHHHHHHHHhhcCcccc
Confidence                               223445899988765332  2233335667899999965432 2122   222222  234


Q ss_pred             cEEEEeccCC
Q psy1090         150 FKVLLTGWYY  159 (169)
Q Consensus       150 ~~~~lT~TP~  159 (169)
                      ....+|||.-
T Consensus       219 Qvmmfsatls  228 (387)
T KOG0329|consen  219 QVMMFSATLS  228 (387)
T ss_pred             eeeeeeeecc
Confidence            4577788853

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.52  E-value=0.0004  Score=56.30  Aligned_cols=41  Identities=24%  Similarity=0.279  Sum_probs=31.5

Q ss_pred             ccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      .++|++|+||+..+-  .....+.+..++...|++|.|=|-|-
T Consensus       258 l~~dvlIiDEaSMvd--~~l~~~ll~al~~~~rlIlvGD~~QL  298 (586)
T TIGR01447       258 LPLDVLVVDEASMVD--LPLMAKLLKALPPNTKLILLGDKNQL  298 (586)
T ss_pred             CcccEEEEcccccCC--HHHHHHHHHhcCCCCEEEEECChhhC
Confidence            578999999999984  34455666777778899998877654

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.

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.49  E-value=0.00054  Score=54.76  Aligned_cols=115  Identities=18%  Similarity=0.174  Sum_probs=63.1

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      .-+.+|+|||+.+.++|.++...+ .+..|+.|.. ++++.-...   |...+          ...-+..+.........
T Consensus         2 f~matgsgkt~~ma~lil~~y~kg-yr~flffvnq~nilekt~~n---ftd~~----------s~kylf~e~i~~~d~~i   67 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKG-YRNFLFFVNQANILEKTKLN---FTDSV----------SSKYLFSENININDENI   67 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhc-hhhEEEEecchhHHHHHHhh---cccch----------hhhHhhhhhhhcCCcee
Confidence            356799999999999999888766 4557777764 666543322   22110          11112222222222233


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHhchhc-------cccc--cccEEEEeCCcccCC
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIENDFGF-------LKKI--TWNCIIVDEGHSVKN  134 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-------~~~~--~~~~vi~DEah~~k~  134 (169)
                      .+++-....+......| +++|-+.+-.+...       +..+  .--+.+-||||++..
T Consensus        68 ~ikkvn~fsehnd~iei-~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~  126 (812)
T COG3421          68 EIKKVNNFSEHNDAIEI-YFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNT  126 (812)
T ss_pred             eeeeecccCccCCceEE-EEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhh
Confidence            33333333334466666 89987777554321       1111  112567899999854

>TIGR00376 DNA helicase, putative

Probab=97.47  E-value=0.00066  Score=55.64  Aligned_cols=56  Identities=13%  Similarity=0.219  Sum_probs=39.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhCCCceEEEEe
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFAPFVRTVKYY   62 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~~~~~~~~~~   62 (169)
                      .++...+|+|||.++.+++......+  .++|+++|++. +.+..+.+...  +.+++...
T Consensus       176 ~lI~GpPGTGKT~t~~~ii~~~~~~g--~~VLv~a~sn~Avd~l~e~l~~~--~~~vvRlg  232 (637)
T TIGR00376       176 FLIHGPPGTGKTRTLVELIRQLVKRG--LRVLVTAPSNIAVDNLLERLALC--DQKIVRLG  232 (637)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcC--CCEEEEcCcHHHHHHHHHHHHhC--CCcEEEeC
Confidence            35667899999999988887766554  48999999864 56777777643  34444443

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.46  E-value=0.0012  Score=54.92  Aligned_cols=115  Identities=17%  Similarity=0.048  Sum_probs=64.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIK   82 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   82 (169)
                      .+|.-..|+|||..+-+++..+...+...++++++|.........|..    +..          ...+...-..     
T Consensus       341 ~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~----g~~----------a~Tih~lL~~-----  401 (720)
T TIGR01448       341 VILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT----GLT----------ASTIHRLLGY-----  401 (720)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc----CCc----------cccHHHHhhc-----
Confidence            467788999999877776665544433357888899876654333321    100          0000000000     


Q ss_pred             cccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090          83 VPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus        83 ~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                                    ..+. ..      ..  ..-...+.+++|+|||+.+..  ......+..++...+++|-|=|-|-
T Consensus       402 --------------~~~~-~~------~~--~~~~~~~~~llIvDEaSMvd~--~~~~~Ll~~~~~~~rlilvGD~~QL  455 (720)
T TIGR01448       402 --------------GPDT-FR------HN--HLEDPIDCDLLIVDESSMMDT--WLALSLLAALPDHARLLLVGDTDQL  455 (720)
T ss_pred             --------------cCCc-cc------hh--hhhccccCCEEEEeccccCCH--HHHHHHHHhCCCCCEEEEECccccc
Confidence                          0000 00      00  000124678999999999843  3345556677777899998876654

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.

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

Probab=97.46  E-value=0.00071  Score=47.29  Aligned_cols=41  Identities=24%  Similarity=0.220  Sum_probs=25.4

Q ss_pred             ccccEEEEeCCcccCCcccHHHHHHhccc-cccEEEEeccCCCC
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKLSIKLTALR-ATFKVLLTGWYYPN  161 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~~~~~~~l~-~~~~~~lT~TP~~n  161 (169)
                      .+.+++|+|||..+.  .......+...+ ...++++.|-|-|-
T Consensus        92 ~~~~vliVDEasmv~--~~~~~~ll~~~~~~~~klilvGD~~QL  133 (196)
T PF13604_consen   92 PKKDVLIVDEASMVD--SRQLARLLRLAKKSGAKLILVGDPNQL  133 (196)
T ss_dssp             TSTSEEEESSGGG-B--HHHHHHHHHHS-T-T-EEEEEE-TTSH
T ss_pred             CcccEEEEecccccC--HHHHHHHHHHHHhcCCEEEEECCcchh
Confidence            355799999999984  233444455553 36799999988864

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.46  E-value=0.0018  Score=54.31  Aligned_cols=107  Identities=10%  Similarity=0.055  Sum_probs=61.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch----HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL----NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l----~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|--+.+|-|||+++...+. + ..-..+.+-||.++.-+    .+|...+-+|. ++.+....+.........     
T Consensus       100 G~IAEM~TGEGKTL~atlpay-l-nAL~GkgVhVVTvNdYLA~RDae~m~~vy~~L-GLtvg~i~~~~~~~err~-----  171 (939)
T PRK12902        100 GQIAEMKTGEGKTLVATLPSY-L-NALTGKGVHVVTVNDYLARRDAEWMGQVHRFL-GLSVGLIQQDMSPEERKK-----  171 (939)
T ss_pred             CceeeecCCCChhHHHHHHHH-H-HhhcCCCeEEEeCCHHHHHhHHHHHHHHHHHh-CCeEEEECCCCChHHHHH-----
Confidence            566778899999997543222 2 22223567777777544    27999999998 777776654322211111     


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhchh----ccccccccEEEEeCCcccCC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDFG----FLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~~----~~~~~~~~~vi~DEah~~k~  134 (169)
                                       .-.+|| +-+|...+     +.+..    ....-+++++|+||+..+--
T Consensus       172 -----------------aY~~DI-tYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILI  219 (939)
T PRK12902        172 -----------------NYACDI-TYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILI  219 (939)
T ss_pred             -----------------hcCCCe-EEecCCcccccchhhhhcccccccccCccceEEEecccceee
Confidence                             145566 44443332     33221    22335778899999886543

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.43  E-value=0.002  Score=49.67  Aligned_cols=62  Identities=13%  Similarity=0.080  Sum_probs=35.8

Q ss_pred             ecHHHHHhchhccccccccEEEEeCCcccCCcccHH---HHHHhccc--cccEEEEeccCCCCCchhhc
Q psy1090         104 TTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKL---SIKLTALR--ATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       104 ~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~---~~~~~~l~--~~~~~~lT~TP~~n~~~el~  167 (169)
                      .+++.+......+  ..++++++|++.+........   ...+....  ....++|+||-=++.+.+++
T Consensus       240 ~~~~~l~~~L~~~--~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~  306 (388)
T PRK12723        240 ESFKDLKEEITQS--KDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIF  306 (388)
T ss_pred             CcHHHHHHHHHHh--CCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHH
Confidence            3444444433333  367899999999876432221   12222222  24568899998777777655

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.29  E-value=0.0018  Score=54.15  Aligned_cols=59  Identities=12%  Similarity=-0.013  Sum_probs=38.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch----HHHHHHHHHhCCCceEEEEeC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL----NNWEAEFRKFAPFVRTVKYYG   63 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l----~qW~~e~~~~~~~~~~~~~~g   63 (169)
                      |.|.-..+|-|||+++...+. + ..-..+.+-||+++.-+    .+|...+-+|. ++.+....+
T Consensus        91 G~IaEm~TGEGKTL~a~l~ay-l-~aL~G~~VhVvT~NdyLA~RD~e~m~pvy~~L-GLsvg~i~~  153 (870)
T CHL00122         91 GKIAEMKTGEGKTLVATLPAY-L-NALTGKGVHIVTVNDYLAKRDQEWMGQIYRFL-GLTVGLIQE  153 (870)
T ss_pred             CccccccCCCCchHHHHHHHH-H-HHhcCCceEEEeCCHHHHHHHHHHHHHHHHHc-CCceeeeCC
Confidence            567778899999987543322 1 11123567888887544    26888888888 666666544

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.27  E-value=0.00099  Score=54.29  Aligned_cols=42  Identities=19%  Similarity=0.234  Sum_probs=32.3

Q ss_pred             cccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090         118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       118 ~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      ..++|++|+||+..+-  .......+..++...|++|-|=|-|-
T Consensus       263 ~l~~dvlIvDEaSMvd--~~lm~~ll~al~~~~rlIlvGD~~QL  304 (615)
T PRK10875        263 PLHLDVLVVDEASMVD--LPMMARLIDALPPHARVIFLGDRDQL  304 (615)
T ss_pred             CCCCCeEEEChHhccc--HHHHHHHHHhcccCCEEEEecchhhc
Confidence            3567999999999873  44556677788888899998877654

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

Probab=97.27  E-value=0.0013  Score=55.08  Aligned_cols=134  Identities=12%  Similarity=0.113  Sum_probs=70.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH-HHHHHH-HHhCC--CceE---EEEeCCHHHHHHHHHhh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN-NWEAEF-RKFAP--FVRT---VKYYGNAIERKALQSEA   75 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~-qW~~e~-~~~~~--~~~~---~~~~g~~~~~~~~~~~~   75 (169)
                      .|+.-|+|+|||.+.=-++..... ...+.+.+.-|.-+-. .-.+.+ +.+..  +-.+   +.+....          
T Consensus        68 vii~getGsGKTTqlP~~lle~g~-~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~iRfe~~~----------  136 (845)
T COG1643          68 VIIVGETGSGKTTQLPQFLLEEGL-GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSIRFESKV----------  136 (845)
T ss_pred             EEEeCCCCCChHHHHHHHHHhhhc-ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEEEEeeccC----------
Confidence            478899999999887766654332 2223444444665432 222222 22221  1111   1111111          


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh-ccccccccEEEEeCCcccCCcccHHHH-HHhc----ccc-
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG-FLKKITWNCIIVDEGHSVKNKKSKLSI-KLTA----LRA-  148 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~-~~~~~~~~~vi~DEah~~k~~~~~~~~-~~~~----l~~-  148 (169)
                                         ..+..+ =+.|-..+.+... ...-..++++|+||+|. ++-++...- .++.    .+. 
T Consensus       137 -------------------s~~Tri-k~mTdGiLlrei~~D~~Ls~ys~vIiDEaHE-RSl~tDilLgllk~~~~~rr~D  195 (845)
T COG1643         137 -------------------SPRTRI-KVMTDGILLREIQNDPLLSGYSVVIIDEAHE-RSLNTDILLGLLKDLLARRRDD  195 (845)
T ss_pred             -------------------CCCcee-EEeccHHHHHHHhhCcccccCCEEEEcchhh-hhHHHHHHHHHHHHHHhhcCCC
Confidence                               033344 6666666665543 33345889999999996 212222221 1222    232 


Q ss_pred             ccEEEEeccCCCCCchhhcc
Q psy1090         149 TFKVLLTGWYYPNKWSKQCT  168 (169)
Q Consensus       149 ~~~~~lT~TP~~n~~~el~~  168 (169)
                      -+.++||||-=...++.+|.
T Consensus       196 LKiIimSATld~~rfs~~f~  215 (845)
T COG1643         196 LKLIIMSATLDAERFSAYFG  215 (845)
T ss_pred             ceEEEEecccCHHHHHHHcC
Confidence            45688999987777766654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.23  E-value=0.0015  Score=42.09  Aligned_cols=42  Identities=12%  Similarity=0.010  Sum_probs=27.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      .+|.-++|+|||..+..++..+....  ..++.+.+......+.
T Consensus         5 ~~l~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~~~~~~~~~~~   46 (148)
T smart00382        5 ILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILEEVL   46 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHhccCCCC--CCEEEECCEEccccCH
Confidence            46778899999988877765443222  3567777766554433

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.

>KOG0926|consensus

Probab=97.22  E-value=0.00089  Score=55.24  Aligned_cols=66  Identities=11%  Similarity=0.219  Sum_probs=39.9

Q ss_pred             CCCeEEEecHHHHHhchh-ccccccccEEEEeCCcccCCcccHHH-HHHhc--------------cccccEEEEeccCCC
Q psy1090          97 KLPLILVTTPQIIENDFG-FLKKITWNCIIVDEGHSVKNKKSKLS-IKLTA--------------LRATFKVLLTGWYYP  160 (169)
Q Consensus        97 ~~~ii~i~ty~~~~~~~~-~~~~~~~~~vi~DEah~~k~~~~~~~-~~~~~--------------l~~~~~~~lT~TP~~  160 (169)
                      ...| -+.|-..+.+... .|.-..|..+|+||||. ++-++... -++.+              ++.-..++||||.--
T Consensus       349 ~T~I-kFMTDGVLLrEi~~DflL~kYSvIIlDEAHE-RSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLRV  426 (1172)
T KOG0926|consen  349 DTSI-KFMTDGVLLREIENDFLLTKYSVIILDEAHE-RSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLRV  426 (1172)
T ss_pred             Ccee-EEecchHHHHHHHHhHhhhhceeEEechhhh-ccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEEe
Confidence            3344 8888888877653 44456889999999995 22233221 11111              123346899999765


Q ss_pred             CCch
Q psy1090         161 NKWS  164 (169)
Q Consensus       161 n~~~  164 (169)
                      .++.
T Consensus       427 sDFt  430 (1172)
T KOG0926|consen  427 SDFT  430 (1172)
T ss_pred             cccc
Confidence            5544

>PF13245 AAA_19: Part of AAA domain

Probab=97.18  E-value=0.0013  Score=38.74  Aligned_cols=40  Identities=15%  Similarity=0.263  Sum_probs=30.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh--CCCCceEEEecCcchH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE--QALEPNLIVCPLSVLN   43 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~--~~~~~~Liv~P~~~l~   43 (169)
                      ++.-.+|+|||.+++..+..+...  ...+++|+++|+....
T Consensus        14 vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa   55 (76)
T PF13245_consen   14 VVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAA   55 (76)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHH
Confidence            347789999999999888887743  3356899999985443

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.16  E-value=0.007  Score=50.34  Aligned_cols=38  Identities=18%  Similarity=0.311  Sum_probs=26.9

Q ss_pred             CCCCeEEEecHHHHHhchhc-----cccccccEEEEeCCcccCC
Q psy1090          96 LKLPLILVTTPQIIENDFGF-----LKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~-----~~~~~~~~vi~DEah~~k~  134 (169)
                      ...|+ +|++++.+-.+...     +-..+++.+|+||||++-.
T Consensus       218 ~~Adi-vVtNH~LLladl~~~~~~iLp~~~~~~lViDEAH~L~d  260 (697)
T PRK11747        218 DEADV-VVANHDLVLADLELGGGVVLPDPENLLYVLDEGHHLPD  260 (697)
T ss_pred             hhCCE-EEECcHHHHhhhhccCCcccCCCCCCEEEEECccchHH
Confidence            44566 99999988776531     1122478899999999853

>KOG0351|consensus

Probab=97.14  E-value=0.00053  Score=58.05  Aligned_cols=136  Identities=15%  Similarity=0.117  Sum_probs=75.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHH--HHHHHhhhcC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIER--KALQSEALSL   78 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~--~~~~~~~~~~   78 (169)
                      +++-..+|.||+++.      +.-. -..+-+|||.|. ++++-....+.+.  +++.....+.+...  ..+...... 
T Consensus       282 ~fvlmpTG~GKSLCY------QlPA~l~~gitvVISPL~SLm~DQv~~L~~~--~I~a~~L~s~q~~~~~~~i~q~l~~-  352 (941)
T KOG0351|consen  282 CFVLMPTGGGKSLCY------QLPALLLGGVTVVISPLISLMQDQVTHLSKK--GIPACFLSSIQTAAERLAILQKLAN-  352 (941)
T ss_pred             eEEEeecCCceeeEe------eccccccCCceEEeccHHHHHHHHHHhhhhc--CcceeeccccccHHHHHHHHHHHhC-
Confidence            677789999999543      1111 112468889997 6776545555322  45555555544432  222222111 


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhcc---ccc----cccEEEEeCCcccCCcccHH---HHHHh----
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL---KKI----TWNCIIVDEGHSVKNKKSKL---SIKLT----  144 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~---~~~----~~~~vi~DEah~~k~~~~~~---~~~~~----  144 (169)
                       .              .....+ +-.|++.+.......   ...    ..-++|+||||+........   ++.+.    
T Consensus       353 -~--------------~~~iki-lYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~  416 (941)
T KOG0351|consen  353 -G--------------NPIIKI-LYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRI  416 (941)
T ss_pred             -C--------------CCeEEE-EEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHHHHHHHHHh
Confidence             0              024555 778888886543221   111    25789999999877644221   22222    


Q ss_pred             ccccccEEEEeccCCCCCc
Q psy1090         145 ALRATFKVLLTGWYYPNKW  163 (169)
Q Consensus       145 ~l~~~~~~~lT~TP~~n~~  163 (169)
                      .+...-.++||||-...--
T Consensus       417 ~~~~vP~iALTATAT~~v~  435 (941)
T KOG0351|consen  417 RFPGVPFIALTATATERVR  435 (941)
T ss_pred             hCCCCCeEEeehhccHHHH
Confidence            2344467999999754433

>KOG0948|consensus

Probab=97.14  E-value=0.001  Score=54.56  Aligned_cols=119  Identities=17%  Similarity=0.118  Sum_probs=69.1

Q ss_pred             cCCCCCcHHHHHH-HHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           6 PDPTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         6 ~de~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      .--+.+|||+.|= |+++.+.+ +  .+++.-.|-- +=+|=++|+..=+.  .+..++|+-...               
T Consensus       150 SAHTSAGKTVVAeYAIA~sLr~-k--QRVIYTSPIKALSNQKYREl~~EF~--DVGLMTGDVTIn---------------  209 (1041)
T KOG0948|consen  150 SAHTSAGKTVVAEYAIAMSLRE-K--QRVIYTSPIKALSNQKYRELLEEFK--DVGLMTGDVTIN---------------  209 (1041)
T ss_pred             EeecCCCcchHHHHHHHHHHHh-c--CeEEeeChhhhhcchhHHHHHHHhc--ccceeecceeeC---------------
Confidence            3447789998764 33333333 2  5788888864 44576677654332  344456643210               


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHh----chhccccccccEEEEeCCcccCCcccH-HH-HHHhcc-ccccEEEEec
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIEN----DFGFLKKITWNCIIVDEGHSVKNKKSK-LS-IKLTAL-RATFKVLLTG  156 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~----~~~~~~~~~~~~vi~DEah~~k~~~~~-~~-~~~~~l-~~~~~~~lT~  156 (169)
                                  ..... ++.|-+.++.    ..+.++  +..+||+||.|+++...-- .+ .-+..+ +..+-++|||
T Consensus       210 ------------P~ASC-LVMTTEILRsMLYRGSEvmr--EVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  210 ------------PDASC-LVMTTEILRSMLYRGSEVMR--EVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             ------------CCCce-eeeHHHHHHHHHhccchHhh--eeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence                        33333 7777777653    334444  5567999999999863211 11 223334 4556688999


Q ss_pred             cCC
Q psy1090         157 WYY  159 (169)
Q Consensus       157 TP~  159 (169)
                      |-.
T Consensus       275 TiP  277 (1041)
T KOG0948|consen  275 TIP  277 (1041)
T ss_pred             cCC
Confidence            954

>KOG0920|consensus

Probab=97.12  E-value=0.0048  Score=52.11  Aligned_cols=137  Identities=19%  Similarity=0.127  Sum_probs=72.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCC-ceEEEecCc--c--hHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALE-PNLIVCPLS--V--LNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~-~~Liv~P~~--~--l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      ++..|+|.|||.++-.+|..-....... ++++--|.-  .  +.+++..=+....+ +.+-|.-.-..+.         
T Consensus       192 vIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g-~~VGYqvrl~~~~---------  261 (924)
T KOG0920|consen  192 VISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLG-EEVGYQVRLESKR---------  261 (924)
T ss_pred             EEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccC-CeeeEEEeeeccc---------
Confidence            5778999999999999987654333222 322222542  2  23444322211122 2221111100000         


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhc-cccccccEEEEeCCcccCCcccHH-HHHHhcc----ccccEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGHSVKNKKSKL-SIKLTAL----RATFKV  152 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah~~k~~~~~~-~~~~~~l----~~~~~~  152 (169)
                                      ..... +.++|...+-+.... -.-....-+|+||+|. ++-.+.. ...++.+    +.-+.+
T Consensus       262 ----------------s~~t~-L~fcTtGvLLr~L~~~~~l~~vthiivDEVHE-R~i~~DflLi~lk~lL~~~p~LkvI  323 (924)
T KOG0920|consen  262 ----------------SRETR-LLFCTTGVLLRRLQSDPTLSGVTHIIVDEVHE-RSINTDFLLILLKDLLPRNPDLKVI  323 (924)
T ss_pred             ----------------CCcee-EEEecHHHHHHHhccCcccccCceeeeeeEEE-ccCCcccHHHHHHHHhhhCCCceEE
Confidence                            02233 378888877664432 2223567899999995 2333332 3333332    345579


Q ss_pred             EEeccCCCCCchhhcc
Q psy1090         153 LLTGWYYPNKWSKQCT  168 (169)
Q Consensus       153 ~lT~TP~~n~~~el~~  168 (169)
                      +||||--...+++.|.
T Consensus       324 LMSAT~dae~fs~YF~  339 (924)
T KOG0920|consen  324 LMSATLDAELFSDYFG  339 (924)
T ss_pred             EeeeecchHHHHHHhC
Confidence            9999988666666653

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

Probab=97.09  E-value=0.0015  Score=54.06  Aligned_cols=125  Identities=18%  Similarity=0.202  Sum_probs=69.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHHHhhhcCCCcc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQSEALSLPTIK   82 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   82 (169)
                      +--.||+|||...+-++..... .+..++|+|.=. +++.+-...++... +  ....|.......  +..         
T Consensus        54 VRSpMGTGKTtaLi~wLk~~l~-~~~~~VLvVShRrSL~~sL~~rf~~~~l~--gFv~Y~d~~~~~--i~~---------  119 (824)
T PF02399_consen   54 VRSPMGTGKTTALIRWLKDALK-NPDKSVLVVSHRRSLTKSLAERFKKAGLS--GFVNYLDSDDYI--IDG---------  119 (824)
T ss_pred             EECCCCCCcHHHHHHHHHHhcc-CCCCeEEEEEhHHHHHHHHHHHHhhcCCC--cceeeecccccc--ccc---------
Confidence            4468999999887777655432 345678888664 66677666665442 2  222233221110  000         


Q ss_pred             cccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCC----cc----cHHHHHHhcc--ccccEE
Q psy1090          83 VPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKN----KK----SKLSIKLTAL--RATFKV  152 (169)
Q Consensus        83 ~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~----~~----~~~~~~~~~l--~~~~~~  152 (169)
                                   ...+- +++..+++.+....+. .+||+||+||+-..-+    +.    ......+..+  +++..+
T Consensus       120 -------------~~~~r-LivqIdSL~R~~~~~l-~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI  184 (824)
T PF02399_consen  120 -------------RPYDR-LIVQIDSLHRLDGSLL-DRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVI  184 (824)
T ss_pred             -------------cccCe-EEEEehhhhhcccccc-cccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEE
Confidence                         12334 7777777766544311 2499999999753211    11    1112222222  688888


Q ss_pred             EEeccC
Q psy1090         153 LLTGWY  158 (169)
Q Consensus       153 ~lT~TP  158 (169)
                      +|-||-
T Consensus       185 ~~DA~l  190 (824)
T PF02399_consen  185 VMDADL  190 (824)
T ss_pred             EecCCC
Confidence            888774

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.05  E-value=0.01  Score=50.84  Aligned_cols=66  Identities=9%  Similarity=-0.095  Sum_probs=39.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec-CcchHHHHHHHHHhC--CCceEEEEeCCHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP-LSVLNNWEAEFRKFA--PFVRTVKYYGNAIERK   69 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P-~~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~   69 (169)
                      +-.-.+|.|||+.=.-++..+......-+.-|..= .++.-|-.+++++-.  .+...-+..|+...+.
T Consensus       435 vNMASTGcGKT~aNARImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~L~~ddLAVlIGs~Av~~  503 (1110)
T TIGR02562       435 VNMASTGCGKTLANARAMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLNLSDDDLAVLIGGTAVQT  503 (1110)
T ss_pred             EEecCCCcchHHHHHHHHHHhCCCCCCceEEEEccccceeccchHHHHHhcCCCccceEEEECHHHHHH
Confidence            44568999999765444444433333234444443 355567778877544  4566677777665544

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.04  E-value=0.0029  Score=46.19  Aligned_cols=24  Identities=8%  Similarity=-0.115  Sum_probs=17.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+|.-++|+|||..+-++...+..
T Consensus        45 vll~GppGtGKTtlA~~ia~~l~~   68 (261)
T TIGR02881        45 MIFKGNPGTGKTTVARILGKLFKE   68 (261)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHh
Confidence            467889999999888776655433

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.

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

Probab=97.02  E-value=0.0041  Score=43.51  Aligned_cols=34  Identities=9%  Similarity=0.109  Sum_probs=23.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      +|.-.+|.|||.++.-+..++..+  ..++.+++-.
T Consensus         5 ~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D   38 (196)
T PF00448_consen    5 ALVGPTGVGKTTTIAKLAARLKLK--GKKVALISAD   38 (196)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEES
T ss_pred             EEECCCCCchHhHHHHHHHHHhhc--cccceeecCC
Confidence            456789999999998888777655  4556666654

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 ....

>KOG0334|consensus

Probab=97.02  E-value=0.0037  Score=52.79  Aligned_cols=137  Identities=19%  Similarity=0.244  Sum_probs=77.3

Q ss_pred             ccccCCCCCcHHHHHH-HHHHHHHHhCC----CCc-eEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVI-AFFCKIIEEQA----LEP-NLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i-~~i~~~~~~~~----~~~-~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~   73 (169)
                      +|=.-.+|+|||+.-+ -.+..+..+.+    .+| .+|+||. .+..|-.+++.+|.  -+.+++..+|......++..
T Consensus       405 vIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiae  484 (997)
T KOG0334|consen  405 VIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAE  484 (997)
T ss_pred             eEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHH
Confidence            4445679999997652 22333332221    255 5899997 66667666666665  35666666655444444443


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHH----Hhchhccccc-cccEEEEeCCcccCC--cccHHHHHHhcc
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQII----ENDFGFLKKI-TWNCIIVDEGHSVKN--KKSKLSIKLTAL  146 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~----~~~~~~~~~~-~~~~vi~DEah~~k~--~~~~~~~~~~~l  146 (169)
                      ..                    ....| +|.|....    ..+...+.++ ..-++|+|||.++-.  ...+..+.+..+
T Consensus       485 lk--------------------Rg~eI-vV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nl  543 (997)
T KOG0334|consen  485 LK--------------------RGAEI-VVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNL  543 (997)
T ss_pred             Hh--------------------cCCce-EEeccchhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhc
Confidence            32                    23556 66665443    3333333333 355899999998642  234445566666


Q ss_pred             cc-ccEEEEeccCCC
Q psy1090         147 RA-TFKVLLTGWYYP  160 (169)
Q Consensus       147 ~~-~~~~~lT~TP~~  160 (169)
                      +. +..++.|||-+.
T Consensus       544 rpdrQtvlfSatfpr  558 (997)
T KOG0334|consen  544 RPDRQTVLFSATFPR  558 (997)
T ss_pred             chhhhhhhhhhhhhH
Confidence            43 334556666543

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.00  E-value=0.0081  Score=51.07  Aligned_cols=60  Identities=7%  Similarity=-0.087  Sum_probs=36.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH---HHHHHHHHhCCCceEEEEeC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN---NWEAEFRKFAPFVRTVKYYG   63 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~---qW~~e~~~~~~~~~~~~~~g   63 (169)
                      |.|--+.+|=|||+++..-+ ++-.-...+-.+|-+...+..   +|...+-+|. ++.+.....
T Consensus       153 G~IAEM~TGEGKTLvatlp~-yLnAL~G~gVHvVTvNDYLA~RDaewm~p~y~fl-GLtVg~i~~  215 (1025)
T PRK12900        153 GKISEMATGEGKTLVSTLPT-FLNALTGRGVHVVTVNDYLAQRDKEWMNPVFEFH-GLSVGVILN  215 (1025)
T ss_pred             CCccccCCCCCcchHhHHHH-HHHHHcCCCcEEEeechHhhhhhHHHHHHHHHHh-CCeeeeeCC
Confidence            55667889999998754222 111112234455555556653   7999999998 666665543

>PRK06526 transposase; Provisional

Probab=96.98  E-value=0.0048  Score=44.93  Aligned_cols=43  Identities=16%  Similarity=0.225  Sum_probs=27.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      +.+|...+|+|||..+.++.......+  .+++++.    ..+|.+++.
T Consensus       100 nlll~Gp~GtGKThLa~al~~~a~~~g--~~v~f~t----~~~l~~~l~  142 (254)
T PRK06526        100 NVVFLGPPGTGKTHLAIGLGIRACQAG--HRVLFAT----AAQWVARLA  142 (254)
T ss_pred             eEEEEeCCCCchHHHHHHHHHHHHHCC--Cchhhhh----HHHHHHHHH
Confidence            456778999999999988876655433  3444432    234555553

>KOG0344|consensus

Probab=96.96  E-value=0.00056  Score=54.15  Aligned_cols=113  Identities=19%  Similarity=0.198  Sum_probs=64.2

Q ss_pred             ccccCCCCCcHHHHHHHH-HHHHHHhC----CC-CceEEEecC-cchHHHHHHHHHhC--CCc--eEEEEeCCHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAF-FCKIIEEQ----AL-EPNLIVCPL-SVLNNWEAEFRKFA--PFV--RTVKYYGNAIERKAL   71 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~-i~~~~~~~----~~-~~~Liv~P~-~~l~qW~~e~~~~~--~~~--~~~~~~g~~~~~~~~   71 (169)
                      ++-+-.+|.|||+.-..= +..+....    .. -..+|+.|. .+..|-++|..++.  +..  ....+..+.....  
T Consensus       176 ~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~q--  253 (593)
T KOG0344|consen  176 VLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQ--  253 (593)
T ss_pred             eEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhh--
Confidence            455678999998654433 22332222    22 378999997 67789999998886  211  1111111100000  


Q ss_pred             HHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc----cccccccEEEEeCCcccCCc
Q psy1090          72 QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF----LKKITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~----~~~~~~~~vi~DEah~~k~~  135 (169)
                                       +.........|+ ++.|+..+......    +.-....++|+|||..+..+
T Consensus       254 -----------------k~a~~~~~k~di-li~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~  303 (593)
T KOG0344|consen  254 -----------------KPAFLSDEKYDI-LISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEP  303 (593)
T ss_pred             -----------------ccchhHHHHHHH-HhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhCh
Confidence                             000011144455 88888777665543    22335678999999999887

>KOG0333|consensus

Probab=96.95  E-value=0.0021  Score=50.70  Aligned_cols=111  Identities=17%  Similarity=0.232  Sum_probs=65.4

Q ss_pred             ccccCCCCCcHHHH----HHHHHHHHH-----HhCCCC-ceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHH
Q psy1090           3 TVIPDPTRYRKSGK----VIAFFCKII-----EEQALE-PNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERK   69 (169)
Q Consensus         3 ~iL~de~G~GKT~~----~i~~i~~~~-----~~~~~~-~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~   69 (169)
                      -|..-|+|+|||..    .+..|..+-     +....+ ..+|++|. .+.+|-.+|-.+|..  +.+++...|...-..
T Consensus       285 ~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EE  364 (673)
T KOG0333|consen  285 PIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEE  364 (673)
T ss_pred             eeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhh
Confidence            45667999999932    333333221     122223 57999997 666788888888873  456665555433222


Q ss_pred             HHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCC
Q psy1090          70 ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~  134 (169)
                      +-...                    ...+.+ ++.|+..+..-.+  .+...+-.++|+|||.++-.
T Consensus       365 q~fql--------------------s~gcei-viatPgrLid~Lenr~lvl~qctyvvldeadrmiD  410 (673)
T KOG0333|consen  365 QGFQL--------------------SMGCEI-VIATPGRLIDSLENRYLVLNQCTYVVLDEADRMID  410 (673)
T ss_pred             hhhhh--------------------hcccee-eecCchHHHHHHHHHHHHhccCceEeccchhhhhc
Confidence            11111                    156677 8888877654322  12223556899999997654

>KOG0332|consensus

Probab=96.94  E-value=0.0016  Score=49.30  Aligned_cols=132  Identities=11%  Similarity=0.159  Sum_probs=69.2

Q ss_pred             cCCCCCcHHHH-HHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           6 PDPTRYRKSGK-VIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         6 ~de~G~GKT~~-~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      ....|+|||.. +++.++.....-..-..+-++|. .+..|-.+-+.+......+-..+.-.+.+..             
T Consensus       135 QsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~-------------  201 (477)
T KOG0332|consen  135 QSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAK-------------  201 (477)
T ss_pred             hhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCcccc-------------
Confidence            45689999965 33333322222222235556897 6667766666655532222222221111100             


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHhchhcccc---ccccEEEEeCCcccCCcc---cHHHHHHhccc-cccEEEEec
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK---ITWNCIIVDEGHSVKNKK---SKLSIKLTALR-ATFKVLLTG  156 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~---~~~~~vi~DEah~~k~~~---~~~~~~~~~l~-~~~~~~lT~  156 (169)
                              ....-..+ |++-|...+......+..   .....+++|||..+-+..   -...+.-+.+. ....++.||
T Consensus       202 --------rG~~i~eq-IviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSA  272 (477)
T KOG0332|consen  202 --------RGNKLTEQ-IVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSA  272 (477)
T ss_pred             --------cCCcchhh-eeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeec
Confidence                    00002223 488888887766555443   356799999999765533   11223333443 556788898


Q ss_pred             cCC
Q psy1090         157 WYY  159 (169)
Q Consensus       157 TP~  159 (169)
                      |-.
T Consensus       273 Tf~  275 (477)
T KOG0332|consen  273 TFV  275 (477)
T ss_pred             hhH
Confidence            854

>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=96.91  E-value=0.0082  Score=38.90  Aligned_cols=41  Identities=20%  Similarity=0.122  Sum_probs=25.0

Q ss_pred             cccEEEEeCCcccCCcc-cHHHHHHhcc------ccccEEEEeccCCC
Q psy1090         120 TWNCIIVDEGHSVKNKK-SKLSIKLTAL------RATFKVLLTGWYYP  160 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~-~~~~~~~~~l------~~~~~~~lT~TP~~  160 (169)
                      +..++++||++.+.... ......+..+      .....+++++.+..
T Consensus        84 ~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          84 KPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             CCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence            45689999999873222 2223334433      24667888888665

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.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.88  E-value=0.013  Score=45.04  Aligned_cols=46  Identities=11%  Similarity=0.030  Sum_probs=31.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRK   51 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~   51 (169)
                      ++.-++|.|||..++.++......  .++++++.-.....|......+
T Consensus        86 LI~G~pG~GKStLllq~a~~~a~~--g~~VlYvs~EEs~~qi~~Ra~r  131 (372)
T cd01121          86 LIGGDPGIGKSTLLLQVAARLAKR--GGKVLYVSGEESPEQIKLRADR  131 (372)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCcCHHHHHHHHHH
Confidence            567799999998888877655443  2578888766555665544443

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

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.85  E-value=0.0097  Score=49.09  Aligned_cols=53  Identities=15%  Similarity=0.199  Sum_probs=40.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKY   61 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~   61 (169)
                      +|..-+|+|||+++..++..     ..+|+|||+|+. ...||..|++.|+|+-.+..|
T Consensus        33 ~l~Gvtgs~kt~~~a~~~~~-----~~~p~Lvi~~n~~~A~ql~~el~~f~p~~~V~~f   86 (655)
T TIGR00631        33 TLLGVTGSGKTFTMANVIAQ-----VNRPTLVIAHNKTLAAQLYNEFKEFFPENAVEYF   86 (655)
T ss_pred             EEECCCCcHHHHHHHHHHHH-----hCCCEEEEECCHHHHHHHHHHHHHhCCCCeEEEE
Confidence            35566899999988766543     246999999985 556999999999987545544

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.80  E-value=0.023  Score=44.00  Aligned_cols=33  Identities=9%  Similarity=0.073  Sum_probs=22.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      .|....|+|||.++..+...+...  ..++.++..
T Consensus       245 ~LVGptGvGKTTTiaKLA~~L~~~--GkkVglI~a  277 (436)
T PRK11889        245 ALIGPTGVGKTTTLAKMAWQFHGK--KKTVGFITT  277 (436)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHc--CCcEEEEec
Confidence            456679999998888776655432  245655554

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=96.80  E-value=0.012  Score=50.28  Aligned_cols=59  Identities=7%  Similarity=-0.051  Sum_probs=36.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH---HHHHHHHHhCCCceEEEEe
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN---NWEAEFRKFAPFVRTVKYY   62 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~---qW~~e~~~~~~~~~~~~~~   62 (169)
                      |.|--+.+|=|||+++..-+. +-.-...+-.+|-+...+..   +|...+-+|. ++.+....
T Consensus       184 G~IAEM~TGEGKTLvAtlp~y-LnAL~GkgVHvVTVNDYLA~RDaewmgply~fL-GLsvg~i~  245 (1112)
T PRK12901        184 GKIAEMATGEGKTLVATLPVY-LNALTGNGVHVVTVNDYLAKRDSEWMGPLYEFH-GLSVDCID  245 (1112)
T ss_pred             CceeeecCCCCchhHHHHHHH-HHHHcCCCcEEEEechhhhhccHHHHHHHHHHh-CCceeecC
Confidence            556678899999987643221 11112234455555556653   7999999998 67666553

>KOG0951|consensus

Probab=96.79  E-value=0.006  Score=52.84  Aligned_cols=104  Identities=20%  Similarity=0.270  Sum_probs=70.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-----HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-----NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-----~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.+++-..|+|||+++--.+..   ....++++-++|.+.+     ..|...|... .+..+...+|...-..++.    
T Consensus      1161 ~v~vga~~gsgkt~~ae~a~l~---~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~-~G~~~~~l~ge~s~~lkl~---- 1232 (1674)
T KOG0951|consen 1161 NVLVGAPNGSGKTACAELALLR---PDTIGRAVYIAPLEEIADEQYRDWEKKFSKL-LGLRIVKLTGETSLDLKLL---- 1232 (1674)
T ss_pred             eEEEecCCCCchhHHHHHHhcC---CccceEEEEecchHHHHHHHHHHHHHhhccc-cCceEEecCCccccchHHh----
Confidence            3578889999999766433222   3345688999998754     3577777666 4777787887654433222    


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKK  136 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~  136 (169)
                                         ...++ +|.|++......   .-...++.|+||.|.+.+..
T Consensus      1233 -------------------~~~~v-ii~tpe~~d~lq---~iQ~v~l~i~d~lh~igg~~ 1269 (1674)
T KOG0951|consen 1233 -------------------QKGQV-IISTPEQWDLLQ---SIQQVDLFIVDELHLIGGVY 1269 (1674)
T ss_pred             -------------------hhcce-EEechhHHHHHh---hhhhcceEeeehhhhhcccC
Confidence                               44555 888887765442   23467899999999987644

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

Probab=96.79  E-value=0.0043  Score=47.05  Aligned_cols=41  Identities=27%  Similarity=0.275  Sum_probs=29.4

Q ss_pred             cccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCC
Q psy1090         118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus       118 ~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                      .++-.++|+||||.+.-  ...--.+.+.-...++++||-|-|
T Consensus       349 Sl~~~FiIIDEaQNLTp--heikTiltR~G~GsKIVl~gd~aQ  389 (436)
T COG1875         349 SLPDSFIIIDEAQNLTP--HELKTILTRAGEGSKIVLTGDPAQ  389 (436)
T ss_pred             ccccceEEEehhhccCH--HHHHHHHHhccCCCEEEEcCCHHH
Confidence            34556899999999852  233344556677889999998875

>KOG0326|consensus

Probab=96.74  E-value=0.0035  Score=46.68  Aligned_cols=128  Identities=15%  Similarity=0.127  Sum_probs=75.6

Q ss_pred             CCCCcHHHHHH-HHHHHHHHhCCCCceEEEecC-cch---HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcc
Q psy1090           8 PTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPL-SVL---NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIK   82 (169)
Q Consensus         8 e~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~-~~l---~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   82 (169)
                      -.|+|||-..+ -.+..+......=..+|++|. .+.   .|-..++.++. +..+++.+|...-+..+-...       
T Consensus       130 KNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl~-------  201 (459)
T KOG0326|consen  130 KNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRLN-------  201 (459)
T ss_pred             cCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeeec-------
Confidence            46999995422 222222222222368999996 332   35667777777 688888888655444332211       


Q ss_pred             cccccCCccccccCCCCeEEEecHHHHHhchh----ccccccccEEEEeCCcccCCccc--HHHHHHhcc-ccccEEEEe
Q psy1090          83 VPAKKGKTKKQISLKLPLILVTTPQIIENDFG----FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL-RATFKVLLT  155 (169)
Q Consensus        83 ~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~----~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l-~~~~~~~lT  155 (169)
                                   ....+ ++.|+..+.....    .++  +-.++|+|||..+-+.+-  ...+.+..+ +.+..++.|
T Consensus       202 -------------~~VH~-~vgTPGRIlDL~~KgVa~ls--~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~rQillyS  265 (459)
T KOG0326|consen  202 -------------QTVHL-VVGTPGRILDLAKKGVADLS--DCVILVMDEADKLLSVDFQPIVEKLISFLPKERQILLYS  265 (459)
T ss_pred             -------------CceEE-EEcCChhHHHHHhcccccch--hceEEEechhhhhhchhhhhHHHHHHHhCCccceeeEEe
Confidence                         33344 8888877654332    222  345899999998765332  223444445 566678889


Q ss_pred             ccCC
Q psy1090         156 GWYY  159 (169)
Q Consensus       156 ~TP~  159 (169)
                      ||-.
T Consensus       266 ATFP  269 (459)
T KOG0326|consen  266 ATFP  269 (459)
T ss_pred             cccc
Confidence            9854

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.74  E-value=0.01  Score=49.81  Aligned_cols=59  Identities=10%  Similarity=-0.102  Sum_probs=36.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-ch---HHHHHHHHHhCCCceEEEEeC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VL---NNWEAEFRKFAPFVRTVKYYG   63 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l---~qW~~e~~~~~~~~~~~~~~g   63 (169)
                      |.|--+.+|=|||+++..-+ + ...-..+.+=||..+. +.   .+|...+-+|. ++.+.+...
T Consensus        93 G~IAEMkTGEGKTLvAtLpa-y-LnAL~GkgVhVVTvNdYLA~RDae~mg~vy~fL-GLsvG~i~~  155 (925)
T PRK12903         93 GSVAEMKTGEGKTITSIAPV-Y-LNALTGKGVIVSTVNEYLAERDAEEMGKVFNFL-GLSVGINKA  155 (925)
T ss_pred             CCeeeecCCCCccHHHHHHH-H-HHHhcCCceEEEecchhhhhhhHHHHHHHHHHh-CCceeeeCC
Confidence            55667889999998764322 2 1111124455555554 43   37999999888 666665543

>KOG1132|consensus

Probab=96.74  E-value=0.037  Score=46.42  Aligned_cols=37  Identities=11%  Similarity=0.159  Sum_probs=23.9

Q ss_pred             CCCCeEEEecHHHHHhch-hccc--cccccEEEEeCCcccC
Q psy1090          96 LKLPLILVTTPQIIENDF-GFLK--KITWNCIIVDEGHSVK  133 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~-~~~~--~~~~~~vi~DEah~~k  133 (169)
                      ...|+ +++.|+.+.+.. ....  +++-.+||+||||.+-
T Consensus       221 edAdI-IF~PYnYLiDp~iR~~~~v~LknsIVIfDEAHNiE  260 (945)
T KOG1132|consen  221 EDADI-IFCPYNYLIDPKIRRSHKVDLKNSIVIFDEAHNIE  260 (945)
T ss_pred             ccCcE-EEechhhhcCHhhhccccccccccEEEEeccccHH
Confidence            45566 889998886432 1111  2334599999999863

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

Probab=96.62  E-value=0.018  Score=44.40  Aligned_cols=87  Identities=11%  Similarity=0.103  Sum_probs=59.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      +++-|+|.||+...+-+++.+..++   ++|.|.=....+||.-...+..-                             
T Consensus        97 LIgGdPGIGKSTLLLQva~~lA~~~---~vLYVsGEES~~QiklRA~RL~~-----------------------------  144 (456)
T COG1066          97 LIGGDPGIGKSTLLLQVAARLAKRG---KVLYVSGEESLQQIKLRADRLGL-----------------------------  144 (456)
T ss_pred             EEccCCCCCHHHHHHHHHHHHHhcC---cEEEEeCCcCHHHHHHHHHHhCC-----------------------------
Confidence            5788999999977776666554433   89999999999999988877641                             


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCc
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~  135 (169)
                                  ...++ .+.....+..-...+.+.+++++|+|-.|.+-++
T Consensus       145 ------------~~~~l-~l~aEt~~e~I~~~l~~~~p~lvVIDSIQT~~s~  183 (456)
T COG1066         145 ------------PTNNL-YLLAETNLEDIIAELEQEKPDLVVIDSIQTLYSE  183 (456)
T ss_pred             ------------Cccce-EEehhcCHHHHHHHHHhcCCCEEEEeccceeecc
Confidence                        11112 4444444444445555678888888888876543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.58  E-value=0.013  Score=45.51  Aligned_cols=38  Identities=16%  Similarity=0.197  Sum_probs=22.0

Q ss_pred             ccEEEEeCCcccCCcccH---HHHHHhcc-ccccEEEEeccC
Q psy1090         121 WNCIIVDEGHSVKNKKSK---LSIKLTAL-RATFKVLLTGWY  158 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~---~~~~~~~l-~~~~~~~lT~TP  158 (169)
                      .+++++||.|.+.+....   ....+..+ .....+++|++-
T Consensus       200 ~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~  241 (405)
T TIGR00362       200 VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDR  241 (405)
T ss_pred             CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCC
Confidence            578999999988653221   12222222 334567777763

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

>PRK08116 hypothetical protein; Validated

Probab=96.54  E-value=0.015  Score=42.69  Aligned_cols=34  Identities=15%  Similarity=0.110  Sum_probs=25.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      |.+|.-++|+|||..+.+++..+...+  .+++++-
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~--~~v~~~~  149 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKG--VPVIFVN  149 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEE
Confidence            467888999999999988887776542  4555444

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.54  E-value=0.036  Score=43.46  Aligned_cols=34  Identities=9%  Similarity=0.077  Sum_probs=21.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .+.-.+|+|||.++..++..+.......++.+|.
T Consensus       225 ~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~  258 (424)
T PRK05703        225 ALVGPTGVGKTTTLAKLAARYALLYGKKKVALIT  258 (424)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            3556799999999888776654122224555554

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.47  E-value=0.014  Score=46.05  Aligned_cols=40  Identities=18%  Similarity=0.164  Sum_probs=22.3

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHh---cc-ccccEEEEeccCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLT---AL-RATFKVLLTGWYY  159 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~---~l-~~~~~~~lT~TP~  159 (169)
                      ..+++++||.|.+.+........+.   .+ .....+++|++-.
T Consensus       211 ~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~  254 (450)
T PRK00149        211 SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRP  254 (450)
T ss_pred             cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCC
Confidence            4678999999998653321112222   22 2334577776543

>PRK14974 cell division protein FtsY; Provisional

Probab=96.44  E-value=0.031  Score=42.43  Aligned_cols=45  Identities=9%  Similarity=0.028  Sum_probs=27.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC----cchHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL----SVLNNWEAEFR   50 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~----~~l~qW~~e~~   50 (169)
                      ++...+|+|||.++..++..+...+  .+++++...    ....||.....
T Consensus       144 ~~~G~~GvGKTTtiakLA~~l~~~g--~~V~li~~Dt~R~~a~eqL~~~a~  192 (336)
T PRK14974        144 VFVGVNGTGKTTTIAKLAYYLKKNG--FSVVIAAGDTFRAGAIEQLEEHAE  192 (336)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHcC--CeEEEecCCcCcHHHHHHHHHHHH
Confidence            3566899999988877766554332  456555543    23456654444

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.44  E-value=0.018  Score=45.45  Aligned_cols=38  Identities=13%  Similarity=0.182  Sum_probs=21.5

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEecc
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGW  157 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~T  157 (169)
                      ..+++|+||.|.+.+.....-..+..+    .....+++|+.
T Consensus       206 ~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd  247 (450)
T PRK14087        206 QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSD  247 (450)
T ss_pred             cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECC
Confidence            457899999998865332212222222    33446777743

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.40  E-value=0.066  Score=41.36  Aligned_cols=121  Identities=13%  Similarity=0.186  Sum_probs=64.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCce-EEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPN-LIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIK   82 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~-Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   82 (169)
                      .|...+|.|||.+..-++..+......+++ +|-.-+.-+. -.++++.|+.                    .       
T Consensus       207 ~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIG-A~EQLk~Ya~--------------------i-------  258 (407)
T COG1419         207 ALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIG-AVEQLKTYAD--------------------I-------  258 (407)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhh-HHHHHHHHHH--------------------H-------
Confidence            467799999998877776655522223344 4433343322 1223433320                    0       


Q ss_pred             cccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEeccC
Q psy1090          83 VPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGWY  158 (169)
Q Consensus        83 ~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~TP  158 (169)
                                   -..++.++.+..-+......+.+  .|+|.+|=+-+...+..+..+.-..+    .....+.||+|-
T Consensus       259 -------------m~vp~~vv~~~~el~~ai~~l~~--~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~  323 (407)
T COG1419         259 -------------MGVPLEVVYSPKELAEAIEALRD--CDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATT  323 (407)
T ss_pred             -------------hCCceEEecCHHHHHHHHHHhhc--CCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCc
Confidence                         22233366666666665555553  37888887665443333322222212    345568888887


Q ss_pred             CCCCchhhc
Q psy1090         159 YPNKWSKQC  167 (169)
Q Consensus       159 ~~n~~~el~  167 (169)
                      =.+++.++|
T Consensus       324 K~~dlkei~  332 (407)
T COG1419         324 KYEDLKEII  332 (407)
T ss_pred             chHHHHHHH
Confidence            777766654

>PRK08727 hypothetical protein; Validated

Probab=96.36  E-value=0.038  Score=39.69  Aligned_cols=22  Identities=14%  Similarity=0.166  Sum_probs=15.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      +|..++|+|||-.+-++.....
T Consensus        45 ~l~G~~G~GKThL~~a~~~~~~   66 (233)
T PRK08727         45 YLSGPAGTGKTHLALALCAAAE   66 (233)
T ss_pred             EEECCCCCCHHHHHHHHHHHHH
Confidence            5677889999977766655543

>KOG0924|consensus

Probab=96.35  E-value=0.0056  Score=49.97  Aligned_cols=48  Identities=19%  Similarity=0.195  Sum_probs=28.2

Q ss_pred             ccccEEEEeCCcccCCcccHH-HHHHhcc----ccccEEEEeccCCCCCchhhc
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKL-SIKLTAL----RATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~-~~~~~~l----~~~~~~~lT~TP~~n~~~el~  167 (169)
                      .++.++|+||||.=. -++.. .-.++.+    +.-..++.|||.=...+.++|
T Consensus       467 ~kYSviImDEAHERs-lNtDilfGllk~~larRrdlKliVtSATm~a~kf~nfF  519 (1042)
T KOG0924|consen  467 DKYSVIIMDEAHERS-LNTDILFGLLKKVLARRRDLKLIVTSATMDAQKFSNFF  519 (1042)
T ss_pred             hheeEEEechhhhcc-cchHHHHHHHHHHHHhhccceEEEeeccccHHHHHHHh
Confidence            378899999999521 22322 2223322    222357788998766666655

>PLN03025 replication factor C subunit; Provisional

Probab=96.30  E-value=0.033  Score=41.92  Aligned_cols=42  Identities=14%  Similarity=0.143  Sum_probs=24.7

Q ss_pred             cccEEEEeCCcccCCcccHH-HHHHhccccccEEEEeccCCCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKL-SIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~-~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      .+.++|+||+|.+....... .+.+.......+++++.++...
T Consensus        99 ~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~  141 (319)
T PLN03025         99 RHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSK  141 (319)
T ss_pred             CeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccc
Confidence            57899999999985322111 1222222444567777766543

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.30  E-value=0.031  Score=45.87  Aligned_cols=118  Identities=9%  Similarity=0.058  Sum_probs=62.5

Q ss_pred             CcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHH----hCCCceEEEEeCCHHHHHHHHHhhhcCCCccccc
Q psy1090          11 YRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRK----FAPFVRTVKYYGNAIERKALQSEALSLPTIKVPA   85 (169)
Q Consensus        11 ~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~----~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   85 (169)
                      -|||..+...+..+...-..-.+++++|. .+.+.-.+|+..    |+|...+-...|.        ...+...      
T Consensus       265 ~GKTwivv~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkGe--------~I~i~f~------  330 (738)
T PHA03368        265 HGKTWFLVPLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKGE--------TISFSFP------  330 (738)
T ss_pred             CCchhhHHHHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecCc--------EEEEEec------
Confidence            59998777666666554445678999986 555566666654    4332222111110        0000000      


Q ss_pred             ccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHH--hccccccEEEEecc
Q psy1090          86 KKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKL--TALRATFKVLLTGW  157 (169)
Q Consensus        86 ~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~--~~l~~~~~~~lT~T  157 (169)
                               .+....|.+.|   . ++.+..+...++++|+||||.++.  ......+  ..-.....+.+|-|
T Consensus       331 ---------nG~kstI~FaS---a-rntNsiRGqtfDLLIVDEAqFIk~--~al~~ilp~l~~~n~k~I~ISS~  389 (738)
T PHA03368        331 ---------DGSRSTIVFAS---S-HNTNGIRGQDFNLLFVDEANFIRP--DAVQTIMGFLNQTNCKIIFVSST  389 (738)
T ss_pred             ---------CCCccEEEEEe---c-cCCCCccCCcccEEEEechhhCCH--HHHHHHHHHHhccCccEEEEecC
Confidence                     01111224431   1 333455667999999999999974  2222222  22245667777755

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.20  E-value=0.04  Score=39.06  Aligned_cols=39  Identities=15%  Similarity=0.250  Sum_probs=22.8

Q ss_pred             cEEEEeCCcccCCccc---HHHHHHhcc-ccccEEEEeccCCC
Q psy1090         122 NCIIVDEGHSVKNKKS---KLSIKLTAL-RATFKVLLTGWYYP  160 (169)
Q Consensus       122 ~~vi~DEah~~k~~~~---~~~~~~~~l-~~~~~~~lT~TP~~  160 (169)
                      +++|+||+|.+.....   .....+... ..+.++++|++...
T Consensus        92 ~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~  134 (226)
T TIGR03420        92 DLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAP  134 (226)
T ss_pred             CEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCCh
Confidence            6799999998864321   122222222 23457888887543

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.17  E-value=0.027  Score=44.42  Aligned_cols=47  Identities=11%  Similarity=0.045  Sum_probs=33.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-++|+|||..++.++......  ..+++.+.-.....|......++
T Consensus        84 lI~G~pG~GKTtL~lq~a~~~a~~--g~~vlYvs~Ees~~qi~~ra~rl  130 (446)
T PRK11823         84 LIGGDPGIGKSTLLLQVAARLAAA--GGKVLYVSGEESASQIKLRAERL  130 (446)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccccHHHHHHHHHHc
Confidence            578899999998888887655432  35788888776666665555544

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

Probab=96.16  E-value=0.032  Score=40.71  Aligned_cols=46  Identities=20%  Similarity=0.247  Sum_probs=31.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      |.+|--.+|+|||..+.|+...+...  ..+++++.-+.++.+....+
T Consensus       107 nl~l~G~~G~GKThLa~Ai~~~l~~~--g~sv~f~~~~el~~~Lk~~~  152 (254)
T COG1484         107 NLVLLGPPGVGKTHLAIAIGNELLKA--GISVLFITAPDLLSKLKAAF  152 (254)
T ss_pred             cEEEECCCCCcHHHHHHHHHHHHHHc--CCeEEEEEHHHHHHHHHHHH
Confidence            46778899999999999988877632  24566665555555544444

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.15  E-value=0.042  Score=44.83  Aligned_cols=40  Identities=15%  Similarity=0.179  Sum_probs=22.9

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEeccCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGWYY  159 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~TP~  159 (169)
                      ..|++|+|+.|.+.+........+..+    .....+++|+.-.
T Consensus       377 ~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~  420 (617)
T PRK14086        377 EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRP  420 (617)
T ss_pred             cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCC
Confidence            358899999998876443222222222    2344566666543

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.06  E-value=0.018  Score=39.33  Aligned_cols=54  Identities=15%  Similarity=0.144  Sum_probs=34.7

Q ss_pred             hccccccccEEEEeCCcccCCc----ccHHHHHHhccccccEEEEeccCCCCCchhhc
Q psy1090         114 GFLKKITWNCIIVDEGHSVKNK----KSKLSIKLTALRATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       114 ~~~~~~~~~~vi~DEah~~k~~----~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el~  167 (169)
                      ..+..-++|++|+||.-..-+.    .......+..-+...-++|||--.+..+.|+.
T Consensus        91 ~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~A  148 (173)
T TIGR00708        91 EMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELA  148 (173)
T ss_pred             HHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhC
Confidence            3344568999999998743332    23344555555566689999987766555543

Alternate name: corrinoid adenosyltransferase.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.04  E-value=0.048  Score=45.60  Aligned_cols=41  Identities=20%  Similarity=0.272  Sum_probs=25.8

Q ss_pred             ccccEEEEeCCcccCCcccHHHHHHhcc---ccccEEEEeccCCCC
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKLSIKLTAL---RATFKVLLTGWYYPN  161 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~~~~~~~l---~~~~~~~lT~TP~~n  161 (169)
                      -+|.++||||+|.+...  .....++.+   ....+++|+.|-.+.
T Consensus       118 gr~KVIIIDEah~LT~~--A~NALLKtLEEPP~~v~FILaTtd~~K  161 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNH--AFNAMLKTLEEPPPHVKFILATTDPQK  161 (830)
T ss_pred             CCceEEEEeChhhCCHH--HHHHHHHHHHhcCCCeEEEEEECChhh
Confidence            36789999999999542  233344444   344567777665443

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

Probab=96.03  E-value=0.024  Score=38.90  Aligned_cols=47  Identities=13%  Similarity=0.103  Sum_probs=36.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-++|+|||..++.++......  ..+++++.......+..+.+..+
T Consensus         3 li~G~~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e~~~~~~~~~~~~~   49 (187)
T cd01124           3 LLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLEESPEELIENAESL   49 (187)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHC--CCcEEEEECCCCHHHHHHHHHHc
Confidence            567899999999998887765533  36889998887777777666655

A related protein is found in archaea.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.03  E-value=0.037  Score=42.29  Aligned_cols=24  Identities=13%  Similarity=0.180  Sum_probs=19.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .++..+.|+|||..+..++..+..
T Consensus        48 ~L~~G~~G~GKttlA~~lA~~Llc   71 (351)
T PRK09112         48 LLFEGPEGIGKATLAFHLANHILS   71 (351)
T ss_pred             EeeECCCCCCHHHHHHHHHHHHcC
Confidence            456889999999999888777665

>KOG0327|consensus

Probab=95.93  E-value=0.013  Score=44.47  Aligned_cols=137  Identities=16%  Similarity=0.172  Sum_probs=72.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH-hCCCCceEEEecCcchHH-HHHHHHHhCCCceEEE--EeC-CHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE-EQALEPNLIVCPLSVLNN-WEAEFRKFAPFVRTVK--YYG-NAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~-~~~~~~~Liv~P~~~l~q-W~~e~~~~~~~~~~~~--~~g-~~~~~~~~~~~~~~   77 (169)
                      .+..-+.|+|||.+-...+..... .....-+|+++|..-+.+ -..-...+.+..++.+  ..| ....+....-..  
T Consensus        66 v~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~--  143 (397)
T KOG0327|consen   66 VIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLK--  143 (397)
T ss_pred             eeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhc--
Confidence            344567899999873322222211 122236899999976654 3333333433333322  223 221111111110  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCc--ccHHHHHHhccc-cccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNK--KSKLSIKLTALR-ATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~--~~~~~~~~~~l~-~~~~~  152 (169)
                                        ....+ ++.|+..+..-.  ..+..-...++++||+..+...  ..+.+..+..++ ....+
T Consensus       144 ------------------~~~hi-vvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~vQv~  204 (397)
T KOG0327|consen  144 ------------------DKPHI-VVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDVQVV  204 (397)
T ss_pred             ------------------cCcee-ecCCchhHHHhhccccccccceeEEeecchHhhhccchHHHHHHHHHHcCcchhhe
Confidence                              22333 777764443221  2445556789999999975543  344555556664 45678


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||...
T Consensus       205 l~SAT~p~  212 (397)
T KOG0327|consen  205 LLSATMPS  212 (397)
T ss_pred             eecccCcH
Confidence            88999763

>PTZ00293 thymidine kinase; Provisional

Probab=95.92  E-value=0.085  Score=37.30  Aligned_cols=34  Identities=9%  Similarity=0.070  Sum_probs=24.3

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +--.|++|||.+.|-.+......  .++++++-|..
T Consensus         9 i~GpMfSGKTteLLr~i~~y~~a--g~kv~~~kp~~   42 (211)
T PTZ00293          9 IIGPMFSGKTTELMRLVKRFTYS--EKKCVVIKYSK   42 (211)
T ss_pred             EECCCCChHHHHHHHHHHHHHHc--CCceEEEEecc
Confidence            45689999998777766544433  36788888864

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.90  E-value=0.055  Score=43.46  Aligned_cols=23  Identities=4%  Similarity=-0.168  Sum_probs=18.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++....|+|||..+..+...+..
T Consensus        42 Lf~Gp~G~GKTt~A~~lAk~l~c   64 (509)
T PRK14958         42 LFTGTRGVGKTTISRILAKCLNC   64 (509)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcC
Confidence            57788999999888877766544

>KOG0925|consensus

Probab=95.87  E-value=0.011  Score=46.45  Aligned_cols=48  Identities=17%  Similarity=0.234  Sum_probs=27.8

Q ss_pred             ccccEEEEeCCcccCCcccHHHH-HHhcc----ccccEEEEeccCCCCCchhhc
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKLSI-KLTAL----RATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~~~-~~~~l----~~~~~~~lT~TP~~n~~~el~  167 (169)
                      -.|+++|+||||.=. -.+.... .++.+    .--+.++||+|.....+...|
T Consensus       158 ~~y~viiLDeahERt-lATDiLmGllk~v~~~rpdLk~vvmSatl~a~Kfq~yf  210 (699)
T KOG0925|consen  158 GRYGVIILDEAHERT-LATDILMGLLKEVVRNRPDLKLVVMSATLDAEKFQRYF  210 (699)
T ss_pred             ccccEEEechhhhhh-HHHHHHHHHHHHHHhhCCCceEEEeecccchHHHHHHh
Confidence            379999999999621 1122211 11221    233468899998766555544

>KOG0989|consensus

Probab=95.83  E-value=0.0074  Score=44.74  Aligned_cols=21  Identities=19%  Similarity=0.230  Sum_probs=16.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~   25 (169)
                      +-..+|+|||.++.++...+.
T Consensus        62 FyGPpGTGKTStalafar~L~   82 (346)
T KOG0989|consen   62 FYGPPGTGKTSTALAFARALN   82 (346)
T ss_pred             eeCCCCCcHhHHHHHHHHHhc
Confidence            345789999999999877654

>CHL00181 cbbX CbbX; Provisional

Probab=95.81  E-value=0.03  Score=41.60  Aligned_cols=25  Identities=4%  Similarity=-0.063  Sum_probs=18.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      .+|.-++|+|||..|-++...+...
T Consensus        62 ill~G~pGtGKT~lAr~la~~~~~~   86 (287)
T CHL00181         62 MSFTGSPGTGKTTVALKMADILYKL   86 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc
Confidence            3677899999998887776655443

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.78  E-value=0.28  Score=33.12  Aligned_cols=53  Identities=17%  Similarity=0.208  Sum_probs=34.2

Q ss_pred             ccccccccEEEEeCCcccCC----cccHHHHHHhccccccEEEEeccCCCCCchhhc
Q psy1090         115 FLKKITWNCIIVDEGHSVKN----KKSKLSIKLTALRATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       115 ~~~~~~~~~vi~DEah~~k~----~~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el~  167 (169)
                      .+..-++|++|+||.-..-+    +.......+..-+...-++|||--.+..+.|+.
T Consensus        90 ~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~A  146 (159)
T cd00561          90 AIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAA  146 (159)
T ss_pred             HHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhC
Confidence            33456899999999775422    223344555555566689999987766655543

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.73  E-value=0.063  Score=44.22  Aligned_cols=23  Identities=4%  Similarity=-0.126  Sum_probs=18.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      +|..+.|+|||..+..+...+..
T Consensus        42 LFtGP~GvGKTTLAriLAkaLnC   64 (700)
T PRK12323         42 LFTGTRGVGKTTLSRILAKSLNC   64 (700)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcC
Confidence            56789999999998888776654

>TIGR00416 sms DNA repair protein RadA

Probab=95.71  E-value=0.044  Score=43.36  Aligned_cols=47  Identities=15%  Similarity=0.159  Sum_probs=34.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-++|+|||..++.++......  .+++|.+.......|......++
T Consensus        98 lI~G~pGsGKTTL~lq~a~~~a~~--g~kvlYvs~EEs~~qi~~ra~rl  144 (454)
T TIGR00416        98 LIGGDPGIGKSTLLLQVACQLAKN--QMKVLYVSGEESLQQIKMRAIRL  144 (454)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEECcCCHHHHHHHHHHc
Confidence            577899999998888876655443  35788888877777766555544

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.65  E-value=0.075  Score=42.20  Aligned_cols=23  Identities=9%  Similarity=-0.002  Sum_probs=18.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..++..+..
T Consensus        44 Lf~GP~GtGKTTlAriLAk~Lnc   66 (484)
T PRK14956         44 IFFGPRGVGKTTIARILAKRLNC   66 (484)
T ss_pred             EEECCCCCCHHHHHHHHHHhcCc
Confidence            67889999999888887766543

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=95.64  E-value=0.037  Score=41.74  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=18.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .++..++|+|||..+-++...+.
T Consensus        39 lll~Gp~GtGKT~la~~~~~~l~   61 (337)
T PRK12402         39 LLVQGPPGSGKTAAVRALARELY   61 (337)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            36778999999999888876654

>PRK08084 DNA replication initiation factor; Provisional

Probab=95.61  E-value=0.077  Score=38.17  Aligned_cols=37  Identities=11%  Similarity=0.144  Sum_probs=21.2

Q ss_pred             ccEEEEeCCcccCCcccH---HHHHHhcc-cc-ccEEEEecc
Q psy1090         121 WNCIIVDEGHSVKNKKSK---LSIKLTAL-RA-TFKVLLTGW  157 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~---~~~~~~~l-~~-~~~~~lT~T  157 (169)
                      .+++++||.|.+......   ....+..+ .. +.++++|++
T Consensus        98 ~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~  139 (235)
T PRK08084         98 LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGD  139 (235)
T ss_pred             CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCC
Confidence            478999999998643211   11222222 22 346888887

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.61  E-value=0.073  Score=42.05  Aligned_cols=39  Identities=3%  Similarity=0.066  Sum_probs=22.8

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEeccC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGWY  158 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~TP  158 (169)
                      ..+++++||.|.+.+........+..+    .....+++|++-
T Consensus       202 ~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~  244 (445)
T PRK12422        202 NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTC  244 (445)
T ss_pred             cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCC
Confidence            467899999999865332222222221    234567787753

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.60  E-value=0.12  Score=40.87  Aligned_cols=16  Identities=13%  Similarity=0.297  Sum_probs=12.7

Q ss_pred             cccEEEEeCCcccCCc
Q psy1090         120 TWNCIIVDEGHSVKNK  135 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~  135 (169)
                      ..+++++||.|.+.+.
T Consensus       194 ~~dvLlIDDi~~l~~~  209 (440)
T PRK14088        194 KVDVLLIDDVQFLIGK  209 (440)
T ss_pred             cCCEEEEechhhhcCc
Confidence            4688999999987543

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=95.58  E-value=0.0073  Score=41.31  Aligned_cols=38  Identities=16%  Similarity=0.200  Sum_probs=24.7

Q ss_pred             CCCCeEEEecHHHHHhchh--cc--ccccccEEEEeCCcccCC
Q psy1090          96 LKLPLILVTTPQIIENDFG--FL--KKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~--~~--~~~~~~~vi~DEah~~k~  134 (169)
                      ...|+ ++.+|..+-....  .+  ...+-.++|+||||.+-+
T Consensus       118 ~~adi-vi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  118 KNADI-VICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             GG-SE-EEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGG
T ss_pred             ccCCE-EEeCHHHHhhHHHHhhhccccccCcEEEEecccchHH
Confidence            66777 9999998865322  11  223556899999999843

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>PRK08181 transposase; Validated

Probab=95.57  E-value=0.07  Score=39.27  Aligned_cols=24  Identities=25%  Similarity=0.130  Sum_probs=17.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+|..++|+|||..+.++......
T Consensus       109 lll~Gp~GtGKTHLa~Aia~~a~~  132 (269)
T PRK08181        109 LLLFGPPGGGKSHLAAAIGLALIE  132 (269)
T ss_pred             EEEEecCCCcHHHHHHHHHHHHHH
Confidence            467778899999887777665544

>KOG0923|consensus

Probab=95.56  E-value=0.023  Score=46.38  Aligned_cols=66  Identities=18%  Similarity=0.132  Sum_probs=35.5

Q ss_pred             EEecHHHHHhchh-ccccccccEEEEeCCcccCCcccHHHHHHhc---cccc-cEEEEeccCCCCCchhhc
Q psy1090         102 LVTTPQIIENDFG-FLKKITWNCIIVDEGHSVKNKKSKLSIKLTA---LRAT-FKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       102 ~i~ty~~~~~~~~-~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~---l~~~-~~~~lT~TP~~n~~~el~  167 (169)
                      =..|-.++.+..- ...--.+.++|+||||.=.-..-..+-.++.   ++.. ..++.|||.=...++++|
T Consensus       359 KYMTDGmLlREfL~epdLasYSViiiDEAHERTL~TDILfgLvKDIar~RpdLKllIsSAT~DAekFS~fF  429 (902)
T KOG0923|consen  359 KYMTDGMLLREFLSEPDLASYSVIIVDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAEKFSAFF  429 (902)
T ss_pred             eeecchhHHHHHhccccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcceEEeeccccCHHHHHHhc
Confidence            3355556655332 2222367899999999622122222333333   3333 346678997666666554

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

Probab=95.55  E-value=0.066  Score=39.00  Aligned_cols=39  Identities=15%  Similarity=0.215  Sum_probs=22.6

Q ss_pred             ccEEEEeCCcccCCcccHHHHHHhccc----cccEEEEeccCC
Q psy1090         121 WNCIIVDEGHSVKNKKSKLSIKLTALR----ATFKVLLTGWYY  159 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~~~~~~~~l~----~~~~~~lT~TP~  159 (169)
                      .-++|+||+|.+....-...+.+....    ....++++|+|-
T Consensus       124 ~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~  166 (269)
T TIGR03015       124 RALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE  166 (269)
T ss_pred             CeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH
Confidence            357999999998533222222333322    223568999884

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.

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

Probab=95.55  E-value=0.067  Score=39.79  Aligned_cols=45  Identities=20%  Similarity=0.215  Sum_probs=26.8

Q ss_pred             hccccccccEEEEeCCcccC-CcccHH---HHHHhccc--cccEEEEeccC
Q psy1090         114 GFLKKITWNCIIVDEGHSVK-NKKSKL---SIKLTALR--ATFKVLLTGWY  158 (169)
Q Consensus       114 ~~~~~~~~~~vi~DEah~~k-~~~~~~---~~~~~~l~--~~~~~~lT~TP  158 (169)
                      ..+...+..++|+||.|++- +...+.   ..+++.+.  -+--+++-||+
T Consensus       139 ~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~  189 (302)
T PF05621_consen  139 RLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTR  189 (302)
T ss_pred             HHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccH
Confidence            45566788999999999853 333332   23334442  23345666775

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

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.54  E-value=0.11  Score=39.10  Aligned_cols=30  Identities=7%  Similarity=0.006  Sum_probs=19.5

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      =.|+|||.+.--+..++..++  .++++.+--
T Consensus       147 VNG~GKTTTIaKLA~~l~~~g--~~VllaA~D  176 (340)
T COG0552         147 VNGVGKTTTIAKLAKYLKQQG--KSVLLAAGD  176 (340)
T ss_pred             cCCCchHhHHHHHHHHHHHCC--CeEEEEecc
Confidence            469999988777666655443  555555543

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=95.54  E-value=0.1  Score=36.27  Aligned_cols=34  Identities=18%  Similarity=0.100  Sum_probs=22.7

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ....|.+|||.+.|-.+......+  .++++..|..
T Consensus         9 i~gpM~SGKT~eLl~r~~~~~~~g--~~v~vfkp~i   42 (201)
T COG1435           9 IYGPMFSGKTEELLRRARRYKEAG--MKVLVFKPAI   42 (201)
T ss_pred             EEccCcCcchHHHHHHHHHHHHcC--CeEEEEeccc
Confidence            456899999987766554443333  5778877763

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=95.48  E-value=0.11  Score=42.36  Aligned_cols=119  Identities=15%  Similarity=0.112  Sum_probs=60.5

Q ss_pred             CcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHH----HHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccccc
Q psy1090          11 YRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNN----WEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPA   85 (169)
Q Consensus        11 ~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~q----W~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   85 (169)
                      -|||...+.+|+.++..-..=.+..++-. ++.+-    -...+++|+|.-++..-.+..        ..+..++     
T Consensus       213 HGKTWf~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~k~~t--------I~~s~pg-----  279 (668)
T PHA03372        213 HGKTWFIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIENKDNV--------ISIDHRG-----  279 (668)
T ss_pred             CCceehHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeeecCcE--------EEEecCC-----
Confidence            38998777777766653322356666653 44333    333456788755543221110        0000000     


Q ss_pred             ccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEecc
Q psy1090          86 KKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGW  157 (169)
Q Consensus        86 ~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~T  157 (169)
                                .+.-. ++.+    ..+.+.++...|+++++||||-++.+.-...--+...+....+.+|.|
T Consensus       280 ----------~Kst~-~fas----c~n~NsiRGQ~fnll~VDEA~FI~~~a~~tilgfm~q~~~KiIfISS~  336 (668)
T PHA03372        280 ----------AKSTA-LFAS----CYNTNSIRGQNFHLLLVDEAHFIKKDAFNTILGFLAQNTTKIIFISST  336 (668)
T ss_pred             ----------Cccee-eehh----hccCccccCCCCCEEEEehhhccCHHHHHHhhhhhcccCceEEEEeCC
Confidence                      11111 2222    022346667899999999999987433222222333355566666654

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.45  E-value=0.028  Score=43.66  Aligned_cols=33  Identities=9%  Similarity=-0.071  Sum_probs=22.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      ++-=.|+|||.++.-+..++.. . ..++++|+-.
T Consensus       105 mvGLQGsGKTTt~~KLA~~lkk-~-~~kvllVaaD  137 (451)
T COG0541         105 MVGLQGSGKTTTAGKLAKYLKK-K-GKKVLLVAAD  137 (451)
T ss_pred             EEeccCCChHhHHHHHHHHHHH-c-CCceEEEecc
Confidence            3444799999999888888776 3 3555555543

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

Probab=95.37  E-value=0.2  Score=35.62  Aligned_cols=36  Identities=17%  Similarity=0.244  Sum_probs=22.8

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHh-cc----ccccEEEEec
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLT-AL----RATFKVLLTG  156 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~-~l----~~~~~~~lT~  156 (169)
                      ..|++++|..|.+.+... +-..+. .+    .....+++|+
T Consensus        97 ~~DlL~iDDi~~l~~~~~-~q~~lf~l~n~~~~~~k~li~ts  137 (219)
T PF00308_consen   97 SADLLIIDDIQFLAGKQR-TQEELFHLFNRLIESGKQLILTS  137 (219)
T ss_dssp             TSSEEEEETGGGGTTHHH-HHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cCCEEEEecchhhcCchH-HHHHHHHHHHHHHhhCCeEEEEe
Confidence            678999999999986432 222222 22    3456777776

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

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.37  E-value=0.12  Score=42.78  Aligned_cols=22  Identities=5%  Similarity=-0.114  Sum_probs=17.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++....|+|||..|..++..+.
T Consensus        41 LF~GPpGvGKTTlAriLAK~Ln   62 (702)
T PRK14960         41 LFTGTRGVGKTTIARILAKCLN   62 (702)
T ss_pred             EEECCCCCCHHHHHHHHHHHhC
Confidence            6788999999988887766654

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

Probab=95.34  E-value=0.075  Score=40.10  Aligned_cols=57  Identities=21%  Similarity=0.274  Sum_probs=33.4

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHH-HHHHH----HHhCCCceEEEEeCCHH
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNN-WEAEF----RKFAPFVRTVKYYGNAI   66 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~q-W~~e~----~~~~~~~~~~~~~g~~~   66 (169)
                      -=|.|||.++.|+.....+.+  +++|+|.  |.+-+.+ ...|+    ++-.|++..........
T Consensus        10 KGGVGKTT~aaA~A~~lA~~g--~kvLlvStDPAhsL~d~f~~elg~~~~~I~~nL~a~eiD~~~~   73 (322)
T COG0003          10 KGGVGKTTIAAATAVKLAESG--KKVLLVSTDPAHSLGDVFDLELGHDPRKVGPNLDALELDPEKA   73 (322)
T ss_pred             CCcccHHHHHHHHHHHHHHcC--CcEEEEEeCCCCchHhhhccccCCchhhcCCCCceeeecHHHH
Confidence            458999999999877776666  3366653  5565543 22222    23335566555554433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.30  E-value=0.11  Score=41.81  Aligned_cols=24  Identities=4%  Similarity=-0.130  Sum_probs=19.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+|..+.|+|||..+-.++..+..
T Consensus        46 ~Lf~Gp~G~GKTT~ArilAk~Lnc   69 (507)
T PRK06645         46 YLLTGIRGVGKTTSARIIAKAVNC   69 (507)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcC
Confidence            467889999999998888766544

>KOG0952|consensus

Probab=95.27  E-value=0.03  Score=47.86  Aligned_cols=107  Identities=14%  Similarity=0.185  Sum_probs=68.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchH----HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLN----NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~----qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ..+.+.+|.|||+.+-..+-......+.+++++++|. .++.    .|...+.  .|+.+++..+|.......-      
T Consensus       946 ~~~g~ptgsgkt~~ae~a~~~~~~~~p~~kvvyIap~kalvker~~Dw~~r~~--~~g~k~ie~tgd~~pd~~~------ 1017 (1230)
T KOG0952|consen  946 FLLGAPTGSGKTVVAELAIFRALSYYPGSKVVYIAPDKALVKERSDDWSKRDE--LPGIKVIELTGDVTPDVKA------ 1017 (1230)
T ss_pred             hhhcCCccCcchhHHHHHHHHHhccCCCccEEEEcCCchhhcccccchhhhcc--cCCceeEeccCccCCChhh------
Confidence            4678899999998876665555566667899999996 4443    4543332  3567777777654432110      


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhcc-c-c--ccccEEEEeCCcccCCc
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL-K-K--ITWNCIIVDEGHSVKNK  135 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~-~-~--~~~~~vi~DEah~~k~~  135 (169)
                                       ....++ +++|++........- . +  .....+++||.|.++.+
T Consensus      1018 -----------------v~~~~~-~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~ 1061 (1230)
T KOG0952|consen 1018 -----------------VREADI-VITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED 1061 (1230)
T ss_pred             -----------------eecCce-EEcccccccCccccccchhhhccccceeecccccccCC
Confidence                             144455 899988764432210 0 1  14557999999998764

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.23  E-value=0.13  Score=43.35  Aligned_cols=39  Identities=10%  Similarity=-0.216  Sum_probs=26.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      .+|....|+|||...-+++..+...  ..++++++|.....
T Consensus       371 ~il~G~aGTGKTtll~~i~~~~~~~--g~~V~~~ApTg~Aa  409 (744)
T TIGR02768       371 AVVVGRAGTGKSTMLKAAREAWEAA--GYRVIGAALSGKAA  409 (744)
T ss_pred             EEEEecCCCCHHHHHHHHHHHHHhC--CCeEEEEeCcHHHH
Confidence            3677789999997766655443332  35788888987554

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.

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

Probab=95.22  E-value=0.19  Score=36.06  Aligned_cols=44  Identities=11%  Similarity=0.218  Sum_probs=31.8

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHHHHHHH
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWEAEFRK   51 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~~e~~~   51 (169)
                      ..-=|.|||..+++++..+..++  +++.++=  |+.-+..|.+...+
T Consensus         8 s~KGGaGKTT~~~~LAs~la~~G--~~V~lIDaDpn~pl~~W~~~a~~   53 (231)
T PF07015_consen    8 SSKGGAGKTTAAMALASELAARG--ARVALIDADPNQPLAKWAENAQR   53 (231)
T ss_pred             cCCCCCcHHHHHHHHHHHHHHCC--CeEEEEeCCCCCcHHHHHHhccc
Confidence            34459999999999888876655  4555554  67778899776544

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

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.21  E-value=0.077  Score=36.89  Aligned_cols=54  Identities=17%  Similarity=0.188  Sum_probs=34.9

Q ss_pred             hccccccccEEEEeCCcccCCc----ccHHHHHHhccccccEEEEeccCCCCCchhhc
Q psy1090         114 GFLKKITWNCIIVDEGHSVKNK----KSKLSIKLTALRATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       114 ~~~~~~~~~~vi~DEah~~k~~----~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el~  167 (169)
                      ..+..-+||++|+||.-..-+.    .......+..-+...-++|||--.+..+.|+.
T Consensus       109 ~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~A  166 (191)
T PRK05986        109 RMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAA  166 (191)
T ss_pred             HHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhC
Confidence            3444668999999997754332    23344555554556689999987666555543

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.20  E-value=0.12  Score=41.04  Aligned_cols=45  Identities=7%  Similarity=-0.034  Sum_probs=30.7

Q ss_pred             CCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhC
Q psy1090           9 TRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFA   53 (169)
Q Consensus         9 ~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~   53 (169)
                      -|+|||.....=+..+...++..+++|-+-.-++ ++..+-+.+|+
T Consensus       185 AGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         185 AGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             cCCCchhHHHHHHHHHhcCCCCceEEEEeehHHHHHHHHHHHHHHH
Confidence            4899997655555666667888899999976544 45555455543

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.19  E-value=0.11  Score=40.36  Aligned_cols=97  Identities=11%  Similarity=0.088  Sum_probs=53.4

Q ss_pred             CCceEEEecC-----cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEe
Q psy1090          30 LEPNLIVCPL-----SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVT  104 (169)
Q Consensus        30 ~~~~Liv~P~-----~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~  104 (169)
                      ..|.+|..|.     |+++-|..++....|+.+++..+....-........                           --
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~---------------------------~~  165 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALR---------------------------DN  165 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHH---------------------------hh
Confidence            3466666664     366778888888877777766554433222211110                           00


Q ss_pred             cHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEec--cCC
Q psy1090         105 TPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTG--WYY  159 (169)
Q Consensus       105 ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~--TP~  159 (169)
                      +.+.+.+   .   ...|++++|..|.+.+....--..+.-+    .....+++|+  +|-
T Consensus       166 ~~~~Fk~---~---y~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~  220 (408)
T COG0593         166 EMEKFKE---K---YSLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPK  220 (408)
T ss_pred             hHHHHHH---h---hccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCch
Confidence            1112222   1   1568899999999877543333334433    3444788888  554

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.14  E-value=0.42  Score=36.90  Aligned_cols=36  Identities=8%  Similarity=0.063  Sum_probs=23.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      +|...+|+|||.++..++..........++.++...
T Consensus       141 ~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D  176 (374)
T PRK14722        141 ALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTD  176 (374)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecc
Confidence            467789999999988887765433222345555543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.11  E-value=0.1  Score=39.86  Aligned_cols=24  Identities=17%  Similarity=0.032  Sum_probs=18.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .++.-++|+|||..+-.++..+.+
T Consensus        43 i~I~G~~GtGKT~l~~~~~~~l~~   66 (365)
T TIGR02928        43 VFIYGKTGTGKTAVTKYVMKELEE   66 (365)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            567788999999888777765543

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

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.01  E-value=0.24  Score=39.63  Aligned_cols=23  Identities=4%  Similarity=-0.104  Sum_probs=17.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      -++....|+|||..+..+...+.
T Consensus        38 ~Lf~Gp~G~GKTT~ArilAk~Ln   60 (491)
T PRK14964         38 ILLVGASGVGKTTCARIISLCLN   60 (491)
T ss_pred             EEEECCCCccHHHHHHHHHHHHc
Confidence            35778899999988877765544

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=94.99  E-value=0.18  Score=42.45  Aligned_cols=58  Identities=10%  Similarity=-0.042  Sum_probs=36.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cch---HHHHHHHHHhCCCceEEEEe
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVL---NNWEAEFRKFAPFVRTVKYY   62 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l---~qW~~e~~~~~~~~~~~~~~   62 (169)
                      |.|.-+-+|=|||+++..-..  ...=..+.+.+|..+ .+.   ..|...+-+|. ++.+.+..
T Consensus        95 g~iaEM~TGEGKTL~atlp~y--lnaL~gkgVhvVTvNdYLA~RDae~m~~l~~~L-GlsvG~~~  156 (822)
T COG0653          95 GDIAEMRTGEGKTLVATLPAY--LNALAGKGVHVVTVNDYLARRDAEWMGPLYEFL-GLSVGVIL  156 (822)
T ss_pred             CceeeeecCCchHHHHHHHHH--HHhcCCCCcEEeeehHHhhhhCHHHHHHHHHHc-CCceeecc
Confidence            567778899999988754322  222122456666665 444   37999999998 55555533

>KOG0780|consensus

Probab=94.92  E-value=0.048  Score=41.91  Aligned_cols=32  Identities=6%  Similarity=-0.029  Sum_probs=20.3

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      -=.|.|||.+.-.++.++..++ .++.||++-.
T Consensus       108 GLqG~GKTTtc~KlA~y~kkkG-~K~~LvcaDT  139 (483)
T KOG0780|consen  108 GLQGSGKTTTCTKLAYYYKKKG-YKVALVCADT  139 (483)
T ss_pred             eccCCCcceeHHHHHHHHHhcC-CceeEEeecc
Confidence            3469999988777776665444 4445555443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=94.90  E-value=0.34  Score=41.61  Aligned_cols=22  Identities=14%  Similarity=0.060  Sum_probs=17.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++...+|+|||.++-.++..+.
T Consensus       785 YIyG~PGTGKTATVK~VLrELq  806 (1164)
T PTZ00112        785 YISGMPGTGKTATVYSVIQLLQ  806 (1164)
T ss_pred             EEECCCCCCHHHHHHHHHHHHH
Confidence            3788999999999887766554

>PRK05642 DNA replication initiation factor; Validated

Probab=94.90  E-value=0.21  Score=35.91  Aligned_cols=39  Identities=10%  Similarity=0.124  Sum_probs=22.7

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEeccC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGWY  158 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~TP  158 (169)
                      +.+++|+|+.|.+.+........+.-+    ....++++|++-
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~  139 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASK  139 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCC
Confidence            347899999998764322112222222    245678888874

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.88  E-value=0.37  Score=37.05  Aligned_cols=22  Identities=5%  Similarity=-0.044  Sum_probs=17.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++..+.|+|||..+-+++..+.
T Consensus        42 L~~Gp~G~GKTtla~~la~~l~   63 (363)
T PRK14961         42 LLSGTRGVGKTTIARLLAKSLN   63 (363)
T ss_pred             EEecCCCCCHHHHHHHHHHHhc
Confidence            6788999999988888776554

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.88  E-value=0.11  Score=44.39  Aligned_cols=23  Identities=9%  Similarity=-0.039  Sum_probs=18.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+-.++..+..
T Consensus        42 LFtGPpGtGKTTLARiLAk~Lnc   64 (944)
T PRK14949         42 LFTGTRGVGKTSLARLFAKGLNC   64 (944)
T ss_pred             EEECCCCCCHHHHHHHHHHhccC
Confidence            57889999999988888766543

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

Probab=94.86  E-value=0.76  Score=31.13  Aligned_cols=32  Identities=9%  Similarity=0.079  Sum_probs=21.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      ++..++|+|||..+..++..+...+  .+++++.
T Consensus         4 ~~~G~~G~GKTt~~~~la~~~~~~g--~~v~~i~   35 (173)
T cd03115           4 LLVGLQGVGKTTTAAKLALYLKKKG--KKVLLVA   35 (173)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEE
Confidence            4567899999999888876655442  3444443

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

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=94.84  E-value=0.063  Score=38.92  Aligned_cols=38  Identities=24%  Similarity=0.308  Sum_probs=23.4

Q ss_pred             cEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEeccCC
Q psy1090         122 NCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGWYY  159 (169)
Q Consensus       122 ~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~TP~  159 (169)
                      -.+++||+|.+..+.-...+.+.++    ....++++-|-|-
T Consensus       133 v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~  174 (269)
T COG3267         133 VVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPK  174 (269)
T ss_pred             eEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcc
Confidence            5689999999875544444444443    2234566666664

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=94.81  E-value=0.081  Score=43.70  Aligned_cols=44  Identities=9%  Similarity=0.043  Sum_probs=25.8

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHh
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKF   52 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~   52 (169)
                      +=|-|||..+..++..+.... ...+++.+|. +..++-.+++++.
T Consensus       195 PRqrGKS~iVgi~l~~La~f~-Gi~IlvTAH~~~ts~evF~rv~~~  239 (752)
T PHA03333        195 PRRCGKTTIMAIILAAMISFL-EIDIVVQAQRKTMCLTLYNRVETV  239 (752)
T ss_pred             ccCCCcHHHHHHHHHHHHHhc-CCeEEEECCChhhHHHHHHHHHHH
Confidence            458899977665554444322 3578888896 4444444444433

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=94.81  E-value=0.21  Score=38.87  Aligned_cols=24  Identities=17%  Similarity=0.151  Sum_probs=18.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      ++..+.|+|||..+.++...+...
T Consensus        40 Lf~Gp~G~GKt~lA~~lA~~l~c~   63 (394)
T PRK07940         40 LFTGPPGSGRSVAARAFAAALQCT   63 (394)
T ss_pred             EEECCCCCcHHHHHHHHHHHhCCC
Confidence            467889999999888887665543

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

Probab=94.65  E-value=0.091  Score=37.38  Aligned_cols=48  Identities=17%  Similarity=0.219  Sum_probs=35.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++.-++|+|||.-++.++.....+ +  .++++|.-.....+..+++..+.
T Consensus        23 li~G~~GsGKT~l~~q~l~~~~~~~g--e~vlyvs~ee~~~~l~~~~~s~g   71 (226)
T PF06745_consen   23 LISGPPGSGKTTLALQFLYNGLKNFG--EKVLYVSFEEPPEELIENMKSFG   71 (226)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHHHT----EEEEESSS-HHHHHHHHHTTT
T ss_pred             EEEeCCCCCcHHHHHHHHHHhhhhcC--CcEEEEEecCCHHHHHHHHHHcC
Confidence            466799999999999888766555 4  57888887777777777777654

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.64  E-value=0.45  Score=39.02  Aligned_cols=23  Identities=9%  Similarity=0.073  Sum_probs=18.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++....|+|||..+..++..+..
T Consensus        39 Lf~Gp~G~GKTt~A~~lAk~l~c   61 (584)
T PRK14952         39 LFSGPRGCGKTSSARILARSLNC   61 (584)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcc
Confidence            57789999999999888776654

>PRK06893 DNA replication initiation factor; Validated

Probab=94.60  E-value=0.29  Score=35.04  Aligned_cols=15  Identities=13%  Similarity=0.197  Sum_probs=12.1

Q ss_pred             cccEEEEeCCcccCC
Q psy1090         120 TWNCIIVDEGHSVKN  134 (169)
Q Consensus       120 ~~~~vi~DEah~~k~  134 (169)
                      +.+++++||.|.+.+
T Consensus        91 ~~dlLilDDi~~~~~  105 (229)
T PRK06893         91 QQDLVCLDDLQAVIG  105 (229)
T ss_pred             cCCEEEEeChhhhcC
Confidence            457899999998754

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=94.57  E-value=0.35  Score=40.06  Aligned_cols=24  Identities=8%  Similarity=-0.074  Sum_probs=19.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      ++..+.|+|||..+..+...+...
T Consensus        42 Lf~Gp~GvGKTTlAr~lAk~L~c~   65 (647)
T PRK07994         42 LFSGTRGVGKTTIARLLAKGLNCE   65 (647)
T ss_pred             EEECCCCCCHHHHHHHHHHhhhhc
Confidence            577899999999988887766543

>KOG0950|consensus

Probab=94.54  E-value=0.19  Score=42.70  Aligned_cols=135  Identities=13%  Similarity=0.104  Sum_probs=72.6

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++|.+-.++.|||+.+=-+ +......  .+.++.+.|-- ++..=..++..|..  ++.+--|.|....          
T Consensus       242 nliys~Pts~gktlvaeilml~~~l~~--rr~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g~~~p----------  309 (1008)
T KOG0950|consen  242 NLIYSLPTSAGKTLVAEILMLREVLCR--RRNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAGRFPP----------  309 (1008)
T ss_pred             ceEEeCCCccchHHHHHHHHHHHHHHH--hhceeEecceeehhHHHHhhhhhhccccCCcchhhcccCCC----------
Confidence            4678889999999754222 2222222  24688888864 33333344444432  3333334432111          


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhcccc----ccccEEEEeCCcccCCcccH-HHHH-Hhcc---c-
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKK----ITWNCIIVDEGHSVKNKKSK-LSIK-LTAL---R-  147 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~----~~~~~vi~DEah~~k~~~~~-~~~~-~~~l---~-  147 (169)
                                    .....+..+ .++|-+......+.+..    ...++||+||-|.+....-- .... +..+   . 
T Consensus       310 --------------~~~~k~~sv-~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y~~~  374 (1008)
T KOG0950|consen  310 --------------EKRRKRESV-AIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLAKILYENL  374 (1008)
T ss_pred             --------------CCcccceee-eeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHHHHHHhcc
Confidence                          011144445 88887777665554332    35689999999988643211 1111 1111   1 


Q ss_pred             --cccEEEEeccCCCCCc
Q psy1090         148 --ATFKVLLTGWYYPNKW  163 (169)
Q Consensus       148 --~~~~~~lT~TP~~n~~  163 (169)
                        .-..++||||...|+.
T Consensus       375 ~~~~~iIGMSATi~N~~l  392 (1008)
T KOG0950|consen  375 ETSVQIIGMSATIPNNSL  392 (1008)
T ss_pred             ccceeEeeeecccCChHH
Confidence              1236999999887754

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.50  E-value=1.8  Score=34.04  Aligned_cols=52  Identities=13%  Similarity=0.098  Sum_probs=29.8

Q ss_pred             HHHHHhchhccccccccEEE---EeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090         106 PQIIENDFGFLKKITWNCII---VDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       106 y~~~~~~~~~~~~~~~~~vi---~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      ++.+......+...+.+-+|   +||+.++.    .....+...+.+-.++-+|.-+++
T Consensus       313 ~~~~~~~~~~f~~~~~~~~I~TKlDEt~~~G----~~l~~~~~~~lPi~yvt~Gq~VP~  367 (420)
T PRK14721        313 GDTLDEVISAYQGHGIHGCIITKVDEAASLG----IALDAVIRRKLVLHYVTNGQKVPE  367 (420)
T ss_pred             HHHHHHHHHHhcCCCCCEEEEEeeeCCCCcc----HHHHHHHHhCCCEEEEECCCCchh
Confidence            44455555666667777666   79987653    234444444555555555544433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=94.40  E-value=0.32  Score=36.45  Aligned_cols=40  Identities=18%  Similarity=0.128  Sum_probs=23.2

Q ss_pred             cccEEEEeCCcccCCcccH--HHHHHhccccccEEEEeccCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSK--LSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~--~~~~~~~l~~~~~~~lT~TP~  159 (169)
                      +.+++|+||+|.+......  ....+.......++++|++..
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~  141 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNK  141 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCCh
Confidence            4578999999988332211  111123334566788877654

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

Probab=94.36  E-value=0.044  Score=37.70  Aligned_cols=38  Identities=13%  Similarity=0.176  Sum_probs=25.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV   41 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~   41 (169)
                      |.+|..++|+|||..+.+++......+  .+++++--..+
T Consensus        49 ~l~l~G~~G~GKThLa~ai~~~~~~~g--~~v~f~~~~~L   86 (178)
T PF01695_consen   49 NLILYGPPGTGKTHLAVAIANEAIRKG--YSVLFITASDL   86 (178)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT----EEEEEHHHH
T ss_pred             EEEEEhhHhHHHHHHHHHHHHHhccCC--cceeEeecCce
Confidence            456777899999999999887766633  45666544333

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=94.33  E-value=0.13  Score=38.90  Aligned_cols=25  Identities=12%  Similarity=0.177  Sum_probs=20.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|+|||..+..++..+...+
T Consensus        26 Lf~G~~G~GK~~~A~~~A~~llC~~   50 (328)
T PRK05707         26 LLHGPAGIGKRALAERLAAALLCEA   50 (328)
T ss_pred             eeECCCCCCHHHHHHHHHHHHcCCC
Confidence            4678899999999999988777543

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.24  E-value=0.7  Score=37.43  Aligned_cols=33  Identities=15%  Similarity=0.182  Sum_probs=21.5

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      |....|.|||.++..++..+...+..+++.++.
T Consensus       355 LVGPtGvGKTTtaakLAa~la~~~~gkkVaLId  387 (559)
T PRK12727        355 LVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVT  387 (559)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHhcCCCceEEEe
Confidence            446789999988877766554443334555554

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.21  E-value=1  Score=33.22  Aligned_cols=44  Identities=7%  Similarity=0.038  Sum_probs=24.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC----cchHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL----SVLNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~----~~l~qW~~e~   49 (169)
                      .+....|+|||.....+...+...  ..++.++...    ..+.||....
T Consensus        79 ~~~G~~g~GKTtl~~~l~~~l~~~--~~~v~~i~~D~~ri~~~~ql~~~~  126 (270)
T PRK06731         79 ALIGPTGVGKTTTLAKMAWQFHGK--KKTVGFITTDHSRIGTVQQLQDYV  126 (270)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHc--CCeEEEEecCCCCHHHHHHHHHHh
Confidence            355679999997766555443322  2445555542    2455665433

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.20  E-value=0.32  Score=37.87  Aligned_cols=23  Identities=9%  Similarity=-0.015  Sum_probs=18.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..+...+..
T Consensus        42 lf~Gp~G~GKtt~A~~~a~~l~c   64 (397)
T PRK14955         42 IFSGLRGVGKTTAARVFAKAVNC   64 (397)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcC
Confidence            46779999999999888776654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.18  E-value=0.54  Score=40.13  Aligned_cols=23  Identities=9%  Similarity=0.073  Sum_probs=18.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      +|.-..|+|||..+..+...+..
T Consensus        41 Lf~Gp~G~GKTt~A~~lAr~L~C   63 (824)
T PRK07764         41 LFSGPRGCGKTSSARILARSLNC   63 (824)
T ss_pred             EEECCCCCCHHHHHHHHHHHhCc
Confidence            57788999999998888776654

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.11  E-value=0.36  Score=39.81  Aligned_cols=23  Identities=4%  Similarity=-0.120  Sum_probs=18.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++....|+|||..+..+...+..
T Consensus        42 Lf~Gp~GvGKTtlAr~lAk~LnC   64 (618)
T PRK14951         42 LFTGTRGVGKTTVSRILAKSLNC   64 (618)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcC
Confidence            56778999999988888766654

>KOG0991|consensus

Probab=94.11  E-value=0.14  Score=36.95  Aligned_cols=17  Identities=29%  Similarity=0.319  Sum_probs=13.3

Q ss_pred             cccccEEEEeCCcccCC
Q psy1090         118 KITWNCIIVDEGHSVKN  134 (169)
Q Consensus       118 ~~~~~~vi~DEah~~k~  134 (169)
                      .-.+..+|+|||..+..
T Consensus       111 ~grhKIiILDEADSMT~  127 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTA  127 (333)
T ss_pred             CCceeEEEeeccchhhh
Confidence            34677899999998754

>PHA00012 I assembly protein

Probab=94.02  E-value=0.25  Score=37.32  Aligned_cols=24  Identities=4%  Similarity=-0.067  Sum_probs=17.9

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      +.--+|+|||..+++-|.....++
T Consensus         6 ITGkPGSGKSl~aV~~I~~~L~~G   29 (361)
T PHA00012          6 VTGKLGAGKTLVAVSRIQDKLVKG   29 (361)
T ss_pred             EecCCCCCchHHHHHHHHHHHHcC
Confidence            445689999999998766655555

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=94.01  E-value=0.095  Score=39.56  Aligned_cols=44  Identities=18%  Similarity=0.227  Sum_probs=31.8

Q ss_pred             ccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCch
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWS  164 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~~  164 (169)
                      ++--+||+||||. . .-.+--+.+.++-...+..+||.+.|=++.
T Consensus       242 L~dAfVIlDEaQN-t-T~~QmKMfLTRiGf~skmvItGD~tQiDLp  285 (348)
T COG1702         242 LNDAFVILDEAQN-T-TVGQMKMFLTRIGFESKMVITGDITQIDLP  285 (348)
T ss_pred             CCCeEEEEecccc-c-chhhhceeeeeecCCceEEEEcCcccccCC
Confidence            4556899999998 2 233444556677888899999999876553

>PRK05973 replicative DNA helicase; Provisional

Probab=94.00  E-value=0.18  Score=36.36  Aligned_cols=47  Identities=4%  Similarity=-0.014  Sum_probs=33.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      +++-.+|+|||.-++.++.....+  ..+++++.-...-.+-.+.+..+
T Consensus        68 LIaG~PG~GKT~lalqfa~~~a~~--Ge~vlyfSlEes~~~i~~R~~s~  114 (237)
T PRK05973         68 LLGARPGHGKTLLGLELAVEAMKS--GRTGVFFTLEYTEQDVRDRLRAL  114 (237)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEEEeCCHHHHHHHHHHc
Confidence            678899999999998887765543  36788888766555555555444

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

Probab=94.00  E-value=0.08  Score=37.85  Aligned_cols=50  Identities=10%  Similarity=0.185  Sum_probs=36.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      +.++..-||-|||...+=+++....++ ..=+-+++|+.++.|-.+.++.-
T Consensus        43 n~v~QlnMGeGKTsVI~Pmla~~LAdg-~~LvrviVpk~Ll~q~~~~L~~~   92 (229)
T PF12340_consen   43 NSVMQLNMGEGKTSVIVPMLALALADG-SRLVRVIVPKALLEQMRQMLRSR   92 (229)
T ss_pred             CeEeeecccCCccchHHHHHHHHHcCC-CcEEEEEcCHHHHHHHHHHHHHH
Confidence            467788899999977766665555443 34577888999999888777644

There are two conserved sequence motifs: LLE and NMG.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=93.97  E-value=0.029  Score=45.56  Aligned_cols=132  Identities=11%  Similarity=0.090  Sum_probs=70.5

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHH-HHHHhC---CCceEEEEeC-CHHHHHHHHHhhhcCC
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEA-EFRKFA---PFVRTVKYYG-NAIERKALQSEALSLP   79 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~-e~~~~~---~~~~~~~~~g-~~~~~~~~~~~~~~~~   79 (169)
                      .-..-+|||..++.++.+.... ...|+|++.|. .....|.. .|...+   |.++-.+... .++..+.+....+   
T Consensus        39 ~k~aQ~GkT~~~~n~~g~~i~~-~P~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l~~~~~~~~~~~~~~t~~~k~f---  114 (557)
T PF05876_consen   39 MKSAQVGKTELLLNWIGYSIDQ-DPGPMLYVQPTDDAAKDFSKERLDPMIRASPVLRRKLSPSKSRDSGNTILYKRF---  114 (557)
T ss_pred             EEcchhhHhHHHHhhceEEEEe-CCCCEEEEEEcHHHHHHHHHHHHHHHHHhCHHHHHHhCchhhcccCCchhheec---
Confidence            3456689999887777765544 35899999998 45566763 344333   2222111110 0000000000000   


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccC----CcccHHHHH---HhccccccEE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVK----NKKSKLSIK---LTALRATFKV  152 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k----~~~~~~~~~---~~~l~~~~~~  152 (169)
                                      ....+ .+....+    ...+.....+++++||....-    +...-...+   ...+....++
T Consensus       115 ----------------~gg~l-~~~ga~S----~~~l~s~~~r~~~~DEvD~~p~~~~~eGdp~~la~~R~~tf~~~~K~  173 (557)
T PF05876_consen  115 ----------------PGGFL-YLVGANS----PSNLRSRPARYLLLDEVDRYPDDVGGEGDPVELAEKRTKTFGSNRKI  173 (557)
T ss_pred             ----------------CCCEE-EEEeCCC----CcccccCCcCEEEEechhhccccCccCCCHHHHHHHHHhhhccCcEE
Confidence                            11222 3333222    234556788999999999773    222222222   2334567899


Q ss_pred             EEeccCCCCC
Q psy1090         153 LLTGWYYPNK  162 (169)
Q Consensus       153 ~lT~TP~~n~  162 (169)
                      ++..||...+
T Consensus       174 ~~~STPt~~~  183 (557)
T PF05876_consen  174 LRISTPTIEG  183 (557)
T ss_pred             EEeCCCCCCC
Confidence            9999999764

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.97  E-value=0.52  Score=38.19  Aligned_cols=23  Identities=4%  Similarity=-0.110  Sum_probs=18.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+-.++..+..
T Consensus        42 Lf~Gp~G~GKTt~A~~lAk~l~c   64 (527)
T PRK14969         42 LFTGTRGVGKTTLARILAKSLNC   64 (527)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcC
Confidence            57789999999888877766543

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.96  E-value=0.25  Score=39.56  Aligned_cols=48  Identities=10%  Similarity=0.004  Sum_probs=36.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++.-++|+|||..++.++.....+  ..+++++.-.....|-......+.
T Consensus       267 li~G~~G~GKt~l~~~f~~~~~~~--ge~~~y~s~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       267 LATGATGTGKTLLVSKFLENACAN--KERAILFAYEESRAQLLRNAYSWG  314 (484)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEEeeCCHHHHHHHHHHcC
Confidence            577899999999988887765543  368899888888887777766553

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=93.94  E-value=0.17  Score=43.27  Aligned_cols=23  Identities=13%  Similarity=0.219  Sum_probs=17.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      +.+|.-|+|+|||..+=+++..+
T Consensus       210 n~lLvG~pGvGKTal~~~La~~i  232 (852)
T TIGR03345       210 NPILTGEAGVGKTAVVEGLALRI  232 (852)
T ss_pred             ceeEECCCCCCHHHHHHHHHHHH
Confidence            46788999999997776655544

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK04195 replication factor C large subunit; Provisional

Probab=93.93  E-value=0.17  Score=40.41  Aligned_cols=15  Identities=20%  Similarity=0.357  Sum_probs=12.4

Q ss_pred             cccEEEEeCCcccCC
Q psy1090         120 TWNCIIVDEGHSVKN  134 (169)
Q Consensus       120 ~~~~vi~DEah~~k~  134 (169)
                      +..+||+||+|.+..
T Consensus        98 ~~kvIiIDEaD~L~~  112 (482)
T PRK04195         98 RRKLILLDEVDGIHG  112 (482)
T ss_pred             CCeEEEEecCccccc
Confidence            467899999999864

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.90  E-value=0.49  Score=37.13  Aligned_cols=33  Identities=12%  Similarity=0.059  Sum_probs=21.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      ++.-..|+|||.++..++....... ..++.++.
T Consensus       227 ~lvGptGvGKTTtaaKLA~~~~~~~-G~~V~Lit  259 (432)
T PRK12724        227 FFVGPTGSGKTTSIAKLAAKYFLHM-GKSVSLYT  259 (432)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHhc-CCeEEEec
Confidence            3567899999999888876543222 23444444

>PRK10867 signal recognition particle protein; Provisional

Probab=93.78  E-value=0.38  Score=37.94  Aligned_cols=34  Identities=9%  Similarity=0.017  Sum_probs=23.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      ++.-.+|+|||.++..++.++.... ..++++|+-
T Consensus       104 ~~vG~~GsGKTTtaakLA~~l~~~~-G~kV~lV~~  137 (433)
T PRK10867        104 MMVGLQGAGKTTTAGKLAKYLKKKK-KKKVLLVAA  137 (433)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHhc-CCcEEEEEc
Confidence            4567899999999988887766552 245555553

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=93.77  E-value=0.23  Score=37.62  Aligned_cols=23  Identities=4%  Similarity=0.001  Sum_probs=16.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|.|||..+..++..+..
T Consensus        32 Lf~G~~G~gk~~~a~~la~~l~c   54 (329)
T PRK08058         32 LFEGAKGTGKKATALWLAKSLFC   54 (329)
T ss_pred             EEECCCCCCHHHHHHHHHHHHCC
Confidence            46677888888777777666554

>PHA02533 17 large terminase protein; Provisional

Probab=93.75  E-value=0.18  Score=40.79  Aligned_cols=43  Identities=14%  Similarity=0.209  Sum_probs=26.8

Q ss_pred             cccccccEEEEeCCcccCCcccHHHHHHhc-cc--cccEEEEeccCC
Q psy1090         116 LKKITWNCIIVDEGHSVKNKKSKLSIKLTA-LR--ATFKVLLTGWYY  159 (169)
Q Consensus       116 ~~~~~~~~vi~DEah~~k~~~~~~~~~~~~-l~--~~~~~~lT~TP~  159 (169)
                      .+....+++++||+|..++.. +...++.. +.  ...++.+..||.
T Consensus       165 ~rG~~~~~liiDE~a~~~~~~-e~~~ai~p~lasg~~~r~iiiSTp~  210 (534)
T PHA02533        165 VRGNSFAMIYIDECAFIPNFI-DFWLAIQPVISSGRSSKIIITSTPN  210 (534)
T ss_pred             cCCCCCceEEEeccccCCCHH-HHHHHHHHHHHcCCCceEEEEECCC
Confidence            445677899999999887532 33333322 22  224678888884

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=93.73  E-value=0.12  Score=40.16  Aligned_cols=38  Identities=11%  Similarity=0.084  Sum_probs=25.8

Q ss_pred             ccEEEEeCCcccCCcccHHHHHHhccc---cccEEEEeccCCC
Q psy1090         121 WNCIIVDEGHSVKNKKSKLSIKLTALR---ATFKVLLTGWYYP  160 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~~~~~~~~l~---~~~~~~lT~TP~~  160 (169)
                      ++++.+|||..+..  ....+....++   .+.++++|.||-.
T Consensus       102 ~~~~~idEa~~~~~--~~~~~l~~rlr~~~~~~~i~~t~NP~~  142 (396)
T TIGR01547       102 IAIIWFEEASQLTF--EDIKELIPRLRETGGKKFIIFSSNPES  142 (396)
T ss_pred             eeeehhhhhhhcCH--HHHHHHHHHhhccCCccEEEEEcCcCC
Confidence            58999999998842  34444444454   2235999999964

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=93.72  E-value=0.64  Score=36.72  Aligned_cols=33  Identities=6%  Similarity=-0.080  Sum_probs=22.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      ++...+|+|||.++..++..+...+  .++++|..
T Consensus        99 ~lvG~~GsGKTTtaakLA~~L~~~g--~kV~lV~~  131 (437)
T PRK00771         99 MLVGLQGSGKTTTAAKLARYFKKKG--LKVGLVAA  131 (437)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHcC--CeEEEecC
Confidence            4567899999999988877665433  35555544

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=93.71  E-value=0.39  Score=39.49  Aligned_cols=24  Identities=8%  Similarity=-0.024  Sum_probs=19.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      +|....|+|||..+..++..+...
T Consensus        50 L~~Gp~GvGKTt~Ar~lAk~L~c~   73 (598)
T PRK09111         50 MLTGVRGVGKTTTARILARALNYE   73 (598)
T ss_pred             EEECCCCCCHHHHHHHHHHhhCcC
Confidence            566789999999998887776544

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=93.69  E-value=0.64  Score=34.45  Aligned_cols=34  Identities=12%  Similarity=0.214  Sum_probs=22.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .+...+|+|||.++..++.++.......++.+|.
T Consensus       198 ~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       198 ALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            3556799999999988877765442223555554

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.66  E-value=0.52  Score=37.08  Aligned_cols=33  Identities=9%  Similarity=0.039  Sum_probs=22.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      .+.--+|+|||.++..++.++...+  .++++|+-
T Consensus       104 ~lvG~~GvGKTTtaaKLA~~l~~~G--~kV~lV~~  136 (429)
T TIGR01425       104 MFVGLQGSGKTTTCTKLAYYYQRKG--FKPCLVCA  136 (429)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CCEEEEcC
Confidence            3556799999999888877655433  45666654

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

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

Probab=93.62  E-value=1  Score=32.95  Aligned_cols=46  Identities=7%  Similarity=-0.053  Sum_probs=30.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+++-.+|+|||..++.++...... ...+++++.-.....+....+
T Consensus        33 ~~i~g~~G~GKT~l~~~~~~~~~~~-~g~~vl~iS~E~~~~~~~~r~   78 (271)
T cd01122          33 IILTAGTGVGKTTFLREYALDLITQ-HGVRVGTISLEEPVVRTARRL   78 (271)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHh-cCceEEEEEcccCHHHHHHHH
Confidence            3678899999998888877655433 135777777655444444444

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

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=93.47  E-value=0.56  Score=40.80  Aligned_cols=42  Identities=24%  Similarity=0.218  Sum_probs=28.2

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEeccCCCCCc
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLTGWYYPNKW  163 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT~TP~~n~~  163 (169)
                      +.+++|+||+..+..  ....+.++.. ....+++|.|=|-|-.+
T Consensus       433 ~~~vlIVDEASMv~~--~~m~~LL~~a~~~garvVLVGD~~QLps  475 (988)
T PRK13889        433 SRDVLVIDEAGMVGT--RQLERVLSHAADAGAKVVLVGDPQQLQA  475 (988)
T ss_pred             cCcEEEEECcccCCH--HHHHHHHHhhhhCCCEEEEECCHHHcCC
Confidence            557899999998843  2334444433 56778999887766543

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=93.44  E-value=0.035  Score=38.15  Aligned_cols=33  Identities=24%  Similarity=0.245  Sum_probs=18.9

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhccccccEEEEecc
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGW  157 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~T  157 (169)
                      ..|++|+|||-.+-  -....+.   ++...++++|.|
T Consensus        90 ~~DlliVDEAAaIp--~p~L~~l---l~~~~~vv~stT  122 (177)
T PF05127_consen   90 QADLLIVDEAAAIP--LPLLKQL---LRRFPRVVFSTT  122 (177)
T ss_dssp             --SCEEECTGGGS---HHHHHHH---HCCSSEEEEEEE
T ss_pred             CCCEEEEechhcCC--HHHHHHH---HhhCCEEEEEee
Confidence            46999999998873  2222222   344556777665

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.43  E-value=0.29  Score=34.76  Aligned_cols=48  Identities=8%  Similarity=-0.025  Sum_probs=35.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++..++|+|||.-++.++.....+  ..+++++.......+-.+.+..+.
T Consensus        20 li~G~~G~GKt~~~~~~~~~~~~~--g~~~~y~s~e~~~~~l~~~~~~~~   67 (224)
T TIGR03880        20 VVIGEYGTGKTTFSLQFLYQGLKN--GEKAMYISLEEREERILGYAKSKG   67 (224)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCHHHHHHHHHHcC
Confidence            457789999999888887654433  478889888877777666666553

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=93.39  E-value=0.3  Score=41.72  Aligned_cols=24  Identities=8%  Similarity=0.145  Sum_probs=18.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      +.+|..++|+|||..+-+++..+.
T Consensus       202 n~lL~G~pGvGKTal~~~la~~i~  225 (821)
T CHL00095        202 NPILIGEPGVGKTAIAEGLAQRIV  225 (821)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHH
Confidence            457889999999988766665544

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.38  E-value=0.78  Score=36.98  Aligned_cols=25  Identities=8%  Similarity=0.025  Sum_probs=19.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|+|||..+.+++..+...+
T Consensus        40 Lf~GppGtGKTTlA~~lA~~l~c~~   64 (504)
T PRK14963         40 LFSGPRGVGKTTTARLIAMAVNCSG   64 (504)
T ss_pred             EEECCCCCCHHHHHHHHHHHHhccC
Confidence            6778999999999988877765433

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=93.38  E-value=0.79  Score=37.46  Aligned_cols=22  Identities=14%  Similarity=0.161  Sum_probs=16.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++..+.|+|||..+-.+...+.
T Consensus        42 Lf~Gp~GtGKTt~Ak~lAkal~   63 (559)
T PRK05563         42 LFSGPRGTGKTSAAKIFAKAVN   63 (559)
T ss_pred             EEECCCCCCHHHHHHHHHHHhc
Confidence            4578899999988877765544

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.36  E-value=0.32  Score=34.92  Aligned_cols=46  Identities=9%  Similarity=-0.032  Sum_probs=30.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRK   51 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~   51 (169)
                      ++..++|+|||..++.++......+  .+.+.++......+-.+++..
T Consensus        28 ~i~G~~G~GKTtl~~~~~~~~~~~g--~~~~yi~~e~~~~~~~~~~~~   73 (230)
T PRK08533         28 LIEGDESTGKSILSQRLAYGFLQNG--YSVSYVSTQLTTTEFIKQMMS   73 (230)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhCC--CcEEEEeCCCCHHHHHHHHHH
Confidence            4678999999998888877654433  577777766554444444433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=93.35  E-value=0.99  Score=33.67  Aligned_cols=38  Identities=13%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             cccEEEEeCCcccCCccc-HHHHHHhccccccEEEEecc
Q psy1090         120 TWNCIIVDEGHSVKNKKS-KLSIKLTALRATFKVLLTGW  157 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~-~~~~~~~~l~~~~~~~lT~T  157 (169)
                      +..++++||+|.+..... ...+.+.......+++++++
T Consensus       102 ~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~  140 (319)
T PRK00440        102 PFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCN  140 (319)
T ss_pred             CceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeC
Confidence            456899999998854221 12222333344456666654

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.33  E-value=1.1  Score=34.88  Aligned_cols=44  Identities=5%  Similarity=0.095  Sum_probs=27.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC----cchHHHHHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL----SVLNNWEAEFR   50 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~----~~l~qW~~e~~   50 (169)
                      +....|+|||.++..+...+...+  .++.+|.-.    ..+.||..-..
T Consensus       211 lvGptGvGKTTt~akLA~~l~~~g--~~V~lItaDtyR~gAveQLk~yae  258 (407)
T PRK12726        211 LIGQTGVGKTTTLVKLGWQLLKQN--RTVGFITTDTFRSGAVEQFQGYAD  258 (407)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCCccCccHHHHHHHHhh
Confidence            556789999998888776554433  455555532    23667765444

>PRK07952 DNA replication protein DnaC; Validated

Probab=93.29  E-value=0.17  Score=36.70  Aligned_cols=33  Identities=12%  Similarity=0.134  Sum_probs=24.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      |-+|...+|+|||..+.+++..+...+  .+++++
T Consensus       101 ~~~l~G~~GtGKThLa~aia~~l~~~g--~~v~~i  133 (244)
T PRK07952        101 SFIFSGKPGTGKNHLAAAICNELLLRG--KSVLII  133 (244)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEE
Confidence            357888999999999999888776543  445555

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.27  E-value=0.49  Score=37.82  Aligned_cols=33  Identities=9%  Similarity=0.144  Sum_probs=21.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      |.-..|.|||.++..+...+.......++.+|.
T Consensus       261 LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~  293 (484)
T PRK06995        261 LMGPTGVGKTTTTAKLAARCVMRHGASKVALLT  293 (484)
T ss_pred             EECCCCccHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence            566899999988877776654433223444333

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.26  E-value=0.72  Score=37.50  Aligned_cols=23  Identities=4%  Similarity=-0.207  Sum_probs=18.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..++..+..
T Consensus        42 Lf~Gp~GvGKTTlAr~lAk~L~c   64 (546)
T PRK14957         42 LFTGTRGVGKTTLGRLLAKCLNC   64 (546)
T ss_pred             EEECCCCCCHHHHHHHHHHHhCC
Confidence            57789999999988888766553

>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=93.19  E-value=0.14  Score=37.84  Aligned_cols=37  Identities=11%  Similarity=0.085  Sum_probs=27.5

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhC--CCCceEEEecCcc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQ--ALEPNLIVCPLSV   41 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~--~~~~~Liv~P~~~   41 (169)
                      +.-..|+|||.+.+.-+.++...+  ....+|+++++..
T Consensus        18 V~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~   56 (315)
T PF00580_consen   18 VNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNA   56 (315)
T ss_dssp             EEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHH
T ss_pred             EEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHH
Confidence            344589999999988888777665  3457899998753

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 ....

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=93.09  E-value=0.28  Score=41.41  Aligned_cols=23  Identities=9%  Similarity=0.140  Sum_probs=16.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      +.+|.-++|+|||..+=++...+
T Consensus       209 n~LLvGppGvGKT~lae~la~~i  231 (758)
T PRK11034        209 NPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHH
Confidence            35778899999997766665443

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.05  E-value=0.36  Score=34.73  Aligned_cols=47  Identities=15%  Similarity=0.081  Sum_probs=33.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-++|+|||..++.++.....+  ..++++|.-.....+-.+.+..+
T Consensus        25 lI~G~pGsGKT~la~~~l~~~~~~--ge~~lyvs~ee~~~~i~~~~~~~   71 (237)
T TIGR03877        25 LLSGGPGTGKSIFSQQFLWNGLQM--GEPGIYVALEEHPVQVRRNMAQF   71 (237)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEEEeeCCHHHHHHHHHHh
Confidence            467899999999988887665433  36788888766665555555443

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.00  E-value=0.59  Score=38.53  Aligned_cols=23  Identities=9%  Similarity=-0.041  Sum_probs=18.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..++..+..
T Consensus        42 Lf~GPpG~GKTtiArilAk~L~C   64 (624)
T PRK14959         42 LFSGTRGVGKTTIARIFAKALNC   64 (624)
T ss_pred             EEECCCCCCHHHHHHHHHHhccc
Confidence            46789999999998888766653

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.96  E-value=0.99  Score=34.12  Aligned_cols=32  Identities=9%  Similarity=-0.006  Sum_probs=22.1

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +.-..|.|||.++..++..+...  .++++++.-
T Consensus       119 lvGpnGsGKTTt~~kLA~~l~~~--g~~V~Li~~  150 (318)
T PRK10416        119 VVGVNGVGKTTTIGKLAHKYKAQ--GKKVLLAAG  150 (318)
T ss_pred             EECCCCCcHHHHHHHHHHHHHhc--CCeEEEEec
Confidence            34589999999888877665533  356666653

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=92.90  E-value=1.6  Score=32.95  Aligned_cols=36  Identities=11%  Similarity=0.051  Sum_probs=19.1

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +.-..|+|||......+.......+..+.++++|..
T Consensus         2 i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~   37 (384)
T PF03237_consen    2 INGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTY   37 (384)
T ss_dssp             EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESS
T ss_pred             CcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCH
Confidence            344679999987655544444444444566666653

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]

Probab=92.88  E-value=0.54  Score=33.64  Aligned_cols=27  Identities=26%  Similarity=0.429  Sum_probs=18.8

Q ss_pred             cHHHHHhchhccccccccEEEEeCCcc
Q psy1090         105 TPQIIENDFGFLKKITWNCIIVDEGHS  131 (169)
Q Consensus       105 ty~~~~~~~~~~~~~~~~~vi~DEah~  131 (169)
                      |.+.+..-.+.+....||++|||----
T Consensus        98 t~E~v~~vv~eL~~~~fDyIi~DsPAG  124 (272)
T COG2894          98 TPEGVKKVVNELKAMDFDYIIIDSPAG  124 (272)
T ss_pred             CHHHHHHHHHHHHhcCCCEEEecCcch
Confidence            555666666666667888999887543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=92.82  E-value=0.41  Score=36.87  Aligned_cols=25  Identities=12%  Similarity=0.111  Sum_probs=21.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++.-..|+||+..+.+++..+...+
T Consensus        45 Lf~Gp~G~GK~~lA~~~A~~Llc~~   69 (365)
T PRK07471         45 LIGGPQGIGKATLAYRMARFLLATP   69 (365)
T ss_pred             EEECCCCCCHHHHHHHHHHHHhCCC
Confidence            4677899999999999998887654

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=92.78  E-value=0.63  Score=34.78  Aligned_cols=25  Identities=16%  Similarity=0.240  Sum_probs=20.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|+|||..+.++...+...+
T Consensus        28 L~~Gp~G~Gktt~a~~lA~~l~~~~   52 (325)
T COG0470          28 LFYGPPGVGKTTAALALAKELLCEN   52 (325)
T ss_pred             eeeCCCCCCHHHHHHHHHHHHhCCC
Confidence            5667889999999999988877554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.75  E-value=0.8  Score=36.60  Aligned_cols=22  Identities=9%  Similarity=0.060  Sum_probs=17.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++..++|+|||..+-.++..+.
T Consensus        40 Lf~GPpGtGKTTlA~~lA~~l~   61 (472)
T PRK14962         40 IFAGPRGTGKTTVARILAKSLN   61 (472)
T ss_pred             EEECCCCCCHHHHHHHHHHHhc
Confidence            6788999999988877766554

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=92.72  E-value=0.33  Score=34.48  Aligned_cols=41  Identities=20%  Similarity=0.304  Sum_probs=25.3

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCc
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKW  163 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~  163 (169)
                      ..+.+++||++.+-.  . ....+........+.+-|=|.|-..
T Consensus        62 ~~~~liiDE~~~~~~--g-~l~~l~~~~~~~~~~l~GDp~Q~~~  102 (234)
T PF01443_consen   62 SYDTLIIDEAQLLPP--G-YLLLLLSLSPAKNVILFGDPLQIPY  102 (234)
T ss_pred             cCCEEEEeccccCCh--H-HHHHHHhhccCcceEEEECchhccC
Confidence            578899999998632  1 2233444433446677787777544

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=92.71  E-value=1.4  Score=35.82  Aligned_cols=23  Identities=9%  Similarity=0.060  Sum_probs=18.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+-.++..+..
T Consensus        40 Lf~Gp~G~GKTt~Ar~LAk~L~c   62 (535)
T PRK08451         40 LFSGLRGSGKTSSARIFARALVC   62 (535)
T ss_pred             EEECCCCCcHHHHHHHHHHHhcC
Confidence            57789999999888888776654

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=92.70  E-value=1  Score=30.41  Aligned_cols=29  Identities=17%  Similarity=0.211  Sum_probs=20.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEP   32 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~   32 (169)
                      ++..+.|.||+..+.+++..+........
T Consensus        23 L~~G~~g~gk~~~a~~~a~~ll~~~~~~~   51 (162)
T PF13177_consen   23 LFHGPSGSGKKTLALAFARALLCSNPNED   51 (162)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHC-TT-CTT
T ss_pred             EEECCCCCCHHHHHHHHHHHHcCCCCCCC
Confidence            45667899999888888887776554433

...

>PRK08506 replicative DNA helicase; Provisional

Probab=92.57  E-value=1  Score=36.02  Aligned_cols=45  Identities=7%  Similarity=-0.042  Sum_probs=33.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      +++-.+|+|||.-++.++.....  ...+++++.......|....+.
T Consensus       196 vIaarpg~GKT~fal~ia~~~~~--~g~~V~~fSlEMs~~ql~~Rll  240 (472)
T PRK08506        196 IIAARPSMGKTTLCLNMALKALN--QDKGVAFFSLEMPAEQLMLRML  240 (472)
T ss_pred             EEEcCCCCChHHHHHHHHHHHHh--cCCcEEEEeCcCCHHHHHHHHH
Confidence            67889999999988888766543  2468888887766666665553

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=92.43  E-value=0.37  Score=32.99  Aligned_cols=54  Identities=17%  Similarity=0.202  Sum_probs=28.7

Q ss_pred             hhccccccccEEEEeCCcccCC----cccHHHHHHhccccccEEEEeccCCCCCchhh
Q psy1090         113 FGFLKKITWNCIIVDEGHSVKN----KKSKLSIKLTALRATFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       113 ~~~~~~~~~~~vi~DEah~~k~----~~~~~~~~~~~l~~~~~~~lT~TP~~n~~~el  166 (169)
                      ...+..-.||++|+||.-..-+    +.......+..-+...-++|||--.+..+.|+
T Consensus        89 ~~~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~  146 (172)
T PF02572_consen   89 KEAISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEA  146 (172)
T ss_dssp             HHHTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH
T ss_pred             HHHHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHh
Confidence            3444567899999999764322    12333444554456678999997766555444

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=92.40  E-value=0.48  Score=39.43  Aligned_cols=53  Identities=15%  Similarity=0.217  Sum_probs=39.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKY   61 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~   61 (169)
                      ++..-.|+|||+.+.+++..     ..+|+|||+|. ....+|.+++..|.|+..+..|
T Consensus        36 ll~Gl~gs~ka~lia~l~~~-----~~r~vLIVt~~~~~A~~l~~dL~~~~~~~~v~~f   89 (652)
T PRK05298         36 TLLGVTGSGKTFTMANVIAR-----LQRPTLVLAHNKTLAAQLYSEFKEFFPENAVEYF   89 (652)
T ss_pred             EEEcCCCcHHHHHHHHHHHH-----hCCCEEEEECCHHHHHHHHHHHHHhcCCCeEEEe
Confidence            35566899999886654432     24689999998 5567999999999887656555

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=92.25  E-value=0.53  Score=33.51  Aligned_cols=46  Identities=11%  Similarity=0.052  Sum_probs=30.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRK   51 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~   51 (169)
                      ++.-++|+|||..+..++......  ..+++++.......+..+....
T Consensus        24 ~i~G~~G~GKT~l~~~~~~~~~~~--g~~~~~is~e~~~~~i~~~~~~   69 (229)
T TIGR03881        24 AVTGEPGTGKTIFCLHFAYKGLRD--GDPVIYVTTEESRESIIRQAAQ   69 (229)
T ss_pred             EEECCCCCChHHHHHHHHHHHHhc--CCeEEEEEccCCHHHHHHHHHH
Confidence            467899999998888776544432  3577777766555554444433

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.24  E-value=1.4  Score=37.36  Aligned_cols=35  Identities=9%  Similarity=0.188  Sum_probs=21.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      .|....|.|||.+...+...+......+++.++.-
T Consensus       189 ~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~  223 (767)
T PRK14723        189 ALVGPTGVGKTTTTAKLAARCVAREGADQLALLTT  223 (767)
T ss_pred             EEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecC
Confidence            46778999999887777655533332234544443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.17  E-value=1.1  Score=37.10  Aligned_cols=24  Identities=8%  Similarity=-0.000  Sum_probs=19.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      ++..+.|+|||..+.+++..+...
T Consensus        42 Lf~Gp~G~GKttlA~~lAk~L~c~   65 (620)
T PRK14948         42 LFTGPRGTGKTSSARILAKSLNCL   65 (620)
T ss_pred             EEECCCCCChHHHHHHHHHHhcCC
Confidence            577899999999999888776643

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=92.16  E-value=0.81  Score=35.91  Aligned_cols=45  Identities=11%  Similarity=0.039  Sum_probs=31.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      +++-.+|+|||.-++.++...... ...+++++....--.+....+
T Consensus       198 viag~pg~GKT~~al~ia~~~a~~-~g~~v~~fSlEm~~~~l~~Rl  242 (421)
T TIGR03600       198 VIGARPSMGKTTLALNIAENVALR-EGKPVLFFSLEMSAEQLGERL  242 (421)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHh-CCCcEEEEECCCCHHHHHHHH
Confidence            678899999998888887554322 246788888665555555444

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=92.05  E-value=1.3  Score=38.97  Aligned_cols=41  Identities=22%  Similarity=0.220  Sum_probs=28.5

Q ss_pred             ccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEeccCCCCCc
Q psy1090         121 WNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLTGWYYPNKW  163 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT~TP~~n~~  163 (169)
                      -+++|+||+..+..  ......++.. +...+++|-|=|-|-.+
T Consensus       469 ~~vlVIDEAsMv~~--~~m~~Ll~~~~~~garvVLVGD~~QL~~  510 (1102)
T PRK13826        469 KTVFVLDEAGMVAS--RQMALFVEAVTRAGAKLVLVGDPEQLQP  510 (1102)
T ss_pred             CcEEEEECcccCCH--HHHHHHHHHHHhcCCEEEEECCHHHcCC
Confidence            46899999998842  3334555555 46789999988776543

>PHA00350 putative assembly protein

Probab=92.03  E-value=0.49  Score=36.85  Aligned_cols=15  Identities=13%  Similarity=0.087  Sum_probs=12.2

Q ss_pred             cCCCCCcHHHHHHHH
Q psy1090           6 PDPTRYRKSGKVIAF   20 (169)
Q Consensus         6 ~de~G~GKT~~~i~~   20 (169)
                      ---+|+|||..++..
T Consensus         7 tG~pGSGKT~~aV~~   21 (399)
T PHA00350          7 VGRPGSYKSYEAVVY   21 (399)
T ss_pred             ecCCCCchhHHHHHH
Confidence            345899999999875

>PRK13342 recombination factor protein RarA; Reviewed

Probab=92.01  E-value=1.1  Score=35.18  Aligned_cols=19  Identities=11%  Similarity=0.025  Sum_probs=13.9

Q ss_pred             ccccCCCCCcHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFF   21 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i   21 (169)
                      .+|.-++|+|||..+-.+.
T Consensus        39 ilL~GppGtGKTtLA~~ia   57 (413)
T PRK13342         39 MILWGPPGTGKTTLARIIA   57 (413)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4667889999997665553

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.99  E-value=0.56  Score=33.55  Aligned_cols=47  Identities=9%  Similarity=0.074  Sum_probs=34.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++..++|+|||.-+..++.....+  ..+++++.-.....+..+++..+
T Consensus        29 ~i~G~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~~~~~~~~~~~~~   75 (234)
T PRK06067         29 LIEGDHGTGKSVLSQQFVYGALKQ--GKKVYVITTENTSKSYLKQMESV   75 (234)
T ss_pred             EEECCCCCChHHHHHHHHHHHHhC--CCEEEEEEcCCCHHHHHHHHHHC
Confidence            566899999999988887654432  46788888777777777766655

>PRK10865 protein disaggregation chaperone; Provisional

Probab=91.99  E-value=0.75  Score=39.57  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=18.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      +.+|..++|+|||..+-++...+.
T Consensus       201 n~lL~G~pGvGKT~l~~~la~~i~  224 (857)
T PRK10865        201 NPVLIGEPGVGKTAIVEGLAQRII  224 (857)
T ss_pred             ceEEECCCCCCHHHHHHHHHHHhh
Confidence            467889999999988766665543

>PRK12377 putative replication protein; Provisional

Probab=91.98  E-value=0.35  Score=35.17  Aligned_cols=39  Identities=13%  Similarity=0.122  Sum_probs=26.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      -+|..++|+|||..+.+++..+...+  .+++++.-..++.
T Consensus       104 l~l~G~~GtGKThLa~AIa~~l~~~g--~~v~~i~~~~l~~  142 (248)
T PRK12377        104 FVFSGKPGTGKNHLAAAIGNRLLAKG--RSVIVVTVPDVMS  142 (248)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcC--CCeEEEEHHHHHH
Confidence            46778899999999998888776543  3454444345544

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

Probab=91.87  E-value=1.6  Score=31.74  Aligned_cols=31  Identities=13%  Similarity=0.049  Sum_probs=21.7

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE--ecCc
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV--CPLS   40 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv--~P~~   40 (169)
                      -=|.|||..+.++...+...+  +++|+|  +|.+
T Consensus        10 kGGvG~TTltAnLA~aL~~~G--~~VlaID~dpqN   42 (243)
T PF06564_consen   10 KGGVGKTTLTANLAWALARLG--ESVLAIDLDPQN   42 (243)
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CcEEEEeCCcHH
Confidence            348999999888887776655  456665  3544

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

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=91.85  E-value=4  Score=30.15  Aligned_cols=32  Identities=9%  Similarity=0.100  Sum_probs=22.4

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +.-.+|.|||.++..++..+...+  .+++++.-
T Consensus        77 l~G~~G~GKTTt~akLA~~l~~~g--~~V~li~~  108 (272)
T TIGR00064        77 FVGVNGVGKTTTIAKLANKLKKQG--KSVLLAAG  108 (272)
T ss_pred             EECCCCCcHHHHHHHHHHHHHhcC--CEEEEEeC
Confidence            346899999999888877664332  56666653

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=91.83  E-value=0.67  Score=39.82  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=17.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      +.+|.-++|+|||..+-+++..+.
T Consensus       196 n~lL~G~pGvGKT~l~~~la~~i~  219 (852)
T TIGR03346       196 NPVLIGEPGVGKTAIVEGLAQRIV  219 (852)
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHh
Confidence            356778999999987766655443

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK08760 replicative DNA helicase; Provisional

Probab=91.78  E-value=0.67  Score=37.09  Aligned_cols=48  Identities=2%  Similarity=-0.109  Sum_probs=36.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      +++-.+|+|||.-++.++...... ...+++++.......|+...+...
T Consensus       233 vIaarPg~GKTafal~iA~~~a~~-~g~~V~~fSlEMs~~ql~~Rl~a~  280 (476)
T PRK08760        233 ILAARPAMGKTTFALNIAEYAAIK-SKKGVAVFSMEMSASQLAMRLISS  280 (476)
T ss_pred             EEEeCCCCChhHHHHHHHHHHHHh-cCCceEEEeccCCHHHHHHHHHHh
Confidence            678899999999888887665432 235788888888788888776543

>PRK04132 replication factor C small subunit; Provisional

Probab=91.77  E-value=1.8  Score=37.11  Aligned_cols=42  Identities=12%  Similarity=0.252  Sum_probs=26.7

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc---ccccEEEEeccCCCCCc
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL---RATFKVLLTGWYYPNKW  163 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l---~~~~~~~lT~TP~~n~~  163 (169)
                      ++.++|+||+|.+...  .....++.+   ....++++..++...-+
T Consensus       630 ~~KVvIIDEaD~Lt~~--AQnALLk~lEep~~~~~FILi~N~~~kIi  674 (846)
T PRK04132        630 SFKIIFLDEADALTQD--AQQALRRTMEMFSSNVRFILSCNYSSKII  674 (846)
T ss_pred             CCEEEEEECcccCCHH--HHHHHHHHhhCCCCCeEEEEEeCChhhCc
Confidence            5789999999998532  222222233   45668888888765443

>KOG0739|consensus

Probab=91.69  E-value=0.21  Score=37.42  Aligned_cols=47  Identities=19%  Similarity=0.195  Sum_probs=31.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      |.+|-..+|+||+..+=++..     ......+=|..+.++..|.-|-++..
T Consensus       168 giLLyGPPGTGKSYLAKAVAT-----EAnSTFFSvSSSDLvSKWmGESEkLV  214 (439)
T KOG0739|consen  168 GILLYGPPGTGKSYLAKAVAT-----EANSTFFSVSSSDLVSKWMGESEKLV  214 (439)
T ss_pred             eEEEeCCCCCcHHHHHHHHHh-----hcCCceEEeehHHHHHHHhccHHHHH
Confidence            557788999999966555432     22244555555678889998876553

>PRK04328 hypothetical protein; Provisional

Probab=91.64  E-value=0.66  Score=33.71  Aligned_cols=47  Identities=17%  Similarity=0.111  Sum_probs=31.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-++|+|||..++.++......  ..+.++|.-...-.+-.+.+..+
T Consensus        27 li~G~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee~~~~i~~~~~~~   73 (249)
T PRK04328         27 LLSGGPGTGKSIFSQQFLWNGLQM--GEPGVYVALEEHPVQVRRNMRQF   73 (249)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeCCHHHHHHHHHHc
Confidence            367899999999888887664433  36777777655555544444444

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

Probab=91.60  E-value=0.36  Score=40.08  Aligned_cols=48  Identities=15%  Similarity=-0.021  Sum_probs=32.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRK   51 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~   51 (169)
                      +++--++|+|||+..++......... ..+++|.++... ..|-.++...
T Consensus        37 ~~iEapTGtGKTl~yL~~al~~~~~~-~~~viist~t~~lq~q~~~~~~~   85 (654)
T COG1199          37 LLIEAPTGTGKTLAYLLPALAYAREE-GKKVIISTRTKALQEQLLEEDLP   85 (654)
T ss_pred             EEEECCCCccHHHHHHHHHHHHHHHc-CCcEEEECCCHHHHHHHHHhhcc
Confidence            56778999999999887766555443 256666666654 4466666543

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

Probab=91.58  E-value=0.74  Score=33.54  Aligned_cols=48  Identities=23%  Similarity=0.228  Sum_probs=34.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++.-++|+|||.-++.++......  ..|++.|.-...-.+-.+.+..|.
T Consensus        27 lI~G~pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e~~~~l~~~~~~~g   74 (260)
T COG0467          27 LITGPPGTGKTIFALQFLYEGARE--GEPVLYVSTEESPEELLENARSFG   74 (260)
T ss_pred             EEEcCCCCcHHHHHHHHHHHHHhc--CCcEEEEEecCCHHHHHHHHHHcC
Confidence            456789999999999998877665  478999987665554444444443

>PHA00673 acetyltransferase domain containing protein

Probab=91.51  E-value=0.27  Score=33.02  Aligned_cols=45  Identities=18%  Similarity=0.037  Sum_probs=35.2

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhcc---ccccEEEEeccCCCCCch
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTAL---RATFKVLLTGWYYPNKWS  164 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l---~~~~~~~lT~TP~~n~~~  164 (169)
                      ..+.+.+|+.|+=++-..+..+.+...   .-..++.+||||.+|.+.
T Consensus        87 ~Ie~l~V~~~~RGqGIG~~Ll~~A~~~Ar~~Gc~~lyis~~p~~~tv~  134 (154)
T PHA00673         87 TTESIFVAAAHRPGGAGMALLRATEALARDLGATGLYVSGPTEGRLVQ  134 (154)
T ss_pred             EEEEEEEChhccCCCHHHHHHHHHHHHHHHCCCCEEEEecCCCccchH
Confidence            467899999999877777666665543   456899999999999764

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=91.47  E-value=2.4  Score=26.90  Aligned_cols=45  Identities=11%  Similarity=0.025  Sum_probs=26.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-..|.|||..+..+...+.+.  ..+++++--..  +++.+++...
T Consensus         3 ~~~GkgG~GKTt~a~~la~~l~~~--g~~V~~id~D~--~~~~~~~~~~   47 (116)
T cd02034           3 AITGKGGVGKTTIAALLARYLAEK--GKPVLAIDADP--DDLPERLSVE   47 (116)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHC--CCcEEEEECCc--hhhHHHHhhc
Confidence            355678999998887776665443  34565555322  4444444433

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=91.43  E-value=0.28  Score=36.35  Aligned_cols=27  Identities=4%  Similarity=-0.102  Sum_probs=20.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      +.+|..++|+|||..|-++...+...+
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g   86 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLG   86 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            346778999999998877776665543

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=91.42  E-value=0.19  Score=39.04  Aligned_cols=22  Identities=18%  Similarity=0.157  Sum_probs=14.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+.-+.|+|||..+-.+...+.
T Consensus       173 lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        173 LIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             EEeCCCCCChhHHHHHHHHHHH
Confidence            4456789999976655544443

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

Probab=91.39  E-value=0.4  Score=39.18  Aligned_cols=44  Identities=14%  Similarity=0.188  Sum_probs=29.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCC----CCceEEEecCcchHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQA----LEPNLIVCPLSVLNNWEA   47 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~----~~~~Liv~P~~~l~qW~~   47 (169)
                      ++....|+|||..|+-=++++....+    .+++||+.|+.+......
T Consensus       230 VVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis  277 (747)
T COG3973         230 VVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYIS  277 (747)
T ss_pred             EEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHH
Confidence            45567899999887755555444322    357999999987665543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.37  E-value=1.9  Score=35.38  Aligned_cols=23  Identities=4%  Similarity=-0.061  Sum_probs=18.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..++..+..
T Consensus        42 Lf~Gp~G~GKtt~A~~lak~l~c   64 (576)
T PRK14965         42 LFTGARGVGKTSTARILAKALNC   64 (576)
T ss_pred             EEECCCCCCHHHHHHHHHHhhcC
Confidence            46778999999988888766553

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=91.19  E-value=1.2  Score=33.79  Aligned_cols=25  Identities=4%  Similarity=-0.013  Sum_probs=20.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|.||+..+.+++..+...+
T Consensus        28 Lf~G~~G~GK~~lA~~~A~~llC~~   52 (325)
T PRK06871         28 LFKADSGLGTEQLIRALAQWLMCQT   52 (325)
T ss_pred             EeECCCCCCHHHHHHHHHHHHcCCC
Confidence            3677899999999999988877644

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=91.12  E-value=2.1  Score=29.42  Aligned_cols=23  Identities=13%  Similarity=0.131  Sum_probs=18.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..++..+..
T Consensus        18 L~~G~~G~gkt~~a~~~~~~l~~   40 (188)
T TIGR00678        18 LFAGPEGVGKELLALALAKALLC   40 (188)
T ss_pred             EEECCCCCCHHHHHHHHHHHHcC
Confidence            46778999999888888776654

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]

Probab=91.08  E-value=0.78  Score=30.67  Aligned_cols=36  Identities=14%  Similarity=0.149  Sum_probs=27.3

Q ss_pred             eEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHH
Q psy1090          33 NLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIER   68 (169)
Q Consensus        33 ~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~   68 (169)
                      ..||+=+.+-.+..+.++.-.|++.++...|+....
T Consensus        69 ~~vi~CSALKr~YRD~LR~~~~~~~Fv~L~g~~~~i  104 (161)
T COG3265          69 HVVIACSALKRSYRDLLREANPGLRFVYLDGDFDLI  104 (161)
T ss_pred             ceEEecHHHHHHHHHHHhccCCCeEEEEecCCHHHH
Confidence            344444566778888888888999999999987663

>TIGR00347 bioD dethiobiotin synthase

Probab=91.07  E-value=0.47  Score=31.94  Aligned_cols=33  Identities=18%  Similarity=-0.009  Sum_probs=25.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      |.+.++|.|||..+++++..+.+++  .++.++=|
T Consensus         2 I~~t~~~~GKT~va~~L~~~l~~~g--~~V~~~kP   34 (166)
T TIGR00347         2 VTGTDTGVGKTVASSALAAKLKKAG--YSVGYYKP   34 (166)
T ss_pred             eecCCCCccHHHHHHHHHHHHHHCC--CcEEEEEe
Confidence            3467899999999999988887655  45666644

Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor.

>PF12846 AAA_10: AAA-like domain

Probab=91.03  E-value=0.54  Score=34.54  Aligned_cols=36  Identities=19%  Similarity=0.179  Sum_probs=24.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      .++.-.+|+|||..+..++......+  .+++|+=|..
T Consensus         4 ~~i~G~tGsGKT~~~~~l~~~~~~~g--~~~~i~D~~g   39 (304)
T PF12846_consen    4 TLILGKTGSGKTTLLKNLLEQLIRRG--PRVVIFDPKG   39 (304)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHcC--CCEEEEcCCc
Confidence            56778999999988877766555444  3445554443

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

Probab=90.96  E-value=0.39  Score=32.46  Aligned_cols=32  Identities=9%  Similarity=-0.041  Sum_probs=23.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-.-|.|||..++.+...+...+  .++|+|-
T Consensus         4 v~s~kgG~GKTt~a~~LA~~la~~g--~~vllvD   35 (169)
T cd02037           4 VMSGKGGVGKSTVAVNLALALAKLG--YKVGLLD   35 (169)
T ss_pred             EecCCCcCChhHHHHHHHHHHHHcC--CcEEEEe
Confidence            4566789999999988877665543  5777773

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

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=90.94  E-value=0.38  Score=40.93  Aligned_cols=58  Identities=14%  Similarity=0.129  Sum_probs=39.8

Q ss_pred             EEecHHHHHhch--hccccccccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEeccCCC
Q psy1090         102 LVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGWYYP  160 (169)
Q Consensus       102 ~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~TP~~  160 (169)
                      ++.|...+..|.  +.+.--.+..+|+||||++.+..+-.+ .++.+    +..+..++|+.|-.
T Consensus        11 ~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaF-I~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596        11 FSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAF-ILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             EEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHH-HHHHHHHhCCCcceEEecCCCcc
Confidence            778887777654  233334678999999999976444333 22322    46789999999976

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

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

Probab=90.81  E-value=0.34  Score=35.39  Aligned_cols=27  Identities=11%  Similarity=-0.039  Sum_probs=20.0

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      -=|.|||.+++.+...+.+.+  +++|+|
T Consensus         8 KGGVGKTT~~~nLA~~La~~g--~rVLli   34 (268)
T TIGR01281         8 KGGIGKSTTSSNLSVAFAKLG--KRVLQI   34 (268)
T ss_pred             CCcCcHHHHHHHHHHHHHhCC--CeEEEE
Confidence            569999999988877665443  567776

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=90.77  E-value=0.51  Score=35.44  Aligned_cols=38  Identities=8%  Similarity=-0.074  Sum_probs=26.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV   41 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~   41 (169)
                      |-+|-..+|+|||..+.|++..+...+  .++.++--+.+
T Consensus       158 gl~L~G~~G~GKThLa~Aia~~l~~~g--~~v~~~~~~~l  195 (306)
T PRK08939        158 GLYLYGDFGVGKSYLLAAIANELAKKG--VSSTLLHFPEF  195 (306)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcC--CCEEEEEHHHH
Confidence            456778899999999988888776443  44555543333

>PRK13235 nifH nitrogenase reductase; Reviewed

Probab=90.77  E-value=0.35  Score=35.51  Aligned_cols=27  Identities=15%  Similarity=0.069  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      -=|.|||.+++.+...+.+.+  +++|+|
T Consensus         9 KGGVGKTT~~~nLA~~La~~G--~rVLlI   35 (274)
T PRK13235          9 KGGIGKSTTTQNTVAGLAEMG--KKVMVV   35 (274)
T ss_pred             CCCccHHHHHHHHHHHHHHCC--CcEEEE
Confidence            559999999988877666544  577777

>TIGR00682 lpxK tetraacyldisaccharide 4'-kinase

Probab=90.65  E-value=2.4  Score=32.01  Aligned_cols=19  Identities=11%  Similarity=-0.036  Sum_probs=15.5

Q ss_pred             CCcHHHHHHHHHHHHHHhC
Q psy1090          10 RYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus        10 G~GKT~~~i~~i~~~~~~~   28 (169)
                      |+|||-.++.++..+..++
T Consensus        40 GTGKTP~v~~La~~l~~~G   58 (311)
T TIGR00682        40 GTGKTPVVVWLAELLKDRG   58 (311)
T ss_pred             CcChHHHHHHHHHHHHHCC
Confidence            8999999998888776543

Also called lipid-A 4'-kinase. This essential gene encodes an enzyme in the pathway of lipid A biosynthesis in Gram-negative organisms. A single copy of this protein is found in Gram-negative bacteria. PSI-BLAST converges on this set of apparent orthologs without identifying any other homologs.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.65  E-value=2.3  Score=34.23  Aligned_cols=22  Identities=9%  Similarity=0.027  Sum_probs=16.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++..+.|+|||..+-.+...+.
T Consensus        42 Lf~Gp~G~GKTtlAr~lAk~L~   63 (486)
T PRK14953         42 IFAGPRGTGKTTIARILAKVLN   63 (486)
T ss_pred             EEECCCCCCHHHHHHHHHHHhc
Confidence            4688999999987777665543

>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []

Probab=90.64  E-value=2.9  Score=31.76  Aligned_cols=41  Identities=15%  Similarity=-0.080  Sum_probs=28.0

Q ss_pred             CCcHHHHHHHHHHHHHHhCCC------------C-ceEEEecCcchHHHHHHHH
Q psy1090          10 RYRKSGKVIAFFCKIIEEQAL------------E-PNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus        10 G~GKT~~~i~~i~~~~~~~~~------------~-~~Liv~P~~~l~qW~~e~~   50 (169)
                      |+|||-.++.++..+.+.+..            + ..++|.|.+.-.+--+|-.
T Consensus        47 GTGKTP~v~~L~~~L~~~G~~~~IlSRGYg~~~~~~~~~v~~~~~~~~~GDEp~  100 (326)
T PF02606_consen   47 GTGKTPLVIWLARLLQARGYRPAILSRGYGRKSKGEPILVSDGSDAEEVGDEPL  100 (326)
T ss_pred             CCCchHHHHHHHHHHHhcCCceEEEcCCCCCCCCCCeEEEeCCCChhhhcCHHH
Confidence            899999999998887765311            1 2677777775555556643

This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS).; GO: 0005524 ATP binding, 0009029 tetraacyldisaccharide 4'-kinase activity, 0009245 lipid A biosynthetic process

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=90.58  E-value=0.36  Score=35.56  Aligned_cols=28  Identities=21%  Similarity=0.176  Sum_probs=21.1

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .-=|.|||.+++.+...+...+  +++|+|
T Consensus         8 gKGGVGKTT~a~nLA~~La~~G--~rVLli   35 (279)
T PRK13230          8 GKGGIGKSTTVCNIAAALAESG--KKVLVV   35 (279)
T ss_pred             CCCCCcHHHHHHHHHHHHHhCC--CEEEEE
Confidence            3569999999988877776544  567777

>PRK05636 replicative DNA helicase; Provisional

Probab=90.53  E-value=0.91  Score=36.60  Aligned_cols=45  Identities=9%  Similarity=0.034  Sum_probs=31.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      +++-.+|+|||.-++.++...... ...+++++.......|....+
T Consensus       269 iiaarpg~GKT~~al~~a~~~a~~-~g~~v~~fSlEMs~~ql~~R~  313 (505)
T PRK05636        269 IVAARPGVGKSTLALDFMRSASIK-HNKASVIFSLEMSKSEIVMRL  313 (505)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHh-CCCeEEEEEeeCCHHHHHHHH
Confidence            678899999998888776554322 235788887766666665554

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=90.50  E-value=1.2  Score=33.90  Aligned_cols=25  Identities=12%  Similarity=0.073  Sum_probs=20.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|+||+..+.++...+...+
T Consensus        28 Lf~G~~G~Gk~~lA~~~A~~LlC~~   52 (334)
T PRK07993         28 LIQALPGMGDDALIYALSRWLMCQQ   52 (334)
T ss_pred             eeECCCCCCHHHHHHHHHHHHcCCC
Confidence            4678899999999999988887643

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=90.41  E-value=3.2  Score=34.89  Aligned_cols=23  Identities=4%  Similarity=-0.084  Sum_probs=17.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      +|....|+|||..+..+...+..
T Consensus        42 Lf~GP~GvGKTTlAriLAk~LnC   64 (709)
T PRK08691         42 LLTGTRGVGKTTIARILAKSLNC   64 (709)
T ss_pred             EEECCCCCcHHHHHHHHHHHhcc
Confidence            67788999999888877665543

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.32  E-value=1.2  Score=36.87  Aligned_cols=23  Identities=9%  Similarity=-0.015  Sum_probs=18.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..|..+...+..
T Consensus        42 Lf~Gp~GvGKttlA~~lAk~L~c   64 (620)
T PRK14954         42 IFSGLRGVGKTTAARVFAKAVNC   64 (620)
T ss_pred             EEECCCCCCHHHHHHHHHHHhCC
Confidence            46788999999999888776654

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=90.29  E-value=0.64  Score=34.95  Aligned_cols=47  Identities=19%  Similarity=0.336  Sum_probs=30.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cch-----HHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVL-----NNWEAEFR   50 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l-----~qW~~e~~   50 (169)
                      ++-..+|.||+--.=.++...+-......+++|+|. ..+     .-|..++.
T Consensus        91 ~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mIpp~E~~aW~~Ql~  143 (369)
T PF02456_consen   91 VVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMIPPQEITAWETQLC  143 (369)
T ss_pred             EEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCCCHHHHHHHHHHHH
Confidence            445689999995444444444444555678999996 444     34777765

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PRK10037 cell division protein; Provisional

Probab=90.29  E-value=0.42  Score=34.64  Aligned_cols=31  Identities=10%  Similarity=-0.036  Sum_probs=22.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +...-=|.|||.+++.+...+.+.+  +++|+|
T Consensus         6 v~n~KGGvGKTT~a~nLA~~La~~G--~rVLlI   36 (250)
T PRK10037          6 LQGVRGGVGTTSITAALAWSLQMLG--ENVLVI   36 (250)
T ss_pred             EecCCCCccHHHHHHHHHHHHHhcC--CcEEEE
Confidence            3455669999999988877766544  567777

>PRK06921 hypothetical protein; Provisional

Probab=89.95  E-value=0.73  Score=33.88  Aligned_cols=39  Identities=10%  Similarity=0.006  Sum_probs=25.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL   42 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l   42 (169)
                      .+|.-++|+|||..+.+++..+.... ...++.+....++
T Consensus       120 l~l~G~~G~GKThLa~aia~~l~~~~-g~~v~y~~~~~l~  158 (266)
T PRK06921        120 IALLGQPGSGKTHLLTAAANELMRKK-GVPVLYFPFVEGF  158 (266)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhhhc-CceEEEEEHHHHH
Confidence            46777999999999888877766542 2344444433433

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=89.92  E-value=1.6  Score=34.90  Aligned_cols=32  Identities=28%  Similarity=0.240  Sum_probs=22.0

Q ss_pred             hchhccccccccEEEEeCCcccCCcccHHHHHHh
Q psy1090         111 NDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLT  144 (169)
Q Consensus       111 ~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~  144 (169)
                      ++.........+++|+||.|..++.  ..+.++.
T Consensus       114 ~~~~~~dG~~~~~~i~DE~h~~~~~--~~~~~l~  145 (477)
T PF03354_consen  114 SDADSLDGLNPSLAIFDELHAHKDD--ELYDALE  145 (477)
T ss_pred             cCCCCccCCCCceEEEeCCCCCCCH--HHHHHHH
Confidence            3445555677899999999998753  3455554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=89.87  E-value=0.47  Score=34.71  Aligned_cols=28  Identities=11%  Similarity=-0.027  Sum_probs=20.9

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .--|.|||.++..+...+...+  +++|+|
T Consensus         9 ~KGGVGKTT~~~nLA~~la~~G--~kVLli   36 (270)
T PRK13185          9 GKGGIGKSTTSSNLSAAFAKLG--KKVLQI   36 (270)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCC--CeEEEE
Confidence            3679999999988877766543  567777

>PHA02518 ParA-like protein; Provisional

Probab=89.84  E-value=0.84  Score=31.80  Aligned_cols=41  Identities=12%  Similarity=0.153  Sum_probs=28.4

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHHHH
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWEAE   48 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~~e   48 (169)
                      ..-=|.|||..++.+...+...+  .++++|-  |.....+|...
T Consensus         7 ~~KGGvGKTT~a~~la~~la~~g--~~vlliD~D~q~~~~~~~~~   49 (211)
T PHA02518          7 NQKGGAGKTTVATNLASWLHADG--HKVLLVDLDPQGSSTDWAEA   49 (211)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhCC--CeEEEEeCCCCCChHHHHHh
Confidence            34458999999988877665443  5676664  66677788653

>PRK06835 DNA replication protein DnaC; Validated

Probab=89.81  E-value=0.48  Score=35.97  Aligned_cols=38  Identities=5%  Similarity=-0.045  Sum_probs=25.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV   41 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~   41 (169)
                      |-+|..++|+|||..+.+++..+...+  ..++.+.-..+
T Consensus       185 ~Lll~G~~GtGKThLa~aIa~~l~~~g--~~V~y~t~~~l  222 (329)
T PRK06835        185 NLLFYGNTGTGKTFLSNCIAKELLDRG--KSVIYRTADEL  222 (329)
T ss_pred             cEEEECCCCCcHHHHHHHHHHHHHHCC--CeEEEEEHHHH
Confidence            346777899999999888877776543  34444433333

>PRK07004 replicative DNA helicase; Provisional

Probab=89.73  E-value=0.95  Score=36.07  Aligned_cols=45  Identities=7%  Similarity=-0.077  Sum_probs=32.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      +++-.+|+|||.-++.++...... ...+++++.....-.|....+
T Consensus       217 viaarpg~GKT~~al~ia~~~a~~-~~~~v~~fSlEM~~~ql~~R~  261 (460)
T PRK07004        217 IVAGRPSMGKTAFSMNIGEYVAVE-YGLPVAVFSMEMPGTQLAMRM  261 (460)
T ss_pred             EEEeCCCCCccHHHHHHHHHHHHH-cCCeEEEEeCCCCHHHHHHHH
Confidence            678899999998888877654332 236788887776666766555

>TIGR02012 tigrfam_recA protein RecA

Probab=89.53  E-value=3.6  Score=31.21  Aligned_cols=38  Identities=11%  Similarity=0.045  Sum_probs=28.1

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNN   44 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~q   44 (169)
                      +.-+.|+|||..++.++......  .+++++|-..+...+
T Consensus        60 I~G~~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~~~~~   97 (321)
T TIGR02012        60 IYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDP   97 (321)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccchhHH
Confidence            66789999999888877665543  467888877766654

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

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

Probab=89.51  E-value=0.55  Score=33.08  Aligned_cols=27  Identities=19%  Similarity=0.035  Sum_probs=20.8

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      --|.|||.++..+...+.+.+  +++|+|
T Consensus         8 KGGvGKTt~~~nLA~~la~~G--~rvLli   34 (212)
T cd02117           8 KGGIGKSTTSQNLSAALAEMG--KKVLQV   34 (212)
T ss_pred             CCcCcHHHHHHHHHHHHHHCC--CcEEEE
Confidence            679999998888877776654  567777

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

>TIGR00767 rho transcription termination factor Rho

Probab=89.40  E-value=1.1  Score=34.97  Aligned_cols=21  Identities=14%  Similarity=0.074  Sum_probs=14.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~   23 (169)
                      +.+..++|+|||..+-.+...
T Consensus       171 ~~IvG~~g~GKTtL~~~i~~~  191 (415)
T TIGR00767       171 GLIVAPPKAGKTVLLQKIAQA  191 (415)
T ss_pred             EEEECCCCCChhHHHHHHHHh
Confidence            456678999999765554443

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

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

Probab=89.39  E-value=3  Score=31.71  Aligned_cols=37  Identities=11%  Similarity=0.012  Sum_probs=27.9

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      +.-+.|+|||..++.++......  .+++++|-+.+...
T Consensus        60 I~Gp~GsGKTtLal~~~~~~~~~--g~~~vyId~E~~~~   96 (325)
T cd00983          60 IYGPESSGKTTLALHAIAEAQKL--GGTVAFIDAEHALD   96 (325)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHc--CCCEEEECccccHH
Confidence            56689999998888877665443  46888888877665

RecA couples ATP hydrolysis to DNA strand exchange.

>CHL00072 chlL photochlorophyllide reductase subunit L

Probab=89.39  E-value=0.53  Score=35.03  Aligned_cols=28  Identities=11%  Similarity=-0.025  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      -=|.|||.+++.+...+.+.+  +++|+|=
T Consensus         8 KGGVGKTTta~nLA~~La~~G--~rVLlID   35 (290)
T CHL00072          8 KGGIGKSTTSCNISIALARRG--KKVLQIG   35 (290)
T ss_pred             CCCCcHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            559999999988877766544  4677663

>PRK06321 replicative DNA helicase; Provisional

Probab=89.38  E-value=1.7  Score=34.84  Aligned_cols=46  Identities=7%  Similarity=-0.026  Sum_probs=32.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      +++--+|+|||.-++.++...... ...+++++.....-.|+.+.+.
T Consensus       230 iiaarPgmGKTafal~ia~~~a~~-~g~~v~~fSLEMs~~ql~~Rll  275 (472)
T PRK06321        230 ILAARPAMGKTALALNIAENFCFQ-NRLPVGIFSLEMTVDQLIHRII  275 (472)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHh-cCCeEEEEeccCCHHHHHHHHH
Confidence            678899999998887765544322 2467888887776777766653

>cd02032 Bchl_like This family of proteins contains bchL and chlL

Probab=89.36  E-value=0.55  Score=34.31  Aligned_cols=27  Identities=11%  Similarity=0.026  Sum_probs=20.0

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      --|.|||.++..+...+.+.+  +++|+|
T Consensus         8 KGGvGKTT~a~nLA~~la~~G--~rvlli   34 (267)
T cd02032           8 KGGIGKSTTSSNLSVALAKRG--KKVLQI   34 (267)
T ss_pred             CCCCCHHHHHHHHHHHHHHCC--CcEEEE
Confidence            569999999888877665444  567666

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

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=89.36  E-value=0.63  Score=34.03  Aligned_cols=34  Identities=24%  Similarity=0.066  Sum_probs=25.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      +++-++|+|||.-++.++......  ..+++++.-.
T Consensus        40 lI~G~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~E   73 (259)
T TIGR03878        40 NITGVSDTGKSLMVEQFAVTQASR--GNPVLFVTVE   73 (259)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEec
Confidence            467899999999888887654433  4678888744

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK09165 replicative DNA helicase; Provisional

Probab=89.11  E-value=1.8  Score=34.89  Aligned_cols=48  Identities=2%  Similarity=-0.124  Sum_probs=33.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC-------------CCCceEEEecCcchHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ-------------ALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~-------------~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      .+++--+|+|||.-++.++.......             ...+++++.....-.|....+.
T Consensus       220 ivIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEMs~~ql~~R~l  280 (497)
T PRK09165        220 IILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEMSAEQLATRIL  280 (497)
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcCCHHHHHHHHH
Confidence            36788999999988888776554331             1357888877766677666653

>PRK13849 putative crown gall tumor protein VirC1; Provisional

Probab=89.02  E-value=1.1  Score=32.20  Aligned_cols=42  Identities=7%  Similarity=0.108  Sum_probs=29.0

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHHHHH
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWEAEF   49 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~~e~   49 (169)
                      ..-=|.|||.+++.+...+...+  .++++|=  |...+..|....
T Consensus         8 n~KGGvGKTT~a~nLA~~la~~G--~~VlliD~DpQ~s~~~w~~~~   51 (231)
T PRK13849          8 SFKGGAGKTTALMGLCAALASDG--KRVALFEADENRPLTRWKENA   51 (231)
T ss_pred             CCCCCccHHHHHHHHHHHHHhCC--CcEEEEeCCCCCCHHHHHHhh
Confidence            34459999999988877766544  4666664  566777887543

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=88.98  E-value=2.9  Score=34.52  Aligned_cols=24  Identities=17%  Similarity=0.091  Sum_probs=19.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      ++..+.|+|||..|..++..+...
T Consensus        42 Lf~GP~GvGKTTlA~~lAk~L~C~   65 (605)
T PRK05896         42 IFSGPRGIGKTSIAKIFAKAINCL   65 (605)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcCC
Confidence            467899999999988887766543

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

Probab=88.93  E-value=0.59  Score=34.06  Aligned_cols=27  Identities=19%  Similarity=0.105  Sum_probs=19.9

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      -=|.|||.++..+...+...+  .++|+|
T Consensus         9 KGGvGKTT~~~nLA~~La~~G--~kVlli   35 (270)
T cd02040           9 KGGIGKSTTTQNLSAALAEMG--KKVMIV   35 (270)
T ss_pred             CCcCCHHHHHHHHHHHHHhCC--CeEEEE
Confidence            459999999888877766533  567766

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

>TIGR00665 DnaB replicative DNA helicase

Probab=88.90  E-value=1.9  Score=33.93  Aligned_cols=46  Identities=4%  Similarity=-0.033  Sum_probs=32.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      +++-.+|+|||.-++.++...... ...+++++.....-.+..+.+.
T Consensus       199 vi~g~pg~GKT~~~l~~a~~~a~~-~g~~vl~~SlEm~~~~i~~R~~  244 (434)
T TIGR00665       199 ILAARPSMGKTAFALNIAENAAIK-EGKPVAFFSLEMSAEQLAMRML  244 (434)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHh-CCCeEEEEeCcCCHHHHHHHHH
Confidence            678899999998888887665432 2357888887765555544443

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>KOG1133|consensus

Probab=88.88  E-value=0.3  Score=40.32  Aligned_cols=38  Identities=16%  Similarity=0.182  Sum_probs=26.6

Q ss_pred             CCCCeEEEecHHHHHhchhc---cccccccEEEEeCCcccCC
Q psy1090          96 LKLPLILVTTPQIIENDFGF---LKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~---~~~~~~~~vi~DEah~~k~  134 (169)
                      ...++ |+-.|+.+-.....   -..++=.+||+||||++-+
T Consensus       322 p~aql-V~LPYQ~LL~~stR~slgI~LkdsIvIiDEAHNlid  362 (821)
T KOG1133|consen  322 PQAQL-VTLPYQLLLHESTRKSLGISLKDSIVIIDEAHNLID  362 (821)
T ss_pred             ccccE-EeccHHHHHhHHHHHhcCccccccEEEEechhHHHH
Confidence            56677 88999998654321   1234556899999998755

>PF13500 AAA_26: AAA domain; PDB: 3OF5_A 2IOJ_A 4A0G_B 4A0R_A 4A0H_B 4A0F_B 3FMI_C 3FPA_D 3FMF_C 3FGN_A

Probab=88.81  E-value=0.79  Score=31.89  Aligned_cols=33  Identities=9%  Similarity=-0.066  Sum_probs=24.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      |.+.++|.|||..+++++..+.+++  .++-++=|
T Consensus         5 I~~t~t~vGKT~vslgL~~~l~~~g--~~v~~~KP   37 (199)
T PF13500_consen    5 ITGTDTGVGKTVVSLGLARALRRRG--IKVGYFKP   37 (199)
T ss_dssp             EEESSSSSSHHHHHHHHHHHHHHTT--SEEEEEEE
T ss_pred             EEeCCCCCCHHHHHHHHHHHHHhCC--CceEEEee
Confidence            4578999999999999998887654  34444444

...

>TIGR01287 nifH nitrogenase iron protein

Probab=88.76  E-value=0.62  Score=34.20  Aligned_cols=27  Identities=19%  Similarity=0.098  Sum_probs=20.5

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      -=|.|||.++..+...+...+  +++|+|
T Consensus         8 KGGVGKTT~a~nLA~~La~~G--~~Vlli   34 (275)
T TIGR01287         8 KGGIGKSTTTQNIAAALAEMG--KKVMIV   34 (275)
T ss_pred             CCcCcHHHHHHHHHHHHHHCC--CeEEEE
Confidence            459999999988877776554  567775

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

>PRK05748 replicative DNA helicase; Provisional

Probab=88.73  E-value=2.1  Score=33.97  Aligned_cols=45  Identities=4%  Similarity=-0.032  Sum_probs=32.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      +++-.+|+|||.-++.++...... ...+++++.....-.|....+
T Consensus       207 vIaarpg~GKT~~al~ia~~~a~~-~g~~v~~fSlEms~~~l~~R~  251 (448)
T PRK05748        207 IVAARPSVGKTAFALNIAQNVATK-TDKNVAIFSLEMGAESLVMRM  251 (448)
T ss_pred             EEEeCCCCCchHHHHHHHHHHHHh-CCCeEEEEeCCCCHHHHHHHH
Confidence            678899999998888887654322 235788887776666666555

>KOG1807|consensus

Probab=88.72  E-value=1.1  Score=37.76  Aligned_cols=60  Identities=13%  Similarity=0.165  Sum_probs=41.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC----CCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ----ALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYG   63 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~----~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g   63 (169)
                      .++...+|+|||.+++..+..+....    ...|+||+|-. +.++|....+... ....++...+
T Consensus       396 sliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligiy~~-qrpsImr~gs  460 (1025)
T KOG1807|consen  396 SLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGIYYH-QRPSIMRQGS  460 (1025)
T ss_pred             heeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHHHhc-CCceEEEecc
Confidence            36778999999999888877776543    34599999975 7888877666542 2334444433

>KOG0738|consensus

Probab=88.68  E-value=0.66  Score=36.03  Aligned_cols=43  Identities=14%  Similarity=0.170  Sum_probs=30.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFR   50 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~   50 (169)
                      |.++...+|+|||+.|=|+...      ++.+++=+.++ +...|.-|-+
T Consensus       247 gvLm~GPPGTGKTlLAKAvATE------c~tTFFNVSsstltSKwRGeSE  290 (491)
T KOG0738|consen  247 GVLMVGPPGTGKTLLAKAVATE------CGTTFFNVSSSTLTSKWRGESE  290 (491)
T ss_pred             eeeeeCCCCCcHHHHHHHHHHh------hcCeEEEechhhhhhhhccchH
Confidence            6788999999999877665543      34677777764 5568986643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=88.68  E-value=0.51  Score=39.80  Aligned_cols=39  Identities=15%  Similarity=0.124  Sum_probs=23.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNW   45 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW   45 (169)
                      |.+|.-.+|+|||..+=++....     ..+.+.+-++.++..|
T Consensus       489 giLL~GppGtGKT~lakalA~e~-----~~~fi~v~~~~l~~~~  527 (733)
T TIGR01243       489 GVLLFGPPGTGKTLLAKAVATES-----GANFIAVRGPEILSKW  527 (733)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhc-----CCCEEEEehHHHhhcc
Confidence            56788899999997776654331     1345555554444443

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF13173 AAA_14: AAA domain

Probab=88.62  E-value=0.51  Score=30.37  Aligned_cols=41  Identities=20%  Similarity=0.106  Sum_probs=25.5

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      +-.++++||+|++.+. ....+.+..-....++++||.-...
T Consensus        61 ~~~~i~iDEiq~~~~~-~~~lk~l~d~~~~~~ii~tgS~~~~  101 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPDW-EDALKFLVDNGPNIKIILTGSSSSL  101 (128)
T ss_pred             CCcEEEEehhhhhccH-HHHHHHHHHhccCceEEEEccchHH
Confidence            4567999999998642 2223333332345789998875543

>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed

Probab=88.61  E-value=7.3  Score=29.65  Aligned_cols=59  Identities=15%  Similarity=-0.058  Sum_probs=32.5

Q ss_pred             CCcHHHHHHHHHHHHHHhCCC-------------CceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHH
Q psy1090          10 RYRKSGKVIAFFCKIIEEQAL-------------EPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIER   68 (169)
Q Consensus        10 G~GKT~~~i~~i~~~~~~~~~-------------~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~   68 (169)
                      |+|||-.++.++..+..++..             +...+|.+.+.-.+--+|-........+.+.-+.++.+
T Consensus        61 GtGKTP~v~~L~~~l~~~g~~~~ilsRGYg~~~~~~~~~v~~~~~~~~~GDEp~lla~~~~~~V~V~~dR~~  132 (325)
T PRK00652         61 GTGKTPVVIALAEQLQARGLKPGVVSRGYGGKLEKGPLLVDPDHTAAEVGDEPLLIARRTGAPVAVSPDRVA  132 (325)
T ss_pred             CCChHHHHHHHHHHHHHCCCeEEEECCCCCCCcCCCCEEeCCCCChhhhCcHHHHhccCCCceEEEcCcHHH
Confidence            899999998888777653310             11255556554445556654444222334444544443

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=88.58  E-value=1.4  Score=35.28  Aligned_cols=49  Identities=18%  Similarity=0.135  Sum_probs=35.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++.-++|+|||.-++-++..-..+ ...+.|.|.-.....+..+....+.
T Consensus        25 Li~G~pGsGKT~la~qfl~~g~~~-~ge~~lyvs~eE~~~~l~~~~~~~G   73 (484)
T TIGR02655        25 LVSGTSGTGKTLFSIQFLYNGIIH-FDEPGVFVTFEESPQDIIKNARSFG   73 (484)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHh-CCCCEEEEEEecCHHHHHHHHHHcC
Confidence            467899999999998887654333 1357888887777777776666554

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]

Probab=88.57  E-value=1.2  Score=37.75  Aligned_cols=26  Identities=8%  Similarity=0.077  Sum_probs=21.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      .+|+..+|.|||..++.-...+++++
T Consensus        25 If~G~apGVGKTyaML~~a~~~~~~G   50 (890)
T COG2205          25 IFLGAAPGVGKTYAMLSEAQRLLAEG   50 (890)
T ss_pred             EEeecCCCccHHHHHHHHHHHHHHcC
Confidence            36788999999999988877776655

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=88.57  E-value=0.59  Score=34.99  Aligned_cols=25  Identities=16%  Similarity=0.177  Sum_probs=19.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      +.+++-.+|+|||..+-+++..+..
T Consensus       134 ~ilI~G~tGSGKTTll~al~~~i~~  158 (299)
T TIGR02782       134 NILVVGGTGSGKTTLANALLAEIAK  158 (299)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhhc
Confidence            4578889999999888777665543

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.

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

Probab=88.57  E-value=0.72  Score=34.65  Aligned_cols=35  Identities=17%  Similarity=0.209  Sum_probs=24.2

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHH
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNN   44 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~q   44 (169)
                      -=|.|||..+.+......+.+  .++|+|.  |.+-+..
T Consensus         9 KGGVGKTT~aaA~A~~~A~~G--~rtLlvS~Dpa~~L~d   45 (305)
T PF02374_consen    9 KGGVGKTTVAAALALALARRG--KRTLLVSTDPAHSLSD   45 (305)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--S-EEEEESSTTTHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhhCC--CCeeEeecCCCccHHH
Confidence            459999999888877666543  6788886  5555543

...

>PRK10263 DNA translocase FtsK; Provisional

Probab=88.51  E-value=2.2  Score=38.16  Aligned_cols=38  Identities=16%  Similarity=0.151  Sum_probs=27.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCC-C-ceEEEecCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQAL-E-PNLIVCPLS   40 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~-~-~~Liv~P~~   40 (169)
                      .+++-.+|+|||...-++|..+...... . ++++|=|+.
T Consensus      1013 LLIAGaTGSGKSv~LntLIlSLl~~~sPeeVrl~LIDPK~ 1052 (1355)
T PRK10263       1013 LLVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPKM 1052 (1355)
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHhCCccceEEEEECCCc
Confidence            5778899999999888888766554332 2 456666775

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=88.50  E-value=0.69  Score=33.95  Aligned_cols=28  Identities=14%  Similarity=0.043  Sum_probs=20.4

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .-=|.|||.+++.+...+.+.+  +++|+|
T Consensus         8 gKGGVGKTT~a~nLA~~La~~G--~rVllv   35 (273)
T PRK13232          8 GKGGIGKSTTTQNLTAALSTMG--NKILLV   35 (273)
T ss_pred             CCCCCcHHHHHHHHHHHHHhhC--CCeEEE
Confidence            3569999999888777665543  567776

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

Probab=88.49  E-value=3.1  Score=28.05  Aligned_cols=51  Identities=14%  Similarity=0.023  Sum_probs=31.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCC-----------------------------------------CceEEEecCcchH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQAL-----------------------------------------EPNLIVCPLSVLN   43 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~-----------------------------------------~~~Liv~P~~~l~   43 (169)
                      |.--.|+|||..+-++-..+...+..                                         +-++|++..+...
T Consensus         7 ltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~lR~~l~~dl~fs~~dR~e~~rr~~~~A~ll~~~G~ivIva~isp~~   86 (156)
T PF01583_consen    7 LTGLSGSGKTTLARALERRLFARGIKVYLLDGDNLRHGLNADLGFSKEDREENIRRIAEVAKLLADQGIIVIVAFISPYR   86 (156)
T ss_dssp             EESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHHCTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTTSEEEEE----SH
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcchhhccCCCCCCCHHHHHHHHHHHHHHHHHHHhCCCeEEEeeccCch
Confidence            45568999998777776666544322                                         4566666666667


Q ss_pred             HHHHHHHHhCCC
Q psy1090          44 NWEAEFRKFAPF   55 (169)
Q Consensus        44 qW~~e~~~~~~~   55 (169)
                      .+.+..++..+.
T Consensus        87 ~~R~~~R~~~~~   98 (156)
T PF01583_consen   87 EDREWARELIPN   98 (156)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCc
Confidence            777777666653

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

>PF05729 NACHT: NACHT domain

Probab=88.33  E-value=0.93  Score=30.00  Aligned_cols=25  Identities=20%  Similarity=0.115  Sum_probs=19.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      +|..+.|.|||..+-.++.......
T Consensus         4 ~I~G~~G~GKStll~~~~~~~~~~~   28 (166)
T PF05729_consen    4 WISGEPGSGKSTLLRKLAQQLAEEE   28 (166)
T ss_pred             EEECCCCCChHHHHHHHHHHHHhcC
Confidence            5678999999988877776665554

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=88.24  E-value=1.2  Score=29.27  Aligned_cols=37  Identities=14%  Similarity=0.023  Sum_probs=25.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL   42 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l   42 (169)
                      ++.-++|+|||..+..++.....  ..++++++......
T Consensus         3 ~i~G~~G~GKT~l~~~i~~~~~~--~~~~v~~~~~e~~~   39 (165)
T cd01120           3 LVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEI   39 (165)
T ss_pred             eEeCCCCCCHHHHHHHHHHHHHh--cCCEEEEEECCcch
Confidence            45678999999888877665543  34567766655433

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=88.19  E-value=0.73  Score=34.90  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=18.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      +.+++-.+|+|||...-+++..+.
T Consensus       146 nilI~G~tGSGKTTll~aL~~~i~  169 (323)
T PRK13833        146 NIVISGGTGSGKTTLANAVIAEIV  169 (323)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHh
Confidence            457889999999988877766554

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

Probab=88.05  E-value=1.5  Score=30.12  Aligned_cols=51  Identities=12%  Similarity=0.103  Sum_probs=33.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh--------CCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE--------QALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~--------~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      .++.-+.|+|||..++.++..+...        ....++|++....-..+..+.+....
T Consensus        35 ~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~~~~~~rl~~~~   93 (193)
T PF13481_consen   35 TLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDSESQIARRLRALL   93 (193)
T ss_dssp             EEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-HHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCCHHHHHHHHHHHh
Confidence            3567789999999888887766532        13457888888777667776666554

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=88.00  E-value=3.9  Score=33.54  Aligned_cols=23  Identities=17%  Similarity=0.160  Sum_probs=18.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+-+++..+..
T Consensus        42 Lf~Gp~G~GKTt~Ar~lAk~L~c   64 (563)
T PRK06647         42 IFSGPRGVGKTSSARAFARCLNC   64 (563)
T ss_pred             EEECCCCCCHHHHHHHHHHhhcc
Confidence            57789999999988888766654

>TIGR01969 minD_arch cell division ATPase MinD, archaeal

Probab=87.92  E-value=0.78  Score=32.94  Aligned_cols=31  Identities=6%  Similarity=-0.032  Sum_probs=22.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +.+.-=|.|||.+++.+...+...+  .++|+|
T Consensus         5 v~~~KGGvGKTt~a~~LA~~la~~g--~~Vlli   35 (251)
T TIGR01969         5 IASGKGGTGKTTITANLGVALAKLG--KKVLAL   35 (251)
T ss_pred             EEcCCCCCcHHHHHHHHHHHHHHCC--CeEEEE
Confidence            3445569999999988877666543  567776

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

>PRK13236 nitrogenase reductase; Reviewed

Probab=87.89  E-value=0.77  Score=34.26  Aligned_cols=27  Identities=22%  Similarity=0.106  Sum_probs=19.7

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      -=|.|||.+++.+...+.+.+  +++|+|
T Consensus        14 KGGVGKTt~a~NLA~~La~~G--~rVLli   40 (296)
T PRK13236         14 KGGIGKSTTSQNTLAAMAEMG--QRILIV   40 (296)
T ss_pred             CCcCCHHHHHHHHHHHHHHCC--CcEEEE
Confidence            348999999988877766543  566666

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

Probab=87.88  E-value=0.93  Score=31.06  Aligned_cols=33  Identities=9%  Similarity=-0.019  Sum_probs=22.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +.+.--|.|||..+..+...+...  ..++|++--
T Consensus         3 v~~~kGG~GKTt~a~~la~~la~~--g~~VlliD~   35 (195)
T PF01656_consen    3 VTSGKGGVGKTTIAANLAQALARK--GKKVLLIDL   35 (195)
T ss_dssp             EEESSTTSSHHHHHHHHHHHHHHT--TS-EEEEEE
T ss_pred             EEcCCCCccHHHHHHHHHhccccc--ccccccccc
Confidence            345567999999998887777663  366766654

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

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

Probab=87.78  E-value=1.1  Score=26.56  Aligned_cols=30  Identities=7%  Similarity=0.037  Sum_probs=19.7

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      ....|+|||..+..++..+.+.+  .+++++-
T Consensus         5 ~g~~G~Gktt~~~~l~~~l~~~g--~~v~~~~   34 (99)
T cd01983           5 TGKGGVGKTTLAANLAAALAKRG--KRVLLID   34 (99)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCC--CeEEEEC
Confidence            33459999999888877765532  3454443

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

>PRK09354 recA recombinase A; Provisional

Probab=87.67  E-value=6.1  Score=30.36  Aligned_cols=38  Identities=11%  Similarity=0.045  Sum_probs=28.4

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNN   44 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~q   44 (169)
                      +.-+.|+|||..++.++......  .+++++|-..+...+
T Consensus        65 I~G~~GsGKTtLal~~~~~~~~~--G~~~~yId~E~s~~~  102 (349)
T PRK09354         65 IYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDP  102 (349)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchHH
Confidence            55689999999888877655433  477888888777664

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=87.54  E-value=2  Score=34.69  Aligned_cols=48  Identities=13%  Similarity=-0.006  Sum_probs=34.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++..++|+|||.-++.++......  ..+++++.-.....+-.+.+..+.
T Consensus       277 li~G~~G~GKT~l~~~~~~~~~~~--g~~~~yis~e~~~~~i~~~~~~~g  324 (509)
T PRK09302        277 LVSGATGTGKTLLASKFAEAACRR--GERCLLFAFEESRAQLIRNARSWG  324 (509)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecCCHHHHHHHHHHcC
Confidence            467799999999998887665443  367888877666666555555543

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=87.28  E-value=2.1  Score=32.47  Aligned_cols=25  Identities=8%  Similarity=0.069  Sum_probs=20.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|+||+..+..++..+...+
T Consensus        29 L~~G~~G~Gk~~lA~~~a~~llC~~   53 (319)
T PRK06090         29 LLQSDEGLGVESLVELFSRALLCQN   53 (319)
T ss_pred             eeECCCCCCHHHHHHHHHHHHcCCC
Confidence            4677899999999999888877654

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

Probab=87.21  E-value=0.6  Score=38.76  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=26.2

Q ss_pred             CCCCeEEEecHHHHHhchhcccc----ccccEEEEeCCcccCC
Q psy1090          96 LKLPLILVTTPQIIENDFGFLKK----ITWNCIIVDEGHSVKN  134 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~~~~----~~~~~vi~DEah~~k~  134 (169)
                      ...++ ++++++.+..+...-..    .+-.++|+||||++-.
T Consensus       193 ~~ad~-vv~nh~~~~~~~~~~~~~~~~p~~~v~v~DEAH~l~d  234 (654)
T COG1199         193 ENADL-VVTNHALLLADVALEESRILLPENDVVVFDEAHNLPD  234 (654)
T ss_pred             hhCCE-EEEccHHHHhHHHhhhhhccCCcccEEEEeccccchH
Confidence            45677 88888887764432222    2467999999999854

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=87.13  E-value=4  Score=30.92  Aligned_cols=25  Identities=16%  Similarity=0.239  Sum_probs=20.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|+||+..+.+++..+...+
T Consensus        30 Lf~Gp~G~GK~~lA~~lA~~LlC~~   54 (319)
T PRK08769         30 LICGPEGLGKRAVALALAEHVLASG   54 (319)
T ss_pred             eeECCCCCCHHHHHHHHHHHHhCCC
Confidence            4677899999999999988877654

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=87.10  E-value=1.2  Score=31.66  Aligned_cols=35  Identities=20%  Similarity=0.183  Sum_probs=25.9

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +.--+|+|||.++-.++..+.. ....+++|+=|..
T Consensus        28 I~G~TGsGKS~~~~~ll~~l~~-~~~~~~ii~D~~G   62 (229)
T PF01935_consen   28 IFGTTGSGKSNTVKVLLEELLK-KKGAKVIIFDPHG   62 (229)
T ss_pred             EECCCCCCHHHHHHHHHHHHHh-cCCCCEEEEcCCC
Confidence            4457899999999888887764 3345777777764

It contains several conserved aspartates and histidines that could be metal ligands.

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

Probab=87.00  E-value=2.1  Score=33.05  Aligned_cols=25  Identities=24%  Similarity=0.239  Sum_probs=17.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      .++-..+|+|||.++--++..+...
T Consensus        45 ~~iyG~~GTGKT~~~~~v~~~l~~~   69 (366)
T COG1474          45 IIIYGPTGTGKTATVKFVMEELEES   69 (366)
T ss_pred             EEEECCCCCCHhHHHHHHHHHHHhh
Confidence            4566789999998886666555443

>cd01394 radB RadB

Probab=86.93  E-value=1.1  Score=31.68  Aligned_cols=34  Identities=9%  Similarity=-0.007  Sum_probs=24.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      .+.-++|+|||..++.++......  ..+++++.-.
T Consensus        23 ~i~G~~GsGKT~l~~~~a~~~~~~--g~~v~yi~~e   56 (218)
T cd01394          23 QVYGPPGTGKTNIAIQLAVETAGQ--GKKVAYIDTE   56 (218)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEECC
Confidence            466799999999988887665433  3567777543

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

>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2

Probab=86.77  E-value=1.4  Score=30.24  Aligned_cols=33  Identities=18%  Similarity=0.116  Sum_probs=22.9

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      .-.|++|||...+..+..+...+  .+++++-|..
T Consensus         7 ~GpM~sGKS~eLi~~~~~~~~~~--~~v~~~kp~~   39 (176)
T PF00265_consen    7 TGPMFSGKSTELIRRIHRYEIAG--KKVLVFKPAI   39 (176)
T ss_dssp             EESTTSSHHHHHHHHHHHHHHTT---EEEEEEEST
T ss_pred             ECCcCChhHHHHHHHHHHHHhCC--CeEEEEEecc
Confidence            45799999998887766554333  6677777763

7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....

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

Probab=86.73  E-value=1  Score=32.63  Aligned_cols=31  Identities=6%  Similarity=0.055  Sum_probs=21.2

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .--=|.|||.+++-+...+...+ ..++|+|=
T Consensus         9 n~KGGvGKTT~a~nLa~~La~~~-~~kVLliD   39 (259)
T COG1192           9 NQKGGVGKTTTAVNLAAALAKRG-GKKVLLID   39 (259)
T ss_pred             ecCCCccHHHHHHHHHHHHHHhc-CCcEEEEe
Confidence            34459999999998877765333 25676665

>PRK10689 transcription-repair coupling factor; Provisional

Probab=86.61  E-value=24  Score=31.83  Aligned_cols=92  Identities=16%  Similarity=0.137  Sum_probs=58.0

Q ss_pred             CCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHH--HHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecH
Q psy1090          30 LEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIE--RKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTP  106 (169)
Q Consensus        30 ~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty  106 (169)
                      .+.++|+||. ..+....+.+.+..|+.++..++|....  +...-.....                  ++.++ +++| 
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~------------------Gk~~V-LVaT-  868 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHH------------------QRFNV-LVCT-  868 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHh------------------cCCCE-EEEC-
Confidence            4689999987 4456677788888888999999986433  3222222221                  67788 7777 


Q ss_pred             HHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc
Q psy1090         107 QIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL  146 (169)
Q Consensus       107 ~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l  146 (169)
                      +.+.+..+.   -+.+.+|++.++++.  -++.++...+.
T Consensus       869 dIierGIDI---P~v~~VIi~~ad~fg--laq~~Qr~GRv  903 (1147)
T PRK10689        869 TIIETGIDI---PTANTIIIERADHFG--LAQLHQLRGRV  903 (1147)
T ss_pred             chhhccccc---ccCCEEEEecCCCCC--HHHHHHHhhcc
Confidence            445443331   246788998887653  24455555444

>PHA02542 41 41 helicase; Provisional

Probab=86.59  E-value=1.8  Score=34.60  Aligned_cols=45  Identities=9%  Similarity=-0.060  Sum_probs=32.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+++-.+|+|||.-++.++.....  ...+++++.-..-..|+...+
T Consensus       193 iiIaarPgmGKTtfalniA~~~a~--~g~~Vl~fSLEM~~~ql~~Rl  237 (473)
T PHA02542        193 NVLLAGVNVGKSLGLCSLAADYLQ--QGYNVLYISMEMAEEVIAKRI  237 (473)
T ss_pred             EEEEcCCCccHHHHHHHHHHHHHh--cCCcEEEEeccCCHHHHHHHH
Confidence            368889999999998888766543  246788886555556665554

>KOG2825|consensus

Probab=86.54  E-value=3  Score=30.60  Aligned_cols=44  Identities=16%  Similarity=0.253  Sum_probs=26.7

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchH-HHHHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLN-NWEAEFR   50 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~-qW~~e~~   50 (169)
                      ++.-=|.|||.++.+++..+  .+...++|||.  |.|.+. .+.+.|-
T Consensus        24 VGGKGGVGKTTcs~sLAvql--a~~r~~vLiISTDPAHNlSDAF~qkft   70 (323)
T KOG2825|consen   24 VGGKGGVGKTTCSCSLAVQL--AKVRESVLIISTDPAHNLSDAFSQKFT   70 (323)
T ss_pred             EcCcCCcCccchhhHHHHHH--hccCCceEEeecCcccchHHHHHHHhc
Confidence            34456999998887765433  33345688887  455554 3444443

>PRK13695 putative NTPase; Provisional

Probab=86.51  E-value=4.9  Score=27.22  Aligned_cols=130  Identities=17%  Similarity=0.047  Sum_probs=0.0

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhh-cCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEAL-SLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~~   79 (169)
                      |-..|..+.|+|||...-.++..+.. ......-+++         +++.............-....+..+....+ ...
T Consensus         1 ~~i~ltG~~G~GKTTll~~i~~~l~~-~G~~~~g~~~---------~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   70 (174)
T PRK13695          1 MKIGITGPPGVGKTTLVLKIAELLKE-EGYKVGGFYT---------EEVREGGKRIGFKIIDLDTGEEGILARVGFPSRP   70 (174)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEEc---------HHHHhcCCccceEEEEcCCCCeEEccccCCCCCC


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEe
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLT  155 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT  155 (169)
                      ..              ..+-. .+...+.+........-.+.+++++||.-.+-.......+.+..+ .....++++
T Consensus        71 ~~--------------~~~~~-~lsgle~~~~~l~~~~l~~~~~lllDE~~~~e~~~~~~~~~l~~~~~~~~~~i~v  132 (174)
T PRK13695         71 RV--------------GKYVV-NLEDLERIGIPALERALEEADVIIIDEIGKMELKSPKFVKAVEEVLDSEKPVIAT  132 (174)
T ss_pred             ce--------------eeEEE-ehHHHHHHHHHHHHhccCCCCEEEEECCCcchhhhHHHHHHHHHHHhCCCeEEEE

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=86.44  E-value=2.4  Score=30.28  Aligned_cols=37  Identities=16%  Similarity=0.129  Sum_probs=27.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV   41 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~   41 (169)
                      +|+-.+|+|||..++.++....... ..+++++.....
T Consensus        17 lI~G~~G~GKT~~~~~~~~~~~~~~-g~~vly~s~E~~   53 (242)
T cd00984          17 IIAARPSMGKTAFALNIAENIAKKQ-GKPVLFFSLEMS   53 (242)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHhC-CCceEEEeCCCC
Confidence            5788999999988888876655442 467888886543

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=86.29  E-value=1.2  Score=34.51  Aligned_cols=24  Identities=21%  Similarity=0.068  Sum_probs=19.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+++-++|+|||.+.-+++.++.+
T Consensus       152 ilI~G~TGSGKTT~l~al~~~i~~  175 (372)
T TIGR02525       152 GLICGETGSGKSTLAASIYQHCGE  175 (372)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            467889999999988888777654

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).

>PHA02519 plasmid partition protein SopA; Reviewed

Probab=86.23  E-value=1  Score=35.02  Aligned_cols=31  Identities=10%  Similarity=0.060  Sum_probs=23.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +...-=|.|||.+++.+...+...+  .++|+|
T Consensus       111 v~n~KGGVGKTTta~nLA~~LA~~G--~rVLlI  141 (387)
T PHA02519        111 VMSHKGGVYKTSSAVHTAQWLALQG--HRVLLI  141 (387)
T ss_pred             EecCCCCCcHHHHHHHHHHHHHhCC--CcEEEE
Confidence            4456679999999988877766544  578777

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=85.96  E-value=4.9  Score=37.09  Aligned_cols=40  Identities=13%  Similarity=0.111  Sum_probs=25.9

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhccc-cccEEEEeccCCCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTALR-ATFKVLLTGWYYPN  161 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l~-~~~~~~lT~TP~~n  161 (169)
                      +.+++|+|||-.+.+  ....+.+..+. ...|++|-|=+-|.
T Consensus       930 ~~~llIVDEASMV~~--~~m~~ll~~~~~~garvVLVGD~~QL  970 (1623)
T PRK14712        930 SNTLFLLDESSMVGN--TDMARAYALIAAGGGRAVASGDTDQL  970 (1623)
T ss_pred             CCcEEEEEccccccH--HHHHHHHHhhhhCCCEEEEEcchhhc
Confidence            457999999999854  23334444443 34688887765544

>PRK13234 nifH nitrogenase reductase; Reviewed

Probab=85.82  E-value=1.2  Score=33.31  Aligned_cols=28  Identities=21%  Similarity=0.157  Sum_probs=20.7

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .--|.|||.++..+...+.+.+  +++|+|
T Consensus        11 ~KGGvGKTt~~~nLa~~la~~g--~kVLli   38 (295)
T PRK13234         11 GKGGIGKSTTSQNTLAALVEMG--QKILIV   38 (295)
T ss_pred             CCCCccHHHHHHHHHHHHHHCC--CeEEEE
Confidence            4569999998888776665544  567777

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=85.79  E-value=1.1  Score=32.80  Aligned_cols=28  Identities=11%  Similarity=-0.162  Sum_probs=19.7

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      -=|.|||.+++.+...+.+. ..+++|+|
T Consensus        10 KGGVGKTT~a~nLA~~La~~-~G~rvLli   37 (275)
T PRK13233         10 KGGIGKSTTTQNTAAAMAYF-HDKKVFIH   37 (275)
T ss_pred             CCCCcHHHHHHHHHHHHHHh-cCCeEEEe
Confidence            55999999998876666542 12567776

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=85.78  E-value=2.9  Score=29.61  Aligned_cols=34  Identities=9%  Similarity=0.038  Sum_probs=24.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      .+.-++|+|||..++.++......  ..+++++.-.
T Consensus        27 ~i~G~~GsGKT~l~~~la~~~~~~--~~~v~yi~~e   60 (225)
T PRK09361         27 QIYGPPGSGKTNICLQLAVEAAKN--GKKVIYIDTE   60 (225)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEECC
Confidence            467799999999998887765543  3566666655

>PRK10818 cell division inhibitor MinD; Provisional

Probab=85.72  E-value=1.2  Score=32.55  Aligned_cols=30  Identities=7%  Similarity=0.108  Sum_probs=20.5

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      ..--=|.|||..++.+...+...+  +++++|
T Consensus         8 ~s~KGGvGKTt~a~nlA~~la~~g--~~vllv   37 (270)
T PRK10818          8 TSGKGGVGKTTSSAAIATGLAQKG--KKTVVI   37 (270)
T ss_pred             EeCCCCCcHHHHHHHHHHHHHHCC--CeEEEE
Confidence            344569999999988877665443  455555

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=85.70  E-value=2.5  Score=34.12  Aligned_cols=49  Identities=14%  Similarity=0.139  Sum_probs=35.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      ++.-++|+|||.-++.++...... ...++++|.-.....+-.+.+..+.
T Consensus        35 li~G~pGsGKT~l~~qf~~~~~~~-~ge~~lyis~ee~~~~i~~~~~~~g   83 (509)
T PRK09302         35 LVSGTAGTGKTLFALQFLVNGIKR-FDEPGVFVTFEESPEDIIRNVASFG   83 (509)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHh-cCCCEEEEEccCCHHHHHHHHHHcC
Confidence            567899999999988887654443 1367888887777666666665553

>TIGR02016 BchX chlorophyllide reductase iron protein subunit X

Probab=85.68  E-value=1.2  Score=33.28  Aligned_cols=29  Identities=14%  Similarity=-0.081  Sum_probs=21.0

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .--|.|||.++..+...+.+.+  +++|+|-
T Consensus         7 gKGGvGKTT~a~nLA~~La~~g--~rVLlID   35 (296)
T TIGR02016         7 GKGGSGKSFTTTNLSHMMAEMG--KRVLQLG   35 (296)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCC--CeEEEEE
Confidence            3569999999988877766543  5666654

This model represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or "iron" protein.

>PRK13705 plasmid-partitioning protein SopA; Provisional

Probab=85.60  E-value=1.1  Score=34.81  Aligned_cols=40  Identities=13%  Similarity=0.085  Sum_probs=27.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE-e--cCcchHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV-C--PLSVLNNW   45 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv-~--P~~~l~qW   45 (169)
                      +....=|.|||.+++.+...+...+  .++|+| +  |...+..|
T Consensus       111 i~n~KGGVGKTT~a~nLA~~LA~~G--~rVLlID~~DpQ~nlt~~  153 (388)
T PRK13705        111 VAAHKGGVYKTSVSVHLAQDLALKG--LRVLLVEGNDPQGTASMY  153 (388)
T ss_pred             EECCCCCchHHHHHHHHHHHHHhcC--CCeEEEcCCCCCCchhhh
Confidence            4455679999999988877665544  678877 3  65555444

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=85.53  E-value=5.2  Score=37.30  Aligned_cols=39  Identities=13%  Similarity=0.131  Sum_probs=25.7

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhccc-cccEEEEeccCCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTALR-ATFKVLLTGWYYP  160 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l~-~~~~~~lT~TP~~  160 (169)
                      .-+++|+||+-.+.+  ......+..+. ...+++|-|=+-|
T Consensus      1062 ~~~llIVDEaSMv~~--~~m~~Ll~~~~~~garvVLVGD~~Q 1101 (1747)
T PRK13709       1062 SNTLFLLDESSMVGN--TDMARAYALIAAGGGRAVSSGDTDQ 1101 (1747)
T ss_pred             CCcEEEEEccccccH--HHHHHHHHhhhcCCCEEEEecchHh
Confidence            447899999999853  33344555554 3568888775554

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=85.44  E-value=2.8  Score=30.13  Aligned_cols=38  Identities=8%  Similarity=0.028  Sum_probs=25.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH----------hCCCCceEEEecCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE----------EQALEPNLIVCPLS   40 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~----------~~~~~~~Liv~P~~   40 (169)
                      ++|+-+.|+|||..++.++.....          ....+++|+++-..
T Consensus         4 ~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed   51 (239)
T cd01125           4 SALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED   51 (239)
T ss_pred             eEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC
Confidence            578889999999988887665431          12345677777543

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK13869 plasmid-partitioning protein RepA; Provisional

Probab=85.37  E-value=1.2  Score=34.89  Aligned_cols=41  Identities=15%  Similarity=-0.056  Sum_probs=27.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWE   46 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~   46 (169)
                      +...-=|.|||.+++.+...+...+  .++|+|=  |...+..|.
T Consensus       126 v~n~KGGvGKTTta~nLA~~LA~~G--~rVLlIDlDpQ~~lt~~~  168 (405)
T PRK13869        126 VTNFKGGSGKTTTSAHLAQYLALQG--YRVLAVDLDPQASLSALL  168 (405)
T ss_pred             EEcCCCCCCHHHHHHHHHHHHHhcC--CceEEEcCCCCCCHHHHc
Confidence            3445679999999988877665544  5677763  555555553

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

Probab=85.34  E-value=1.5  Score=31.90  Aligned_cols=14  Identities=21%  Similarity=0.339  Sum_probs=10.4

Q ss_pred             cccCCCCCcHHHHH
Q psy1090           4 VIPDPTRYRKSGKV   17 (169)
Q Consensus         4 iL~de~G~GKT~~~   17 (169)
                      .+.-+.|.|||..+
T Consensus        20 ~I~G~~G~GKTTLl   33 (249)
T cd01128          20 LIVAPPKAGKTTLL   33 (249)
T ss_pred             EEECCCCCCHHHHH
Confidence            45567999999544

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

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=85.27  E-value=6.8  Score=30.05  Aligned_cols=25  Identities=8%  Similarity=-0.011  Sum_probs=20.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      ++..+.|.||+..+..+...+...+
T Consensus        25 Lf~Gp~G~GK~~lA~~~A~~LlC~~   49 (342)
T PRK06964         25 LLHGQAGIGKLDFAQHLAQGLLCET   49 (342)
T ss_pred             EEECCCCCCHHHHHHHHHHHHcCCC
Confidence            4677899999999999988776644

>PRK00090 bioD dithiobiotin synthetase; Reviewed

Probab=85.22  E-value=1.7  Score=30.78  Aligned_cols=25  Identities=20%  Similarity=0.026  Sum_probs=20.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      |.+.++|.|||..+++++..+.+++
T Consensus         4 I~~t~t~~GKT~vs~~L~~~l~~~g   28 (222)
T PRK00090          4 VTGTDTDVGKTVVTAALAQALREAG   28 (222)
T ss_pred             EEeCCCCcCHHHHHHHHHHHHHHcC
Confidence            4567899999999999988877665

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=85.20  E-value=3.5  Score=28.76  Aligned_cols=35  Identities=9%  Similarity=0.019  Sum_probs=24.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      .+.-++|+|||.-++.++......  ..+++.+.-..
T Consensus        16 ~i~G~~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~   50 (209)
T TIGR02237        16 QIYGPPGSGKTNICMILAVNAARQ--GKKVVYIDTEG   50 (209)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC
Confidence            356789999999888877655433  35777777654

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

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=85.19  E-value=1.3  Score=33.48  Aligned_cols=34  Identities=18%  Similarity=0.177  Sum_probs=21.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEE
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLI   35 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Li   35 (169)
                      +.+++-.+|+|||...-+++..+.......++++
T Consensus       150 ~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivt  183 (319)
T PRK13894        150 NILVIGGTGSGKTTLVNAIINEMVIQDPTERVFI  183 (319)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEE
Confidence            3577889999999776666655432233334443

>PRK11054 helD DNA helicase IV; Provisional

Probab=85.11  E-value=1.7  Score=36.49  Aligned_cols=49  Identities=10%  Similarity=-0.022  Sum_probs=33.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCC--CCceEEEecCcchHHHHH-HHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQA--LEPNLIVCPLSVLNNWEA-EFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~--~~~~Liv~P~~~l~qW~~-e~~~~   52 (169)
                      ++.-..|+|||.+.++-+.++...+.  ...+|+++.+.-..+... .+...
T Consensus       213 lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~  264 (684)
T PRK11054        213 LVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRER  264 (684)
T ss_pred             EEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHh
Confidence            34456899999999999888876543  347899998765544333 34433

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=85.10  E-value=7  Score=29.86  Aligned_cols=47  Identities=17%  Similarity=0.181  Sum_probs=27.7

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcc-----hHHHHHHHHHhC
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSV-----LNNWEAEFRKFA   53 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~-----l~qW~~e~~~~~   53 (169)
                      +.-.+|+|||...-.++..+...+  .++.|+.  |.+.     +-.|........
T Consensus        61 i~G~~GaGKSTl~~~l~~~l~~~g--~~v~vi~~Dp~s~~~~gallgd~~r~~~~~  114 (332)
T PRK09435         61 ITGVPGVGKSTFIEALGMHLIEQG--HKVAVLAVDPSSTRTGGSILGDKTRMERLS  114 (332)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCC--CeEEEEEeCCCccccchhhhchHhHHHhhc
Confidence            445689999977666666555433  3444443  5543     345766666544

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

Probab=85.10  E-value=1.6  Score=29.47  Aligned_cols=31  Identities=6%  Similarity=-0.007  Sum_probs=23.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +..---|.|||..+..+...+.+.+  .++++|
T Consensus         4 v~~~kgG~GKtt~a~~la~~l~~~g--~~vllv   34 (179)
T cd02036           4 VTSGKGGVGKTTTTANLGTALAQLG--YKVVLI   34 (179)
T ss_pred             EeeCCCCCCHHHHHHHHHHHHHhCC--CeEEEE
Confidence            4455679999999988877765543  678887

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

>TIGR01007 eps_fam capsular exopolysaccharide family

Probab=84.92  E-value=1.6  Score=30.38  Aligned_cols=32  Identities=9%  Similarity=0.005  Sum_probs=23.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-..|.|||..+..+...+.+.+  .++|+|=
T Consensus        22 v~s~kgG~GKTt~a~~LA~~la~~G--~rVllID   53 (204)
T TIGR01007        22 ITSVKPGEGKSTTSANIAVAFAQAG--YKTLLID   53 (204)
T ss_pred             EecCCCCCCHHHHHHHHHHHHHhCC--CeEEEEe
Confidence            4456789999999888877665543  5677763

This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes.

>PRK01906 tetraacyldisaccharide 4'-kinase; Provisional

Probab=84.86  E-value=10  Score=29.09  Aligned_cols=59  Identities=15%  Similarity=-0.033  Sum_probs=32.4

Q ss_pred             CCcHHHHHHHHHHHHHHhCCC------------CceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHH
Q psy1090          10 RYRKSGKVIAFFCKIIEEQAL------------EPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIER   68 (169)
Q Consensus        10 G~GKT~~~i~~i~~~~~~~~~------------~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~   68 (169)
                      |+|||-.++.++..+...+..            +...+|.|.+.-.+--+|-........+-+.-+..+.+
T Consensus        68 GTGKTP~v~~La~~l~~~G~~~~IlSRGYg~~~~~~~~v~~~~~~~~~GDEpllla~~~~~~V~V~~dR~~  138 (338)
T PRK01906         68 GTGKTPTVIALVDALRAAGFTPGVVSRGYGAKIKHPTAVTPASRASDAGDEPLLIARRTDAPVWVCPDRVA  138 (338)
T ss_pred             CCChHHHHHHHHHHHHHcCCceEEEecCCCCCCCCCeEEcCCCChhhhCcHHHHhhhcCCCeEEEeCcHHH
Confidence            899999999988877664311            11355666654444445543333222334444444443

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=84.62  E-value=3  Score=30.36  Aligned_cols=41  Identities=15%  Similarity=-0.019  Sum_probs=30.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNN   44 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~q   44 (169)
                      .+|+-.+|.|||.-++.++......+ ..+++++.....-.+
T Consensus        22 ~vi~a~pg~GKT~~~l~ia~~~a~~~-~~~vly~SlEm~~~~   62 (259)
T PF03796_consen   22 TVIAARPGVGKTAFALQIALNAALNG-GYPVLYFSLEMSEEE   62 (259)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT-SSEEEEEESSS-HHH
T ss_pred             EEEEecccCCchHHHHHHHHHHHHhc-CCeEEEEcCCCCHHH
Confidence            36788899999999988887766543 278888888755554

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=84.43  E-value=7  Score=37.06  Aligned_cols=38  Identities=11%  Similarity=-0.097  Sum_probs=26.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      ++.-..|+|||...-+++......  ..++++++|..-..
T Consensus       450 ii~G~aGTGKTt~l~~l~~~~~~~--G~~V~~lAPTgrAA  487 (1960)
T TIGR02760       450 IINGFGGTGSTEIAQLLLHLASEQ--GYEIQIITAGSLSA  487 (1960)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHhc--CCeEEEEeCCHHHH
Confidence            556678999997766665544333  36789999987544

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

>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ

Probab=84.41  E-value=1.7  Score=31.19  Aligned_cols=32  Identities=13%  Similarity=0.033  Sum_probs=22.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+.--|.|||..++.+...+.+.+  .++|+|=
T Consensus         6 v~s~KGGvGKTt~a~nla~~la~~g--~~VlliD   37 (246)
T TIGR03371         6 IVGVKGGVGKTTLTANLASALKLLG--EPVLAID   37 (246)
T ss_pred             EEeCCCCccHHHHHHHHHHHHHhCC--CcEEEEe
Confidence            3445679999999988877766543  5666664

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

>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=84.33  E-value=0.86  Score=33.34  Aligned_cols=23  Identities=26%  Similarity=0.268  Sum_probs=17.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+++-++|+|||.+.-+++..+.
T Consensus       130 ili~G~tGSGKTT~l~all~~i~  152 (270)
T PF00437_consen  130 ILISGPTGSGKTTLLNALLEEIP  152 (270)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHCH
T ss_pred             EEEECCCccccchHHHHHhhhcc
Confidence            46778999999988877765544

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 ....

>TIGR01968 minD_bact septum site-determining protein MinD

Probab=83.58  E-value=1.9  Score=31.12  Aligned_cols=31  Identities=3%  Similarity=0.018  Sum_probs=22.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +.+-.-|.|||..+..+...+...+  .++++|
T Consensus         6 v~s~kGGvGKTt~a~~lA~~la~~g--~~vlli   36 (261)
T TIGR01968         6 ITSGKGGVGKTTTTANLGTALARLG--KKVVLI   36 (261)
T ss_pred             EecCCCCccHHHHHHHHHHHHHHcC--CeEEEE
Confidence            4456679999999988877666433  456666

This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.

>KOG2028|consensus

Probab=83.23  E-value=3.9  Score=31.79  Aligned_cols=14  Identities=14%  Similarity=0.154  Sum_probs=9.1

Q ss_pred             cccCCCCCcHHHHH
Q psy1090           4 VIPDPTRYRKSGKV   17 (169)
Q Consensus         4 iL~de~G~GKT~~~   17 (169)
                      ||=..+|+|||..+
T Consensus       166 IlWGppG~GKTtlA  179 (554)
T KOG2028|consen  166 ILWGPPGTGKTTLA  179 (554)
T ss_pred             EEecCCCCchHHHH
Confidence            45567788888443

>PF02702 KdpD: Osmosensitive K+ channel His kinase sensor domain; InterPro: IPR003852 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []

Probab=83.18  E-value=1.5  Score=30.87  Aligned_cols=26  Identities=8%  Similarity=0.033  Sum_probs=20.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      .+|+..+|.|||..++.-...+..++
T Consensus         8 IflG~apGVGKTy~ML~ea~~l~~~G   33 (211)
T PF02702_consen    8 IFLGAAPGVGKTYAMLQEAHRLKEQG   33 (211)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHHHTT
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHCC
Confidence            36788999999999988777666554

Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the N-terminal domain found in KdpD sensor kinase proteins, which regulate the kdpFABC operon responsible for potassium transport []. The N-terminal domain forms part of the cytoplasmic region of the protein, which may be the sensor domain responsible for sensing turgor pressure [].; GO: 0000155 two-component sensor activity, 0004673 protein histidine kinase activity, 0000160 two-component signal transduction system (phosphorelay), 0016020 membrane; PDB: 2R8R_B.

>PRK09183 transposase/IS protein; Provisional

Probab=83.03  E-value=2.2  Score=31.24  Aligned_cols=38  Identities=16%  Similarity=0.129  Sum_probs=23.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL   42 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l   42 (169)
                      .+|..++|+|||..+.++.......+  .+++++-...++
T Consensus       105 v~l~Gp~GtGKThLa~al~~~a~~~G--~~v~~~~~~~l~  142 (259)
T PRK09183        105 IVLLGPSGVGKTHLAIALGYEAVRAG--IKVRFTTAADLL  142 (259)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEeHHHHH
Confidence            45677999999988887755433322  455555434444

>PRK07773 replicative DNA helicase; Validated

Probab=82.96  E-value=4.6  Score=35.06  Aligned_cols=48  Identities=6%  Similarity=-0.092  Sum_probs=34.0

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRK   51 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~   51 (169)
                      .+++-.+|+|||.-++.++...... ...+++++.-...-.|....+..
T Consensus       220 ivIagrPg~GKT~fal~ia~~~a~~-~~~~V~~fSlEms~~ql~~R~~s  267 (886)
T PRK07773        220 IIVAARPSMGKTTFGLDFARNCAIR-HRLAVAIFSLEMSKEQLVMRLLS  267 (886)
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHHHh-cCCeEEEEecCCCHHHHHHHHHH
Confidence            3678899999999888887665433 23578888776666666655543

>PRK06904 replicative DNA helicase; Validated

Probab=82.89  E-value=3.6  Score=33.00  Aligned_cols=47  Identities=6%  Similarity=0.010  Sum_probs=34.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      .+++--+|+|||.-++.++...... ...+++++.....-.|+...+.
T Consensus       224 iiIaarPg~GKTafalnia~~~a~~-~g~~Vl~fSlEMs~~ql~~Rll  270 (472)
T PRK06904        224 IIVAARPSMGKTTFAMNLCENAAMA-SEKPVLVFSLEMPAEQIMMRML  270 (472)
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHh-cCCeEEEEeccCCHHHHHHHHH
Confidence            3678899999998887776554322 2468889888877777776654

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=82.89  E-value=2.2  Score=30.31  Aligned_cols=22  Identities=9%  Similarity=-0.046  Sum_probs=14.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      -+|..+.|+|||..+-++....
T Consensus        45 ~~l~G~~G~GKT~La~ai~~~~   66 (227)
T PRK08903         45 FYLWGEAGSGRSHLLQALVADA   66 (227)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            3566788888887666555443

>cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell

Probab=82.85  E-value=2.1  Score=30.27  Aligned_cols=32  Identities=19%  Similarity=0.156  Sum_probs=23.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      ++.-..|.|||..+.++.....+.+  .++++|.
T Consensus         3 ~~~g~~g~Gkt~~~~~la~~~a~~g--~~~~l~~   34 (217)
T cd02035           3 FFTGKGGVGKTTIAAATAVRLAEEG--KKVLLVS   34 (217)
T ss_pred             EEeCCCCchHHHHHHHHHHHHHHCC--CcEEEEE
Confidence            4556789999999888877666544  5666664

This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.

>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]

Probab=82.85  E-value=3.8  Score=27.55  Aligned_cols=44  Identities=20%  Similarity=0.197  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCc
Q psy1090          13 KSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFV   56 (169)
Q Consensus        13 KT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~   56 (169)
                      |+.++..-+...+-++..+|.|||.|..+=++|.+..-++...+
T Consensus        19 K~at~~p~v~ammIkkAkrPLlivGp~~~dee~~E~~vKi~ekf   62 (170)
T COG1880          19 KTATAVPEVVAMMIKKAKRPLLIVGPLALDEELLELAVKIIEKF   62 (170)
T ss_pred             chhccccHHHHHHHHhcCCceEEecccccCHHHHHHHHHHHHhc
Confidence            55554433333444555689999999988678988877776433

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

Probab=82.83  E-value=0.54  Score=30.62  Aligned_cols=21  Identities=10%  Similarity=-0.015  Sum_probs=13.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~   23 (169)
                      ++|-+.+|+|||..+-++...
T Consensus         2 vLleg~PG~GKT~la~~lA~~   22 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS   22 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH
T ss_pred             EeeECCCccHHHHHHHHHHHH
Confidence            467899999999888766544

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

>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=82.79  E-value=1.4  Score=28.62  Aligned_cols=22  Identities=9%  Similarity=0.105  Sum_probs=16.0

Q ss_pred             ccccCCCCCcHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      .+|.-++|+|||..+-.++..+
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~   23 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL   23 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4677899999997765555443

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.

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

Probab=82.75  E-value=2.2  Score=29.76  Aligned_cols=38  Identities=16%  Similarity=0.106  Sum_probs=22.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh-CCCCc-eEEEecCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE-QALEP-NLIVCPLS   40 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~-~Liv~P~~   40 (169)
                      .+++-.+|+|||....+++..+... .+..- +.++=|+.
T Consensus        41 ~li~G~tgsGKS~~l~~ll~~l~~~~~p~~~~l~iiD~k~   80 (205)
T PF01580_consen   41 LLIAGATGSGKSTLLRTLLLSLALTYSPDDVQLYIIDPKG   80 (205)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTS
T ss_pred             EEEEcCCCCCccHHHHHHHHHHHHHhcCCccEEEEEcCCc
Confidence            5678899999999888887776653 22333 34444553

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

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=82.75  E-value=4.3  Score=30.50  Aligned_cols=14  Identities=14%  Similarity=0.219  Sum_probs=11.6

Q ss_pred             cccEEEEeCCcccC
Q psy1090         120 TWNCIIVDEGHSVK  133 (169)
Q Consensus       120 ~~~~vi~DEah~~k  133 (169)
                      ++.++|+||+|.+.
T Consensus        93 ~~kv~iI~~ad~m~  106 (313)
T PRK05564         93 DKKVIIIYNSEKMT  106 (313)
T ss_pred             CceEEEEechhhcC
Confidence            67789999999874

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.70  E-value=9.5  Score=31.75  Aligned_cols=22  Identities=18%  Similarity=0.078  Sum_probs=16.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++..+.|+|||..+..+...+.
T Consensus        43 Lf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         43 LFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             EEECCCCCCHHHHHHHHHHHhC
Confidence            5678899999987766665553

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=82.57  E-value=1.3  Score=35.61  Aligned_cols=46  Identities=17%  Similarity=0.121  Sum_probs=32.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      |.+|...+|+|||+.+-++...     ...+.+-+-...++..|.-|..+.
T Consensus       278 giLl~GpPGtGKT~lAkava~~-----~~~~fi~v~~~~l~sk~vGesek~  323 (494)
T COG0464         278 GVLLYGPPGTGKTLLAKAVALE-----SRSRFISVKGSELLSKWVGESEKN  323 (494)
T ss_pred             eeEEECCCCCCHHHHHHHHHhh-----CCCeEEEeeCHHHhccccchHHHH
Confidence            5688999999999887666542     124566555558888898776543

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=82.47  E-value=1.1  Score=34.57  Aligned_cols=23  Identities=13%  Similarity=0.206  Sum_probs=18.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      |.+++.++|+|||..|+++...+
T Consensus        67 giLi~GppgTGKTAlA~gIa~eL   89 (450)
T COG1224          67 GILIVGPPGTGKTALAMGIAREL   89 (450)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHh
Confidence            46789999999998888876554

>TIGR00959 ffh signal recognition particle protein

Probab=82.45  E-value=2.1  Score=33.78  Aligned_cols=33  Identities=12%  Similarity=0.031  Sum_probs=22.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +++..+|+|||.++..++.++.... ..++++|.
T Consensus       103 ~~vG~~GsGKTTtaakLA~~l~~~~-g~kV~lV~  135 (428)
T TIGR00959       103 LMVGLQGSGKTTTCGKLAYYLKKKQ-GKKVLLVA  135 (428)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHhC-CCeEEEEe
Confidence            4677899999999988877754333 23455444

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

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=82.38  E-value=2.3  Score=32.71  Aligned_cols=24  Identities=25%  Similarity=0.216  Sum_probs=18.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+++.++|+|||.+.-+++..+..
T Consensus       137 ilI~GpTGSGKTTtL~aLl~~i~~  160 (358)
T TIGR02524       137 VFITGATGSGKSTLLAAIIRELAE  160 (358)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhh
Confidence            467889999999888777766543

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.

>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA)

Probab=82.35  E-value=2  Score=31.30  Aligned_cols=40  Identities=18%  Similarity=0.161  Sum_probs=26.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNW   45 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW   45 (169)
                      ++.-..|.|||..+.++.......+  .++|+|-  |.+.+..+
T Consensus         4 ~~~gkgG~GKtt~a~~la~~~a~~g--~~vLlvd~D~~~sl~~~   45 (254)
T cd00550           4 FFGGKGGVGKTTISAATAVRLAEQG--KKVLLVSTDPAHSLSDS   45 (254)
T ss_pred             EEECCCCchHHHHHHHHHHHHHHCC--CCceEEeCCCcccHHHH
Confidence            3455689999999988877765544  5677664  44444443

This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity.

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

Probab=82.30  E-value=2.8  Score=25.61  Aligned_cols=31  Identities=10%  Similarity=0.116  Sum_probs=21.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +.+-.-|.|||..+..+...+...  ..+++++
T Consensus         4 ~~~~kgG~Gkst~~~~la~~~~~~--~~~vl~~   34 (104)
T cd02042           4 VANQKGGVGKTTTAVNLAAALARR--GKRVLLI   34 (104)
T ss_pred             EEeCCCCcCHHHHHHHHHHHHHhC--CCcEEEE
Confidence            445567999999888877766542  3466665

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

>KOG2543|consensus

Probab=82.11  E-value=3.4  Score=32.13  Aligned_cols=41  Identities=17%  Similarity=0.199  Sum_probs=30.6

Q ss_pred             ccEEEEeCCcccCCcccHHHHHHhcc-----ccccEEEEeccCCCC
Q psy1090         121 WNCIIVDEGHSVKNKKSKLSIKLTAL-----RATFKVLLTGWYYPN  161 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~~~~~~~~l-----~~~~~~~lT~TP~~n  161 (169)
                      --++|+|-++.++..++.....+.++     ....++++++++..+
T Consensus       116 ~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~  161 (438)
T KOG2543|consen  116 KVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEK  161 (438)
T ss_pred             eEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHH
Confidence            34789999999998777766666544     246678888888754

>PRK05595 replicative DNA helicase; Provisional

Probab=81.80  E-value=4.3  Score=32.19  Aligned_cols=46  Identities=7%  Similarity=-0.112  Sum_probs=33.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      +++-.+|+|||.-++.++...... ...+++++.....-.|....+.
T Consensus       205 viaarpg~GKT~~al~ia~~~a~~-~g~~vl~fSlEms~~~l~~R~~  250 (444)
T PRK05595        205 LIAARPSMGKTTFALNIAEYAALR-EGKSVAIFSLEMSKEQLAYKLL  250 (444)
T ss_pred             EEEecCCCChHHHHHHHHHHHHHH-cCCcEEEEecCCCHHHHHHHHH
Confidence            678899999999888887654322 2367888877766667666643

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=81.78  E-value=16  Score=32.06  Aligned_cols=92  Identities=18%  Similarity=0.185  Sum_probs=55.4

Q ss_pred             CCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHH--HHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecH
Q psy1090          30 LEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAI--ERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTP  106 (169)
Q Consensus        30 ~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty  106 (169)
                      .+.++|+||. .-+....+.+++..|+.++..++|.-.  ++...-.....                  +..++ +++| 
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~------------------Gk~~I-LVaT-  719 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYK------------------GEFQV-LVCT-  719 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHc------------------CCCCE-EEEC-
Confidence            4689999997 445556677777778899999999643  33322222211                  66777 7776 


Q ss_pred             HHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc
Q psy1090         107 QIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL  146 (169)
Q Consensus       107 ~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l  146 (169)
                      +.+.+..+.   -+.+.+|++.+++..  -+..++...+.
T Consensus       720 ~iie~GIDI---p~v~~VIi~~a~~~g--ls~l~Qr~GRv  754 (926)
T TIGR00580       720 TIIETGIDI---PNANTIIIERADKFG--LAQLYQLRGRV  754 (926)
T ss_pred             Chhhccccc---ccCCEEEEecCCCCC--HHHHHHHhcCC
Confidence            344443332   245678888886642  23444444443

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.

>PRK13768 GTPase; Provisional

Probab=81.66  E-value=2  Score=31.32  Aligned_cols=31  Identities=16%  Similarity=-0.051  Sum_probs=21.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      ++....|+|||..+..+...+...+  .++++|
T Consensus         6 ~v~G~~G~GKTt~~~~~~~~l~~~g--~~v~~i   36 (253)
T PRK13768          6 FFLGTAGSGKTTLTKALSDWLEEQG--YDVAIV   36 (253)
T ss_pred             EEECCCCccHHHHHHHHHHHHHhcC--CceEEE
Confidence            4566799999998888777665433  455554

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=81.63  E-value=4.8  Score=31.88  Aligned_cols=48  Identities=6%  Similarity=-0.000  Sum_probs=37.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++|.=+|+|||.-++.++..... ...+|+.|+.-.-.-.||...+...
T Consensus       200 i~AaRP~mGKTafalnia~n~a~-~~~~~v~iFSLEM~~eql~~R~Ls~  247 (435)
T COG0305         200 IVAARPGMGKTALALNIALNAAA-DGRKPVAIFSLEMSEEQLVMRLLSS  247 (435)
T ss_pred             EEccCCCCChHHHHHHHHHHHHH-hcCCCeEEEEccCCHHHHHHHhhcc
Confidence            67888999999988888877665 3356777777777788988877543

>CHL00175 minD septum-site determining protein; Validated

Probab=81.14  E-value=2.5  Score=31.09  Aligned_cols=31  Identities=6%  Similarity=-0.046  Sum_probs=22.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      +.+..-|.|||..+..+...+.+.+  .++|+|
T Consensus        20 v~s~KGGvGKTt~a~nLA~~La~~g--~~vlli   50 (281)
T CHL00175         20 ITSGKGGVGKTTTTANLGMSIARLG--YRVALI   50 (281)
T ss_pred             EEcCCCCCcHHHHHHHHHHHHHhCC--CeEEEE
Confidence            4556789999999888877666543  467766

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=80.83  E-value=2  Score=33.44  Aligned_cols=39  Identities=10%  Similarity=0.038  Sum_probs=24.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNW   45 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW   45 (169)
                      |.+|.-++|+|||..+-++....     ..+.+.+....+...|
T Consensus       167 gvLL~GppGtGKT~lAkaia~~~-----~~~~i~v~~~~l~~~~  205 (389)
T PRK03992        167 GVLLYGPPGTGKTLLAKAVAHET-----NATFIRVVGSELVQKF  205 (389)
T ss_pred             ceEEECCCCCChHHHHHHHHHHh-----CCCEEEeehHHHhHhh
Confidence            56788999999998876664432     2345555444554433

>PTZ00301 uridine kinase; Provisional

Probab=80.53  E-value=3.4  Score=29.26  Aligned_cols=21  Identities=14%  Similarity=0.191  Sum_probs=15.1

Q ss_pred             ccCCCCCcHHHHHHHHHHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++-.+|+|||..+-.+...+.
T Consensus         8 IaG~SgSGKTTla~~l~~~l~   28 (210)
T PTZ00301          8 ISGASGSGKSSLSTNIVSELM   28 (210)
T ss_pred             EECCCcCCHHHHHHHHHHHHH
Confidence            577899999977755554443

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=80.47  E-value=0.75  Score=35.47  Aligned_cols=35  Identities=14%  Similarity=0.142  Sum_probs=22.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      -+|+.++|+|||..++++...+   +..-|...+.-+.
T Consensus        53 iLiaGppGtGKTAlA~~ia~eL---G~~~PF~~isgSE   87 (398)
T PF06068_consen   53 ILIAGPPGTGKTALAMAIAKEL---GEDVPFVSISGSE   87 (398)
T ss_dssp             EEEEE-TTSSHHHHHHHHHHHC---TTTS-EEEEEGGG
T ss_pred             EEEeCCCCCCchHHHHHHHHHh---CCCCCeeEcccce
Confidence            5788999999998887776543   3344666555544

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=80.29  E-value=2.4  Score=30.78  Aligned_cols=35  Identities=11%  Similarity=0.205  Sum_probs=24.0

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      .++....|+|||...+.++......  ...+++++|.
T Consensus        16 ~viIG~sGSGKT~li~~lL~~~~~~--f~~I~l~t~~   50 (241)
T PF04665_consen   16 MVIIGKSGSGKTTLIKSLLYYLRHK--FDHIFLITPE   50 (241)
T ss_pred             EEEECCCCCCHHHHHHHHHHhhccc--CCEEEEEecC
Confidence            4677789999998887777554332  2556666674

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

>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms

Probab=80.03  E-value=3.8  Score=26.62  Aligned_cols=34  Identities=12%  Similarity=-0.014  Sum_probs=24.3

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ..-++|.|||..+..++..+.+++  .++..+=|..
T Consensus         4 ~~~~~~~Gkt~~~~~l~~~l~~~~--~~v~~~kp~~   37 (134)
T cd03109           4 FGTGTDIGKTVATAILARALKEKG--YRVAPLKPVQ   37 (134)
T ss_pred             EeCCCCcCHHHHHHHHHHHHHHCC--CeEEEEecCC
Confidence            445789999999999988876554  4555555543

The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	169
1z6a_A	500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN		1e-13
1z63_A	500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COM		1e-13
3mwy_W	800	Crystal Structure Of The Chromodomain-atpase Portio		3e-11

>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN Length = 500

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/158 (28%), Positives = 78/158 (49%), Gaps = 27/158 (17%)
Query: 5   IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGN 64
           + D     K+ + IA F    +E  L P+L++CPLSVL NWE E  KFAP +R   ++  
Sbjct: 61  LADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFH-- 118
Query: 65  AIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCI 124
                                   + + +I L+   I++TT  ++  D   LK++ W  I
Sbjct: 119 ------------------------EDRSKIKLEDYDIILTTYAVLLRD-TRLKEVEWKYI 153
Query: 125 IVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNK 162
           ++DE  ++KN ++K+   +  L++ +++ LTG    NK
Sbjct: 154 VIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENK 191

>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX With Dsdna Length = 500

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/158 (28%), Positives = 78/158 (49%), Gaps = 27/158 (17%)
Query: 5   IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGN 64
           + D     K+ + IA F    +E  L P+L++CPLSVL NWE E  KFAP +R   ++  
Sbjct: 61  LADDXGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFH-- 118
Query: 65  AIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCI 124
                                   + + +I L+   I++TT  ++  D   LK++ W  I
Sbjct: 119 ------------------------EDRSKIKLEDYDIILTTYAVLLRD-TRLKEVEWKYI 153
Query: 125 IVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNK 162
           ++DE  ++KN ++K+   +  L++ +++ LTG    NK
Sbjct: 154 VIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENK 191

>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of The Yeast Chd1 Chromatin Remodeler Length = 800

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 10/154 (6%)
Query: 4   VIPDPTRYRKSGKVIAFFCKII-EEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYY 62
           ++ D     K+ + +AF   +I   +   P++IV PLS +  W   F K+AP +  + Y 
Sbjct: 259 ILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYM 318
Query: 63  GNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWN 122
           GN   R  ++           P  KGK   + +     +L+TT + I  D   L  I W 
Sbjct: 319 GNQKSRDTIREYEFYTN----PRAKGKKTMKFN-----VLLTTYEYILKDRAELGSIKWQ 369
Query: 123 CIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
            + VDE H +KN +S L   L + +   ++L+TG
Sbjct: 370 FMAVDEAHRLKNAESSLYESLNSFKVANRMLITG 403

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	169
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	3e-38
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	1e-25
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	8e-25
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	4e-14

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Length = 800

 Score =  137 bits (346), Expect = 3e-38
 Identities = 42/146 (28%), Positives = 64/146 (43%), Gaps = 13/146 (8%)

Query: 15  GK---VIAFFCKIIEEQALE-PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKA 70
           GK    +AF   +I  +    P++IV PLS +  W   F K+AP +  + Y GN   R  
Sbjct: 267 GKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDT 326

Query: 71  LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGH 130
           ++             K  K           +L+TT + I  D   L  I W  + VDE H
Sbjct: 327 IREYEFYTNPRAKGKKTMKFN---------VLLTTYEYILKDRAELGSIKWQFMAVDEAH 377

Query: 131 SVKNKKSKLSIKLTALRATFKVLLTG 156
            +KN +S L   L + +   ++L+TG
Sbjct: 378 RLKNAESSLYESLNSFKVANRMLITG 403

>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 Length = 644

 Score =  101 bits (253), Expect = 1e-25
 Identities = 26/128 (20%), Positives = 53/128 (41%), Gaps = 14/128 (10%)

Query: 30  LEPNLIVCPLSVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLPTIKVPAKKG 88
           ++  ++V P S++ NW  E  K+    V+ V   G + +    +          +  +  
Sbjct: 114 IDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVNF------ISQQGM 167

Query: 89  KTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRA 148
           +    I       L+ + +        L K     +I DEGH +KN  ++  + L ++ A
Sbjct: 168 RIPTPI-------LIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNA 220

Query: 149 TFKVLLTG 156
             +VL++G
Sbjct: 221 QRRVLISG 228

>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 Length = 500

 Score = 98.4 bits (246), Expect = 8e-25
 Identities = 42/145 (28%), Positives = 71/145 (48%), Gaps = 30/145 (20%)

Query: 15  GK---VIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKAL 71
           GK    IA F    +E  L P+L++CPLSVL NWE E  KFAP +R   ++ +  + K  
Sbjct: 68  GKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLE 127

Query: 72  QSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHS 131
             +                          I++TT  ++  D   LK++ W  I++DE  +
Sbjct: 128 DYD--------------------------IILTTYAVLLRDTR-LKEVEWKYIVIDEAQN 160

Query: 132 VKNKKSKLSIKLTALRATFKVLLTG 156
           +KN ++K+   +  L++ +++ LTG
Sbjct: 161 IKNPQTKIFKAVKELKSKYRIALTG 185

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 68.2 bits (166), Expect = 4e-14
 Identities = 25/153 (16%), Positives = 46/153 (30%), Gaps = 31/153 (20%)

Query: 15  GK---VIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF-RKFAPFVRTVKYYGNAIERKA 70
           GK         + +   A E  LI+ P ++ + W  E  R+F    R   +         
Sbjct: 182 GKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRFNL--RFALFDDERYAEAQ 239

Query: 71  LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDE 128
             +                          L++ +      +      L +  W+ ++VDE
Sbjct: 240 HDAY------------------NPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDE 281

Query: 129 GHSVKNKKSKLS-----IKLTALRATFKVLLTG 156
            H +   +   S     I+  A      +LLT 
Sbjct: 282 AHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTA 314

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.96
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.91
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.86
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.85
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.84
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.84
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.83
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.82
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.81
3h1t_A	590	Type I site-specific restriction-modification syst	99.81
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.8
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.77
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.77
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.75
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.75
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.74
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.74
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.73
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.72
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.72
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.72
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.72
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.71
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.71
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.7
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.69
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.69
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.69
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.68
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.68
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.67
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.67
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.66
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.66
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.66
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.62
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.62
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.62
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.61
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.6
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.59
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.59
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.53
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.52
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.52
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.52
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.51
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.5
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.49
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.48
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.48
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.48
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.46
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.45
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.44
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.31
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.31
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.19
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.13
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.11
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.07
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.04
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.04
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.03
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.97
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.78
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.76
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.57
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.56
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.54
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.44
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.43
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.39
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.14
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.01
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.95
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.8
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.77
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.76
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.74
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.73
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.63
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.54
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.53
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.5
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.48
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.31
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.21
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.85
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.85
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	96.8
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.59
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	96.57
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	96.52
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.52
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.44
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.4
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.28
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.06
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.98
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	95.55
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	95.39
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	95.24
3bos_A	242	Putative DNA replication factor; P-loop containing	95.18
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	94.93
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.83
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	94.54
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	94.52
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	94.37
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.27
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	94.03
3io5_A	333	Recombination and repair protein; storage dimer, i	93.6
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	93.6
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	93.23
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	93.19
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	93.12
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	92.85
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	92.72
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	92.69
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	92.68
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	92.64
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	92.48
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	92.06
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	91.89
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	91.78
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.69
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.17
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	91.02
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.01
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	90.98
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	90.09
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	90.08
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.86
2qgz_A	308	Helicase loader, putative primosome component; str	89.8
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	89.56
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	89.53
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	88.92
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	88.66
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	88.54
3fwy_A	314	Light-independent protochlorophyllide reductase I	88.45
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	87.99
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	87.93
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	87.65
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	87.64
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	87.55
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	87.51
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	87.32
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	87.17
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	87.15
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	87.13
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	87.13
3end_A	307	Light-independent protochlorophyllide reductase ir	87.13
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	87.1
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	87.09
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	86.66
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	86.61
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	86.42
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	86.38
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	86.08
3of5_A	228	Dethiobiotin synthetase; structural genomics, cent	86.07
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	85.93
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	85.86
3qxc_A	242	Dethiobiotin synthetase; DTBS, structural genomics	85.85
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	85.75
1xp8_A	366	RECA protein, recombinase A; recombination, radior	85.66
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	85.64
2xj4_A	286	MIPZ; replication, cell division, ATPase, WACA; 1.	85.15
1wcv_1	257	SOJ, segregation protein; ATPase, bacterial, chrom	84.93
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	84.78
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	84.73
3fgn_A	251	Dethiobiotin synthetase; biotin biosynthesis, BIOD	84.19
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	83.94
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	83.91
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	83.82
3cwq_A	209	Para family chromosome partitioning protein; alpha	83.54
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	83.17
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	83.02
1u94_A	356	RECA protein, recombinase A; homologous recombinat	82.81
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	82.72
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	82.65
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	82.2
2r6a_A	454	DNAB helicase, replicative helicase; replication,	82.14
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	82.07
3pg5_A	361	Uncharacterized protein; structural genomics, PSI-	81.21
2chg_A	226	Replication factor C small subunit; DNA-binding pr	81.06
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	81.05
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	80.96
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	80.73
2xxa_A	433	Signal recognition particle protein; protein trans	80.14
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	80.07

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.4e-37  Score=254.33  Aligned_cols=160  Identities=28%  Similarity=0.434  Sum_probs=138.2

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      .||||+|+||+|||+++++++..+... ...+|+|||||.+++.||.+|+.+|+|++++..++|....+..+....+...
T Consensus       256 ~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P~sll~qW~~E~~~~~p~~~v~~~~g~~~~r~~~~~~~~~~~  335 (800)
T 3mwy_W          256 DNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTN  335 (800)
T ss_dssp             CCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECCTTTHHHHHHHHHHHSTTCCEEECCCSSHHHHHHHHHHSCSC
T ss_pred             CCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEECchHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHHHhhcc
Confidence            379999999999999999999877644 5568999999999999999999999999999999999988877666554321


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                      ..        ........+++ +++||+.+.++...+....|++||+||||++||..++.++++..+++++||+|||||+
T Consensus       336 ~~--------~~~~~~~~~dv-vitTy~~l~~~~~~l~~~~w~~vIvDEaH~lkn~~s~~~~~l~~l~~~~rl~LTgTPi  406 (800)
T 3mwy_W          336 PR--------AKGKKTMKFNV-LLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPL  406 (800)
T ss_dssp             C-------------CCCCCSE-EEECTTHHHHTHHHHHTSEEEEEEETTGGGGCCSSSHHHHHHTTSEEEEEEEECSCCC
T ss_pred             cc--------ccccccccCCE-EEecHHHHHhhHHHHhcCCcceeehhhhhhhcCchhHHHHHHHHhhhccEEEeeCCcC
Confidence            11        01112256788 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhhccC
Q psy1090         160 PNKWSKQCTL  169 (169)
Q Consensus       160 ~n~~~el~~l  169 (169)
                      +|++.|||+|
T Consensus       407 qN~l~el~~l  416 (800)
T 3mwy_W          407 QNNIKELAAL  416 (800)
T ss_dssp             SSCSHHHHHH
T ss_pred             CCCHHHHHHH
Confidence            9999999974

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=100.00  E-value=7.3e-36  Score=239.36  Aligned_cols=154  Identities=21%  Similarity=0.331  Sum_probs=124.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC-----CCceEEEecCcchHHHHHHHHHhCCC-ceEEEEeC-CHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA-----LEPNLIVCPLSVLNNWEAEFRKFAPF-VRTVKYYG-NAIERKALQSE   74 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~-----~~~~Liv~P~~~l~qW~~e~~~~~~~-~~~~~~~g-~~~~~~~~~~~   74 (169)
                      ||||+||||+|||+++++++..+...+.     .+++|||||.+++.||.+|+.+|.|. ..++.+++ ..+........
T Consensus        81 g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~sll~qW~~E~~~~~~~~~~~~~~~~g~~~~~~~~~~~  160 (644)
T 1z3i_X           81 GCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVN  160 (644)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHHHHHHHHHHHHHHHGGGCCEEEECSSCHHHHHHHHHH
T ss_pred             CeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecHHHHHHHHHHHHHHcCCCeeEEEEeCCCHHHHHHHHHH
Confidence            6899999999999999999988776542     35799999999999999999999864 55555554 43332222111


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEE
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLL  154 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~l  154 (169)
                      ......             .....++ +++||+.+..+...+....|+++|+||||++||+.++.++++..+++++||+|
T Consensus       161 ~~~~~~-------------~~~~~~v-vi~ty~~l~~~~~~l~~~~~~~vI~DEaH~ikn~~~~~~~al~~l~~~~rl~L  226 (644)
T 1z3i_X          161 FISQQG-------------MRIPTPI-LIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLI  226 (644)
T ss_dssp             HHCCCS-------------SCCSCCE-EEEEHHHHHHHTTTTTTSCCCEEEETTGGGCCTTCHHHHHHHHHHCCSEEEEE
T ss_pred             HHHhcC-------------CCCCCcE-EEeeHHHHHhhHHHhhcCCccEEEEECceecCChhhHHHHHHHhcccCcEEEE
Confidence            111000             0134567 99999999998888888999999999999999999999999999999999999


Q ss_pred             eccCCCCCchhhccC
Q psy1090         155 TGWYYPNKWSKQCTL  169 (169)
Q Consensus       155 T~TP~~n~~~el~~l  169 (169)
                      ||||++|++.|||+|
T Consensus       227 TgTPiqN~l~El~sl  241 (644)
T 1z3i_X          227 SGTPIQNDLLEYFSL  241 (644)
T ss_dssp             CSSCSGGGGGGCHHH
T ss_pred             ecCcccCCHHHHHHH
Confidence            999999999999975

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=100.00  E-value=4.1e-35  Score=229.09  Aligned_cols=141  Identities=30%  Similarity=0.539  Sum_probs=124.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      ||+|+|+||+|||+++++++..+...+..+++|||||.+++.||.+|+.+|.|+.++..++|....      .       
T Consensus        58 ~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P~~l~~qw~~e~~~~~~~~~v~~~~g~~~~------~-------  124 (500)
T 1z63_A           58 GICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSK------I-------  124 (500)
T ss_dssp             CEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECSTTHHHHHHHHHHHCTTSCEEECSSSTTS------C-------
T ss_pred             CEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEccHHHHHHHHHHHHHHCCCceEEEEecCchh------c-------
Confidence            789999999999999999998888777778999999999999999999999999999888876521      0       


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                                  .....++ +++||+.+.++.. +....|+++|+||||+++|..++.++++..++++++++|||||++|
T Consensus       125 ------------~~~~~~i-vi~t~~~l~~~~~-l~~~~~~~vIvDEaH~~kn~~~~~~~~l~~l~~~~~l~LTaTP~~n  190 (500)
T 1z63_A          125 ------------KLEDYDI-ILTTYAVLLRDTR-LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIEN  190 (500)
T ss_dssp             ------------CGGGSSE-EEEEHHHHTTCHH-HHTCCEEEEEEETGGGGSCTTSHHHHHHHTSCEEEEEEECSSCSTT
T ss_pred             ------------cccCCcE-EEeeHHHHhccch-hcCCCcCEEEEeCccccCCHhHHHHHHHHhhccCcEEEEecCCCCC
Confidence                        0145677 9999999987765 6677999999999999999999999999999999999999999999


Q ss_pred             CchhhccC
Q psy1090         162 KWSKQCTL  169 (169)
Q Consensus       162 ~~~el~~l  169 (169)
                      ++.|||++
T Consensus       191 ~~~el~~l  198 (500)
T 1z63_A          191 KVDDLWSI  198 (500)
T ss_dssp             CHHHHHHH
T ss_pred             CHHHHHHH
Confidence            99999864

>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=99.96  E-value=4.7e-30  Score=213.18  Aligned_cols=148  Identities=14%  Similarity=0.137  Sum_probs=118.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      +++|+|+||+|||+++++++......+..+++|||||.+++.||..|+.+++ +..+.++++............    . 
T Consensus       172 ~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~sLl~Qw~~E~~~~f-~l~v~v~~~~~~~~~~~~~~~----~-  245 (968)
T 3dmq_A          172 RVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETLQHQWLVEMLRRF-NLRFALFDDERYAEAQHDAYN----P-  245 (968)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCTTTHHHHHHHHHHHS-CCCCEECCHHHHHHHHHTTCS----S-
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCHHHHHHHHHHHHHHh-CCCEEEEccchhhhhhhhccc----c-
Confidence            6899999999999999999988888887889999999999999999998887 677777766543321111000    0 


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhch---hccccccccEEEEeCCcccCCcccHH---HHHHhcc--ccccEEE
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDF---GFLKKITWNCIIVDEGHSVKNKKSKL---SIKLTAL--RATFKVL  153 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~---~~~~~~~~~~vi~DEah~~k~~~~~~---~~~~~~l--~~~~~~~  153 (169)
                                   ....++ +++||+.+.++.   ..+....|+++|+||||++++..++.   ++.+..+  +++++|+
T Consensus       246 -------------~~~~dI-vI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~~~~L~  311 (968)
T 3dmq_A          246 -------------FDTEQL-VICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLL  311 (968)
T ss_dssp             -------------STTCSE-EEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTCSSEEE
T ss_pred             -------------cccCCE-EEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcCCcEEE
Confidence                         145677 999999997754   34566789999999999999876553   7777776  6788999


Q ss_pred             EeccCCCCCchhhccC
Q psy1090         154 LTGWYYPNKWSKQCTL  169 (169)
Q Consensus       154 lT~TP~~n~~~el~~l  169 (169)
                      |||||++|++.|+|++
T Consensus       312 LTATPi~n~~~el~sl  327 (968)
T 3dmq_A          312 LTATPEQLGMESHFAR  327 (968)
T ss_dssp             SCSSCSSSCSSCTHHH
T ss_pred             EEcCCccCCHHHHHHH
Confidence            9999999999999863

>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=99.91  E-value=4.2e-24  Score=164.96  Aligned_cols=140  Identities=19%  Similarity=0.194  Sum_probs=103.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +++++++||+|||++++.++..... +..+++|||||. .++.||.+++.+|.  +...+..++|..........  .  
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~-~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~--~--   99 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLT-KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKA--W--   99 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHH-HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHH--H--
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHh-cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhh--c--
Confidence            5799999999999999998876655 446789999998 78899999999998  55688888887544322111  1  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcccHHHH--HHh-ccccccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKSKLSI--KLT-ALRATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~~~~~--~~~-~l~~~~~~~  153 (169)
                                       ...++ +++||+.+.+...  .+...+|+++|+||||++++.......  .+. ..+..++++
T Consensus       100 -----------------~~~~i-vv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~  161 (494)
T 1wp9_A          100 -----------------ARAKV-IVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIG  161 (494)
T ss_dssp             -----------------HHCSE-EEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEE
T ss_pred             -----------------cCCCE-EEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCeEEE
Confidence                             23456 9999999987544  445568999999999999865332221  111 235788999


Q ss_pred             EeccCCCCCchh
Q psy1090         154 LTGWYYPNKWSK  165 (169)
Q Consensus       154 lT~TP~~n~~~e  165 (169)
                      |||||. |+..+
T Consensus       162 lTaTp~-~~~~~  172 (494)
T 1wp9_A          162 LTASPG-STPEK  172 (494)
T ss_dssp             EESCSC-SSHHH
T ss_pred             EecCCC-CCcHH
Confidence            999999 44333

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.86  E-value=1.2e-21  Score=142.84  Aligned_cols=132  Identities=19%  Similarity=0.170  Sum_probs=94.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +++|+++||+|||.+++.++......+ .+++||++|. .++.||.+++.+|..  ...+....+......         
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~~~~-~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~---------  199 (282)
T 1rif_A          130 RRILNLPTSAGRSLIQALLARYYLENY-EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDD---------  199 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHC-SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSSTT---------
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHcC-CCeEEEEECCHHHHHHHHHHHHHhcccccceEEEEeCCCcchh---------
Confidence            368899999999999988776655433 4589999997 788999999999963  334444444321110         


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEecc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLTGW  157 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT~T  157 (169)
                                    ......++ +++||+.+.+.... ....++++|+||||++.++  .....+..+ +..++++||||
T Consensus       200 --------------~~~~~~~I-~v~T~~~l~~~~~~-~~~~~~~vIiDEaH~~~~~--~~~~il~~~~~~~~~l~lSAT  261 (282)
T 1rif_A          200 --------------KYKNDAPV-VVGTWQTVVKQPKE-WFSQFGMMMNDECHLATGK--SISSIISGLNNCMFKFGLSGS  261 (282)
T ss_dssp             --------------CCCTTCSE-EEECHHHHTTSCGG-GGGGEEEEEEETGGGCCHH--HHHHHTTTCTTCCEEEEECSS
T ss_pred             --------------hhccCCcE-EEEchHHHHhhHHH-HHhhCCEEEEECCccCCcc--cHHHHHHHhhcCCeEEEEeCC
Confidence                          01145666 99999998776432 2247899999999999753  445566666 68899999999


Q ss_pred             CCCC
Q psy1090         158 YYPN  161 (169)
Q Consensus       158 P~~n  161 (169)
                      |..+
T Consensus       262 p~~~  265 (282)
T 1rif_A          262 LRDG  265 (282)
T ss_dssp             CCTT
T ss_pred             CCCc
Confidence            9644

>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=99.85  E-value=7e-21  Score=147.68  Aligned_cols=121  Identities=21%  Similarity=0.213  Sum_probs=95.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCce-EEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVR-TVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +++|+++||+|||.+++..+...     ..++||+||. .++.||.+++.+|  +.. +..++|...             
T Consensus       110 ~~ll~~~TGsGKT~~~l~~i~~~-----~~~~Lvl~P~~~L~~Q~~~~~~~~--~~~~v~~~~g~~~-------------  169 (472)
T 2fwr_A          110 RGCIVLPTGSGKTHVAMAAINEL-----STPTLIVVPTLALAEQWKERLGIF--GEEYVGEFSGRIK-------------  169 (472)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH-----CSCEEEEESSHHHHHHHHHHGGGG--CGGGEEEBSSSCB-------------
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHc-----CCCEEEEECCHHHHHHHHHHHHhC--CCcceEEECCCcC-------------
Confidence            37899999999999988877654     4689999999 8889999999995  556 777766532             


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCC
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~  159 (169)
                                      ...++ +++||+.+......+. ..|+++|+||||++.++..  ...+..+++.++++|||||.
T Consensus       170 ----------------~~~~I-vv~T~~~l~~~~~~~~-~~~~liIvDEaH~~~~~~~--~~~~~~~~~~~~l~lSATp~  229 (472)
T 2fwr_A          170 ----------------ELKPL-TVSTYDSAYVNAEKLG-NRFMLLIFDEVHHLPAESY--VQIAQMSIAPFRLGLTATFE  229 (472)
T ss_dssp             ----------------CCCSE-EEEEHHHHHHTHHHHT-TTCSEEEEETGGGTTSTTT--HHHHHTCCCSEEEEEESCCC
T ss_pred             ----------------CcCCE-EEEEcHHHHHHHHHhc-CCCCEEEEECCcCCCChHH--HHHHHhcCCCeEEEEecCcc
Confidence                            23456 9999999887665442 3599999999999987654  34566678899999999999


Q ss_pred             CCC
Q psy1090         160 PNK  162 (169)
Q Consensus       160 ~n~  162 (169)
                      +++
T Consensus       230 ~~~  232 (472)
T 2fwr_A          230 RED  232 (472)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.84  E-value=1.3e-20  Score=134.20  Aligned_cols=122  Identities=21%  Similarity=0.206  Sum_probs=91.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCce-EEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVR-TVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +++..++|+|||.+++.++...     .+++||++|. .++.||.+++.+|  +.. +..+.|...              
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~~-----~~~~liv~P~~~L~~q~~~~~~~~--~~~~v~~~~g~~~--------------  169 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINEL-----STPTLIVVPTLALAEQWKERLGIF--GEEYVGEFSGRIK--------------  169 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS-----CSCEEEEESSHHHHHHHHHHHGGG--CGGGEEEESSSCB--------------
T ss_pred             EEEEeCCCCCHHHHHHHHHHHc-----CCCEEEEeCCHHHHHHHHHHHHhC--CCCeEEEEeCCCC--------------
Confidence            6788999999999988776542     4689999998 7788999999985  455 666666532              


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCC
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                                     ...++ +++||+.+......+. ..|+++|+||+|++.+..  ..+.+..++..++++|||||.+
T Consensus       170 ---------------~~~~i-~v~T~~~l~~~~~~~~-~~~~llIiDEaH~l~~~~--~~~i~~~~~~~~~l~LSATp~r  230 (237)
T 2fz4_A          170 ---------------ELKPL-TVSTYDSAYVNAEKLG-NRFMLLIFDEVHHLPAES--YVQIAQMSIAPFRLGLTATFER  230 (237)
T ss_dssp             ---------------CCCSE-EEEEHHHHHHTHHHHT-TTCSEEEEECSSCCCTTT--HHHHHHTCCCSEEEEEEESCC-
T ss_pred             ---------------CcCCE-EEEeHHHHHhhHHHhc-ccCCEEEEECCccCCChH--HHHHHHhccCCEEEEEecCCCC
Confidence                           23456 9999999887665442 358999999999997643  3455566788999999999998


Q ss_pred             CCch
Q psy1090         161 NKWS  164 (169)
Q Consensus       161 n~~~  164 (169)
                      ++-.
T Consensus       231 ~D~~  234 (237)
T 2fz4_A          231 EDGR  234 (237)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            8644

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.84  E-value=1.2e-20  Score=148.41  Aligned_cols=143  Identities=16%  Similarity=0.135  Sum_probs=102.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC---CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA---LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~---~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      +++++++||+|||++++..+........   ..++|||+|. .+..||.+++.++++  +..+..++|............
T Consensus        21 ~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  100 (555)
T 3tbk_A           21 NTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHII  100 (555)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHH
T ss_pred             CEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHh
Confidence            5789999999999998888776665544   6789999998 888999999999875  678888888764332211111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--c-ccccccEEEEeCCcccCCcccHHHHHHhcc------
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--L-KKITWNCIIVDEGHSVKNKKSKLSIKLTAL------  146 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~-~~~~~~~vi~DEah~~k~~~~~~~~~~~~l------  146 (169)
                                          ...++ +++|++.+.+....  + .-..++++|+||||++.+...........+      
T Consensus       101 --------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  159 (555)
T 3tbk_A          101 --------------------EDNDI-IILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGE  159 (555)
T ss_dssp             --------------------HHCSE-EEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSS
T ss_pred             --------------------cCCCE-EEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhcc
Confidence                                33556 99999998765432  2 234689999999999987654222111222      


Q ss_pred             ---ccccEEEEeccCCCCCchh
Q psy1090         147 ---RATFKVLLTGWYYPNKWSK  165 (169)
Q Consensus       147 ---~~~~~~~lT~TP~~n~~~e  165 (169)
                         ....+++|||||.+++..+
T Consensus       160 ~~~~~~~~l~lSAT~~~~~~~~  181 (555)
T 3tbk_A          160 SRDPLPQVVGLTASVGVGDAKT  181 (555)
T ss_dssp             CCSCCCEEEEEESCCCCTTCCS
T ss_pred             ccCCCCeEEEEecCcccCcccc
Confidence               2357999999998876444

>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=99.84  E-value=1.7e-20  Score=147.74  Aligned_cols=142  Identities=16%  Similarity=0.144  Sum_probs=100.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC---CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA---LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~---~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      +++++++||+|||++++..+........   ..++||++|. .+..||.+++.++++  +.++..++|............
T Consensus        24 ~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  103 (556)
T 4a2p_A           24 NALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI  103 (556)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHH
T ss_pred             CEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhh
Confidence            4789999999999998887776665544   5789999998 788999999999976  678888888764332222111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--c-ccccccEEEEeCCcccCCcccHHHHHH-hcc-----
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--L-KKITWNCIIVDEGHSVKNKKSKLSIKL-TAL-----  146 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~-~~~~~~~vi~DEah~~k~~~~~~~~~~-~~l-----  146 (169)
                                          ...++ +++|++.+.+....  + ....++++|+||||++.+... ....+ ..+     
T Consensus       104 --------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~-~~~~~~~~~~~~~~  161 (556)
T 4a2p_A          104 --------------------EDSDI-IVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHP-YNVLMTRYLEQKFN  161 (556)
T ss_dssp             --------------------HHCSE-EEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSH-HHHHHHHHHHHHHC
T ss_pred             --------------------CCCCE-EEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcch-HHHHHHHHHHhhhc
Confidence                                33556 99999998865432  2 334689999999999987654 22222 211     


Q ss_pred             ---ccccEEEEeccCCCCCchh
Q psy1090         147 ---RATFKVLLTGWYYPNKWSK  165 (169)
Q Consensus       147 ---~~~~~~~lT~TP~~n~~~e  165 (169)
                         +...+++|||||.+++..+
T Consensus       162 ~~~~~~~~l~lSAT~~~~~~~~  183 (556)
T 4a2p_A          162 SASQLPQILGLTASVGVGNAKN  183 (556)
T ss_dssp             C---CCEEEEEESCCCCTTCSS
T ss_pred             ccCCCCeEEEEeCCcccCchhh
Confidence               2367999999998766443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.83  E-value=9.6e-21  Score=148.20  Aligned_cols=131  Identities=18%  Similarity=0.160  Sum_probs=95.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHh--CCCceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKF--APFVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~--~~~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +++|+++||+|||.+++..+......+ .+++||++|. .+..||.+++.+|  .+...+....|.......        
T Consensus       130 ~~ll~~~tGsGKT~~~~~~~~~~~~~~-~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~~~~~~~~~~~--------  200 (510)
T 2oca_A          130 RRILNLPTSAGRSLIQALLARYYLENY-EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDK--------  200 (510)
T ss_dssp             EEEEECCSTTTHHHHHHHHHHHHHHHC-SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEECGGGCCTTGG--------
T ss_pred             CcEEEeCCCCCHHHHHHHHHHHHHhCC-CCeEEEEECcHHHHHHHHHHHHHhhcCCccceEEEecCCccccc--------
Confidence            579999999999999987766555433 3599999998 6788999999998  455566666654322111        


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEecc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLTGW  157 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT~T  157 (169)
                                     .....++ +++|++.+.+.... .-.+++++|+||||++.+  ......+..+ ++..+++||||
T Consensus       201 ---------------~~~~~~I-~i~T~~~l~~~~~~-~~~~~~liIiDE~H~~~~--~~~~~il~~~~~~~~~l~lSAT  261 (510)
T 2oca_A          201 ---------------YKNDAPV-VVGTWQTVVKQPKE-WFSQFGMMMNDECHLATG--KSISSIISGLNNCMFKFGLSGS  261 (510)
T ss_dssp             ---------------GCTTCSE-EEEEHHHHTTSCGG-GGGGEEEEEEETGGGCCH--HHHHHHGGGCTTCCEEEEEESC
T ss_pred             ---------------cccCCcE-EEEeHHHHhhchhh-hhhcCCEEEEECCcCCCc--ccHHHHHHhcccCcEEEEEEeC
Confidence                           1155677 99999998765322 224789999999999975  3344455666 67789999999


Q ss_pred             CCC
Q psy1090         158 YYP  160 (169)
Q Consensus       158 P~~  160 (169)
                      |..
T Consensus       262 p~~  264 (510)
T 2oca_A          262 LRD  264 (510)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            943

>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=99.83  E-value=4.6e-20  Score=151.20  Aligned_cols=142  Identities=16%  Similarity=0.145  Sum_probs=101.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC---CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA---LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~---~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      +++++++||+|||++++..+........   .+++|||||. .++.||.+++.++++  +.++..++|............
T Consensus       265 ~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~  344 (797)
T 4a2q_A          265 NALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI  344 (797)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHH
T ss_pred             CEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhh
Confidence            5789999999999998888776666544   6789999997 688999999999986  788888888764433222211


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--c-ccccccEEEEeCCcccCCcccHHHHHHhcc------
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--L-KKITWNCIIVDEGHSVKNKKSKLSIKLTAL------  146 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~-~~~~~~~vi~DEah~~k~~~~~~~~~~~~l------  146 (169)
                                          ...++ +++|++.+.+....  + .-..++++|+||||++.+... ....+..+      
T Consensus       345 --------------------~~~~I-vv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~-~~~i~~~~~~~~~~  402 (797)
T 4a2q_A          345 --------------------EDSDI-IVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHP-YNVLMTRYLEQKFN  402 (797)
T ss_dssp             --------------------HTCSE-EEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSH-HHHHHHHHHHHHHT
T ss_pred             --------------------CCCCE-EEEchHHHHHHHHhccccccccCCEEEEECccccCCCcc-HHHHHHHHHHHhhc
Confidence                                44566 99999998765432  2 234689999999999987654 22222221      


Q ss_pred             ---ccccEEEEeccCCCCCchh
Q psy1090         147 ---RATFKVLLTGWYYPNKWSK  165 (169)
Q Consensus       147 ---~~~~~~~lT~TP~~n~~~e  165 (169)
                         ....+++|||||.+++..+
T Consensus       403 ~~~~~~~~l~lSATp~~~~~~~  424 (797)
T 4a2q_A          403 SASQLPQILGLTASVGVGNAKN  424 (797)
T ss_dssp             TCCCCCEEEEEESCCCCTTCCS
T ss_pred             cCCCCCeEEEEcCCcccccccc
Confidence               2367999999998765443

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.82  E-value=9e-20  Score=147.37  Aligned_cols=141  Identities=17%  Similarity=0.148  Sum_probs=99.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCC---CceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQAL---EPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~---~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      +++++++||+|||++++..+.........   +++||++|. .+..||.+++.++.+  +.++..++|....+.......
T Consensus        30 ~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~  109 (696)
T 2ykg_A           30 NTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIV  109 (696)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCSSSCHHHHH
T ss_pred             CEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHHHhccCCceEEEEeCCccccccHHHhc
Confidence            57899999999999988777655544432   689999997 888999999999986  678888887643321111111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--c-ccccccEEEEeCCcccCCcccHHHHHHhcc------
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--L-KKITWNCIIVDEGHSVKNKKSKLSIKLTAL------  146 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~-~~~~~~~vi~DEah~~k~~~~~~~~~~~~l------  146 (169)
                                          ...++ +++|++.+.+....  + ....++++|+||||++.+...........+      
T Consensus       110 --------------------~~~~I-iv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~l~~~~~~  168 (696)
T 2ykg_A          110 --------------------ENNDI-IILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGG  168 (696)
T ss_dssp             --------------------HTCSE-EEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHTT
T ss_pred             --------------------cCCCE-EEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHHHHHhhcc
Confidence                                34566 99999999775442  2 344789999999999987653222221111      


Q ss_pred             ---ccccEEEEeccCCCCCc
Q psy1090         147 ---RATFKVLLTGWYYPNKW  163 (169)
Q Consensus       147 ---~~~~~~~lT~TP~~n~~  163 (169)
                         ....+++|||||..++.
T Consensus       169 ~~~~~~~il~LTATp~~~~~  188 (696)
T 2ykg_A          169 SSGPLPQVIGLTASVGVGDA  188 (696)
T ss_dssp             CCSCCCEEEEEESCCCCSSC
T ss_pred             cCCCCCeEEEEeCccccCcc
Confidence               45789999999986543

>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=99.81  E-value=4e-20  Score=153.57  Aligned_cols=143  Identities=16%  Similarity=0.140  Sum_probs=100.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC---CCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA---LEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~---~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~   75 (169)
                      +++++++||+|||++++..+........   .+++|||+|. .++.||.+++.++++  +.++..++|............
T Consensus       265 ~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~G~~~~~~~~~~~~  344 (936)
T 4a2w_A          265 NALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI  344 (936)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECCC-----CCHHHH
T ss_pred             CEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEECCcchhhHHHHhc
Confidence            5789999999999998877765544433   5789999997 688999999999986  788888888764432211111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--c-ccccccEEEEeCCcccCCcccHHHHHHhcc------
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--L-KKITWNCIIVDEGHSVKNKKSKLSIKLTAL------  146 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~-~~~~~~~vi~DEah~~k~~~~~~~~~~~~l------  146 (169)
                                          ...++ +++|++.+.+....  + ....++++|+||||++.+... ....+..+      
T Consensus       345 --------------------~~~~I-vI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~-~~~i~~~~~~~~~~  402 (936)
T 4a2w_A          345 --------------------EDSDI-IVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHP-YNVLMTRYLEQKFN  402 (936)
T ss_dssp             --------------------HHCSE-EEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCH-HHHHHHHHHHHHHT
T ss_pred             --------------------cCCCE-EEecHHHHHHHHHcCccccccCCCEEEEECccccCCCcc-HHHHHHHHHHHhhc
Confidence                                33566 99999999865432  2 233689999999999987654 23222222      


Q ss_pred             ---ccccEEEEeccCCCCCchhh
Q psy1090         147 ---RATFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       147 ---~~~~~~~lT~TP~~n~~~el  166 (169)
                         ....+++|||||.+++..++
T Consensus       403 ~~~~~~~~l~LSATp~~~~~~~l  425 (936)
T 4a2w_A          403 SASQLPQILGLTASVGVGNAKNI  425 (936)
T ss_dssp             TCSCCCEEEEEESCCCCTTCCSH
T ss_pred             cCCCcCeEEEecCCcccccchhH
Confidence               23679999999988765443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.81  E-value=1.7e-20  Score=149.23  Aligned_cols=133  Identities=15%  Similarity=0.124  Sum_probs=82.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC-------CCCceEEEecC-cchHHHH-HHHHHhCCCceEEEEeCCHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ-------ALEPNLIVCPL-SVLNNWE-AEFRKFAPFVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~-------~~~~~Liv~P~-~~l~qW~-~e~~~~~~~~~~~~~~g~~~~~~~~~~   73 (169)
                      ++++++||+|||++++.++..+...+       ..+++||+||. .+..||. +++..|.+....  ..+..        
T Consensus       201 ~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~~~~~~~~~--~~~~~--------  270 (590)
T 3h1t_A          201 SLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFTPFGDARHK--IEGGK--------  270 (590)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCTTTCSSEEE--CCC----------
T ss_pred             eEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHHhcchhhhh--hhccC--------
Confidence            68999999999999998888777665       66899999995 7778999 788877643221  11110        


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhch------hccccccccEEEEeCCcccCCcc-cHHHHHHhcc
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF------GFLKKITWNCIIVDEGHSVKNKK-SKLSIKLTAL  146 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~------~~~~~~~~~~vi~DEah~~k~~~-~~~~~~~~~l  146 (169)
                                          .....++ +++||+.+....      ..+....|+++|+||||++.+.. +.....+..+
T Consensus       271 --------------------~~~~~~I-~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~il~~~  329 (590)
T 3h1t_A          271 --------------------VVKSREI-YFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARDNSNWREILEYF  329 (590)
T ss_dssp             --------------------CCSSCSE-EEEEGGGC------CCGGGGSCTTSCSEEEESCCC---------CHHHHHHS
T ss_pred             --------------------CCCCCcE-EEEEhhhhccccccccccccCCCCccCEEEEECCccccccchHHHHHHHHhC
Confidence                                0145567 999999987642      23334568999999999997643 3334555667


Q ss_pred             ccccEEEEeccCCCCCchhh
Q psy1090         147 RATFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       147 ~~~~~~~lT~TP~~n~~~el  166 (169)
                      +...+++|||||..+...++
T Consensus       330 ~~~~~l~lTATP~~~~~~~~  349 (590)
T 3h1t_A          330 EPAFQIGMTATPLREDNRDT  349 (590)
T ss_dssp             TTSEEEEEESSCSCTTTHHH
T ss_pred             CcceEEEeccccccccchhH
Confidence            77899999999998765543

>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=99.80  E-value=5e-20  Score=148.91  Aligned_cols=141  Identities=16%  Similarity=0.181  Sum_probs=95.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC----CCceEEEecC-cchHHH-HHHHHHhCCC-ceEEEEeCCHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA----LEPNLIVCPL-SVLNNW-EAEFRKFAPF-VRTVKYYGNAIERKALQSE   74 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~----~~~~Liv~P~-~~l~qW-~~e~~~~~~~-~~~~~~~g~~~~~~~~~~~   74 (169)
                      +++++++||+|||++++..+......+.    .+++|||+|. .++.|| .+++.++.+. ..+..++|...........
T Consensus        24 ~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~~~~v~~~~g~~~~~~~~~~~  103 (699)
T 4gl2_A           24 NIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEV  103 (699)
T ss_dssp             CEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTTTSCEEEEC----CCCCHHHH
T ss_pred             CEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCcCceEEEEeCCcchhhHHHhh
Confidence            5789999999999998887765544332    3789999997 578899 9999999865 8888888865432211111


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhch--------hccccccccEEEEeCCcccCCccc--HHHH-HH
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--------GFLKKITWNCIIVDEGHSVKNKKS--KLSI-KL  143 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--------~~~~~~~~~~vi~DEah~~k~~~~--~~~~-~~  143 (169)
                      .                    ...++ +++|++.+.+..        ..+....|+++|+||||++.....  .... .+
T Consensus       104 ~--------------------~~~~I-lv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l  162 (699)
T 4gl2_A          104 V--------------------KSCDI-IISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYL  162 (699)
T ss_dssp             H--------------------HSCSE-EEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHH
T ss_pred             h--------------------cCCCE-EEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHH
Confidence            1                    44566 999999998644        223445789999999998754321  1111 11


Q ss_pred             hc-c-------------ccccEEEEeccCCCCCc
Q psy1090         144 TA-L-------------RATFKVLLTGWYYPNKW  163 (169)
Q Consensus       144 ~~-l-------------~~~~~~~lT~TP~~n~~  163 (169)
                      .. +             ....+++|||||..++.
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~  196 (699)
T 4gl2_A          163 MQKLKNNRLKKENKPVIPLPQILGLTASPGVGGA  196 (699)
T ss_dssp             HHHHHHHHHHC----CCCCCEEEEECSCCCCCSC
T ss_pred             HhhhcccccccccccCCCCCEEEEeccccccccc
Confidence            11 1             44679999999998744

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.77  E-value=4e-18  Score=119.78  Aligned_cols=140  Identities=14%  Similarity=0.140  Sum_probs=93.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC-CCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA-LEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~-~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ++++..++|+|||..++..+........ ..++||++|. .+..||.++++++.   ++.++..+.|.............
T Consensus        53 ~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~  132 (220)
T 1t6n_A           53 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK  132 (220)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHH
T ss_pred             CEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhc
Confidence            4688999999999887766554433322 3489999998 77889999999886   46788888876443332222111


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc---HHHHHHhccc-ccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS---KLSIKLTALR-ATF  150 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~---~~~~~~~~l~-~~~  150 (169)
                                         ...++ +++|++.+.....  .+.-..++++|+||||++.....   .....+..++ ...
T Consensus       133 -------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~  192 (220)
T 1t6n_A          133 -------------------NCPHI-VVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ  192 (220)
T ss_dssp             -------------------SCCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSE
T ss_pred             -------------------CCCCE-EEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHHHHHHHHHhCCCcCe
Confidence                               34566 9999998865432  22234688999999998854211   1122233343 567


Q ss_pred             EEEEeccCCCC
Q psy1090         151 KVLLTGWYYPN  161 (169)
Q Consensus       151 ~~~lT~TP~~n  161 (169)
                      .+++||||..+
T Consensus       193 ~i~~SAT~~~~  203 (220)
T 1t6n_A          193 VMMFSATLSKE  203 (220)
T ss_dssp             EEEEESCCCTT
T ss_pred             EEEEEeecCHH
Confidence            89999999654

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.77  E-value=5e-18  Score=118.06  Aligned_cols=138  Identities=15%  Similarity=0.127  Sum_probs=93.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh----CCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE----QALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~----~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ++++..++|+|||.+++..+......    +...++||++|. .+..||.+++.++.+..++..+.|............ 
T Consensus        40 ~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  118 (207)
T 2gxq_A           40 DLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL-  118 (207)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH-
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh-
Confidence            46888999999998865554433321    234579999998 778899999999998888888777544332222211 


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhccc-cccE
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-ATFK  151 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~~~~  151 (169)
                                         ...++ +++|++.+.+...  .+.-..++++|+||||++....  ......+..++ ....
T Consensus       119 -------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~  178 (207)
T 2gxq_A          119 -------------------RGADA-VVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQT  178 (207)
T ss_dssp             -------------------HCCSE-EEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTTCHHHHHHHHHTSCTTSEE
T ss_pred             -------------------CCCCE-EEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccchHHHHHHHHHhCCccCeE
Confidence                               34566 9999988865432  2233468999999999875432  22233334443 4568


Q ss_pred             EEEeccCCC
Q psy1090         152 VLLTGWYYP  160 (169)
Q Consensus       152 ~~lT~TP~~  160 (169)
                      +++||||..
T Consensus       179 i~~SAT~~~  187 (207)
T 2gxq_A          179 LLFSATLPS  187 (207)
T ss_dssp             EEECSSCCH
T ss_pred             EEEEEecCH
Confidence            999999854

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.75  E-value=1e-18  Score=122.14  Aligned_cols=134  Identities=16%  Similarity=0.215  Sum_probs=83.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh----CCCCceEEEecC-cchHH-HHHHHHHhCC-CceEEEEeCCHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE----QALEPNLIVCPL-SVLNN-WEAEFRKFAP-FVRTVKYYGNAIERKALQSE   74 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~----~~~~~~Liv~P~-~~l~q-W~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~   74 (169)
                      ++++..++|+|||+.++..+......    ....++||+||. .+..| |.+++.++.+ ...+..+.|...........
T Consensus        50 ~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~  129 (216)
T 3b6e_A           50 NIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEV  129 (216)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTTTSCEEECCC---CCCCHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhccCceEEEEeCCcccchhHHhh
Confidence            47889999999999988777655433    225689999998 56678 9899998874 46677666654322111110


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--------cccccccEEEEeCCcccCCcccHHHHHHhcc
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--------LKKITWNCIIVDEGHSVKNKKSKLSIKLTAL  146 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--------~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l  146 (169)
                      .                    ...++ +++|++.+......        +....++++|+||||++...... ...+..+
T Consensus       130 ~--------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~-~~~~~~~  187 (216)
T 3b6e_A          130 V--------------------KSCDI-IISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVY-NNIMRHY  187 (216)
T ss_dssp             H--------------------HHCSE-EEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CH-HHHHHHH
T ss_pred             c--------------------cCCCE-EEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcH-HHHHHHH
Confidence            0                    23456 99999998765433        22357899999999998643222 2221111


Q ss_pred             ------------------ccccEEEEecc
Q psy1090         147 ------------------RATFKVLLTGW  157 (169)
Q Consensus       147 ------------------~~~~~~~lT~T  157 (169)
                                        ...+.++||||
T Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          188 LMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHhcccccccccccCCCCcceEEEeecC
Confidence                              34678999998

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.75  E-value=1.5e-17  Score=118.04  Aligned_cols=137  Identities=12%  Similarity=0.091  Sum_probs=91.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-----CCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-----QALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNAIERKALQS   73 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-----~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~~~~~~~~~   73 (169)
                      ++++..++|+|||+.++..+......     ....++||++|. .+..||.+++.++...  ..+..+.|..........
T Consensus        64 ~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  143 (236)
T 2pl3_A           64 DVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAER  143 (236)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHH
T ss_pred             CEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHh
Confidence            46889999999999866554433322     234579999998 7788999999998743  677777776543322221


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc---cccccccEEEEeCCcccCCcc--cHHHHHHhccc-
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF---LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-  147 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~---~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-  147 (169)
                      .                     ...++ +++|++.+......   +....++++|+||||++.+.+  ......+..++ 
T Consensus       144 ~---------------------~~~~i-iv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~  201 (236)
T 2pl3_A          144 I---------------------NNINI-LVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPK  201 (236)
T ss_dssp             H---------------------TTCSE-EEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHTTTHHHHHHHHHTSCT
T ss_pred             C---------------------CCCCE-EEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcCCcHHHHHHHHHhCCC
Confidence            1                     34566 99999998654432   233478899999999876433  23334445554 


Q ss_pred             cccEEEEeccCCC
Q psy1090         148 ATFKVLLTGWYYP  160 (169)
Q Consensus       148 ~~~~~~lT~TP~~  160 (169)
                      ....+++|||+..
T Consensus       202 ~~~~l~~SAT~~~  214 (236)
T 2pl3_A          202 KRQTLLFSATQTK  214 (236)
T ss_dssp             TSEEEEEESSCCH
T ss_pred             CCeEEEEEeeCCH
Confidence            4558999999854

>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=99.74  E-value=9.8e-18  Score=125.47  Aligned_cols=138  Identities=16%  Similarity=0.159  Sum_probs=95.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      ++++..++|+|||.+++..+......+...++||++|. .+..||.+++.++.+  ...+....|...........    
T Consensus        46 ~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~----  121 (367)
T 1hv8_A           46 NIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL----  121 (367)
T ss_dssp             EEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH----
T ss_pred             CEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhc----
Confidence            36788999999999887766655444456689999998 677899999999874  45666666654433322211    


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCccc--HHHHHHhcc-ccccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL-RATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l-~~~~~~~  153 (169)
                                       ...++ +++|++.+.+....  +...+++++|+||||++.+...  .....+..+ +....++
T Consensus       122 -----------------~~~~i-iv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~  183 (367)
T 1hv8_A          122 -----------------KNANI-VVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILL  183 (367)
T ss_dssp             -----------------HTCSE-EEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEE
T ss_pred             -----------------CCCCE-EEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCceEEE
Confidence                             23456 99999998765432  2334789999999999865442  122333334 4567799


Q ss_pred             EeccCCCC
Q psy1090         154 LTGWYYPN  161 (169)
Q Consensus       154 lT~TP~~n  161 (169)
                      +||||..+
T Consensus       184 ~SAT~~~~  191 (367)
T 1hv8_A          184 FSATMPRE  191 (367)
T ss_dssp             ECSSCCHH
T ss_pred             EeeccCHH
Confidence            99999754

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.74  E-value=2e-17  Score=117.06  Aligned_cols=137  Identities=12%  Similarity=0.144  Sum_probs=92.2

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ++++..++|+|||+..+.. +..+...+...++||++|. .+..||.+++.++.   ++.++..+.|...........  
T Consensus        63 ~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--  140 (230)
T 2oxc_A           63 DLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL--  140 (230)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT--
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc--
Confidence            4688999999999885443 3333333445689999998 78889999999986   367788888764433222111  


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc---cHHHHHHhccc-ccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK---SKLSIKLTALR-ATF  150 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~---~~~~~~~~~l~-~~~  150 (169)
                                         ...++ +++|++.+.....  .+....++++|+||||++...+   ......+..++ ...
T Consensus       141 -------------------~~~~I-iv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~  200 (230)
T 2oxc_A          141 -------------------KKCHI-AVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQ  200 (230)
T ss_dssp             -------------------TSCSE-EEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTSSHHHHHHHHHHSCSSCE
T ss_pred             -------------------cCCCE-EEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcchHHHHHHHHHhCCCCCe
Confidence                               34566 9999999865432  2223467899999999985432   22223344554 456


Q ss_pred             EEEEeccCCC
Q psy1090         151 KVLLTGWYYP  160 (169)
Q Consensus       151 ~~~lT~TP~~  160 (169)
                      .+++|||+-.
T Consensus       201 ~l~lSAT~~~  210 (230)
T 2oxc_A          201 MLAVSATYPE  210 (230)
T ss_dssp             EEEEESCCCH
T ss_pred             EEEEEeccCH
Confidence            8999999753

>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=99.73  E-value=2.7e-17  Score=124.26  Aligned_cols=140  Identities=14%  Similarity=0.130  Sum_probs=94.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ++++..++|+|||++++..+...... ....++||+||. .+..||.+++.++.   |+.++..+.|.............
T Consensus        47 ~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  126 (391)
T 1xti_A           47 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK  126 (391)
T ss_dssp             CEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHH
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhc
Confidence            47889999999998876665544332 234589999998 77889999999886   46788888876543332222111


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcccHH--H-HHHhcc-cccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKKSKL--S-IKLTAL-RATF  150 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~~~~--~-~~~~~l-~~~~  150 (169)
                                         ...++ +++|++.+......  +....++++|+||||++.......  . ..+... ....
T Consensus       127 -------------------~~~~i-iv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~  186 (391)
T 1xti_A          127 -------------------NCPHI-VVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ  186 (391)
T ss_dssp             -------------------SCCSE-EEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSE
T ss_pred             -------------------CCCCE-EEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCce
Confidence                               34566 99999998754322  233578999999999987532211  1 222233 3566


Q ss_pred             EEEEeccCCCC
Q psy1090         151 KVLLTGWYYPN  161 (169)
Q Consensus       151 ~~~lT~TP~~n  161 (169)
                      .+++||||..+
T Consensus       187 ~i~~SAT~~~~  197 (391)
T 1xti_A          187 VMMFSATLSKE  197 (391)
T ss_dssp             EEEEESSCCST
T ss_pred             EEEEEeeCCHH
Confidence            89999999754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.72  E-value=1.1e-17  Score=117.57  Aligned_cols=142  Identities=16%  Similarity=0.150  Sum_probs=91.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHH-hCCCCceEEEecC-cchHHHHHHHHHhCC------CceEEEEeCCHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIE-EQALEPNLIVCPL-SVLNNWEAEFRKFAP------FVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~-~~~~~~~Liv~P~-~~l~qW~~e~~~~~~------~~~~~~~~g~~~~~~~~~~   73 (169)
                      ++++..++|+|||..++..+..... .+...++||++|. .+..||.+++.++..      ...+..+.|..........
T Consensus        43 ~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  122 (219)
T 1q0u_A           43 SMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEK  122 (219)
T ss_dssp             CEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCC
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHH
Confidence            4678999999999886554433322 2334589999998 777899999988864      4566666665433221100


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhccc-c
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-A  148 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~  148 (169)
                                          .....++ +++|++.+.....  .+....++++|+||||++...+  ......+..++ .
T Consensus       123 --------------------~~~~~~I-iv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~  181 (219)
T 1q0u_A          123 --------------------LNVQPHI-VIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKD  181 (219)
T ss_dssp             --------------------CSSCCSE-EEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTT
T ss_pred             --------------------cCCCCCE-EEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHhhhChHHHHHHHHHhCCcc
Confidence                                0135667 9999988875432  2223467899999999876432  22333444553 4


Q ss_pred             ccEEEEeccCCCCCchh
Q psy1090         149 TFKVLLTGWYYPNKWSK  165 (169)
Q Consensus       149 ~~~~~lT~TP~~n~~~e  165 (169)
                      ...+++|||+. +.+.+
T Consensus       182 ~~~l~~SAT~~-~~~~~  197 (219)
T 1q0u_A          182 LQMLVFSATIP-EKLKP  197 (219)
T ss_dssp             CEEEEEESCCC-GGGHH
T ss_pred             cEEEEEecCCC-HHHHH
Confidence            56899999984 44444

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.72  E-value=7.4e-17  Score=112.09  Aligned_cols=138  Identities=12%  Similarity=0.094  Sum_probs=91.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHH-hCCCCceEEEecC-cchHHHHHHHHHhCC---CceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIE-EQALEPNLIVCPL-SVLNNWEAEFRKFAP---FVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~-~~~~~~~Liv~P~-~~l~qW~~e~~~~~~---~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ++++..++|+|||..++..+..... .....++||++|. .+..||.+++.++..   +..+....|............ 
T Consensus        42 ~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-  120 (206)
T 1vec_A           42 DILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-  120 (206)
T ss_dssp             CEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTT-
T ss_pred             CEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcC-
Confidence            4688899999999876654443322 2334579999998 677899999988863   567777777654443322211 


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhccc-cccE
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTALR-ATFK  151 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l~-~~~~  151 (169)
                                         ...++ +++|++.+.....  ...-..++++|+||||++...+-  .....+..++ ....
T Consensus       121 -------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~  180 (206)
T 1vec_A          121 -------------------DTVHV-VIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQI  180 (206)
T ss_dssp             -------------------SCCSE-EEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEE
T ss_pred             -------------------CCCCE-EEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhCcHHHHHHHHHhCCccceE
Confidence                               45667 9999998865433  12234678999999998765332  1122333443 5678


Q ss_pred             EEEeccCCC
Q psy1090         152 VLLTGWYYP  160 (169)
Q Consensus       152 ~~lT~TP~~  160 (169)
                      +++|||+..
T Consensus       181 l~~SAT~~~  189 (206)
T 1vec_A          181 LLYSATFPL  189 (206)
T ss_dssp             EEEESCCCH
T ss_pred             EEEEeeCCH
Confidence            999999953

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.72  E-value=6e-17  Score=123.64  Aligned_cols=141  Identities=14%  Similarity=0.158  Sum_probs=96.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHH---HHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIE---RKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~---~~~~~~~~~   76 (169)
                      +.++..++|+|||+.++..+....  ....++||++|. .+..||.+++.++.+ +.++..++|....   .........
T Consensus        38 ~~lv~apTGsGKT~~~l~~~~~~~--~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~  115 (414)
T 3oiy_A           38 SFTMVAPTGVGKTTFGMMTALWLA--RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEE  115 (414)
T ss_dssp             CEECCSCSSSSHHHHHHHHHHHHH--TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHh--cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhc
Confidence            468889999999995554443332  445789999998 778899999999875 6788888876543   111221111


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCC-------------cccH-HHHH
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKN-------------KKSK-LSIK  142 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~-------------~~~~-~~~~  142 (169)
                                         +..++ +++|++.+.+....+....++++|+||||++..             .... ....
T Consensus       116 -------------------~~~~I-iv~Tp~~l~~~l~~~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~~~~~~~~~i  175 (414)
T 3oiy_A          116 -------------------DDYHI-LVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKA  175 (414)
T ss_dssp             -------------------TCCSE-EEEEHHHHHHCHHHHTTCCCSEEEESCHHHHHHCHHHHHHHHHHTTCCHHHHHHH
T ss_pred             -------------------CCCCE-EEECHHHHHHHHHHhccccccEEEEeChHhhhhccchhhhHHhhcCCcHHHHHHH
Confidence                               44677 999999998776666666899999999997632             2222 2222


Q ss_pred             Hhcc------------ccccEEEEeccCCCCCch
Q psy1090         143 LTAL------------RATFKVLLTGWYYPNKWS  164 (169)
Q Consensus       143 ~~~l------------~~~~~~~lT~TP~~n~~~  164 (169)
                      +..+            .....+++||||.++...
T Consensus       176 ~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~  209 (414)
T 3oiy_A          176 FSTIKQGKIYERPKNLKPGILVVSSATAKPRGIR  209 (414)
T ss_dssp             HHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSST
T ss_pred             HHhcccchhhhhcccCCCceEEEEecCCCcchhH
Confidence            2222            445788999997776554

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.72  E-value=7.3e-17  Score=115.60  Aligned_cols=138  Identities=14%  Similarity=0.133  Sum_probs=92.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.++..++|+|||.+++..+...... ....++||++|. .+..||.+++.++..  +..+..+.|............  
T Consensus        82 ~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--  159 (249)
T 3ber_A           82 DIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA--  159 (249)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHH--
T ss_pred             CEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhc--
Confidence            46788999999998866555443333 334579999998 677899999998864  566777777544332222211  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhc---cccccccEEEEeCCcccCCcc--cHHHHHHhccc-cccE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF---LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-ATFK  151 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~---~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~~~~  151 (169)
                                        ...++ +++|++.+.+....   +.-..++++|+||||++.+.+  ......+..++ ....
T Consensus       160 ------------------~~~~I-~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~  220 (249)
T 3ber_A          160 ------------------KKPHI-IIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKT  220 (249)
T ss_dssp             ------------------TCCSE-EEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSSEE
T ss_pred             ------------------CCCCE-EEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccChHHHHHHHHHhCCCCCeE
Confidence                              45677 99999998664432   223467899999999876432  22234444553 5668


Q ss_pred             EEEeccCCC
Q psy1090         152 VLLTGWYYP  160 (169)
Q Consensus       152 ~~lT~TP~~  160 (169)
                      +++|||+..
T Consensus       221 l~~SAT~~~  229 (249)
T 3ber_A          221 FLFSATMTK  229 (249)
T ss_dssp             EEEESSCCH
T ss_pred             EEEeccCCH
Confidence            999999864

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.71  E-value=1.1e-16  Score=114.74  Aligned_cols=138  Identities=17%  Similarity=0.174  Sum_probs=90.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC----------CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ----------ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIER   68 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~----------~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~   68 (169)
                      ++++..++|+|||+.++..+.......          ...++||++|. .+..||.+++.++..  ...+....|.....
T Consensus        62 ~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~  141 (253)
T 1wrb_A           62 DIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTH  141 (253)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSH
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHH
Confidence            467889999999988765554433321          12479999998 778899999998864  35666666654333


Q ss_pred             HHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc--cHHHHHHh
Q psy1090          69 KALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK--SKLSIKLT  144 (169)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~--~~~~~~~~  144 (169)
                      .......                    ...++ +++|++.+......  +.-..++++|+||||++...+  ......+.
T Consensus       142 ~~~~~~~--------------------~~~~I-vv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~  200 (253)
T 1wrb_A          142 SQIREVQ--------------------MGCHL-LVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIE  200 (253)
T ss_dssp             HHHHHHS--------------------SCCSE-EEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHhC--------------------CCCCE-EEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCchHHHHHHHHh
Confidence            3222211                    45677 99999998754332  223457899999999875432  22333344


Q ss_pred             cc--c---cccEEEEeccCCC
Q psy1090         145 AL--R---ATFKVLLTGWYYP  160 (169)
Q Consensus       145 ~l--~---~~~~~~lT~TP~~  160 (169)
                      .+  .   ....+++||||-.
T Consensus       201 ~~~~~~~~~~q~l~~SAT~~~  221 (253)
T 1wrb_A          201 ESNMPSGINRQTLMFSATFPK  221 (253)
T ss_dssp             SSCCCCGGGCEEEEEESSCCH
T ss_pred             hccCCCCCCcEEEEEEEeCCH
Confidence            32  2   3458999999854

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.71  E-value=8.3e-17  Score=113.27  Aligned_cols=137  Identities=15%  Similarity=0.124  Sum_probs=86.7

Q ss_pred             CccccCCCCCcHHHHHH-HHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||.+.+ .++..+.......++||++|. .+..||.+++.++.+  +..+..+.|..........    
T Consensus        53 ~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----  128 (224)
T 1qde_A           53 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG----  128 (224)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC--------------
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc----
Confidence            46889999999998844 333333333445689999998 677899999999874  4566666665433221111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l-~~~~~~  152 (169)
                                       ....++ +++|++.+.....  .+....++++|+||||++...+.  .....+..+ +....+
T Consensus       129 -----------------~~~~~i-iv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i  190 (224)
T 1qde_A          129 -----------------LRDAQI-VVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVV  190 (224)
T ss_dssp             -----------------CTTCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEE
T ss_pred             -----------------CCCCCE-EEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhhhHHHHHHHHHhCCccCeEE
Confidence                             023567 9999998865432  22234678999999998754322  222333344 345689


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||+..
T Consensus       191 ~lSAT~~~  198 (224)
T 1qde_A          191 LLSATMPN  198 (224)
T ss_dssp             EEESSCCH
T ss_pred             EEEeecCH
Confidence            99999864

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.70  E-value=7.8e-17  Score=114.55  Aligned_cols=139  Identities=14%  Similarity=0.139  Sum_probs=86.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||..++..+...... ....++||++|. .+..||.+++.++..  +..+....|............  
T Consensus        69 ~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~--  146 (237)
T 3bor_A           69 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQ--  146 (237)
T ss_dssp             CEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC--------------
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHh--
Confidence            46889999999998865544433222 234589999998 778899999999874  455555565443322211110  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCc--ccHHHHHHhccc-cccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNK--KSKLSIKLTALR-ATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~--~~~~~~~~~~l~-~~~~~  152 (169)
                                       ....++ +++|++.+.....  .+....++++|+||||++...  .......+..++ ....+
T Consensus       147 -----------------~~~~~I-lv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i  208 (237)
T 3bor_A          147 -----------------AEAPHI-VVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVV  208 (237)
T ss_dssp             ------------------CCCSE-EEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEE
T ss_pred             -----------------cCCCCE-EEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCeEE
Confidence                             033677 9999988765432  223346889999999987432  233344445553 45679


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||+..
T Consensus       209 ~~SAT~~~  216 (237)
T 3bor_A          209 LLSATMPT  216 (237)
T ss_dssp             EECSSCCH
T ss_pred             EEEEecCH
Confidence            99999964

>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=99.69  E-value=1.1e-16  Score=121.70  Aligned_cols=139  Identities=14%  Similarity=0.123  Sum_probs=93.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||++++..+...... ....++||++|. .+..||.+++.++..  +..+....|............. 
T Consensus        79 ~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  157 (414)
T 3eiq_A           79 DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQM-  157 (414)
T ss_dssp             CEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTT-
T ss_pred             CEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhc-
Confidence            46889999999999876655544333 245689999998 677899999998863  4555555555444333332211 


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~~  152 (169)
                                        ...++ +++|++.+.+....  +....++++|+||||++.+..  ......+..+ .....+
T Consensus       158 ------------------~~~~i-iv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i  218 (414)
T 3eiq_A          158 ------------------EAPHI-IVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV  218 (414)
T ss_dssp             ------------------TCCSE-EEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEE
T ss_pred             ------------------CCCCE-EEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEE
Confidence                              44566 99999887654332  334468899999999875433  2333444455 456679


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      +|||||..
T Consensus       219 ~~SAT~~~  226 (414)
T 3eiq_A          219 LLSATMPS  226 (414)
T ss_dssp             EECSCCCH
T ss_pred             EEEEecCH
Confidence            99999964

>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=99.69  E-value=7.1e-17  Score=134.61  Aligned_cols=134  Identities=17%  Similarity=0.079  Sum_probs=87.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +|++.+.+|+|||++++.++..+...+...++|||||. .+..||.+++.+|.+.. +   .+... ...+.....    
T Consensus       302 ~gli~~~TGSGKT~t~~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~f~~f~~~~-v---~~~~s-~~~l~~~L~----  372 (1038)
T 2w00_A          302 GGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKDLDYQTMKEYQRFSPDS-V---NGSEN-TAGLKRNLD----  372 (1038)
T ss_dssp             SEEEEECTTSSHHHHHHHHHHHHTTCTTCCEEEEEECGGGCCHHHHHHHHTTSTTC-S---SSSCC-CHHHHHHHH----
T ss_pred             CEEEEecCCCCHHHHHHHHHHHHHhcCCCceEEEEeCcHHHHHHHHHHHHHhcccc-c---ccccC-HHHHHHHhc----
Confidence            47999999999999986665433222334689999995 78889999999987541 1   11111 111111100    


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhc---c-ccccccEEEEeCCcccCCcccHHHHHH-hccccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF---L-KKITWNCIIVDEGHSVKNKKSKLSIKL-TALRATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~---~-~~~~~~~vi~DEah~~k~~~~~~~~~~-~~l~~~~~~~lT  155 (169)
                                    ....++ +++|++.+......   + .-..++++|+||||++..  ....+.+ ..++...+++||
T Consensus       373 --------------~~~~~I-iVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~--~~~~~~I~~~~p~a~~lgfT  435 (1038)
T 2w00_A          373 --------------KDDNKI-IVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF--GEAQKNLKKKFKRYYQFGFT  435 (1038)
T ss_dssp             --------------CSSCCE-EEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH--HHHHHHHHHHCSSEEEEEEE
T ss_pred             --------------CCCCCE-EEEEHHHHHHHHhcccchhccccccEEEEEccchhcc--hHHHHHHHHhCCcccEEEEe
Confidence                          034566 99999998764321   1 112678999999999753  2223333 456778999999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||...
T Consensus       436 ATP~~~  441 (1038)
T 2w00_A          436 GTPIFP  441 (1038)
T ss_dssp             SSCCCS
T ss_pred             CCcccc
Confidence            999964

>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=99.69  E-value=2.4e-16  Score=119.97  Aligned_cols=138  Identities=14%  Similarity=0.122  Sum_probs=93.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHH-hCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIE-EQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~-~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||.+++..+..... .....++||++|. .+..||.+++.++..  +..+....|............  
T Consensus        76 ~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--  153 (410)
T 2j0s_A           76 DVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD--  153 (410)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH--
T ss_pred             CEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhh--
Confidence            4788999999999887765544332 2345689999998 678899999999874  456666666544433332221  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l-~~~~~~  152 (169)
                                        ...++ +++|++.+.....  .+....++++|+||||++.+...  .....+..+ .....+
T Consensus       154 ------------------~~~~i-vv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i  214 (410)
T 2j0s_A          154 ------------------YGQHV-VAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV  214 (410)
T ss_dssp             ------------------HCCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEE
T ss_pred             ------------------cCCCE-EEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhhhHHHHHHHHHhCccCceEE
Confidence                              33456 9999988765432  23345689999999998876442  222333344 356789


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++||||..
T Consensus       215 ~~SAT~~~  222 (410)
T 2j0s_A          215 LISATLPH  222 (410)
T ss_dssp             EEESCCCH
T ss_pred             EEEcCCCH
Confidence            99999964

>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=99.68  E-value=1.1e-16  Score=120.95  Aligned_cols=137  Identities=15%  Similarity=0.121  Sum_probs=91.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHH-hCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIE-EQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~-~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||++++..+..... .....++||++|. .+..||.+++.++.+  +.++..+.|...........   
T Consensus        60 ~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---  136 (394)
T 1fuu_A           60 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL---  136 (394)
T ss_dssp             CEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHH---
T ss_pred             CEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhc---
Confidence            4688999999999886544443322 2345689999998 777899999999874  46677777754433222211   


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~~  152 (169)
                                        ...++ +++|++.+.+...  .+....++++|+||||++....  ......+..+ +....+
T Consensus       137 ------------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i  197 (394)
T 1fuu_A          137 ------------------RDAQI-VVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVV  197 (394)
T ss_dssp             ------------------HHCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEE
T ss_pred             ------------------CCCCE-EEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCceEE
Confidence                              22455 9999999865433  2334578999999999874332  2223333344 456689


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++||||..
T Consensus       198 ~~SAT~~~  205 (394)
T 1fuu_A          198 LLSATMPN  205 (394)
T ss_dssp             EECSSCCH
T ss_pred             EEEEecCH
Confidence            99999964

>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=99.68  E-value=3.8e-16  Score=118.45  Aligned_cols=138  Identities=12%  Similarity=0.104  Sum_probs=92.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhC-CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQ-ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~-~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||++++..+....... ...++||++|. .+..||.+++.++.+  +..+....|............  
T Consensus        60 ~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--  137 (400)
T 1s2m_A           60 DILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLN--  137 (400)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTT--
T ss_pred             CEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhc--
Confidence            468899999999988766655433322 34589999998 677899999999875  466777777655443332211  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc-HHHHHH-hcc-ccccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS-KLSIKL-TAL-RATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~-~~~~~~-~~l-~~~~~~  152 (169)
                                        ...++ +++|++.+.+...  ...-..++++|+||||++..... .....+ ..+ .....+
T Consensus       138 ------------------~~~~I-vv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~i~~~~~~~~~~i  198 (400)
T 1s2m_A          138 ------------------ETVHI-LVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSL  198 (400)
T ss_dssp             ------------------SCCSE-EEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEE
T ss_pred             ------------------CCCCE-EEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCcCceEE
Confidence                              45667 9999998865432  22234689999999998765321 112222 233 356689


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||+..
T Consensus       199 ~lSAT~~~  206 (400)
T 1s2m_A          199 LFSATFPL  206 (400)
T ss_dssp             EEESCCCH
T ss_pred             EEEecCCH
Confidence            99999864

>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=99.67  E-value=4.7e-16  Score=131.42  Aligned_cols=136  Identities=18%  Similarity=0.215  Sum_probs=93.0

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCC--ceEEEEeCC--HHHHHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPF--VRTVKYYGN--AIERKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~--~~~~~~~g~--~~~~~~~~~~~   75 (169)
                      |+++++.+||+|||..++..+.....  ...+++|+||.. +..||.+++.++++.  .++..+.+.  .+++.......
T Consensus       625 ~d~ll~~~TGsGKT~val~aa~~~~~--~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l  702 (1151)
T 2eyq_A          625 MDRLVCGDVGFGKTEVAMRAAFLAVD--NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEV  702 (1151)
T ss_dssp             CEEEEECCCCTTTHHHHHHHHHHHHT--TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHH--hCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHH
Confidence            35799999999999887754433333  236899999985 677999999988753  456666653  22222222211


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccc-cccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALR-ATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~-~~~~~~l  154 (169)
                      ..                  +..++ +++|++.+.+...   -.+++++|+||+|++.   ......++.++ ....++|
T Consensus       703 ~~------------------g~~dI-vV~T~~ll~~~~~---~~~l~lvIiDEaH~~g---~~~~~~l~~l~~~~~vl~l  757 (1151)
T 2eyq_A          703 AE------------------GKIDI-LIGTHKLLQSDVK---FKDLGLLIVDEEHRFG---VRHKERIKAMRANVDILTL  757 (1151)
T ss_dssp             HT------------------TCCSE-EEECTHHHHSCCC---CSSEEEEEEESGGGSC---HHHHHHHHHHHTTSEEEEE
T ss_pred             hc------------------CCCCE-EEECHHHHhCCcc---ccccceEEEechHhcC---hHHHHHHHHhcCCCCEEEE
Confidence            11                  56777 9999998865432   3478999999999974   33445555553 4578999


Q ss_pred             eccCCCCCc
Q psy1090         155 TGWYYPNKW  163 (169)
Q Consensus       155 T~TP~~n~~  163 (169)
                      ||||.++..
T Consensus       758 SATp~p~~l  766 (1151)
T 2eyq_A          758 TATPIPRTL  766 (1151)
T ss_dssp             ESSCCCHHH
T ss_pred             cCCCChhhH
Confidence            999987654

>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=99.67  E-value=7.7e-16  Score=114.00  Aligned_cols=133  Identities=14%  Similarity=0.162  Sum_probs=89.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      ++++..++|+|||+.++..+..   .  ..++||++|. .+..||.+++.++.+  +..+..+.|...........    
T Consensus        33 ~~lv~~~TGsGKT~~~~~~~~~---~--~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  103 (337)
T 2z0m_A           33 NVVVRAKTGSGKTAAYAIPILE---L--GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRV----  103 (337)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH---H--TCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHH----
T ss_pred             CEEEEcCCCCcHHHHHHHHHHh---h--cCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhc----
Confidence            4788999999999887665543   1  4689999998 677899999998874  45666677654433322211    


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcccH--HHHHHhccc-cccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKSK--LSIKLTALR-ATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~~--~~~~~~~l~-~~~~~~  153 (169)
                                       ...++ +++|++.+.+...  .+....++++|+||||++.+....  ....+..+. ....++
T Consensus       104 -----------------~~~~i-~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (337)
T 2z0m_A          104 -----------------RNADI-VVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGL  165 (337)
T ss_dssp             -----------------TTCSE-EEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHHHHHCTTCSEEEE
T ss_pred             -----------------CCCCE-EEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHHHhhCCcccEEEE
Confidence                             33566 9999999876432  223457899999999987654321  122233343 344567


Q ss_pred             EeccCCCC
Q psy1090         154 LTGWYYPN  161 (169)
Q Consensus       154 lT~TP~~n  161 (169)
                      +||||..+
T Consensus       166 ~SAT~~~~  173 (337)
T 2z0m_A          166 FSATIPEE  173 (337)
T ss_dssp             EESCCCHH
T ss_pred             EeCcCCHH
Confidence            89999654

>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=99.66  E-value=3.2e-16  Score=127.59  Aligned_cols=136  Identities=12%  Similarity=0.082  Sum_probs=93.0

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHH--HHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERK--ALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~--~~~~~~   75 (169)
                      |++++..++|+|||..++..+......+  ..++|++|. .+..||.+++.++++  +.++..++|......  ......
T Consensus       390 ~~~Ll~a~TGSGKTlvall~il~~l~~g--~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l  467 (780)
T 1gm5_A          390 MNRLLQGDVGSGKTVVAQLAILDNYEAG--FQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGL  467 (780)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHHHT--SCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHH
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHH
Confidence            4678999999999998876665544443  689999998 567799999999875  577888887643322  222111


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhc-cccccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA-LRATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~-l~~~~~~~l  154 (169)
                      .                  .+..++ +++|++.+.+...   -.+++++|+||+|++...  .+ ..+.. ......++|
T Consensus       468 ~------------------~g~~~I-vVgT~~ll~~~~~---~~~l~lVVIDEaHr~g~~--qr-~~l~~~~~~~~vL~m  522 (780)
T 1gm5_A          468 R------------------NGQIDV-VIGTHALIQEDVH---FKNLGLVIIDEQHRFGVK--QR-EALMNKGKMVDTLVM  522 (780)
T ss_dssp             H------------------SSCCCE-EEECTTHHHHCCC---CSCCCEEEEESCCCC--------CCCCSSSSCCCEEEE
T ss_pred             h------------------cCCCCE-EEECHHHHhhhhh---ccCCceEEecccchhhHH--HH-HHHHHhCCCCCEEEE
Confidence            1                  155777 9999988865332   347799999999997422  11 11111 245779999


Q ss_pred             eccCCCCCc
Q psy1090         155 TGWYYPNKW  163 (169)
Q Consensus       155 T~TP~~n~~  163 (169)
                      ||||.++..
T Consensus       523 SATp~p~tl  531 (780)
T 1gm5_A          523 SATPIPRSM  531 (780)
T ss_dssp             ESSCCCHHH
T ss_pred             eCCCCHHHH
Confidence            999987544

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.66  E-value=7.6e-16  Score=108.69  Aligned_cols=138  Identities=13%  Similarity=0.168  Sum_probs=87.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-------CCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-------QALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIERKALQ   72 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-------~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~~~~~~   72 (169)
                      ++++..++|+|||+.++..+......       ....++||++|. .+..||.+++.++. ++..+....|.........
T Consensus        59 ~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  138 (228)
T 3iuy_A           59 DLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIE  138 (228)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHH
T ss_pred             CEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHH
Confidence            46788999999998866544332221       234579999998 67789999999985 4667777666544332222


Q ss_pred             HhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhccc-
Q psy1090          73 SEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-  147 (169)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-  147 (169)
                      ...                    ...++ +++|++.+.....  .+.-..++++|+||||++...+  ......+..++ 
T Consensus       139 ~~~--------------------~~~~i-iv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~  197 (228)
T 3iuy_A          139 DIS--------------------KGVDI-IIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRP  197 (228)
T ss_dssp             HHH--------------------SCCSE-EEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHTTCHHHHHHHHHHSCS
T ss_pred             Hhc--------------------CCCCE-EEECHHHHHHHHHcCCcCcccceEEEEECHHHHhccchHHHHHHHHHhCCc
Confidence            111                    44677 9999998865332  2223457899999999875432  22233344443 


Q ss_pred             cccEEEEeccCCC
Q psy1090         148 ATFKVLLTGWYYP  160 (169)
Q Consensus       148 ~~~~~~lT~TP~~  160 (169)
                      ....+++|||+..
T Consensus       198 ~~~~l~~SAT~~~  210 (228)
T 3iuy_A          198 DRQTVMTSATWPD  210 (228)
T ss_dssp             SCEEEEEESCCCH
T ss_pred             CCeEEEEEeeCCH
Confidence            4567999999754

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.66  E-value=1e-15  Score=110.39  Aligned_cols=138  Identities=13%  Similarity=0.128  Sum_probs=89.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-----CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-----QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-----~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~   73 (169)
                      +.++..++|+|||..++..+......     ....++||++|. .+..||.+++.++..  ...+....|..........
T Consensus        93 ~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  172 (262)
T 3ly5_A           93 DLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK  172 (262)
T ss_dssp             CCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHH
T ss_pred             cEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHH
Confidence            46889999999998865544433322     124579999998 777899999999874  3455666665443332222


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc---cccccccEEEEeCCcccCCcc--cHHHHHHhccc-
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF---LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-  147 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~---~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-  147 (169)
                      ..                    ...++ +++|++.+......   +.-..++++|+||||++...+  ......+..++ 
T Consensus       173 ~~--------------------~~~~I-iv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~  231 (262)
T 3ly5_A          173 LG--------------------NGINI-IVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPT  231 (262)
T ss_dssp             HH--------------------HCCSE-EEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHHSCS
T ss_pred             hc--------------------CCCCE-EEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhhhHHHHHHHHHHhCCC
Confidence            11                    33566 99999888654322   223457899999999865432  22233334443 


Q ss_pred             cccEEEEeccCCC
Q psy1090         148 ATFKVLLTGWYYP  160 (169)
Q Consensus       148 ~~~~~~lT~TP~~  160 (169)
                      ....+++|||+..
T Consensus       232 ~~q~l~~SAT~~~  244 (262)
T 3ly5_A          232 RRQTMLFSATQTR  244 (262)
T ss_dssp             SSEEEEECSSCCH
T ss_pred             CCeEEEEEecCCH
Confidence            4568999999864

>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=99.62  E-value=3.8e-15  Score=114.57  Aligned_cols=138  Identities=16%  Similarity=0.192  Sum_probs=91.2

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHhC-----CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEEQ-----ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQ   72 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~~-----~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~   72 (169)
                      +.++..++|+|||+..+..+. .+....     ...++||++|. .+..||.+++.++..  ..++...+|.........
T Consensus        95 d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~  174 (434)
T 2db3_A           95 DLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNE  174 (434)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHH
T ss_pred             CEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHH
Confidence            467889999999987665444 333322     13479999998 678899999999873  456666666544333222


Q ss_pred             HhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc--
Q psy1090          73 SEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL--  146 (169)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l--  146 (169)
                      ...                    ...++ +++|++.+.+...  .+.-..++++|+||||++...+  ....+.+..+  
T Consensus       175 ~l~--------------------~~~~I-vv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~  233 (434)
T 2db3_A          175 CIT--------------------RGCHV-VIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTM  233 (434)
T ss_dssp             HHT--------------------TCCSE-EEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTTTHHHHHHHHHCTTS
T ss_pred             Hhh--------------------cCCCE-EEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccCcHHHHHHHHHhcCC
Confidence            211                    45677 9999999876433  2223467899999999986543  2223333332  


Q ss_pred             -ccccEEEEeccCCC
Q psy1090         147 -RATFKVLLTGWYYP  160 (169)
Q Consensus       147 -~~~~~~~lT~TP~~  160 (169)
                       .....+++|||+..
T Consensus       234 ~~~~q~l~~SAT~~~  248 (434)
T 2db3_A          234 RPEHQTLMFSATFPE  248 (434)
T ss_dssp             CSSCEEEEEESCCCH
T ss_pred             CCCceEEEEeccCCH
Confidence             34668999999853

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.62  E-value=4.1e-15  Score=105.95  Aligned_cols=138  Identities=10%  Similarity=0.077  Sum_probs=89.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh------CCCCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE------QALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQ   72 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~------~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~   72 (169)
                      +.++..++|+|||+..+..+......      .....+||++|. .+..||.+++.++.  .+..+...+|.........
T Consensus        68 ~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  147 (242)
T 3fe2_A           68 DMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR  147 (242)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHH
T ss_pred             CEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHH
Confidence            46788899999998866554443332      224579999998 67789999988875  3567777776544333222


Q ss_pred             HhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-c
Q psy1090          73 SEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-R  147 (169)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~  147 (169)
                      ...                    ...++ +++|++.+.....  .+.-..++++|+||||++...+  ......+..+ +
T Consensus       148 ~~~--------------------~~~~I-~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~  206 (242)
T 3fe2_A          148 DLE--------------------RGVEI-CIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRP  206 (242)
T ss_dssp             HHH--------------------HCCSE-EEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCS
T ss_pred             Hhc--------------------CCCCE-EEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCc
Confidence            221                    34566 9999988865432  1223467899999999875432  2223334445 3


Q ss_pred             cccEEEEeccCCC
Q psy1090         148 ATFKVLLTGWYYP  160 (169)
Q Consensus       148 ~~~~~~lT~TP~~  160 (169)
                      ....+++|||+..
T Consensus       207 ~~q~~~~SAT~~~  219 (242)
T 3fe2_A          207 DRQTLMWSATWPK  219 (242)
T ss_dssp             SCEEEEEESCCCH
T ss_pred             cceEEEEEeecCH
Confidence            4568999999743

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.62  E-value=3.3e-15  Score=106.50  Aligned_cols=138  Identities=17%  Similarity=0.161  Sum_probs=85.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh--CCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE--QALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~--~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      ++++..++|+|||+.++..+......  ....++||++|. .+..||.+++.++...  ..+....|......     ..
T Consensus        68 ~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~  142 (245)
T 3dkp_A           68 ELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAK-----KF  142 (245)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHT-----TT
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHH-----Hh
Confidence            46788999999998865554443332  223479999998 6778999999998753  34444443322111     00


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc----cccccccEEEEeCCcccCCcc-----cHHHHHHhcc-
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF----LKKITWNCIIVDEGHSVKNKK-----SKLSIKLTAL-  146 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~----~~~~~~~~vi~DEah~~k~~~-----~~~~~~~~~l-  146 (169)
                      ..              ......++ +++|++.+......    +.-..++++|+||||++....     ......+..+ 
T Consensus       143 ~~--------------~~~~~~~I-~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~  207 (245)
T 3dkp_A          143 GP--------------KSSKKFDI-LVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACT  207 (245)
T ss_dssp             ST--------------TSCCCCCE-EEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCC
T ss_pred             hh--------------hhcCCCCE-EEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcC
Confidence            00              01155677 99999988654322    233467899999999875421     1122222232 


Q ss_pred             -ccccEEEEeccCC
Q psy1090         147 -RATFKVLLTGWYY  159 (169)
Q Consensus       147 -~~~~~~~lT~TP~  159 (169)
                       .....++||||+.
T Consensus       208 ~~~~~~~~~SAT~~  221 (245)
T 3dkp_A          208 SHKVRRAMFSATFA  221 (245)
T ss_dssp             CTTCEEEEEESSCC
T ss_pred             CCCcEEEEEeccCC
Confidence             3456899999984

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.61  E-value=7.4e-15  Score=111.85  Aligned_cols=138  Identities=16%  Similarity=0.189  Sum_probs=90.0

Q ss_pred             CccccCCCCCcHHHHHHHHH-HHHHHhCC------------------CCceEEEecC-cchHHHHHHHHHhC--CCceEE
Q psy1090           2 DTVIPDPTRYRKSGKVIAFF-CKIIEEQA------------------LEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTV   59 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i-~~~~~~~~------------------~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~   59 (169)
                      ++++..++|+|||+..+..+ ..+...+.                  ...+||++|. .+..||.+++.++.  .+.++.
T Consensus        54 ~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  133 (417)
T 2i4i_A           54 DLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPC  133 (417)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEE
T ss_pred             CEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEE
Confidence            46789999999998765443 33333221                  1469999998 77889999999886  356777


Q ss_pred             EEeCCHHHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc-
Q psy1090          60 KYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK-  136 (169)
Q Consensus        60 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~-  136 (169)
                      .++|............                    ...++ +++|++.+.+....  +.-..++++|+||||++...+ 
T Consensus       134 ~~~g~~~~~~~~~~~~--------------------~~~~I-~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~~~  192 (417)
T 2i4i_A          134 VVYGGADIGQQIRDLE--------------------RGCHL-LVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGF  192 (417)
T ss_dssp             EECSSSCHHHHHHHHT--------------------TCCSE-EEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHTTC
T ss_pred             EEECCCCHHHHHHHhh--------------------CCCCE-EEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhccCc
Confidence            7777654433332221                    44567 99999998764332  233467899999999875433 


Q ss_pred             cHHHHHH-hc--cc---cccEEEEeccCCC
Q psy1090         137 SKLSIKL-TA--LR---ATFKVLLTGWYYP  160 (169)
Q Consensus       137 ~~~~~~~-~~--l~---~~~~~~lT~TP~~  160 (169)
                      ......+ ..  +.   ....+++||||..
T Consensus       193 ~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~  222 (417)
T 2i4i_A          193 EPQIRRIVEQDTMPPKGVRHTMMFSATFPK  222 (417)
T ss_dssp             HHHHHHHHTSSSCCCBTTBEEEEEESCCCH
T ss_pred             HHHHHHHHHhccCCCcCCcEEEEEEEeCCH
Confidence            1122222 22  21   3568999999954

>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=99.60  E-value=8e-16  Score=116.11  Aligned_cols=134  Identities=10%  Similarity=0.152  Sum_probs=87.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      ++++..++|+|||++++..+...... +...++||++|. .+..||.+++.++..  ........+......        
T Consensus        46 ~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~--------  117 (395)
T 3pey_A           46 NMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN--------  117 (395)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTT--------
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhh--------
Confidence            46889999999999877665543332 345689999998 577899999998863  344444443321100        


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcccH--HHH-HHhcc-ccccE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKSK--LSI-KLTAL-RATFK  151 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~~--~~~-~~~~l-~~~~~  151 (169)
                                      .....++ +++|++.+.....  .+.-.+++++|+||||++.+....  ... ....+ +....
T Consensus       118 ----------------~~~~~~i-iv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~  180 (395)
T 3pey_A          118 ----------------KQINAQV-IVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQL  180 (395)
T ss_dssp             ----------------SCBCCSE-EEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCEE
T ss_pred             ----------------ccCCCCE-EEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcEE
Confidence                            0135677 9999999865432  223346899999999987642221  122 22233 34568


Q ss_pred             EEEeccCCC
Q psy1090         152 VLLTGWYYP  160 (169)
Q Consensus       152 ~~lT~TP~~  160 (169)
                      +++||||..
T Consensus       181 i~~SAT~~~  189 (395)
T 3pey_A          181 VLFSATFAD  189 (395)
T ss_dssp             EEEESCCCH
T ss_pred             EEEEecCCH
Confidence            999999964

>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=99.59  E-value=3e-15  Score=113.68  Aligned_cols=135  Identities=10%  Similarity=0.127  Sum_probs=87.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.++..++|+|||+.++..+...... ....++||++|. .+..||.+.+.++.   ++..+....+......       
T Consensus        66 ~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------  138 (412)
T 3fht_A           66 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER-------  138 (412)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCT-------
T ss_pred             eEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhh-------
Confidence            36888999999998876554433332 334489999998 57789988888775   4556665554322110       


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCc--ccHHH-HHHhcc-ccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNK--KSKLS-IKLTAL-RAT  149 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~--~~~~~-~~~~~l-~~~  149 (169)
                                      ......++ +++|++.+.....   .+.-..++++|+||||++...  ..... .....+ ...
T Consensus       139 ----------------~~~~~~~i-vv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~  201 (412)
T 3fht_A          139 ----------------GQKISEQI-VIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC  201 (412)
T ss_dssp             ----------------TCCCCCSE-EEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTC
T ss_pred             ----------------hhcCCCCE-EEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCc
Confidence                            00134567 9999999876442   233357899999999987431  12222 223333 345


Q ss_pred             cEEEEeccCCC
Q psy1090         150 FKVLLTGWYYP  160 (169)
Q Consensus       150 ~~~~lT~TP~~  160 (169)
                      ..+++||||..
T Consensus       202 ~~i~~SAT~~~  212 (412)
T 3fht_A          202 QMLLFSATFED  212 (412)
T ss_dssp             EEEEEESCCCH
T ss_pred             eEEEEEeecCH
Confidence            68999999864

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.53  E-value=5.4e-14  Score=111.69  Aligned_cols=138  Identities=15%  Similarity=0.095  Sum_probs=88.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCC-----CCceEEEecC-cchHHHHHHHHHhC------CCceEEEEeCCHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQA-----LEPNLIVCPL-SVLNNWEAEFRKFA------PFVRTVKYYGNAIERKA   70 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~-----~~~~Liv~P~-~~l~qW~~e~~~~~------~~~~~~~~~g~~~~~~~   70 (169)
                      .++..++|+|||+..+..+........     ..++|||+|. .+..||.+++.++.      +...+....|.......
T Consensus        63 vlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~  142 (579)
T 3sqw_A           63 VIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAA  142 (579)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHH
T ss_pred             EEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHH
Confidence            577899999999886655443333321     2379999998 67789999998864      34556666665444333


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhcc---ccccccEEEEeCCcccCCccc--HHHHHHhc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL---KKITWNCIIVDEGHSVKNKKS--KLSIKLTA  145 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~---~~~~~~~vi~DEah~~k~~~~--~~~~~~~~  145 (169)
                      ......                   ...++ +++|++.+.......   .-..++++|+||||++....-  .....+..
T Consensus       143 ~~~l~~-------------------~~~~I-lV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~gf~~~~~~i~~~  202 (579)
T 3sqw_A          143 MNKMNK-------------------LRPNI-VIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGI  202 (579)
T ss_dssp             HHHHHH-------------------HCCSE-EEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHH
T ss_pred             HHHHhc-------------------CCCCE-EEECHHHHHHHHHhccccccccCCEEEEEChHHhhcCCCHHHHHHHHHH
Confidence            332211                   34567 999999986543321   223578999999999865431  11112222


Q ss_pred             c---c-----cccEEEEeccCCC
Q psy1090         146 L---R-----ATFKVLLTGWYYP  160 (169)
Q Consensus       146 l---~-----~~~~~~lT~TP~~  160 (169)
                      +   .     ....+++|||+..
T Consensus       203 l~~~~~~~~~~~~~l~~SAT~~~  225 (579)
T 3sqw_A          203 LNEKNSKSADNIKTLLFSATLDD  225 (579)
T ss_dssp             HHHHCSSCTTCCEEEEEESSCCT
T ss_pred             hhhhhcccccCceEEEEeccCCh
Confidence            2   1     3468999999874

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.52  E-value=5.1e-14  Score=117.69  Aligned_cols=126  Identities=14%  Similarity=0.054  Sum_probs=87.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +.+++.++|+|||+.+...+......  ..++|+++|. .+..||.+++.++++  .+..++|.....            
T Consensus       103 ~vLV~apTGSGKTlva~lai~~~l~~--g~rvL~l~PtkaLa~Q~~~~l~~~~~--~vglltGd~~~~------------  166 (1010)
T 2xgj_A          103 SVLVSAHTSAGKTVVAEYAIAQSLKN--KQRVIYTSPIKALSNQKYRELLAEFG--DVGLMTGDITIN------------  166 (1010)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT--TCEEEEEESSHHHHHHHHHHHHHHHS--CEEEECSSCEEC------------
T ss_pred             CEEEECCCCCChHHHHHHHHHHHhcc--CCeEEEECChHHHHHHHHHHHHHHhC--CEEEEeCCCccC------------
Confidence            46889999999999875544443333  3689999997 778899999998875  556666643211            


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~~~lT  155 (169)
                                     ...++ +++|++.+.+...  ...-.+++++|+||+|++.+..  ......+..+ .....++||
T Consensus       167 ---------------~~~~I-vV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~il~LS  230 (1010)
T 2xgj_A          167 ---------------PDAGC-LVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLS  230 (1010)
T ss_dssp             ---------------TTCSE-EEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCEEEEEE
T ss_pred             ---------------CCCCE-EEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCeEEEEc
Confidence                           33566 9999998865322  1222378899999999997642  2223334444 356789999


Q ss_pred             ccCC
Q psy1090         156 GWYY  159 (169)
Q Consensus       156 ~TP~  159 (169)
                      ||+.
T Consensus       231 ATi~  234 (1010)
T 2xgj_A          231 ATIP  234 (1010)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            9964

>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=99.52  E-value=7e-14  Score=110.53  Aligned_cols=138  Identities=14%  Similarity=0.064  Sum_probs=87.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCC-----CCceEEEecC-cchHHHHHHHHHhC------CCceEEEEeCCHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQA-----LEPNLIVCPL-SVLNNWEAEFRKFA------PFVRTVKYYGNAIERKA   70 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~-----~~~~Liv~P~-~~l~qW~~e~~~~~------~~~~~~~~~g~~~~~~~   70 (169)
                      .++..++|+|||+.++..+........     ..++||++|. .+..||.+++.++.      +...+....|.......
T Consensus       114 ~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  193 (563)
T 3i5x_A          114 VIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAA  193 (563)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHH
T ss_pred             EEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHH
Confidence            577899999999886655444333322     2379999997 77789999998863      33456666665444333


Q ss_pred             HHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhcc---ccccccEEEEeCCcccCCccc-HHHH-HHhc
Q psy1090          71 LQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL---KKITWNCIIVDEGHSVKNKKS-KLSI-KLTA  145 (169)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~---~~~~~~~vi~DEah~~k~~~~-~~~~-~~~~  145 (169)
                      ......                   ...++ +++|++.+.......   .-..++++|+||||++....- .... .+..
T Consensus       194 ~~~~~~-------------------~~~~I-iv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~f~~~~~~i~~~  253 (563)
T 3i5x_A          194 MNKMNK-------------------LRPNI-VIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGI  253 (563)
T ss_dssp             HHHHHH-------------------HCCSE-EEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHH
T ss_pred             HHHHhc-------------------CCCCE-EEECcHHHHHHHHhccccccccceEEEEeCHHHHhccchHHHHHHHHHh
Confidence            332211                   45567 999999886543321   123578999999998765431 1111 1122


Q ss_pred             c--------ccccEEEEeccCCC
Q psy1090         146 L--------RATFKVLLTGWYYP  160 (169)
Q Consensus       146 l--------~~~~~~~lT~TP~~  160 (169)
                      +        .....+++||||..
T Consensus       254 l~~~~~~~~~~~~~l~~SAT~~~  276 (563)
T 3i5x_A          254 LNEKNSKSADNIKTLLFSATLDD  276 (563)
T ss_dssp             HHHHCSSCTTCCEEEEEESSCCT
T ss_pred             hhhccccCccCceEEEEEccCCH
Confidence            2        13458999999974

>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=99.52  E-value=2.7e-14  Score=112.16  Aligned_cols=139  Identities=16%  Similarity=0.069  Sum_probs=90.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHH--HHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIE--RKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~   78 (169)
                      ++++..++|+|||+.++..+.  . .  .+.+|||+|. .++.||.+++.++  +.....+++....  .........  
T Consensus        42 d~lv~apTGsGKTl~~~lp~l--~-~--~g~~lvi~P~~aL~~q~~~~l~~~--gi~~~~l~~~~~~~~~~~~~~~~~--  112 (523)
T 1oyw_A           42 DCLVVMPTGGGKSLCYQIPAL--L-L--NGLTVVVSPLISLMKDQVDQLQAN--GVAAACLNSTQTREQQLEVMTGCR--  112 (523)
T ss_dssp             CEEEECSCHHHHHHHHHHHHH--H-S--SSEEEEECSCHHHHHHHHHHHHHT--TCCEEEECTTSCHHHHHHHHHHHH--
T ss_pred             CEEEECCCCcHHHHHHHHHHH--H-h--CCCEEEECChHHHHHHHHHHHHHc--CCcEEEEeCCCCHHHHHHHHHHHh--
Confidence            467889999999976543322  1 1  3689999998 7788999999987  4566666664332  221111111  


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcccH---HHHHHh----ccccc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKKSK---LSIKLT----ALRAT  149 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~~~---~~~~~~----~l~~~  149 (169)
                                      .+..++ +++|++.+...  .+.+...+++++|+||||++...+..   .+..+.    .+...
T Consensus       113 ----------------~~~~~i-lv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~  175 (523)
T 1oyw_A          113 ----------------TGQIRL-LYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL  175 (523)
T ss_dssp             ----------------HTCCSE-EEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCTTS
T ss_pred             ----------------cCCCCE-EEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHHHhCCCC
Confidence                            155677 99999998543  23344568899999999998654321   122232    33456


Q ss_pred             cEEEEeccCCCCCchhh
Q psy1090         150 FKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       150 ~~~~lT~TP~~n~~~el  166 (169)
                      ..++|||||..+...|+
T Consensus       176 ~~i~lSAT~~~~~~~~i  192 (523)
T 1oyw_A          176 PFMALTATADDTTRQDI  192 (523)
T ss_dssp             CEEEEESCCCHHHHHHH
T ss_pred             CEEEEeCCCCHHHHHHH
Confidence            78999999987655444

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.51  E-value=1.7e-13  Score=115.39  Aligned_cols=141  Identities=14%  Similarity=0.164  Sum_probs=95.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC-CCceEEEEeCCHHH---HHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA-PFVRTVKYYGNAIE---RKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~-~~~~~~~~~g~~~~---~~~~~~~~~   76 (169)
                      +.++..++|+|||...+..+....  .....+||++|. .+..|+.+++.++. .+.++..++|....   .........
T Consensus        95 dvlv~ApTGSGKTl~~l~~il~~~--~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~  172 (1104)
T 4ddu_A           95 SFTMVAPTGVGKTTFGMMTALWLA--RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEE  172 (1104)
T ss_dssp             CEEECCSTTCCHHHHHHHHHHHHH--TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHT
T ss_pred             CEEEEeCCCCcHHHHHHHHHHHHH--hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhC
Confidence            467888999999995554444433  344689999998 67789999999976 35688888875433   222222111


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcc-------------cH-HHHH
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKK-------------SK-LSIK  142 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~-------------~~-~~~~  142 (169)
                                         +..++ +++|++.+.+....+....++++|+||||++....             .. ....
T Consensus       173 -------------------g~~~I-lV~Tp~rL~~~l~~l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf~~~~i~~i  232 (1104)
T 4ddu_A          173 -------------------DDYHI-LVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKA  232 (1104)
T ss_dssp             -------------------SCCSE-EEEEHHHHHHSHHHHHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSCCHHHHHHH
T ss_pred             -------------------CCCCE-EEECHHHHHHHHHhhcccCcCEEEEeCCCccccccccchhhhHhcCCCHHHHHHH
Confidence                               44677 99999999776665555689999999999865321             11 1222


Q ss_pred             Hhcc------------ccccEEEEeccCCCCCch
Q psy1090         143 LTAL------------RATFKVLLTGWYYPNKWS  164 (169)
Q Consensus       143 ~~~l------------~~~~~~~lT~TP~~n~~~  164 (169)
                      +..+            .....+++||||....+.
T Consensus       233 l~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~  266 (1104)
T 4ddu_A          233 FSTIKQGKIYERPKNLKPGILVVSSATAKPRGIR  266 (1104)
T ss_dssp             HHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSST
T ss_pred             HHhcccchhhhhhccCCCceEEEEcCCCCcHHHH
Confidence            2222            345689999998776654

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.50  E-value=1.4e-13  Score=115.01  Aligned_cols=128  Identities=14%  Similarity=0.051  Sum_probs=89.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +.++..++|+|||+.+...+.....  ...++||++|. .+..||.+++.+++++..+..++|....             
T Consensus        56 ~vlv~apTGsGKTlv~~~~i~~~~~--~g~~vlvl~PtraLa~Q~~~~l~~~~~~~~v~~l~G~~~~-------------  120 (997)
T 4a4z_A           56 SVFVAAHTSAGKTVVAEYAIAMAHR--NMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQI-------------  120 (997)
T ss_dssp             EEEEECCTTSCSHHHHHHHHHHHHH--TTCEEEEEESCGGGHHHHHHHHHTTC--CCEEEECSSCEE-------------
T ss_pred             CEEEEECCCCcHHHHHHHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHHHHHcCCCeEEEEeCCCcc-------------
Confidence            3678999999999875544444332  23679999997 6778999999998877888888875421             


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCc--ccHHHHHHhccc-cccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNK--KSKLSIKLTALR-ATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~--~~~~~~~~~~l~-~~~~~~lT  155 (169)
                                    ....++ +++|++.+.+....  ..-.+++++|+||||++.+.  .......+..++ ....++||
T Consensus       121 --------------~~~~~I-lV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~~~v~iIlLS  185 (997)
T 4a4z_A          121 --------------NPDANC-LIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLS  185 (997)
T ss_dssp             --------------CTTSSE-EEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCEEEEEE
T ss_pred             --------------CCCCCE-EEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcccCCCEEEEc
Confidence                          144566 99999988654321  12246899999999998653  233444555554 46789999


Q ss_pred             ccCC
Q psy1090         156 GWYY  159 (169)
Q Consensus       156 ~TP~  159 (169)
                      |||.
T Consensus       186 AT~~  189 (997)
T 4a4z_A          186 ATVP  189 (997)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            9985

>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=99.49  E-value=9.2e-14  Score=110.53  Aligned_cols=137  Identities=19%  Similarity=0.165  Sum_probs=87.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHH--HHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIER--KALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~--~~~~~~~~~~   78 (169)
                      ++++..++|+|||+..+..+..     ..+.+|||+|. .++.||.+.+.++  +..+..++|.....  ......... 
T Consensus        61 d~lv~~pTGsGKTl~~~lpal~-----~~g~~lVisP~~~L~~q~~~~l~~~--gi~~~~l~~~~~~~~~~~~~~~l~~-  132 (591)
T 2v1x_A           61 EVFLVMPTGGGKSLCYQLPALC-----SDGFTLVICPLISLMEDQLMVLKQL--GISATMLNASSSKEHVKWVHAEMVN-  132 (591)
T ss_dssp             CEEEECCTTSCTTHHHHHHHHT-----SSSEEEEECSCHHHHHHHHHHHHHH--TCCEEECCSSCCHHHHHHHHHHHHC-
T ss_pred             CEEEEECCCChHHHHHHHHHHH-----cCCcEEEEeCHHHHHHHHHHHHHhc--CCcEEEEeCCCCHHHHHHHHHHhhc-
Confidence            3678899999999765433321     24689999997 7888999999988  56666666653322  211111100 


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhc---hhcc----ccccccEEEEeCCcccCCccc-------HHHHHHh
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIEND---FGFL----KKITWNCIIVDEGHSVKNKKS-------KLSIKLT  144 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~---~~~~----~~~~~~~vi~DEah~~k~~~~-------~~~~~~~  144 (169)
                                     .....++ +++|++.+...   .+.+    ....++++|+||||++...+.       .......
T Consensus       133 ---------------~~~~~~I-lv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~  196 (591)
T 2v1x_A          133 ---------------KNSELKL-IYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKR  196 (591)
T ss_dssp             ---------------TTCCCCE-EEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHH
T ss_pred             ---------------ccCCCCE-EEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHHHHHHHHHHH
Confidence                           0156677 99999987532   1211    233789999999999765321       1112223


Q ss_pred             ccccccEEEEeccCCCCC
Q psy1090         145 ALRATFKVLLTGWYYPNK  162 (169)
Q Consensus       145 ~l~~~~~~~lT~TP~~n~  162 (169)
                      .++....++|||||....
T Consensus       197 ~~~~~~ii~lSAT~~~~v  214 (591)
T 2v1x_A          197 QFPNASLIGLTATATNHV  214 (591)
T ss_dssp             HCTTSEEEEEESSCCHHH
T ss_pred             hCCCCcEEEEecCCCHHH
Confidence            345667899999997653

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.48  E-value=6.8e-14  Score=113.69  Aligned_cols=132  Identities=14%  Similarity=0.141  Sum_probs=87.4

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +.+++.++|+|||.++... +..+...  .+++++++|. .+..||.+++.++.+ +.++...+|.......        
T Consensus        41 ~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~~~~~~~--------  110 (720)
T 2zj8_A           41 NALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDE--------  110 (720)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSGGGHHHHHHHTGGGGGGTCCEEEECSCSSCCCG--------
T ss_pred             cEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcHHHHHHHHHHHHHHHhcCCEEEEecCCCCcccc--------
Confidence            3678999999999987444 4343323  3689999997 777899999977653 5677777774321110        


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhccc--cccccEEEEeCCcccCCcc-cH-HHHHHhccc-cccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLK--KITWNCIIVDEGHSVKNKK-SK-LSIKLTALR-ATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~--~~~~~~vi~DEah~~k~~~-~~-~~~~~~~l~-~~~~~~  153 (169)
                                     .....++ +++|++.+......-.  -.+++++|+||+|.+.... .. ....+..++ ....++
T Consensus       111 ---------------~~~~~~I-iv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~ii~  174 (720)
T 2zj8_A          111 ---------------WLGKYDI-IIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIG  174 (720)
T ss_dssp             ---------------GGGGCSE-EEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHHBTTBEEEE
T ss_pred             ---------------ccCCCCE-EEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHHHHHHHHhhcCCeEEE
Confidence                           0145667 9999988865332211  2367899999999886421 22 222333343 577899


Q ss_pred             EeccCC
Q psy1090         154 LTGWYY  159 (169)
Q Consensus       154 lT~TP~  159 (169)
                      ||||+-
T Consensus       175 lSATl~  180 (720)
T 2zj8_A          175 LSATIG  180 (720)
T ss_dssp             EECCCS
T ss_pred             EcCCcC
Confidence            999985

>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=99.48  E-value=3.5e-14  Score=110.32  Aligned_cols=134  Identities=11%  Similarity=0.164  Sum_probs=83.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      .++..++|+|||...+..+...... +...++||++|. .+..||.+.+.++.   +...+....+......        
T Consensus       134 ~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------  205 (479)
T 3fmp_B          134 LIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER--------  205 (479)
T ss_dssp             EEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCT--------
T ss_pred             EEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccc--------
Confidence            5788999999998865444332222 333479999998 66778877776654   4566655554322100        


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCccc--HHHHHH-hcc-cccc
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNKKS--KLSIKL-TAL-RATF  150 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~~~--~~~~~~-~~l-~~~~  150 (169)
                                     ......++ +++|++.+.....   .+.-..++++|+||+|++.....  .....+ ..+ ....
T Consensus       206 ---------------~~~~~~~I-vv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~  269 (479)
T 3fmp_B          206 ---------------GQKISEQI-VIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQ  269 (479)
T ss_dssp             ---------------TCCCCCSE-EEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSE
T ss_pred             ---------------cccCCCCE-EEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccce
Confidence                           00133466 9999999866442   23334789999999998753211  122222 333 3456


Q ss_pred             EEEEeccCCC
Q psy1090         151 KVLLTGWYYP  160 (169)
Q Consensus       151 ~~~lT~TP~~  160 (169)
                      .+++||||..
T Consensus       270 ~i~~SAT~~~  279 (479)
T 3fmp_B          270 MLLFSATFED  279 (479)
T ss_dssp             EEEEESCCCH
T ss_pred             EEEEeCCCCH
Confidence            8999999964

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.48  E-value=4.9e-14  Score=103.48  Aligned_cols=135  Identities=8%  Similarity=0.105  Sum_probs=84.8

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.++..++|+|||...+.. +..+...+....+||++|. .+..|+.+.+.++.   ++..+....|......       
T Consensus       133 ~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~-------  205 (300)
T 3fmo_B          133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER-------  205 (300)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCT-------
T ss_pred             eEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhh-------
Confidence            3577889999999875533 3333222333479999998 67789888888775   4566666655432110       


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh---ccccccccEEEEeCCcccCCcc---cHHHHHHhccc-cc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG---FLKKITWNCIIVDEGHSVKNKK---SKLSIKLTALR-AT  149 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~---~~~~~~~~~vi~DEah~~k~~~---~~~~~~~~~l~-~~  149 (169)
                                      ......++ +++|++.+.....   .+.-...+++|+||||++-...   ......+..++ ..
T Consensus       206 ----------------~~~~~~~I-lV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~  268 (300)
T 3fmo_B          206 ----------------GQKISEQI-VIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNC  268 (300)
T ss_dssp             ----------------TCCCCCSE-EEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTC
T ss_pred             ----------------hhcCCCCE-EEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCC
Confidence                            00144567 9999999865442   2223467899999999875311   11222233343 45


Q ss_pred             cEEEEeccCCC
Q psy1090         150 FKVLLTGWYYP  160 (169)
Q Consensus       150 ~~~~lT~TP~~  160 (169)
                      ..+++|||+-.
T Consensus       269 q~i~~SAT~~~  279 (300)
T 3fmo_B          269 QMLLFSATFED  279 (300)
T ss_dssp             EEEEEESCCCH
T ss_pred             EEEEEeccCCH
Confidence            68899999864

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.46  E-value=9.2e-14  Score=112.63  Aligned_cols=132  Identities=20%  Similarity=0.169  Sum_probs=87.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.+++.++|+|||.++...+......  .+++++++|. .+..||.++++++.+ +.++...+|......          
T Consensus        42 ~~lv~apTGsGKT~~~~l~il~~~~~--~~~~l~i~P~r~La~q~~~~~~~~~~~g~~v~~~~G~~~~~~----------  109 (702)
T 2p6r_A           42 NLLLAMPTAAGKTLLAEMAMVREAIK--GGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRD----------  109 (702)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHHTTTTTTTCCEEEECSSCBCCS----------
T ss_pred             cEEEEcCCccHHHHHHHHHHHHHHHh--CCcEEEEeCcHHHHHHHHHHHHHHHhcCCEEEEEeCCCCcch----------
Confidence            46889999999999886555443332  4689999998 577899999976654 567777777432110          


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccc--cccccEEEEeCCcccCCcc--cHHHHHHhcc----ccccE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLK--KITWNCIIVDEGHSVKNKK--SKLSIKLTAL----RATFK  151 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~--~~~~~~vi~DEah~~k~~~--~~~~~~~~~l----~~~~~  151 (169)
                                   ......++ +++|++.+......-.  -.+++++|+||+|.+....  ......+..+    +....
T Consensus       110 -------------~~~~~~~I-iv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~~~~i  175 (702)
T 2p6r_A          110 -------------EHLGDCDI-IVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRV  175 (702)
T ss_dssp             -------------SCSTTCSE-EEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEE
T ss_pred             -------------hhccCCCE-EEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHHHHHHHhcCcCceE
Confidence                         00145677 9999988765332211  2367899999999986522  2222222223    35678


Q ss_pred             EEEeccCC
Q psy1090         152 VLLTGWYY  159 (169)
Q Consensus       152 ~~lT~TP~  159 (169)
                      ++||||+-
T Consensus       176 i~lSATl~  183 (702)
T 2p6r_A          176 IGLSATAP  183 (702)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcC
Confidence            99999985

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.45  E-value=1.7e-13  Score=111.31  Aligned_cols=133  Identities=13%  Similarity=0.072  Sum_probs=87.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.+++.++|+|||.++...+...... ..+++++++|.. +..||.++++++.+ +.++...+|.......         
T Consensus        48 ~~lv~apTGsGKT~~~~l~il~~~~~-~~~~il~i~P~r~La~q~~~~~~~~~~~g~~v~~~~G~~~~~~~---------  117 (715)
T 2va8_A           48 RLLLTSPTGSGKTLIAEMGIISFLLK-NGGKAIYVTPLRALTNEKYLTFKDWELIGFKVAMTSGDYDTDDA---------  117 (715)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHH-SCSEEEEECSCHHHHHHHHHHHGGGGGGTCCEEECCSCSSSCCG---------
T ss_pred             cEEEEcCCCCcHHHHHHHHHHHHHHH-CCCeEEEEeCcHHHHHHHHHHHHHhhcCCCEEEEEeCCCCCchh---------
Confidence            46889999999999986555433332 246899999984 77899999976653 5667666664221100         


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhcc--ccccccEEEEeCCcccCCcc-c-HHHHHHhccccccEEEEe
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL--KKITWNCIIVDEGHSVKNKK-S-KLSIKLTALRATFKVLLT  155 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~--~~~~~~~vi~DEah~~k~~~-~-~~~~~~~~l~~~~~~~lT  155 (169)
                                    .....++ +++|++.+......-  .-.+++++|+||+|.+.+.. . .....+..++..+.++||
T Consensus       118 --------------~~~~~~I-iv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l~~i~~~~~~~~ii~lS  182 (715)
T 2va8_A          118 --------------WLKNYDI-IITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVVESVTIRAKRRNLLALS  182 (715)
T ss_dssp             --------------GGGGCSE-EEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHHHHHHHHHHTSEEEEEE
T ss_pred             --------------hcCCCCE-EEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHHHHHHHhcccCcEEEEc
Confidence                          0135667 999998876533221  12367899999999976422 1 122233345567899999


Q ss_pred             ccCC
Q psy1090         156 GWYY  159 (169)
Q Consensus       156 ~TP~  159 (169)
                      |||-
T Consensus       183 ATl~  186 (715)
T 2va8_A          183 ATIS  186 (715)
T ss_dssp             SCCT
T ss_pred             CCCC
Confidence            9985

>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=99.44  E-value=5.2e-13  Score=112.59  Aligned_cols=126  Identities=14%  Similarity=0.055  Sum_probs=86.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +.+++.++|+|||+++...+......  .+++||++|. .+..||.+++.+++.  .+..++|....             
T Consensus       201 dvLV~ApTGSGKTlva~l~i~~~l~~--g~rvlvl~PtraLa~Q~~~~l~~~~~--~VglltGd~~~-------------  263 (1108)
T 3l9o_A          201 SVLVSAHTSAGKTVVAEYAIAQSLKN--KQRVIYTSPIKALSNQKYRELLAEFG--DVGLMTGDITI-------------  263 (1108)
T ss_dssp             CEEEECCSSSHHHHHHHHHHHHHHHT--TCEEEEEESSHHHHHHHHHHHHHHTS--SEEEECSSCBC-------------
T ss_pred             CEEEECCCCCChHHHHHHHHHHHHhc--CCeEEEEcCcHHHHHHHHHHHHHHhC--CccEEeCcccc-------------
Confidence            46889999999998876555544433  4689999998 677899999999875  45556664321             


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~~~lT  155 (169)
                                    ....++ +++|++.+.+....  ..-.++++||+||||++....  ......+..+ .....++||
T Consensus       264 --------------~~~~~I-lV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lS  328 (1108)
T 3l9o_A          264 --------------NPDAGC-LVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLS  328 (1108)
T ss_dssp             --------------CCSCSE-EEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEE
T ss_pred             --------------CCCCCE-EEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHHHHhcCCCceEEEEc
Confidence                          144667 99999887653321  112267899999999986532  2222333444 356789999


Q ss_pred             ccCC
Q psy1090         156 GWYY  159 (169)
Q Consensus       156 ~TP~  159 (169)
                      ||+.
T Consensus       329 ATip  332 (1108)
T 3l9o_A          329 ATIP  332 (1108)
T ss_dssp             CSCS
T ss_pred             CCCC
Confidence            9943

>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=99.31  E-value=6.4e-12  Score=105.73  Aligned_cols=136  Identities=17%  Similarity=0.185  Sum_probs=89.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCC--c----eEEEEeCCHHHHHHHH-H
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPF--V----RTVKYYGNAIERKALQ-S   73 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~----~~~~~~g~~~~~~~~~-~   73 (169)
                      +.++..++|+|||..++..+....  ....++||++|. .+..|+.++++++.+.  .    .+..++|......... .
T Consensus        73 dvlv~apTGSGKTl~~lp~l~~~~--~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~  150 (1054)
T 1gku_B           73 SFAATAPTGVGKTSFGLAMSLFLA--LKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFM  150 (1054)
T ss_dssp             CEECCCCBTSCSHHHHHHHHHHHH--TTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHh--hcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHH
Confidence            468889999999974444444333  334689999998 6778999999988753  3    5667777543322111 1


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-------
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-------  146 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-------  146 (169)
                      ...                   ...++ +++|++.+.+....+.  .++++|+||||++.+........+..+       
T Consensus       151 ~~l-------------------~~~~I-lV~TP~~L~~~l~~L~--~l~~lViDEah~~l~~~~~~~~i~~~lgf~~~~~  208 (1054)
T 1gku_B          151 QNL-------------------RNFKI-VITTTQFLSKHYRELG--HFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLK  208 (1054)
T ss_dssp             HSG-------------------GGCSE-EEEEHHHHHHCSTTSC--CCSEEEESCHHHHHTSTHHHHHHHHHTTEEEETT
T ss_pred             hhc-------------------cCCCE-EEEcHHHHHHHHHHhc--cCCEEEEeChhhhhhccccHHHHHHHhCcchhhh
Confidence            111                   12666 9999999987666544  788999999999776433333333323       


Q ss_pred             -----ccccEEEEeccCCCC
Q psy1090         147 -----RATFKVLLTGWYYPN  161 (169)
Q Consensus       147 -----~~~~~~~lT~TP~~n  161 (169)
                           .....+++|||+...
T Consensus       209 ~~~~~~~~q~~l~SAT~t~~  228 (1054)
T 1gku_B          209 TKSWVGEARGCLMVSTATAK  228 (1054)
T ss_dssp             TTEEEECCSSEEEECCCCSC
T ss_pred             hhhcccCCceEEEEecCCCc
Confidence                 123468889888765

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.31  E-value=6.5e-12  Score=96.52  Aligned_cols=126  Identities=12%  Similarity=0.029  Sum_probs=71.5

Q ss_pred             ccccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++..++|+|||..+ +.++......  ..+++|++|. .+..|+.+.+.    +..+....|......           
T Consensus         5 ~lv~a~TGsGKT~~~l~~~l~~~~~~--g~~~lvl~Pt~~La~Q~~~~~~----~~~v~~~~~~~~~~~-----------   67 (431)
T 2v6i_A            5 TVLDLHPGAGKTRRVLPQLVREAVKK--RLRTVILAPTRVVASEMYEALR----GEPIRYMTPAVQSER-----------   67 (431)
T ss_dssp             EEEECCTTSCTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT----TSCEEEC-------------------
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEECcHHHHHHHHHHHhC----CCeEEEEecCccccC-----------
Confidence            578899999999987 4444344333  3589999998 45568777665    444444333211100           


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhc-hhccccccccEEEEeCCcccCCccc-HHHHHHhcc---ccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIEND-FGFLKKITWNCIIVDEGHSVKNKKS-KLSIKLTAL---RATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~-~~~~~~~~~~~vi~DEah~~k~~~~-~~~~~~~~l---~~~~~~~lT  155 (169)
                                    .....+ .+.+...+.+. .....-.+++++|+||+|++ +... .....+..+   .....++||
T Consensus        68 --------------~~~~~~-~~~~~~~l~~~l~~~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~S  131 (431)
T 2v6i_A           68 --------------TGNEIV-DFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMT  131 (431)
T ss_dssp             ---------------CCCSE-EEEEHHHHHHHHHHTCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEE
T ss_pred             --------------CCCceE-EEEchHHHHHHHhcCccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEe
Confidence                          022223 44455554332 12212246799999999997 3222 122222222   357789999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||...
T Consensus       132 AT~~~~  137 (431)
T 2v6i_A          132 ATPPGT  137 (431)
T ss_dssp             SSCTTC
T ss_pred             CCCCcc
Confidence            999854

>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=99.19  E-value=1.6e-10  Score=100.97  Aligned_cols=133  Identities=15%  Similarity=0.138  Sum_probs=86.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHH-hCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRK-FAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~-~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.+++-++|+|||+.+.-.+.....++..+++++++|. .+..|-.+++.+ |.+  +.++..++|.........     
T Consensus       944 nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~~~----- 1018 (1724)
T 4f92_B          944 NVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLL----- 1018 (1724)
T ss_dssp             CEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHHHHHH-----
T ss_pred             cEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcchhhc-----
Confidence            46788999999999876555544555556789999997 677776777754 433  567888888765433221     


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhccc----cccccEEEEeCCcccCCcccHHHHHH-hc-------
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLK----KITWNCIIVDEGHSVKNKKSKLSIKL-TA-------  145 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~----~~~~~~vi~DEah~~k~~~~~~~~~~-~~-------  145 (169)
                                        ...++ +++|++.+........    -.+.+++|+||+|.+..........+ ..       
T Consensus      1019 ------------------~~~~I-iV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~rg~~le~il~rl~~i~~~ 1079 (1724)
T 4f92_B         1019 ------------------GKGNI-IISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQ 1079 (1724)
T ss_dssp             ------------------HHCSE-EEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGSTTHHHHHHHHHHHHHHHHT
T ss_pred             ------------------CCCCE-EEECHHHHHHHHhCcccccccceeeEEEeechhhcCCCCCccHHHHHHHHHHHHhh
Confidence                              33456 9999998743222111    12568999999999875433322221 11       


Q ss_pred             c-ccccEEEEeccC
Q psy1090         146 L-RATFKVLLTGWY  158 (169)
Q Consensus       146 l-~~~~~~~lT~TP  158 (169)
                      . +..+.++||||-
T Consensus      1080 ~~~~~riI~lSATl 1093 (1724)
T 4f92_B         1080 IERPIRIVALSSSL 1093 (1724)
T ss_dssp             TSSCCEEEEEESCB
T ss_pred             cCCCceEEEEeCCC
Confidence            2 234678999995

>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=99.13  E-value=1.6e-10  Score=89.40  Aligned_cols=126  Identities=13%  Similarity=0.053  Sum_probs=70.0

Q ss_pred             ccccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++..++|+|||.+. +.++..+...  ..++||++|. .+..|+.+++.    +..+....+.....            
T Consensus        24 vlv~a~TGsGKT~~~~l~il~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~----g~~v~~~~~~~~~~------------   85 (459)
T 2z83_A           24 TVLDLHPGSGKTRKILPQIIKDAIQQ--RLRTAVLAPTRVVAAEMAEALR----GLPVRYQTSAVQRE------------   85 (459)
T ss_dssp             EEECCCTTSCTTTTHHHHHHHHHHHT--TCCEEEEECSHHHHHHHHHHTT----TSCEEECC------------------
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEECchHHHHHHHHHHhc----CceEeEEecccccC------------
Confidence            577899999999984 4444444332  3689999998 56778888876    22222111110000            


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhc-hhccccccccEEEEeCCcccCCcccHHH----HHHhccccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIEND-FGFLKKITWNCIIVDEGHSVKNKKSKLS----IKLTALRATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~-~~~~~~~~~~~vi~DEah~~k~~~~~~~----~~~~~l~~~~~~~lT  155 (169)
                                   ......+ .+.+...+.+. .....-.+++++|+||||+.. ......    ...........++||
T Consensus        86 -------------~t~~~~i-~~~~~~~l~~~l~~~~~l~~~~~iViDEaH~~~-~~~~~~~~~~~~~~~~~~~~~il~S  150 (459)
T 2z83_A           86 -------------HQGNEIV-DVMCHATLTHRLMSPNRVPNYNLFVMDEAHFTD-PASIAARGYIATKVELGEAAAIFMT  150 (459)
T ss_dssp             ---------------CCCSE-EEEEHHHHHHHHHSCC-CCCCSEEEESSTTCCS-HHHHHHHHHHHHHHHTTSCEEEEEC
T ss_pred             -------------CCCCcEE-EEEchHHHHHHhhccccccCCcEEEEECCccCC-chhhHHHHHHHHHhccCCccEEEEE
Confidence                         0022233 45555554332 222223367999999999852 111111    111122456789999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||..+
T Consensus       151 AT~~~~  156 (459)
T 2z83_A          151 ATPPGT  156 (459)
T ss_dssp             SSCTTC
T ss_pred             cCCCcc
Confidence            999754

>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=99.11  E-value=2.7e-10  Score=87.99  Aligned_cols=125  Identities=13%  Similarity=0.106  Sum_probs=71.0

Q ss_pred             cccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           4 VIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         4 iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      ++..++|+|||... +.++......  ..++||++|. .+..|+.+++.    +..+. +......              
T Consensus        23 lv~a~TGsGKT~~~~~~~l~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~----g~~v~-~~~~~~~--------------   81 (451)
T 2jlq_A           23 IMDLHPGAGKTKRILPSIVREALLR--RLRTLILAPTRVVAAEMEEALR----GLPIR-YQTPAVK--------------   81 (451)
T ss_dssp             EECCCTTSSCCTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT----TSCEE-ECCTTCS--------------
T ss_pred             EEECCCCCCHhhHHHHHHHHHHHhc--CCcEEEECCCHHHHHHHHHHhc----Cceee-eeecccc--------------
Confidence            67789999999874 4444443332  3689999998 56678887774    22221 1110000              


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhc-cccccccEEEEeCCcccCCcccHHHH-HHh---ccccccEEEEec
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGHSVKNKKSKLSI-KLT---ALRATFKVLLTG  156 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah~~k~~~~~~~~-~~~---~l~~~~~~~lT~  156 (169)
                                ........+ .+.|.+.+.+.... ..-.+++++|+||||++ +....... .+.   .......++|||
T Consensus        82 ----------~~~~~~~~i-~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SA  149 (451)
T 2jlq_A           82 ----------SDHTGREIV-DLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTA  149 (451)
T ss_dssp             ----------CCCCSSCCE-EEEEHHHHHHHHHHCSCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECS
T ss_pred             ----------ccCCCCceE-EEEChHHHHHHhhCcccccCCCEEEEeCCccC-CcchHHHHHHHHHhhcCCCceEEEEcc
Confidence                      001134445 66777766543322 12236799999999987 22222111 111   113567899999


Q ss_pred             cCCCC
Q psy1090         157 WYYPN  161 (169)
Q Consensus       157 TP~~n  161 (169)
                      ||...
T Consensus       150 T~~~~  154 (451)
T 2jlq_A          150 TPPGS  154 (451)
T ss_dssp             SCTTC
T ss_pred             CCCcc
Confidence            99654

>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=99.07  E-value=5.9e-10  Score=85.83  Aligned_cols=126  Identities=15%  Similarity=0.167  Sum_probs=68.7

Q ss_pred             ccccCCCCCcHHHHHH-HHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++..++|+|||..++ .++..+...  ...+||++|. .+..|+.+++..+    .+. +.+..-.          .  
T Consensus        11 vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~----~v~-~~~~~~~----------~--   71 (440)
T 1yks_A           11 TVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----DVK-FHTQAFS----------A--   71 (440)
T ss_dssp             EEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----CEE-EESSCCC----------C--
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC----CeE-Eecccce----------e--
Confidence            6788999999998863 444433332  3589999998 5667888888643    222 1111000          0  


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHh-chhccccccccEEEEeCCcccCCcccHHH-HHHhc---cccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIEN-DFGFLKKITWNCIIVDEGHSVKNKKSKLS-IKLTA---LRATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~-~~~~~~~~~~~~vi~DEah~~k~~~~~~~-~~~~~---l~~~~~~~lT  155 (169)
                                 .. ....-+ -..+...+.. ......-.+++++|+||+|++ +...... ..+..   ......++||
T Consensus        72 -----------v~-Tp~~l~-~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~S  137 (440)
T 1yks_A           72 -----------HG-SGREVI-DAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMT  137 (440)
T ss_dssp             -----------CC-CSSCCE-EEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEC
T ss_pred             -----------cc-CCccce-eeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEe
Confidence                       00 011111 2223333322 112212246789999999998 2221111 11111   1356789999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||..+
T Consensus       138 AT~~~~  143 (440)
T 1yks_A          138 ATPPGT  143 (440)
T ss_dssp             SSCTTC
T ss_pred             CCCCch
Confidence            999765

>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=99.04  E-value=5.2e-10  Score=89.60  Aligned_cols=123  Identities=23%  Similarity=0.145  Sum_probs=75.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      .++.-++|+|||......+.   +.  ..++||++|. .+..|+.+.+.+.. +..+....|...               
T Consensus       235 vlv~ApTGSGKT~a~~l~ll---~~--g~~vLVl~PTReLA~Qia~~l~~~~-g~~vg~~vG~~~---------------  293 (666)
T 3o8b_A          235 AHLHAPTGSGKSTKVPAAYA---AQ--GYKVLVLNPSVAATLGFGAYMSKAH-GIDPNIRTGVRT---------------  293 (666)
T ss_dssp             EEEECCTTSCTTTHHHHHHH---HT--TCCEEEEESCHHHHHHHHHHHHHHH-SCCCEEECSSCE---------------
T ss_pred             EEEEeCCchhHHHHHHHHHH---HC--CCeEEEEcchHHHHHHHHHHHHHHh-CCCeeEEECcEe---------------
Confidence            46778999999966554332   22  3489999998 55568888776655 233333333311               


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccH-HHHHHhccc---cccEEEEecc
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSK-LSIKLTALR---ATFKVLLTGW  157 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~-~~~~~~~l~---~~~~~~lT~T  157 (169)
                                  .....++ ++.|++.+.++ ..+...+++++|+||+|.+...... ....+..+.   ....+++|||
T Consensus       294 ------------~~~~~~I-lV~TPGrLl~~-~~l~l~~l~~lVlDEAH~l~~~~~~~l~~Il~~l~~~~~~llil~SAT  359 (666)
T 3o8b_A          294 ------------ITTGAPV-TYSTYGKFLAD-GGCSGGAYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLATAT  359 (666)
T ss_dssp             ------------ECCCCSE-EEEEHHHHHHT-TSCCTTSCSEEEETTTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEESS
T ss_pred             ------------ccCCCCE-EEECcHHHHhC-CCcccCcccEEEEccchhcCccHHHHHHHHHHhhhhcCCceEEEECCC
Confidence                        0155677 99999988543 2334447899999999876421111 122223332   2236778999


Q ss_pred             CCC
Q psy1090         158 YYP  160 (169)
Q Consensus       158 P~~  160 (169)
                      |..
T Consensus       360 ~~~  362 (666)
T 3o8b_A          360 PPG  362 (666)
T ss_dssp             CTT
T ss_pred             CCc
Confidence            864

>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=99.04  E-value=9.9e-10  Score=77.71  Aligned_cols=138  Identities=13%  Similarity=0.002  Sum_probs=75.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHH-HHhCC--CCceEEEecCc-chHHHHHHHHHhCCC---ceEEEEeCCHHHHHHHHHhh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKI-IEEQA--LEPNLIVCPLS-VLNNWEAEFRKFAPF---VRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~-~~~~~--~~~~Liv~P~~-~l~qW~~e~~~~~~~---~~~~~~~g~~~~~~~~~~~~   75 (169)
                      .++..++|+|||......+... ...+.  ...+++++|.. +..|..+.+.+....   ..+.. . ..          
T Consensus        79 ~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~-~-~~----------  146 (235)
T 3llm_A           79 VIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGY-S-VR----------  146 (235)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEE-E-ET----------
T ss_pred             EEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEE-e-ec----------
Confidence            4678899999997655444332 22222  23688888984 445666666654421   11110 0 00          


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHh----ccccccE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLT----ALRATFK  151 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~----~l~~~~~  151 (169)
                                   ..........++ +++|.+.+.+.... .-.+++++|+||+|...-........++    .......
T Consensus       147 -------------~~~~~~~~~~~I-vv~Tpg~l~~~l~~-~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~~~~~~  211 (235)
T 3llm_A          147 -------------FESILPRPHASI-MFCTVGVLLRKLEA-GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRI  211 (235)
T ss_dssp             -------------TEEECCCSSSEE-EEEEHHHHHHHHHH-CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHCTTSEE
T ss_pred             -------------hhhccCCCCCeE-EEECHHHHHHHHHh-hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhCCCCeE
Confidence                         000000134556 88998777654432 1246789999999973111111111222    2244568


Q ss_pred             EEEeccCCCCCchhhc
Q psy1090         152 VLLTGWYYPNKWSKQC  167 (169)
Q Consensus       152 ~~lT~TP~~n~~~el~  167 (169)
                      +++|||+-.+.+.+.|
T Consensus       212 il~SAT~~~~~~~~~~  227 (235)
T 3llm_A          212 VLMSATIDTSMFCEYF  227 (235)
T ss_dssp             EEEECSSCCHHHHHHT
T ss_pred             EEEecCCCHHHHHHHc
Confidence            9999999876655544

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.03  E-value=2.5e-10  Score=91.96  Aligned_cols=126  Identities=17%  Similarity=0.140  Sum_probs=69.4

Q ss_pred             ccccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++..++|+|||..+ +.++..+..  ....+||++|. .+..|+.+.+..+.  ..   +....-..         .  
T Consensus       244 vlv~apTGSGKTl~~ll~il~~l~~--~~~~~lilaPTr~La~Q~~~~l~~~~--i~---~~~~~l~~---------v--  305 (673)
T 2wv9_A          244 TVLDLHPGAGKTRRILPQIIKDAIQ--KRLRTAVLAPTRVVAAEMAEALRGLP--VR---YLTPAVQR---------E--  305 (673)
T ss_dssp             EEECCCTTTTTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTSC--CE---ECCC---C---------C--
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEccHHHHHHHHHHHHhcCC--ee---eecccccc---------c--
Confidence            578899999999885 444444333  23689999998 56678888887542  11   11110000         0  


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHH-hchhccccccccEEEEeCCcccCCccc-HHHHHHhcc---ccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIE-NDFGFLKKITWNCIIVDEGHSVKNKKS-KLSIKLTAL---RATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~-~~~~~~~~~~~~~vi~DEah~~k~~~~-~~~~~~~~l---~~~~~~~lT  155 (169)
                                   .....-+ -+.+...+. .......-.+++++|+||+|++. ... .....+..+   .....++||
T Consensus       306 -------------~tp~~ll-~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~~-~~~~~~~~~l~~~~~~~~~~vl~~S  370 (673)
T 2wv9_A          306 -------------HSGNEIV-DVMCHATLTHRLMSPLRVPNYNLFVMDEAHFTD-PASIAARGYIATRVEAGEAAAIFMT  370 (673)
T ss_dssp             -------------CCSCCCE-EEEEHHHHHHHHHSSSCCCCCSEEEEESTTCCC-HHHHHHHHHHHHHHHTTSCEEEEEC
T ss_pred             -------------CCHHHHH-HHHHhhhhHHHHhcccccccceEEEEeCCcccC-ccHHHHHHHHHHhccccCCcEEEEc
Confidence                         0011222 333333332 22222223468999999999982 111 111222222   456789999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||..+
T Consensus       371 AT~~~~  376 (673)
T 2wv9_A          371 ATPPGT  376 (673)
T ss_dssp             SSCTTC
T ss_pred             CCCChh
Confidence            999754

>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=99.00  E-value=9.3e-10  Score=96.31  Aligned_cols=133  Identities=15%  Similarity=0.096  Sum_probs=81.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh---------CCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE---------QALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERK   69 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~---------~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~   69 (169)
                      +.+++-++|+|||+.+.-.+.....+         ....++|+|+|. ++..|-.++|.+.+.  +.++..++|+.....
T Consensus        97 N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~~~~gi~V~~~tGd~~~~~  176 (1724)
T 4f92_B           97 NLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCK  176 (1724)
T ss_dssp             CEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHHTTTTCCEEECCSSCSSCC
T ss_pred             cEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHHhhCCCEEEEEECCCCCCc
Confidence            35778899999998876544433322         123479999997 777777788865442  567777777532110


Q ss_pred             HHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhcc----ccccccEEEEeCCcccCCcccHHHHHH--
Q psy1090          70 ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL----KKITWNCIIVDEGHSVKNKKSKLSIKL--  143 (169)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~----~~~~~~~vi~DEah~~k~~~~~~~~~~--  143 (169)
                                             +.....++ +++|++.+..-....    .-...+++|+||+|.+.++-......+  
T Consensus       177 -----------------------~~~~~~~I-lVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d~RG~~lE~~l~  232 (1724)
T 4f92_B          177 -----------------------EEISATQI-IVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVA  232 (1724)
T ss_dssp             -----------------------TTGGGCSE-EEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGSTTHHHHHHHHH
T ss_pred             -----------------------cccCCCCE-EEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCCccHHHHHHHHH
Confidence                                   00145677 999999864321110    012568999999998864322222211  


Q ss_pred             ------hcc-ccccEEEEeccC
Q psy1090         144 ------TAL-RATFKVLLTGWY  158 (169)
Q Consensus       144 ------~~l-~~~~~~~lT~TP  158 (169)
                            ... .....++||||.
T Consensus       233 rl~~~~~~~~~~~riI~LSATl  254 (1724)
T 4f92_B          233 RAIRNIEMTQEDVRLIGLSATL  254 (1724)
T ss_dssp             HHHHHHHHHTCCCEEEEEECSC
T ss_pred             HHHHHHHhCCCCCcEEEEeccc
Confidence                  112 234689999995

>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=98.97  E-value=2e-09  Score=86.12  Aligned_cols=126  Identities=14%  Similarity=0.127  Sum_probs=72.7

Q ss_pred             ccccCCCCCcHHHHH-HHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKV-IAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~-i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++..++|+|||... +.++..+..  ...++||++|. .+..|+.+++..    ..+. +.+....          .  
T Consensus       189 vlv~a~TGSGKT~~~~lpil~~l~~--~~~~vLvl~PtreLa~Qi~~~l~~----~~v~-~~~~~l~----------~--  249 (618)
T 2whx_A          189 TIMDLHPGAGKTKRILPSIVREALK--RRLRTLILAPTRVVAAEMEEALRG----LPIR-YQTPAVK----------S--  249 (618)
T ss_dssp             EEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTT----SCEE-ECCTTSS----------C--
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHh--CCCeEEEEcChHHHHHHHHHHhcC----Ccee-Eecccce----------e--
Confidence            578899999999884 555555443  23589999998 566788877752    2222 2221100          0  


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhch-hccccccccEEEEeCCcccCCcccH-HHHHH-hcc--ccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDF-GFLKKITWNCIIVDEGHSVKNKKSK-LSIKL-TAL--RATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~-~~~~~~~~~~vi~DEah~~k~~~~~-~~~~~-~~l--~~~~~~~lT  155 (169)
                                  .......+ .+.+...+.+.. ....-.+++++|+||||++ +.... ....+ ..+  .....++||
T Consensus       250 ------------~~tp~~~i-~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~-~~~~~~~~~~i~~~l~~~~~q~il~S  315 (618)
T 2whx_A          250 ------------DHTGREIV-DLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMT  315 (618)
T ss_dssp             ------------CCCSSSCE-EEEEHHHHHHHHHHCSSCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHHTSCEEEEEC
T ss_pred             ------------ccCCCceE-EEEChHHHHHHHhccccccCCeEEEEECCCCC-CccHHHHHHHHHHHhcccCccEEEEE
Confidence                        00123333 556666554322 1212346899999999997 22211 11222 222  346789999


Q ss_pred             ccCCCC
Q psy1090         156 GWYYPN  161 (169)
Q Consensus       156 ~TP~~n  161 (169)
                      |||...
T Consensus       316 AT~~~~  321 (618)
T 2whx_A          316 ATPPGS  321 (618)
T ss_dssp             SSCTTC
T ss_pred             CCCchh
Confidence            999654

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.78  E-value=2.1e-08  Score=79.14  Aligned_cols=54  Identities=15%  Similarity=0.002  Sum_probs=36.8

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYG   63 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g   63 (169)
                      +++...+|+|||+..+..+..   .  ..+++|++|+ .+..|+.+++.++  ..++....|
T Consensus        29 ~~~~a~TGtGKT~~~l~~~~~---~--~~~~~~~~~t~~l~~q~~~~~~~l--~~~~~~l~g   83 (540)
T 2vl7_A           29 LLLNAKPGLGKTVFVEVLGMQ---L--KKKVLIFTRTHSQLDSIYKNAKLL--GLKTGFLIG   83 (540)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH---H--TCEEEEEESCHHHHHHHHHHHGGG--TCCEEEC--
T ss_pred             EEEEcCCCCcHHHHHHHHHHh---C--CCcEEEEcCCHHHHHHHHHHHHhc--CCcEEEecC
Confidence            577889999999765443321   1  3689999998 5677999999875  344444443

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.76  E-value=1.8e-08  Score=79.63  Aligned_cols=57  Identities=12%  Similarity=0.027  Sum_probs=41.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGN   64 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~   64 (169)
                      +++...+|+|||+..+.-+..     ...+++|++|. .+..|+.+++.++..  +.++....|.
T Consensus        25 ~~~~a~TGtGKT~~~l~p~l~-----~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~~~~~l~gr   84 (551)
T 3crv_A           25 VALNAPTGSGKTLFSLLVSLE-----VKPKVLFVVRTHNEFYPIYRDLTKIREKRNITFSFLVGK   84 (551)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH-----HCSEEEEEESSGGGHHHHHHHHTTCCCSSCCCEEECCCH
T ss_pred             EEEECCCCccHHHHHHHHHHh-----CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCccEEEEccc
Confidence            467789999999877654433     24689999998 566799999987743  4566665553

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.57  E-value=3.8e-07  Score=74.90  Aligned_cols=127  Identities=10%  Similarity=0.000  Sum_probs=75.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-H---HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-N---NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~---qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |-|....+|.|||+.+...+......  ...++||+|+.-+ .   +|...+-++. ++.+....|......  +...  
T Consensus        94 G~IaeakTGeGKTLvf~Lp~~L~aL~--G~qv~VvTPTreLA~Qdae~m~~l~~~l-GLsv~~i~Gg~~~~~--r~~a--  166 (997)
T 2ipc_A           94 GKIAEMKTGEGKTLVATLAVALNALT--GKGVHVVTVNDYLARRDAEWMGPVYRGL-GLSVGVIQHASTPAE--RRKA--  166 (997)
T ss_dssp             TSEEECCSTHHHHHHHHHHHHHHHTT--CSCCEEEESSHHHHHHHHHHHHHHHHTT-TCCEEECCTTCCHHH--HHHH--
T ss_pred             CceeeccCCCchHHHHHHHHHHHHHh--CCCEEEEeCCHHHHHHHHHHHHHHHHhc-CCeEEEEeCCCCHHH--HHHH--
Confidence            34556789999998654333211222  3479999999654 3   4666666666 677777776433221  1111  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHH-----hch----hccccc---cccEEEEeCCcccCCcccHHHHHHhc
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIE-----NDF----GFLKKI---TWNCIIVDEGHSVKNKKSKLSIKLTA  145 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~-----~~~----~~~~~~---~~~~vi~DEah~~k~~~~~~~~~~~~  145 (169)
                                        ...|| ++.|+..+.     ...    +.+...   +..++|+||+|.+-....        
T Consensus       167 ------------------y~~DI-vyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLiDea--------  219 (997)
T 2ipc_A          167 ------------------YLADV-TYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEA--------  219 (997)
T ss_dssp             ------------------HTSSE-EEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTTSST--------
T ss_pred             ------------------cCCCE-EEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHHhCC--------
Confidence                              33566 888887763     221    122233   678999999996432221        


Q ss_pred             cccccEEEEeccCCCCCchhhc
Q psy1090         146 LRATFKVLLTGWYYPNKWSKQC  167 (169)
Q Consensus       146 l~~~~~~~lT~TP~~n~~~el~  167 (169)
                         ..-+++|| |.+.. .++|
T Consensus       220 ---rtPLIISg-p~~~~-~~lY  236 (997)
T 2ipc_A          220 ---RTPLIISG-PAEKA-TDLY  236 (997)
T ss_dssp             ---TSCEEEEE-SCSSC-HHHH
T ss_pred             ---CCCeeeeC-CCccc-hHHH
Confidence               22388999 76655 4444

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.56  E-value=2e-07  Score=75.15  Aligned_cols=118  Identities=11%  Similarity=0.043  Sum_probs=71.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      .++.-++|+|||..++..+.   ..   +..++++|. .+..|..+++.+.  +..+...+|....         ...+ 
T Consensus       158 vlv~apTGSGKT~~al~~l~---~~---~~gl~l~PtR~LA~Qi~~~l~~~--g~~v~lltG~~~~---------iv~T-  219 (677)
T 3rc3_A          158 IFHSGPTNSGKTYHAIQKYF---SA---KSGVYCGPLKLLAHEIFEKSNAA--GVPCDLVTGEERV---------TVQP-  219 (677)
T ss_dssp             EEEECCTTSSHHHHHHHHHH---HS---SSEEEEESSHHHHHHHHHHHHHT--TCCEEEECSSCEE---------CCST-
T ss_pred             EEEEcCCCCCHHHHHHHHHH---hc---CCeEEEeCHHHHHHHHHHHHHhc--CCcEEEEECCeeE---------EecC-
Confidence            37788999999985443332   22   345999998 5667888888876  5566666665332         0000 


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcc--cHHHHHHhccc--cccEEEEecc
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR--ATFKVLLTGW  157 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~--~~~~~~lT~T  157 (169)
                                  .....++ +..|.+.+..      ...++++|+||+|++.+..  ......+..+.  ....+++|||
T Consensus       220 ------------pGr~~~i-l~~T~e~~~l------~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT  280 (677)
T 3rc3_A          220 ------------NGKQASH-VSCTVEMCSV------TTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAA  280 (677)
T ss_dssp             ------------TCCCCSE-EEEEGGGCCS------SSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGG
T ss_pred             ------------CCcccce-eEecHhHhhh------cccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccch
Confidence                        0023455 7777655321      2467999999999985432  22234444443  3455677777

>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=98.54  E-value=2.5e-07  Score=75.82  Aligned_cols=139  Identities=14%  Similarity=0.072  Sum_probs=72.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC-CCCceEEEecCc-chHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ-ALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~-~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++..++|+|||.+.-.++....... ....+++++|.. +..|+.+.+.... +..+....|...        .+    
T Consensus       112 vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~La~q~~~~l~~~~-~~~v~~~vG~~i--------~~----  178 (773)
T 2xau_A          112 MVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEM-DVKLGEEVGYSI--------RF----  178 (773)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHHHHHHHHHHHHHT-TCCBTTTEEEEE--------TT----
T ss_pred             EEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHHHHHHHHHHHHHh-CCchhheeccee--------cc----
Confidence            47889999999984333322211111 134588999984 4557776665543 111110001000        00    


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchh-ccccccccEEEEeCCcc-cCCccc--HHHHHHhc-cccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG-FLKKITWNCIIVDEGHS-VKNKKS--KLSIKLTA-LRATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~-~~~~~~~~~vi~DEah~-~k~~~~--~~~~~~~~-l~~~~~~~lT  155 (169)
                                ........++ ++.|.+.+.+... ...-.+++++|+||+|. .-+...  ...+.+.. .+....++||
T Consensus       179 ----------~~~~~~~~~I-~v~T~G~l~r~l~~~~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~~~~~iIl~S  247 (773)
T 2xau_A          179 ----------ENKTSNKTIL-KYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMS  247 (773)
T ss_dssp             ----------EEECCTTCSE-EEEEHHHHHHHHHHSTTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHCTTCEEEEEE
T ss_pred             ----------ccccCCCCCE-EEECHHHHHHHHhhCccccCCCEEEecCccccccchHHHHHHHHHHHHhCCCceEEEEe
Confidence                      0001145566 8888888765432 12234789999999995 221111  11122222 2345689999


Q ss_pred             ccCCCCCchh
Q psy1090         156 GWYYPNKWSK  165 (169)
Q Consensus       156 ~TP~~n~~~e  165 (169)
                      ||+-.+.+.+
T Consensus       248 AT~~~~~l~~  257 (773)
T 2xau_A          248 ATLDAEKFQR  257 (773)
T ss_dssp             SCSCCHHHHH
T ss_pred             ccccHHHHHH
Confidence            9995444433

>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=98.44  E-value=1.2e-06  Score=71.99  Aligned_cols=106  Identities=14%  Similarity=0.036  Sum_probs=66.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-ch---HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VL---NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l---~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|....+|.|||+.+..-+......  ...++||+|+. +.   .+|...+.+|. ++.+....|.......  ...  
T Consensus       126 G~Iaem~TGeGKTLa~~LP~~l~aL~--g~~v~VvTpTreLA~Qdae~m~~l~~~l-GLsv~~i~gg~~~~~r--~~~--  198 (922)
T 1nkt_A          126 GNVAEMKTGEGKTLTCVLPAYLNALA--GNGVHIVTVNDYLAKRDSEWMGRVHRFL-GLQVGVILATMTPDER--RVA--  198 (922)
T ss_dssp             TEEEECCTTSCHHHHTHHHHHHHHTT--TSCEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTCCHHHH--HHH--
T ss_pred             CCEEEecCCCccHHHHHHHHHHHHHh--CCCeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHH--HHh--
Confidence            45667889999998654332211112  34799999984 43   35888888887 7888777664332111  111  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhch----hccccccccEEEEeCCcccC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDF----GFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~----~~~~~~~~~~vi~DEah~~k  133 (169)
                                        ..+|| ++.|+..+     ....    +.+...++.++|+|||+++-
T Consensus       199 ------------------y~~DI-vygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmL  244 (922)
T 1nkt_A          199 ------------------YNADI-TYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSIL  244 (922)
T ss_dssp             ------------------HHSSE-EEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHH
T ss_pred             ------------------cCCCE-EEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHH
Confidence                              23466 88887776     3332    23444578899999999865

>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=98.43  E-value=9.3e-07  Score=72.26  Aligned_cols=106  Identities=8%  Similarity=-0.033  Sum_probs=66.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chH---HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLN---NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~---qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|-...+|.|||+.+..-+.....  ....++||+|+. +..   +|...+.+|. ++.+....|..........    
T Consensus        98 G~Iaea~TGeGKTlaf~LP~~l~aL--~g~~vlVltptreLA~qd~e~~~~l~~~l-gl~v~~i~gg~~~~~r~~~----  170 (844)
T 1tf5_A           98 GNIAEMKTGEGKTLTSTLPVYLNAL--TGKGVHVVTVNEYLASRDAEQMGKIFEFL-GLTVGLNLNSMSKDEKREA----  170 (844)
T ss_dssp             TSEEECCTTSCHHHHHHHHHHHHHT--TSSCEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTSCHHHHHHH----
T ss_pred             CCEEEccCCcHHHHHHHHHHHHHHH--cCCCEEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHh----
Confidence            4466788999999865433321111  234799999984 443   4777777776 7787776665332211111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHH-----Hhch----hccccccccEEEEeCCcccC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDF----GFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~-----~~~~----~~~~~~~~~~vi~DEah~~k  133 (169)
                                        ..++| ++.|+..+     ....    ..+...+..++|+|||+++-
T Consensus       171 ------------------~~~dI-v~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mL  216 (844)
T 1tf5_A          171 ------------------YAADI-TYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  216 (844)
T ss_dssp             ------------------HHSSE-EEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             ------------------cCCCE-EEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhh
Confidence                              23466 88888777     4432    23444578899999999864

>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=98.39  E-value=8.8e-07  Score=72.35  Aligned_cols=106  Identities=10%  Similarity=-0.082  Sum_probs=65.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chH---HHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLN---NWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~---qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|-...+|+|||+.+..-+.....  ....++|++|+. +..   +|...+.++. ++.+....|......  +...  
T Consensus        89 G~Iaem~TGsGKTlaf~LP~l~~~l--~g~~vlVltPTreLA~Q~~e~~~~l~~~l-gl~v~~i~GG~~~~~--r~~~--  161 (853)
T 2fsf_A           89 RCIAEMRTGEGKTLTATLPAYLNAL--TGKGVHVVTVNDYLAQRDAENNRPLFEFL-GLTVGINLPGMPAPA--KREA--  161 (853)
T ss_dssp             SEEEECCTTSCHHHHHHHHHHHHHT--TSSCCEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTCCHHH--HHHH--
T ss_pred             CeeeeecCCchHHHHHHHHHHHHHH--cCCcEEEEcCCHHHHHHHHHHHHHHHHhc-CCeEEEEeCCCCHHH--HHHh--
Confidence            3455678999999865433322122  234799999985 433   4666666666 677777776533221  1111  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHH-----hch----hccccccccEEEEeCCcccC
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIE-----NDF----GFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~-----~~~----~~~~~~~~~~vi~DEah~~k  133 (169)
                                        ...+| ++.|+..+.     ...    ..+...+..++|+||||++-
T Consensus       162 ------------------~~~dI-vvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mL  207 (853)
T 2fsf_A          162 ------------------YAADI-TYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSIL  207 (853)
T ss_dssp             ------------------HHSSE-EEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHT
T ss_pred             ------------------cCCCE-EEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHH
Confidence                              23566 899987762     222    22444578899999999765

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.14  E-value=5.2e-06  Score=66.85  Aligned_cols=48  Identities=15%  Similarity=0.268  Sum_probs=37.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKF   52 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~   52 (169)
                      .++.-.+|+|||.+...++..+...+  .++|+++|++. +++..+.+...
T Consensus       208 ~lI~GPPGTGKT~ti~~~I~~l~~~~--~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          208 AIIHGPPGTGKTTTVVEIILQAVKQG--LKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTT--CCEEEEESSHHHHHHHHHHHHHT
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhCC--CeEEEEcCchHHHHHHHHHHHhc
Confidence            35677899999999988888777654  68999999854 56777777654

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.01  E-value=4.2e-05  Score=60.78  Aligned_cols=114  Identities=17%  Similarity=0.013  Sum_probs=66.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCcc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIK   82 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~   82 (169)
                      .++.-.+|+|||.++.+++..+...  ..++++++|+........+..    .....-          +... ..     
T Consensus       207 ~~I~G~pGTGKTt~i~~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~~----~~~a~T----------ih~l-l~-----  264 (574)
T 3e1s_A          207 VVLTGGPGTGKSTTTKAVADLAESL--GLEVGLCAPTGKAARRLGEVT----GRTAST----------VHRL-LG-----  264 (574)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHH----TSCEEE----------HHHH-TT-----
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhc--CCeEEEecCcHHHHHHhHhhh----cccHHH----------HHHH-Hc-----
Confidence            3567789999998887777655543  368999999876654443321    000000          0000 00     


Q ss_pred             cccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCC
Q psy1090          83 VPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNK  162 (169)
Q Consensus        83 ~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~  162 (169)
                                         ...  +.+.  ...-...+++++|+||++.+.  .......+..+....++++.|-|-|..
T Consensus       265 -------------------~~~--~~~~--~~~~~~~~~dvlIIDEasml~--~~~~~~Ll~~~~~~~~lilvGD~~QL~  319 (574)
T 3e1s_A          265 -------------------YGP--QGFR--HNHLEPAPYDLLIVDEVSMMG--DALMLSLLAAVPPGARVLLVGDTDQLP  319 (574)
T ss_dssp             -------------------EET--TEES--CSSSSCCSCSEEEECCGGGCC--HHHHHHHHTTSCTTCEEEEEECTTSCC
T ss_pred             -------------------CCc--chhh--hhhcccccCCEEEEcCccCCC--HHHHHHHHHhCcCCCEEEEEecccccC
Confidence                               000  0000  011123478999999999974  234445566677788999999998854


Q ss_pred             c
Q psy1090         163 W  163 (169)
Q Consensus       163 ~  163 (169)
                      +
T Consensus       320 ~  320 (574)
T 3e1s_A          320 P  320 (574)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=97.95  E-value=0.0001  Score=59.20  Aligned_cols=148  Identities=11%  Similarity=0.198  Sum_probs=76.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhCCCceEEEEeCCHHHH-----------HHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFAPFVRTVKYYGNAIER-----------KAL   71 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~~~~~~~~~~g~~~~~-----------~~~   71 (169)
                      ++.-.+|+|||.+...++..+.. ....++|+++|++. +.+-.+.+.+.  +.+++.......+.           ..+
T Consensus       199 li~GppGTGKT~~~~~~i~~l~~-~~~~~ilv~a~tn~A~~~l~~~l~~~--~~~~~R~~~~~r~~~~~~~~~~tl~~~~  275 (624)
T 2gk6_A          199 LIQGPPGTGKTVTSATIVYHLAR-QGNGPVLVCAPSNIAVDQLTEKIHQT--GLKVVRLCAKSREAIDSPVSFLALHNQI  275 (624)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHT-SSSCCEEEEESSHHHHHHHHHHHHTT--TCCEEECCCTGGGSCCCTTTTTBHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHH-cCCCeEEEEeCcHHHHHHHHHHHHhc--CCeEEeeccccchhhccchhhhhHHHHH
Confidence            56678999999998887766553 24568999999865 45555556543  34444433321110           000


Q ss_pred             H---------HhhhcCCCc-ccccc---cCC-----ccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccC
Q psy1090          72 Q---------SEALSLPTI-KVPAK---KGK-----TKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        72 ~---------~~~~~~~~~-~~~~~---~~~-----~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k  133 (169)
                      .         ......... ..+..   ...     .........++ +++|...+..  ..+....|+++|+|||....
T Consensus       276 ~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~v-I~~T~~~~~~--~~l~~~~fd~viIDEAsQ~~  352 (624)
T 2gk6_A          276 RNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADV-ICCTCVGAGD--PRLAKMQFRSILIDESTQAT  352 (624)
T ss_dssp             TSCSSCHHHHHHHTTCC----CCHHHHHHHHHHHHHHHHHHHHTCSE-EEEETGGGGC--GGGTTCCCSEEEETTGGGSC
T ss_pred             HhccchHHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHHHHHhcCCE-EEEcChhhcc--hhhhcCCCCEEEEecccccC
Confidence            0         000000000 00000   000     00011245567 6666544332  23456789999999997654


Q ss_pred             CcccHHHHHHhccccccEEEEeccCCCC
Q psy1090         134 NKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       134 ~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      .+.  .  .+..+....++++-|=|-|-
T Consensus       353 e~~--~--li~l~~~~~~~ilvGD~~QL  376 (624)
T 2gk6_A          353 EPE--C--MVPVVLGAKQLILVGDHCQL  376 (624)
T ss_dssp             HHH--H--HHHHTTTBSEEEEEECTTSC
T ss_pred             cHH--H--HHHHHhcCCeEEEecChhcc
Confidence            332  1  22222335688888888774

>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=97.80  E-value=0.00016  Score=57.90  Aligned_cols=44  Identities=18%  Similarity=0.194  Sum_probs=32.9

Q ss_pred             ccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCch
Q psy1090         119 ITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWS  164 (169)
Q Consensus       119 ~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~~  164 (169)
                      .+++++|+|||+.+.  .......+..++...+++|-|=|-|-.+.
T Consensus       261 l~~d~lIIDEAsml~--~~~~~~Ll~~l~~~~~liLvGD~~QL~~V  304 (608)
T 1w36_D          261 LHLDVLVVDEASMID--LPMMSRLIDALPDHARVIFLGDRDQLASV  304 (608)
T ss_dssp             CSCSEEEECSGGGCB--HHHHHHHHHTCCTTCEEEEEECTTSGGGT
T ss_pred             CCCCEEEEechhhCC--HHHHHHHHHhCCCCCEEEEEcchhhcCCC
Confidence            478999999999764  23345556677778899999988876553

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.77  E-value=0.00018  Score=49.89  Aligned_cols=34  Identities=15%  Similarity=0.061  Sum_probs=25.6

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +.-+||.|||..++..+......+  .+++|+.|.-
T Consensus        33 itG~MgsGKTT~lL~~a~r~~~~g--~kVli~k~~~   66 (214)
T 2j9r_A           33 ICGSMFSGKSEELIRRVRRTQFAK--QHAIVFKPCI   66 (214)
T ss_dssp             EECSTTSCHHHHHHHHHHHHHHTT--CCEEEEECC-
T ss_pred             EECCCCCcHHHHHHHHHHHHHHCC--CEEEEEEecc
Confidence            456899999999988876655443  6889988863

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=97.76  E-value=0.0002  Score=59.00  Aligned_cols=148  Identities=13%  Similarity=0.211  Sum_probs=76.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhCCCceEEEEeCCHHH-----------HHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAPFVRTVKYYGNAIE-----------RKAL   71 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~~~~~~~~~~g~~~~-----------~~~~   71 (169)
                      ++.-.+|+|||.+...++..+... ...++|+++|++.. .+-.+.+.+.  +.+++......++           ....
T Consensus       375 lI~GppGTGKT~ti~~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~--g~~vvRlg~~~r~~i~~~~~~~tlh~~~  451 (800)
T 2wjy_A          375 LIQGPPGTGKTVTSATIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT--GLKVVRLCAKSREAIDSPVSFLALHNQI  451 (800)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT--TCCEEECCCGGGGGCCCTTGGGBHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh--CcceEeecccchhhhcchhhhhhHHHHH
Confidence            566789999999988877665542 35689999999654 4555555443  3344433322111           0000


Q ss_pred             H---------Hhh-hcCCCccccc---ccCCc-----cccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccC
Q psy1090          72 Q---------SEA-LSLPTIKVPA---KKGKT-----KKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVK  133 (169)
Q Consensus        72 ~---------~~~-~~~~~~~~~~---~~~~~-----~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k  133 (169)
                      .         ... ..........   .....     ........++ +++|...+..  ..+....|+++|+|||....
T Consensus       452 ~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~V-I~~T~~~~~~--~~l~~~~fd~viIDEAsQ~~  528 (800)
T 2wjy_A          452 RNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADV-ICCTCVGAGD--PRLAKMQFRSILIDESTQAT  528 (800)
T ss_dssp             HTCTTCHHHHHHHHHHTTTSCCCHHHHHHHHHHHHHHHHHHHHHCSE-EEEETGGGGC--TTTTTCCCSEEEETTGGGSC
T ss_pred             HcCccHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHhhhccCCE-EEEchhhhCC--hhhhcCCCCEEEEECCCCCC
Confidence            0         000 0000000000   00000     0011134566 6666554432  23456789999999997654


Q ss_pred             CcccHHHHHHhccccccEEEEeccCCCC
Q psy1090         134 NKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       134 ~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      .+.    ..+..+....+++|-|=|-|-
T Consensus       529 e~~----~li~l~~~~~~~ilvGD~~QL  552 (800)
T 2wjy_A          529 EPE----CMVPVVLGAKQLILVGDHCQL  552 (800)
T ss_dssp             HHH----HHHHHTTTBSEEEEEECTTSC
T ss_pred             cHH----HHHHHHhcCCeEEEecccccC
Confidence            321    122233345688888888774

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.74  E-value=0.00043  Score=57.11  Aligned_cols=147  Identities=14%  Similarity=0.176  Sum_probs=76.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhCCCceEEEEeCCHHH-----------HHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFAPFVRTVKYYGNAIE-----------RKAL   71 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~~~~~~~~~~g~~~~-----------~~~~   71 (169)
                      ++.-.+|+|||.++...+..+... ...++|+++|++. +.+-.+.+.+.  +.+++........           ....
T Consensus       379 lI~GppGTGKT~~i~~~i~~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~--g~~ilR~g~~~r~~i~~~~~~~tl~~~~  455 (802)
T 2xzl_A          379 LIQGPPGTGKTVTSATIVYHLSKI-HKDRILVCAPSNVAVDHLAAKLRDL--GLKVVRLTAKSREDVESSVSNLALHNLV  455 (802)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHH-HCCCEEEEESSHHHHHHHHHHHHHT--TCCEEECCCGGGTTSCCTTGGGBHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhC-CCCeEEEEcCcHHHHHHHHHHHHhh--CccEEeecccchhhhcchhhhhhHHHHH
Confidence            566789999999988877665543 3468999999865 45666666654  3344443321110           0000


Q ss_pred             HH-----------hhhcCCCccc-ccccCC-----ccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCC
Q psy1090          72 QS-----------EALSLPTIKV-PAKKGK-----TKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        72 ~~-----------~~~~~~~~~~-~~~~~~-----~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~  134 (169)
                      ..           .......... ......     .........++ +++|...+..  ..+.. .|+.+|+|||+....
T Consensus       456 ~~~~~~~l~~l~~~~~~~~~ls~~~~~~~~~~~~~~~~~~l~~a~V-I~~T~~~~~~--~~L~~-~fd~viIDEA~q~~e  531 (802)
T 2xzl_A          456 GRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADV-VCCTCVGAGD--KRLDT-KFRTVLIDESTQASE  531 (802)
T ss_dssp             HTTCCTHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHHHTCSE-EEEETTGGGC--TTCCS-CCSEEEETTGGGSCH
T ss_pred             HhhcHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHhccCCE-EEechhhcCh--HHHhc-cCCEEEEECccccch
Confidence            00           0000000000 000000     00011245566 6766655432  23344 899999999987643


Q ss_pred             cccHHHHHHhccccccEEEEeccCCCC
Q psy1090         135 KKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       135 ~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      +  .  ..+..+....+++|-|=|-|-
T Consensus       532 ~--~--~li~l~~~~~~lilvGD~~QL  554 (802)
T 2xzl_A          532 P--E--CLIPIVKGAKQVILVGDHQQL  554 (802)
T ss_dssp             H--H--HHHHHTTTBSEEEEEECTTSC
T ss_pred             H--H--HHHHHHhCCCEEEEEeCcccc
Confidence            2  1  122233345688888888774

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.73  E-value=7.7e-05  Score=50.60  Aligned_cols=34  Identities=18%  Similarity=0.204  Sum_probs=25.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      ++.-.||+|||..++..+......+  .+++++.|.
T Consensus         7 vi~G~~gsGKTT~ll~~~~~~~~~g--~~v~~~~~~   40 (184)
T 2orw_A            7 VITGPMYSGKTTELLSFVEIYKLGK--KKVAVFKPK   40 (184)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTT--CEEEEEEEC
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEeec
Confidence            4566899999998887776554433  578888877

>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=97.63  E-value=0.00014  Score=50.78  Aligned_cols=35  Identities=17%  Similarity=0.185  Sum_probs=25.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ++.-+||.|||..++..+..+...+  .+++++.|.-
T Consensus        16 litG~mGsGKTT~ll~~~~r~~~~g--~kVli~~~~~   50 (223)
T 2b8t_A           16 FITGPMFAGKTAELIRRLHRLEYAD--VKYLVFKPKI   50 (223)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTT--CCEEEEEECC
T ss_pred             EEECCCCCcHHHHHHHHHHHHHhcC--CEEEEEEecc
Confidence            4567899999999988877655443  5788887753

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.54  E-value=0.00083  Score=51.86  Aligned_cols=39  Identities=10%  Similarity=0.089  Sum_probs=29.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      ++.-..|+|||..+.+++..+...+ ..++++++|.....
T Consensus        49 li~G~aGTGKT~ll~~~~~~l~~~~-~~~il~~a~T~~Aa   87 (459)
T 3upu_A           49 TINGPAGTGATTLTKFIIEALISTG-ETGIILAAPTHAAK   87 (459)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHHTT-CCCEEEEESSHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHhcC-CceEEEecCcHHHH
Confidence            5667789999988877777766554 25799999987654

>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=97.53  E-value=0.00082  Score=54.66  Aligned_cols=59  Identities=14%  Similarity=-0.101  Sum_probs=40.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH----HHHHHHHHhCCCceEEEEeC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN----NWEAEFRKFAPFVRTVKYYG   63 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~----qW~~e~~~~~~~~~~~~~~g   63 (169)
                      |.|.-+.+|.|||+++...+......  .+.+.||+|+.-+.    +|...+-+|. ++.+.....
T Consensus        90 G~iaEM~TGEGKTLva~lp~~lnAL~--G~~vhVvT~ndyLA~rdae~m~~l~~~L-glsvg~i~~  152 (822)
T 3jux_A           90 GKVAEMKTGEGKTLAATMPIYLNALI--GKGVHLVTVNDYLARRDALWMGPVYLFL-GLRVGVINS  152 (822)
T ss_dssp             TCEEECCTTSCHHHHTHHHHHHHHTT--SSCEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEEEET
T ss_pred             CChhhccCCCCccHHHHHHHHHHHhc--CCceEEEeccHHHHHhHHHHHHHHHHHh-CCEEEEEcC
Confidence            56777889999998754332211112  35699999986542    5888888888 677776665

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.50  E-value=0.00038  Score=47.47  Aligned_cols=34  Identities=21%  Similarity=0.150  Sum_probs=25.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      ++--+||+|||..++..+......+  .+++++.|.
T Consensus        12 v~~G~mgsGKTT~ll~~a~r~~~~g--~kV~v~k~~   45 (191)
T 1xx6_A           12 VIVGPMYSGKSEELIRRIRRAKIAK--QKIQVFKPE   45 (191)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEEEC
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHCC--CEEEEEEec
Confidence            3456799999999888776654333  688998886

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.48  E-value=0.00022  Score=54.68  Aligned_cols=106  Identities=11%  Similarity=0.066  Sum_probs=64.7

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      +.-..|+|||......+.       .++.+|++|. .....|.+.+.+..          ..                  
T Consensus       166 I~G~aGsGKTt~I~~~~~-------~~~~lVlTpT~~aa~~l~~kl~~~~----------~~------------------  210 (446)
T 3vkw_A          166 VDGVPGCGKTKEILSRVN-------FEEDLILVPGRQAAEMIRRRANASG----------II------------------  210 (446)
T ss_dssp             EEECTTSCHHHHHHHHCC-------TTTCEEEESCHHHHHHHHHHHTTTS----------CC------------------
T ss_pred             EEcCCCCCHHHHHHHHhc-------cCCeEEEeCCHHHHHHHHHHhhhcC----------cc------------------
Confidence            455789999977655442       2578999998 55567887774221          00                  


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCC
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                                  ..... -+.|++.+..........+++.+|+||+..+-  .......+...++ .++++.|=|-|-
T Consensus       211 ------------~~~~~-~V~T~dsfL~~~~~~~~~~~d~liiDE~sm~~--~~~l~~l~~~~~~-~~vilvGD~~Ql  272 (446)
T 3vkw_A          211 ------------VATKD-NVRTVDSFLMNYGKGARCQFKRLFIDEGLMLH--TGCVNFLVEMSLC-DIAYVYGDTQQI  272 (446)
T ss_dssp             ------------CCCTT-TEEEHHHHHHTTTSSCCCCCSEEEEETGGGSC--HHHHHHHHHHTTC-SEEEEEECTTSC
T ss_pred             ------------ccccc-eEEEeHHhhcCCCCCCCCcCCEEEEeCcccCC--HHHHHHHHHhCCC-CEEEEecCcccc
Confidence                        01111 35666665443333333568999999999762  2333333344444 889998887764

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.31  E-value=0.0011  Score=46.55  Aligned_cols=34  Identities=18%  Similarity=0.055  Sum_probs=25.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ..-+||.|||..++..+....  ....+++++-|.-
T Consensus        24 ~~G~MgsGKTT~lL~~~~r~~--~~g~kvli~kp~~   57 (234)
T 2orv_A           24 ILGPMFSGKSTELMRRVRRFQ--IAQYKCLVIKYAK   57 (234)
T ss_dssp             EECCTTSCHHHHHHHHHHHHH--TTTCCEEEEEETT
T ss_pred             EECCCCCcHHHHHHHHHHHHH--HCCCeEEEEeecC
Confidence            356799999999888766544  3347888888863

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.21  E-value=0.002  Score=44.69  Aligned_cols=34  Identities=18%  Similarity=0.122  Sum_probs=23.3

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +.-+||.|||...+..+..+...+  .+++|+-|.-
T Consensus        33 itG~M~sGKTT~Llr~~~r~~~~g--~kvli~kp~~   66 (219)
T 3e2i_A           33 ITGSMFSGKSEELIRRLRRGIYAK--QKVVVFKPAI   66 (219)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHTT--CCEEEEEEC-
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcC--CceEEEEecc
Confidence            455799999988887765444333  5678887754

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.85  E-value=0.0028  Score=43.21  Aligned_cols=33  Identities=18%  Similarity=0.067  Sum_probs=23.9

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      +--.||+|||...+-.+......+  .+++++-|.
T Consensus        25 iyG~MgsGKTt~Ll~~i~n~~~~~--~kvl~~kp~   57 (195)
T 1w4r_A           25 ILGPMFSGKSTELMRRVRRFQIAQ--YKCLVIKYA   57 (195)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHTT--CCEEEEEET
T ss_pred             EECCCCCcHHHHHHHHHHHHHHcC--CeEEEEccc
Confidence            456899999977776666554443  678888776

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.85  E-value=0.0073  Score=44.18  Aligned_cols=38  Identities=11%  Similarity=0.104  Sum_probs=22.3

Q ss_pred             ccEEEEeCCcccCCcccHH---HHHHhcc-ccccEEEEeccC
Q psy1090         121 WNCIIVDEGHSVKNKKSKL---SIKLTAL-RATFKVLLTGWY  158 (169)
Q Consensus       121 ~~~vi~DEah~~k~~~~~~---~~~~~~l-~~~~~~~lT~TP  158 (169)
                      .+++++||+|.+.......   ...+..+ ....+++++++.
T Consensus        99 ~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~  140 (324)
T 1l8q_A           99 VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  140 (324)
T ss_dssp             CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             CCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            5789999999986421111   1222222 345678888863

>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=96.80  E-value=0.0026  Score=51.44  Aligned_cols=54  Identities=19%  Similarity=0.234  Sum_probs=40.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYY   62 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~   62 (169)
                      .|..-+|+|||+++..++...     .+|+|||+|+ ....||++++..|+|+..+..|-
T Consensus        32 ~l~g~tgs~kt~~~a~~~~~~-----~~~~lvv~~~~~~A~ql~~el~~~~~~~~V~~fp   86 (664)
T 1c4o_A           32 TLLGATGTGKTVTMAKVIEAL-----GRPALVLAPNKILAAQLAAEFRELFPENAVEYFI   86 (664)
T ss_dssp             EEEECTTSCHHHHHHHHHHHH-----TCCEEEEESSHHHHHHHHHHHHHHCTTSEEEECC
T ss_pred             EEEcCCCcHHHHHHHHHHHHh-----CCCEEEEecCHHHHHHHHHHHHHHCCCCeEEEcC
Confidence            355668999999887766432     3589999998 55679999999999776555443

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.59  E-value=0.0032  Score=50.54  Aligned_cols=61  Identities=16%  Similarity=0.104  Sum_probs=42.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGN   64 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~   64 (169)
                      +++...+|+|||+..+..+...... ...+++|++|+ .+..|+.+++.++.  ..+++....|.
T Consensus        25 ~~~~apTGtGKT~a~l~p~l~~~~~-~~~kvli~t~T~~l~~Qi~~el~~l~~~~~~~~~~l~gr   88 (620)
T 4a15_A           25 VALESPTGSGKTIMALKSALQYSSE-RKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGR   88 (620)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHH-HTCEEEEEESSHHHHHHHHHHHHHHHHHSCCCEEECCCH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhhh-cCCeEEEECCCHHHHHHHHHHHHHHhhccCeEEEEEECC
Confidence            5778899999998876554333322 23689999998 55679999988764  25666666653

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=96.57  E-value=0.0045  Score=45.45  Aligned_cols=22  Identities=18%  Similarity=0.049  Sum_probs=16.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      |.+|.-++|+|||..+-++...
T Consensus        53 ~vLl~GppGtGKT~la~aia~~   74 (322)
T 3eie_A           53 GILLYGPPGTGKSYLAKAVATE   74 (322)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            4578889999999887666543

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=96.52  E-value=0.021  Score=43.79  Aligned_cols=34  Identities=6%  Similarity=-0.033  Sum_probs=19.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .+|..++|+|||..+-++...........+++.+
T Consensus       133 lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v  166 (440)
T 2z4s_A          133 LFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYI  166 (440)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEe
Confidence            4566778888887666665554443323344433

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=96.52  E-value=0.032  Score=42.11  Aligned_cols=126  Identities=9%  Similarity=-0.013  Sum_probs=64.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhC---CC-ceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFA---PF-VRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~---~~-~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +.-.-+.|||..+.+++.+.........+++++|..- ...+.+++..+.   |. ++.......               
T Consensus       183 i~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P~ll~~~~~~~~---------------  247 (385)
T 2o0j_A          183 CNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQPGIVEWN---------------  247 (385)
T ss_dssp             EEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSHHHHHHHHHHHHHHHHHSCTTTSCCEEEEC---------------
T ss_pred             EEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHHHHhChHhhhhhhccCC---------------
Confidence            3445588999887776665444444457888888743 333445555443   21 100000000               


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhc-cc--cccEEEEec
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA-LR--ATFKVLLTG  156 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~-l~--~~~~~~lT~  156 (169)
                               ...........+.++++      +.+.+.....+++|+||+|..++. .....++.. +.  ...++++..
T Consensus       248 ---------~~~I~f~nGs~i~~lsa------~~~slrG~~~~~viiDE~a~~~~~-~el~~al~~~ls~~~~~kiiiiS  311 (385)
T 2o0j_A          248 ---------KGSIELDNGSSIGAYAS------SPDAVRGNSFAMIYIEDCAFIPNF-HDSWLAIQPVISSGRRSKIIITT  311 (385)
T ss_dssp             ---------SSEEEETTSCEEEEEEC------SHHHHHTSCCSEEEEESGGGSTTH-HHHHHHHHHHHHSTTCCEEEEEE
T ss_pred             ---------ccEEEeCCCCEEEEEEC------CCCCccCCCCCEEEechhhhcCCC-HHHHHHHHHHhhcCCCCcEEEEe
Confidence                     00000001111212332      223344567899999999998752 233444432 22  346888889


Q ss_pred             cCCCC
Q psy1090         157 WYYPN  161 (169)
Q Consensus       157 TP~~n  161 (169)
                      ||-..
T Consensus       312 TP~g~  316 (385)
T 2o0j_A          312 TPNGL  316 (385)
T ss_dssp             CCCSS
T ss_pred             CCCCc
Confidence            98644

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=96.44  E-value=0.03  Score=44.82  Aligned_cols=49  Identities=4%  Similarity=-0.010  Sum_probs=34.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC--CCCceEEEecCcc-hHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ--ALEPNLIVCPLSV-LNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~--~~~~~Liv~P~~~-l~qW~~e~~~~   52 (169)
                      ++.-..|+|||.+.+.-+.++...+  ...++|+++++.. ..+..+.+.+.
T Consensus        26 lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~   77 (647)
T 3lfu_A           26 LVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQL   77 (647)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHH
Confidence            3445689999999998888877654  2357999998754 44555556554

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.40  E-value=0.0025  Score=46.20  Aligned_cols=25  Identities=4%  Similarity=-0.094  Sum_probs=19.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      .+|..++|+|||..+-++...+...
T Consensus        70 vll~G~~GtGKT~la~~la~~l~~~   94 (309)
T 3syl_A           70 MSFTGNPGTGKTTVALKMAGLLHRL   94 (309)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhc
Confidence            4678899999998887777665543

>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=96.28  E-value=0.01  Score=47.92  Aligned_cols=53  Identities=17%  Similarity=0.251  Sum_probs=40.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYY   62 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~   62 (169)
                      |..-+|+|||+++..++...     .+|+|||+|+ ....||++|+..|+|+..+..|-
T Consensus        37 l~g~~gs~k~~~~a~~~~~~-----~~~~lvv~~~~~~A~~l~~el~~~~~~~~v~~fp   90 (661)
T 2d7d_A           37 LLGATGTGKTFTVSNLIKEV-----NKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFV   90 (661)
T ss_dssp             EEECTTSCHHHHHHHHHHHH-----CCCEEEECSSHHHHHHHHHHHHHHCTTSEEEEEC
T ss_pred             EECcCCcHHHHHHHHHHHHh-----CCCEEEEECCHHHHHHHHHHHHHHcCCCcEEEcc
Confidence            45568999999887665432     3589999998 55679999999998765555443

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=96.06  E-value=0.04  Score=43.93  Aligned_cols=130  Identities=10%  Similarity=0.047  Sum_probs=64.6

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCccc
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKV   83 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~   83 (169)
                      +.-.-|.|||..+.+++.+.........++++.|.. ......+.+..+.......                .. ... .
T Consensus       183 i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~~qA~~~~~~i~~~i~~~p~~----------------~~-~~~-~  244 (592)
T 3cpe_A          183 CNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELLPDF----------------LQ-PGI-V  244 (592)
T ss_dssp             EEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSHHHHHHHHHHHHHHHTTSCTT----------------TS-CCE-E
T ss_pred             EEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHHHHhChHh----------------hc-ccc-c
Confidence            444568999987766665555444445788888874 3334445555554211000                00 000 0


Q ss_pred             ccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhc-cc--cccEEEEeccCCC
Q psy1090          84 PAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA-LR--ATFKVLLTGWYYP  160 (169)
Q Consensus        84 ~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~-l~--~~~~~~lT~TP~~  160 (169)
                      .  .............+.++++      +...+.....+++|+||+|..++.. ..+.++.. +.  ...++++++||-.
T Consensus       245 ~--~~~~~i~~~nGs~i~~~s~------~~~~lrG~~~~~~iiDE~~~~~~~~-~l~~~~~~~l~~~~~~~ii~isTP~~  315 (592)
T 3cpe_A          245 E--WNKGSIELDNGSSIGAYAS------SPDAVRGNSFAMIYIEDCAFIPNFH-DSWLAIQPVISSGRRSKIIITTTPNG  315 (592)
T ss_dssp             E--ECSSEEEETTSCEEEEEEC------CHHHHHHSCCSEEEEETGGGCTTHH-HHHHHHHHHHSSSSCCEEEEEECCCT
T ss_pred             c--CCccEEEecCCCEEEEEeC------CCCCccCCCcceEEEehhccCCchh-HHHHHHHHHhccCCCceEEEEeCCCC
Confidence            0  0000000001111212221      1223334567899999999987532 34444432 22  3468889999965


Q ss_pred             C
Q psy1090         161 N  161 (169)
Q Consensus       161 n  161 (169)
                      .
T Consensus       316 ~  316 (592)
T 3cpe_A          316 L  316 (592)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=95.98  E-value=0.011  Score=43.98  Aligned_cols=37  Identities=16%  Similarity=0.227  Sum_probs=22.5

Q ss_pred             EEEEeCCcccCCcc-cHH-HHHHhccccccEEEEeccCC
Q psy1090         123 CIIVDEGHSVKNKK-SKL-SIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus       123 ~vi~DEah~~k~~~-~~~-~~~~~~l~~~~~~~lT~TP~  159 (169)
                      ++|+||+|.+.... ... ...+.....+.+++++++..
T Consensus       136 vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~  174 (384)
T 2qby_B          136 IIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDI  174 (384)
T ss_dssp             EEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSST
T ss_pred             EEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCC
Confidence            89999999885432 233 33333333566777776654

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=95.55  E-value=0.014  Score=43.45  Aligned_cols=23  Identities=17%  Similarity=0.036  Sum_probs=17.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      |.+|.-++|+|||..+-+++...
T Consensus        86 ~iLL~GppGtGKT~la~ala~~~  108 (355)
T 2qp9_X           86 GILLYGPPGTGKSYLAKAVATEA  108 (355)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh
Confidence            46788899999998877666543

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=95.39  E-value=0.035  Score=40.46  Aligned_cols=42  Identities=14%  Similarity=0.168  Sum_probs=25.0

Q ss_pred             cccEEEEeCCcccC-Ccc-cHHHHHHhccccccEEEEeccCCCC
Q psy1090         120 TWNCIIVDEGHSVK-NKK-SKLSIKLTALRATFKVLLTGWYYPN  161 (169)
Q Consensus       120 ~~~~vi~DEah~~k-~~~-~~~~~~~~~l~~~~~~~lT~TP~~n  161 (169)
                      ...++++||+|.+. ... ....+.+.......+++++.++...
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~  148 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDG  148 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGG
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccc
Confidence            56789999999985 211 1112222223456778888777653

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=95.24  E-value=0.015  Score=42.69  Aligned_cols=22  Identities=18%  Similarity=0.039  Sum_probs=16.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      |.+|.-++|+|||..+-++...
T Consensus        47 ~iLL~GppGtGKT~la~ala~~   68 (322)
T 1xwi_A           47 GILLFGPPGTGKSYLAKAVATE   68 (322)
T ss_dssp             EEEEESSSSSCHHHHHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHHHHH
Confidence            4577889999999877666543

>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=95.18  E-value=0.035  Score=38.23  Aligned_cols=16  Identities=19%  Similarity=0.416  Sum_probs=12.7

Q ss_pred             cccEEEEeCCcccCCc
Q psy1090         120 TWNCIIVDEGHSVKNK  135 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~  135 (169)
                      ..+++|+||+|.+...
T Consensus       104 ~~~vliiDe~~~~~~~  119 (242)
T 3bos_A          104 QFDLICIDDVDAVAGH  119 (242)
T ss_dssp             GSSEEEEETGGGGTTC
T ss_pred             CCCEEEEeccccccCC
Confidence            4578999999998643

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=94.93  E-value=0.065  Score=41.18  Aligned_cols=31  Identities=13%  Similarity=0.039  Sum_probs=22.2

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      ++-..|+|||.++..++.++...+  .++++++
T Consensus       105 ivG~~G~GKTTt~~kLA~~l~~~G--~kVllv~  135 (443)
T 3dm5_A          105 MVGIQGSGKTTTVAKLARYFQKRG--YKVGVVC  135 (443)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHTTT--CCEEEEE
T ss_pred             EECcCCCCHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            455699999999988887765433  5666665

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=94.83  E-value=0.079  Score=40.62  Aligned_cols=32  Identities=6%  Similarity=-0.139  Sum_probs=22.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      ++.-..|+|||.++..++..+...+  +++++++
T Consensus       101 ~lvG~~GsGKTTt~~kLA~~l~~~G--~kVllv~  132 (433)
T 3kl4_A          101 MLVGVQGSGKTTTAGKLAYFYKKRG--YKVGLVA  132 (433)
T ss_dssp             EECCCTTSCHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEe
Confidence            3456789999998888877665433  5566555

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=94.54  E-value=0.04  Score=41.42  Aligned_cols=37  Identities=11%  Similarity=0.031  Sum_probs=21.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      +.+|.-++|+|||..+-++...     ...+++.+-+..+..
T Consensus       150 ~vLL~GppGtGKT~la~aia~~-----~~~~~~~v~~~~l~~  186 (389)
T 3vfd_A          150 GLLLFGPPGNGKTMLAKAVAAE-----SNATFFNISAASLTS  186 (389)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHH-----TTCEEEEECSCCC--
T ss_pred             eEEEECCCCCCHHHHHHHHHHh-----hcCcEEEeeHHHhhc
Confidence            4578889999999877665332     123444444444443

>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=94.52  E-value=0.11  Score=35.38  Aligned_cols=22  Identities=5%  Similarity=-0.053  Sum_probs=15.8

Q ss_pred             ccccCCCCCcHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      .+|.-+.|+|||..+-.+....
T Consensus        48 ~ll~G~~G~GKT~l~~~~~~~~   69 (250)
T 1njg_A           48 YLFSGTRGVGKTSIARLLAKGL   69 (250)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3577889999997776665443

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=94.37  E-value=0.022  Score=43.72  Aligned_cols=22  Identities=18%  Similarity=0.039  Sum_probs=16.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      |.+|.-++|+|||..+-++...
T Consensus       169 ~vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          169 GILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4577889999999877666543

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.27  E-value=0.016  Score=41.39  Aligned_cols=21  Identities=14%  Similarity=0.015  Sum_probs=15.5

Q ss_pred             CccccCCCCCcHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC   22 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~   22 (169)
                      |.+|..++|+|||..+-++..
T Consensus        53 ~~ll~G~~GtGKT~la~~la~   73 (285)
T 3h4m_A           53 GILLYGPPGTGKTLLAKAVAT   73 (285)
T ss_dssp             EEEEESSSSSSHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHH
Confidence            356788999999977755543

>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=94.03  E-value=0.042  Score=40.32  Aligned_cols=23  Identities=13%  Similarity=0.245  Sum_probs=17.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|..++|+|||..+-++...+.
T Consensus        61 ~ll~G~~G~GKT~la~~la~~l~   83 (353)
T 1sxj_D           61 MLFYGPPGTGKTSTILALTKELY   83 (353)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            46788999999988777766543

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=93.60  E-value=0.34  Score=35.68  Aligned_cols=41  Identities=10%  Similarity=0.059  Sum_probs=30.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNN   44 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~q   44 (169)
                      .+.-++|+|||..++.++......+..++++.|...+.+.+
T Consensus        32 eI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~   72 (333)
T 3io5_A           32 ILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITP   72 (333)
T ss_dssp             EEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhH
Confidence            35678999999988888776665544568888888766554

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=93.60  E-value=0.46  Score=34.84  Aligned_cols=23  Identities=9%  Similarity=0.040  Sum_probs=18.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++..+.|+|||..+..++..+..
T Consensus        28 L~~G~~G~GKt~~a~~la~~l~~   50 (334)
T 1a5t_A           28 LIQALPGMGDDALIYALSRYLLC   50 (334)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHTC
T ss_pred             EEECCCCchHHHHHHHHHHHHhC
Confidence            56789999999998888776653

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.23  E-value=0.13  Score=37.17  Aligned_cols=40  Identities=13%  Similarity=0.150  Sum_probs=22.5

Q ss_pred             cccEEEEeCCcccCCcccH-HHHHHhccccccEEEEeccCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSK-LSIKLTALRATFKVLLTGWYY  159 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~-~~~~~~~l~~~~~~~lT~TP~  159 (169)
                      +..++|+||+|.+...... ..+.+.......++++++++.
T Consensus       107 ~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~  147 (323)
T 1sxj_B          107 KHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  147 (323)
T ss_dssp             CCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             CceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCCh
Confidence            3678999999998532111 122222233455677766554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=93.19  E-value=0.22  Score=36.79  Aligned_cols=23  Identities=9%  Similarity=0.020  Sum_probs=17.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|.-+.|+|||..+-.+.....
T Consensus        47 vll~G~~G~GKT~l~~~~~~~~~   69 (387)
T 2v1u_A           47 ALLYGLTGTGKTAVARLVLRRLE   69 (387)
T ss_dssp             EEECBCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            56778899999988776665543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=93.12  E-value=0.94  Score=33.20  Aligned_cols=24  Identities=17%  Similarity=0.070  Sum_probs=18.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+|.-.+|+|||.++-.++..+..
T Consensus        48 lli~GpPGTGKT~~v~~v~~~L~~   71 (318)
T 3te6_A           48 FYITNADDSTKFQLVNDVMDELIT   71 (318)
T ss_dssp             EEEECCCSHHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            457788999999888777766654

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=92.85  E-value=0.16  Score=37.68  Aligned_cols=40  Identities=10%  Similarity=-0.048  Sum_probs=28.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNW   45 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW   45 (169)
                      .+.-++|+|||..++.++......  .++++++.......++
T Consensus        65 ~I~G~pGsGKTtLal~la~~~~~~--g~~vlyi~~E~~~~~~  104 (349)
T 2zr9_A           65 EIYGPESSGKTTVALHAVANAQAA--GGIAAFIDAEHALDPE  104 (349)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCcCHH
Confidence            466789999998888887665543  3678888776655554

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=92.72  E-value=0.15  Score=39.08  Aligned_cols=46  Identities=7%  Similarity=-0.115  Sum_probs=32.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+++-.+|+|||.-++.++...... ...+++++.......++...+
T Consensus       203 ~ii~G~pg~GKT~lal~ia~~~a~~-~g~~vl~~slE~~~~~l~~R~  248 (444)
T 2q6t_A          203 NIIAARPAMGKTAFALTIAQNAALK-EGVGVGIYSLEMPAAQLTLRM  248 (444)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSSCHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHh-CCCeEEEEECCCCHHHHHHHH
Confidence            3678899999998888777655432 245888888776666666554

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=92.69  E-value=0.5  Score=34.37  Aligned_cols=14  Identities=21%  Similarity=0.352  Sum_probs=12.3

Q ss_pred             cccEEEEeCCcccC
Q psy1090         120 TWNCIIVDEGHSVK  133 (169)
Q Consensus       120 ~~~~vi~DEah~~k  133 (169)
                      ++.++|+||+|.+.
T Consensus        82 ~~kvviIdead~lt   95 (305)
T 2gno_A           82 TRKYVIVHDCERMT   95 (305)
T ss_dssp             SSEEEEETTGGGBC
T ss_pred             CceEEEeccHHHhC
Confidence            57899999999985

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=92.68  E-value=0.17  Score=39.33  Aligned_cols=50  Identities=12%  Similarity=0.125  Sum_probs=36.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEE
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVK   60 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~   60 (169)
                      |..-+|+|||+.+.+++..     ..+|+|||+|+ ....+|.+++..|.|+. +..
T Consensus        19 l~g~~gs~ka~~~a~l~~~-----~~~p~lvv~~~~~~A~~l~~~l~~~~~~~-v~~   69 (483)
T 3hjh_A           19 LGELTGAACATLVAEIAER-----HAGPVVLIAPDMQNALRLHDEISQFTDQM-VMN   69 (483)
T ss_dssp             EECCCTTHHHHHHHHHHHH-----SSSCEEEEESSHHHHHHHHHHHHHTCSSC-EEE
T ss_pred             EeCCCchHHHHHHHHHHHH-----hCCCEEEEeCCHHHHHHHHHHHHhhCCCc-EEE
Confidence            4556899999877665532     24689999998 45679999999998754 443

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=92.64  E-value=0.19  Score=39.27  Aligned_cols=21  Identities=10%  Similarity=0.058  Sum_probs=16.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~   23 (169)
                      .+|.-++|+|||..+-+++..
T Consensus        80 lLL~GppGtGKTtla~~la~~  100 (516)
T 1sxj_A           80 AMLYGPPGIGKTTAAHLVAQE  100 (516)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            567889999999887666544

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=92.48  E-value=0.46  Score=38.90  Aligned_cols=23  Identities=9%  Similarity=0.153  Sum_probs=17.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|.-++|+|||..+-++...+.
T Consensus       210 vlL~G~~GtGKT~la~~la~~l~  232 (758)
T 1r6b_X          210 PLLVGESGVGKTAIAEGLAWRIV  232 (758)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHH
T ss_pred             eEEEcCCCCCHHHHHHHHHHHHH
Confidence            56788999999987776665543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=92.06  E-value=0.64  Score=34.04  Aligned_cols=30  Identities=13%  Similarity=-0.076  Sum_probs=21.0

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      ...|.|||.++..++..+...  .++++++.-
T Consensus       112 G~~G~GKTT~~~~LA~~l~~~--g~kVllid~  141 (320)
T 1zu4_A          112 GVNGTGKTTSLAKMANYYAEL--GYKVLIAAA  141 (320)
T ss_dssp             SSTTSSHHHHHHHHHHHHHHT--TCCEEEEEC
T ss_pred             CCCCCCHHHHHHHHHHHHHHC--CCeEEEEeC
Confidence            459999998887776665543  367777653

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=91.89  E-value=0.063  Score=43.08  Aligned_cols=38  Identities=16%  Similarity=0.118  Sum_probs=25.2

Q ss_pred             CCCCeEEEecHHHHHhchhc------c-ccccccEEEEeCCcccCC
Q psy1090          96 LKLPLILVTTPQIIENDFGF------L-KKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        96 ~~~~ii~i~ty~~~~~~~~~------~-~~~~~~~vi~DEah~~k~  134 (169)
                      ...|+ |+++|+.+-...-.      + ...+-.++|+||||++-+
T Consensus       174 ~~ADv-VV~ny~ylld~~~r~~~~~~~~i~p~~~ivI~DEAHNL~d  218 (620)
T 4a15_A          174 PDADI-VIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPD  218 (620)
T ss_dssp             GGCSE-EEEEHHHHTCHHHHHHHHHHHTCCGGGEEEEETTGGGHHH
T ss_pred             hcCCE-EEeCchhhcCHHHHHHHHHhhccCcCCeEEEEECCCchHH
Confidence            56677 99999886543211      1 123456999999999854

>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=91.78  E-value=0.39  Score=35.39  Aligned_cols=21  Identities=5%  Similarity=-0.026  Sum_probs=15.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~   24 (169)
                      ++..+.|+|||..+-++...+
T Consensus        42 ll~G~~G~GKT~la~~la~~l   62 (373)
T 1jr3_A           42 LFSGTRGVGKTSIARLLAKGL   62 (373)
T ss_dssp             EEESCTTSSHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            577899999998776665543

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.69  E-value=0.41  Score=33.06  Aligned_cols=49  Identities=22%  Similarity=0.207  Sum_probs=32.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      .+++-++|+|||.-++.++....... ..+++++.-.....+..+.+..+
T Consensus        33 ~~i~G~pG~GKT~l~l~~~~~~~~~~-~~~v~~~s~E~~~~~~~~~~~~~   81 (251)
T 2zts_A           33 VLLTGGTGTGKTTFAAQFIYKGAEEY-GEPGVFVTLEERARDLRREMASF   81 (251)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHH-CCCEEEEESSSCHHHHHHHHHTT
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhc-CCCceeecccCCHHHHHHHHHHc
Confidence            36788999999988887765433222 35788887766666655555443

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.17  E-value=0.45  Score=32.77  Aligned_cols=46  Identities=11%  Similarity=0.026  Sum_probs=31.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRK   51 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~   51 (169)
                      ++.-++|+|||..++.++......  .++++++.......+..+.+..
T Consensus        27 ~i~G~~GsGKTtl~~~~~~~~~~~--~~~v~~~~~e~~~~~~~~~~~~   72 (247)
T 2dr3_A           27 LLSGGPGTGKTIFSQQFLWNGLKM--GEPGIYVALEEHPVQVRQNMAQ   72 (247)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHT--TCCEEEEESSSCHHHHHHHHHT
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccCCHHHHHHHHHH
Confidence            467789999998888776665443  3678888776655555555543

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=91.02  E-value=0.26  Score=33.68  Aligned_cols=33  Identities=15%  Similarity=-0.050  Sum_probs=25.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +.+-..|.|||.+++.++..+...+  .+++++=|
T Consensus         6 v~s~kgGvGKTt~a~nLa~~la~~G--~rVll~dp   38 (224)
T 1byi_A            6 VTGTDTEVGKTVASCALLQAAKAAG--YRTAGYKP   38 (224)
T ss_dssp             EEESSTTSCHHHHHHHHHHHHHHTT--CCEEEECS
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CCEEEEcc
Confidence            4456789999999999888776554  57888765

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.01  E-value=0.33  Score=40.43  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=18.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      +.+|.-++|+|||..+-++...+..
T Consensus       193 ~vlL~G~pG~GKT~la~~la~~l~~  217 (854)
T 1qvr_A          193 NPVLIGEPGVGKTAIVEGLAQRIVK  217 (854)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3577889999999877777665543

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=90.98  E-value=0.24  Score=33.26  Aligned_cols=32  Identities=16%  Similarity=0.065  Sum_probs=21.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .+|.-++|+|||..+-++.......  ..+++++
T Consensus        57 ~~l~G~~GtGKT~la~~i~~~~~~~--~~~~~~~   88 (202)
T 2w58_A           57 LYLHGSFGVGKTYLLAAIANELAKR--NVSSLIV   88 (202)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHTT--TCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEE
Confidence            4677899999998877766555432  2444444

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=90.09  E-value=0.26  Score=34.39  Aligned_cols=42  Identities=5%  Similarity=-0.065  Sum_probs=27.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEE-Ee-cCcchHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLI-VC-PLSVLNNWE   46 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Li-v~-P~~~l~qW~   46 (169)
                      .++....|.|||..++.+...+...+  .++++ .+ |..-...|.
T Consensus         9 I~~~~kgGvGKTt~a~~la~~l~~~G--~~V~v~d~D~q~~~~~~a   52 (228)
T 2r8r_A            9 VFLGAAPGVGKTYAMLQAAHAQLRQG--VRVMAGVVETHGRAETEA   52 (228)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHHHHTT--CCEEEEECCCTTCHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCC--CCEEEEEeCCCCChhHHH
Confidence            56788899999999999888776654  34433 33 433444444

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.08  E-value=0.12  Score=39.25  Aligned_cols=42  Identities=12%  Similarity=0.025  Sum_probs=29.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAE   48 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e   48 (169)
                      |.+|--.+|+|||..+=+++...     ..+++.|..+.++..|.-|
T Consensus       184 GvLL~GPPGTGKTllAkAiA~e~-----~~~f~~v~~s~l~sk~vGe  225 (405)
T 4b4t_J          184 GVILYGPPGTGKTLLARAVAHHT-----DCKFIRVSGAELVQKYIGE  225 (405)
T ss_dssp             CEEEESCSSSSHHHHHHHHHHHH-----TCEEEEEEGGGGSCSSTTH
T ss_pred             ceEEeCCCCCCHHHHHHHHHHhh-----CCCceEEEhHHhhccccch
Confidence            77889999999998887766543     2456666667776666533

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.86  E-value=0.62  Score=33.93  Aligned_cols=46  Identities=4%  Similarity=-0.099  Sum_probs=32.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFR   50 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~   50 (169)
                      .+++-.+|+|||.-++.++......+  .+++++.......+....+.
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE~s~~~l~~R~~  116 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEMGKKENIKRLI  116 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESSSCHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECCCCHHHHHHHHH
Confidence            46788999999988877766554333  68888887766666555544

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=89.80  E-value=0.33  Score=35.31  Aligned_cols=33  Identities=9%  Similarity=0.004  Sum_probs=22.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHH-HhCCCCceEEE
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKII-EEQALEPNLIV   36 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~-~~~~~~~~Liv   36 (169)
                      +.+|..++|+|||..+.++..... ..+  .+++++
T Consensus       154 ~lll~G~~GtGKT~La~aia~~~~~~~g--~~v~~~  187 (308)
T 2qgz_A          154 GLYLYGDMGIGKSYLLAAMAHELSEKKG--VSTTLL  187 (308)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHSC--CCEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHhcC--CcEEEE
Confidence            356788999999998888777665 433  344444

>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=89.56  E-value=2.8  Score=30.26  Aligned_cols=31  Identities=10%  Similarity=-0.011  Sum_probs=19.9

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .-..|+|||.++..+...+.... ..+++++.
T Consensus       111 vG~~GsGKTTl~~~LA~~l~~~~-G~~V~lv~  141 (296)
T 2px0_A          111 FGSTGAGKTTTLAKLAAISMLEK-HKKIAFIT  141 (296)
T ss_dssp             EESTTSSHHHHHHHHHHHHHHTT-CCCEEEEE
T ss_pred             ECCCCCCHHHHHHHHHHHHHHhc-CCEEEEEe
Confidence            34579999988877766554322 24566655

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=89.53  E-value=0.44  Score=41.04  Aligned_cols=49  Identities=14%  Similarity=0.150  Sum_probs=35.9

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCC-CceEEEecCcchHHHHHHHHHhC
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQAL-EPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~-~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      +.-..|+|||.+.+.-+.++...+.. .++|+++|....-+-.+.+.+..
T Consensus         6 V~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~TFt~~~rl~~~l   55 (1166)
T 3u4q_B            6 LVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQMTFLMEYELAKTP   55 (1166)
T ss_dssp             EEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGGHHHHHHHHTCCS
T ss_pred             EEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcccHHHHHHHHHhh
Confidence            33457999999998888887766554 68999999887555555555444

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.92  E-value=0.13  Score=39.48  Aligned_cols=40  Identities=10%  Similarity=0.022  Sum_probs=28.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      |.+|-..+|+|||..+=+++...     ..+.+.|-.+.++..|.
T Consensus       217 GvLLyGPPGTGKTllAkAiA~e~-----~~~f~~v~~s~l~~~~v  256 (434)
T 4b4t_M          217 GALMYGPPGTGKTLLARACAAQT-----NATFLKLAAPQLVQMYI  256 (434)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHH-----TCEEEEEEGGGGCSSCS
T ss_pred             eeEEECcCCCCHHHHHHHHHHHh-----CCCEEEEehhhhhhccc
Confidence            67888999999998887766543     24566666667665554

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.66  E-value=0.13  Score=39.55  Aligned_cols=41  Identities=10%  Similarity=0.053  Sum_probs=28.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEA   47 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~   47 (169)
                      |.+|--.+|+|||..+=+++...     ..+++.|-.+.++..|..
T Consensus       217 GvLL~GPPGtGKTllAkAiA~e~-----~~~~~~v~~s~l~sk~~G  257 (437)
T 4b4t_L          217 GVLLYGPPGTGKTLLAKAVAATI-----GANFIFSPASGIVDKYIG  257 (437)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHH-----TCEEEEEEGGGTCCSSSS
T ss_pred             eEEEECCCCCcHHHHHHHHHHHh-----CCCEEEEehhhhccccch
Confidence            67888999999998887776543     235666666666554443

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=88.54  E-value=0.53  Score=32.30  Aligned_cols=33  Identities=9%  Similarity=0.008  Sum_probs=25.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +.+-.-|.|||..++.+...+...+  .++++|-.
T Consensus         7 v~s~kgGvGKTt~a~~LA~~la~~g--~~VlliD~   39 (237)
T 1g3q_A            7 IVSGKGGTGKTTVTANLSVALGDRG--RKVLAVDG   39 (237)
T ss_dssp             EECSSTTSSHHHHHHHHHHHHHHTT--CCEEEEEC
T ss_pred             EecCCCCCCHHHHHHHHHHHHHhcC--CeEEEEeC
Confidence            4456789999999998887776543  67888764

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=88.45  E-value=0.49  Score=34.57  Aligned_cols=27  Identities=11%  Similarity=-0.111  Sum_probs=21.2

Q ss_pred             CCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           9 TRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         9 ~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      =|.|||.+++-+...+.+.+  +++|+|=
T Consensus        57 GGVGKTTtavNLA~aLA~~G--kkVllID   83 (314)
T 3fwy_A           57 GGIGKSTTSSNLSAAFSILG--KRVLQIG   83 (314)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             CccCHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            48999999998887776655  5677775

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=87.99  E-value=0.68  Score=30.91  Aligned_cols=42  Identities=19%  Similarity=0.208  Sum_probs=28.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWEA   47 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~~   47 (169)
                      +.+-.-|.|||..++.+...+...+  .++++|-  |...+..|..
T Consensus         6 v~s~kgG~GKTt~a~~la~~la~~g--~~vlliD~D~~~~~~~~~~   49 (206)
T 4dzz_A            6 FLNPKGGSGKTTAVINIATALSRSG--YNIAVVDTDPQMSLTNWSK   49 (206)
T ss_dssp             ECCSSTTSSHHHHHHHHHHHHHHTT--CCEEEEECCTTCHHHHHHT
T ss_pred             EEeCCCCccHHHHHHHHHHHHHHCC--CeEEEEECCCCCCHHHHHh
Confidence            3455679999999988887776543  5677776  4455556653

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=87.93  E-value=0.55  Score=34.34  Aligned_cols=33  Identities=12%  Similarity=0.001  Sum_probs=24.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +..-.-|.|||.++.++...+...  ..++|+|-.
T Consensus        18 v~sgKGGvGKTTvA~~LA~~lA~~--G~rVLlvD~   50 (324)
T 3zq6_A           18 FIGGKGGVGKTTISAATALWMARS--GKKTLVIST   50 (324)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEEC
T ss_pred             EEeCCCCchHHHHHHHHHHHHHHC--CCcEEEEeC
Confidence            344567999999999888777654  367887764

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=87.65  E-value=0.52  Score=33.11  Aligned_cols=29  Identities=10%  Similarity=-0.035  Sum_probs=21.1

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .--|.|||..++.+...+...  ..++|+|=
T Consensus         8 ~KGGvGKTT~a~nLA~~la~~--G~~VlliD   36 (269)
T 1cp2_A            8 GKGGIGKSTTTQNLTSGLHAM--GKTIMVVG   36 (269)
T ss_dssp             ECTTSSHHHHHHHHHHHHHTT--TCCEEEEE
T ss_pred             cCCCCcHHHHHHHHHHHHHHC--CCcEEEEc
Confidence            356999999998887776643  35777753

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=87.64  E-value=0.24  Score=35.69  Aligned_cols=35  Identities=14%  Similarity=-0.093  Sum_probs=23.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSV   41 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~   41 (169)
                      |.+|.-++|+|||..+-+++..+     ..+++.+-...+
T Consensus        38 ~lLl~GppGtGKT~la~aiA~~l-----~~~~i~v~~~~l   72 (293)
T 3t15_A           38 ILGIWGGKGQGKSFQCELVFRKM-----GINPIMMSAGEL   72 (293)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH-----TCCCEEEEHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-----CCCEEEEeHHHh
Confidence            45677899999998877665544     245555554443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=87.55  E-value=1.8  Score=29.30  Aligned_cols=44  Identities=11%  Similarity=0.108  Sum_probs=27.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .|.-+.|+|||..+..++......+  ++++++.......+....+
T Consensus        27 ~i~G~~GsGKTtl~~~l~~~~~~~~--~~v~~~~~~~~~~~~~~~~   70 (235)
T 2w0m_A           27 ALTGEPGTGKTIFSLHFIAKGLRDG--DPCIYVTTEESRDSIIRQA   70 (235)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHHT--CCEEEEESSSCHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHCC--CeEEEEEcccCHHHHHHHH
Confidence            4678899999988777765544333  5677776554444433333

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=87.51  E-value=0.66  Score=32.29  Aligned_cols=32  Identities=9%  Similarity=0.103  Sum_probs=24.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-.-|.|||..++.+...+...+  .++|+|=
T Consensus         7 v~s~kgGvGKTt~a~~LA~~la~~g--~~VlliD   38 (260)
T 3q9l_A            7 VTSGKGGVGKTTSSAAIATGLAQKG--KKTVVID   38 (260)
T ss_dssp             EECSSTTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EECCCCCCcHHHHHHHHHHHHHhCC--CcEEEEE
Confidence            4456789999999998887776543  5777765

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=87.32  E-value=0.68  Score=32.56  Aligned_cols=32  Identities=13%  Similarity=-0.011  Sum_probs=24.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-.-|.|||..++.+...+...+  .++|+|=
T Consensus        23 v~s~kGGvGKTT~a~nLA~~la~~G--~~VlliD   54 (262)
T 2ph1_A           23 VMSGKGGVGKSTVTALLAVHYARQG--KKVGILD   54 (262)
T ss_dssp             EECSSSCTTHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EEcCCCCCCHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            4456779999999998877776543  5788776

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=87.17  E-value=0.33  Score=32.99  Aligned_cols=40  Identities=20%  Similarity=0.150  Sum_probs=23.7

Q ss_pred             cccEEEEeCCcccCC---cccHHHHHHhccc----cccEEEEeccCC
Q psy1090         120 TWNCIIVDEGHSVKN---KKSKLSIKLTALR----ATFKVLLTGWYY  159 (169)
Q Consensus       120 ~~~~vi~DEah~~k~---~~~~~~~~~~~l~----~~~~~~lT~TP~  159 (169)
                      .-.++|+||||.+-.   ......+.+..+.    ...-++|.+.|.
T Consensus        87 ~~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r~~~~~iil~tq~~  133 (199)
T 2r2a_A           87 IGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHRHQGIDIFVLTQGP  133 (199)
T ss_dssp             TTCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTTTTTCEEEEEESCG
T ss_pred             CceEEEEEChhhhccCccccchhHHHHHHHHhcCcCCeEEEEECCCH
Confidence            356899999999832   2222223444442    334678888883

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.15  E-value=0.17  Score=38.74  Aligned_cols=42  Identities=7%  Similarity=0.016  Sum_probs=29.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAE   48 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e   48 (169)
                      |.+|--.+|+|||..+-+++...     ..+++.+....++..|..|
T Consensus       218 GvLLyGPPGTGKTlLAkAiA~e~-----~~~fi~v~~s~l~sk~vGe  259 (437)
T 4b4t_I          218 GVILYGAPGTGKTLLAKAVANQT-----SATFLRIVGSELIQKYLGD  259 (437)
T ss_dssp             EEEEESSTTTTHHHHHHHHHHHH-----TCEEEEEESGGGCCSSSSH
T ss_pred             CCceECCCCchHHHHHHHHHHHh-----CCCEEEEEHHHhhhccCch
Confidence            67888999999998887776543     2356666666666555433

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10

Probab=87.13  E-value=0.69  Score=32.37  Aligned_cols=32  Identities=13%  Similarity=-0.054  Sum_probs=24.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-.-|.|||..++.+...+...+  .++++|-
T Consensus         7 v~s~kgGvGKTt~a~~LA~~la~~g--~~VlliD   38 (263)
T 1hyq_A            7 VASGKGGTGKTTITANLGVALAQLG--HDVTIVD   38 (263)
T ss_dssp             EEESSSCSCHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EECCCCCCCHHHHHHHHHHHHHhCC--CcEEEEE
Confidence            4456789999999998887776543  5788876

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=87.13  E-value=0.66  Score=33.08  Aligned_cols=29  Identities=17%  Similarity=0.109  Sum_probs=21.4

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .--|.|||..++.+...+...+  .++|+|=
T Consensus         9 ~KGGvGKTT~a~nLA~~La~~G--~rVlliD   37 (289)
T 2afh_E            9 GKGGIGKSTTTQNLVAALAEMG--KKVMIVG   37 (289)
T ss_dssp             ECTTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             CCCcCcHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            3569999999998887776543  5677653

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=87.10  E-value=0.66  Score=33.20  Aligned_cols=38  Identities=13%  Similarity=-0.149  Sum_probs=25.1

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHH
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWE   46 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~   46 (169)
                      .--|.|||..+..+...+...+  .++|+|=  |..-...|.
T Consensus        44 ~KGGvGKTT~a~nLA~~la~~G--~rVlliD~D~q~~~~~~l   83 (298)
T 2oze_A           44 FKGGVGKSKLSTMFAYLTDKLN--LKVLMIDKDLQATLTKDL   83 (298)
T ss_dssp             SSSSSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHHHhCC--CeEEEEeCCCCCCHHHHH
Confidence            4679999999988877666543  5777753  444444443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.09  E-value=0.19  Score=38.81  Aligned_cols=40  Identities=10%  Similarity=0.003  Sum_probs=28.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      |.+|--.+|+|||+.+=+++...     ..+++.|....++..|.
T Consensus       245 GILLyGPPGTGKTlLAkAiA~e~-----~~~fi~vs~s~L~sk~v  284 (467)
T 4b4t_H          245 GILLYGPPGTGKTLCARAVANRT-----DATFIRVIGSELVQKYV  284 (467)
T ss_dssp             EEEECSCTTSSHHHHHHHHHHHH-----TCEEEEEEGGGGCCCSS
T ss_pred             ceEeeCCCCCcHHHHHHHHHhcc-----CCCeEEEEhHHhhcccC
Confidence            67889999999998887766543     23566666666665554

>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=86.66  E-value=0.81  Score=30.02  Aligned_cols=23  Identities=13%  Similarity=0.033  Sum_probs=17.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|.-++|+|||..+-+++..+.
T Consensus        41 ~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           41 LTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             EEECCSSSSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH
Confidence            35677899999988777766554

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.61  E-value=0.2  Score=38.32  Aligned_cols=40  Identities=13%  Similarity=0.024  Sum_probs=27.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      |.+|-..+|+|||..+=+++...     ..+++.|-.+.++..|.
T Consensus       208 GiLL~GPPGtGKT~lakAiA~~~-----~~~~~~v~~~~l~~~~~  247 (428)
T 4b4t_K          208 GVLLYGPPGTGKTMLVKAVANST-----KAAFIRVNGSEFVHKYL  247 (428)
T ss_dssp             EEEEESCTTTTHHHHHHHHHHHH-----TCEEEEEEGGGTCCSSC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh-----CCCeEEEecchhhcccc
Confidence            67888999999998887766543     24566666666655443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=86.42  E-value=1.4  Score=32.59  Aligned_cols=45  Identities=4%  Similarity=-0.023  Sum_probs=32.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+|+-.+|+|||.-++.++.....  ...+++++.......|....+
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fSlEms~~ql~~Rl   93 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFSLEMSAEQLALRA   93 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEESSSCHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEeCCCCHHHHHHHH
Confidence            467889999999888877766554  346888888776655555444

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=86.38  E-value=0.36  Score=33.35  Aligned_cols=30  Identities=7%  Similarity=-0.031  Sum_probs=22.2

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .---|.|||..+..+...+...+  .++|+|=
T Consensus         6 s~kGGvGKTt~a~~LA~~la~~g--~~VlliD   35 (254)
T 3kjh_A            6 AGKGGVGKTTVAAGLIKIMASDY--DKIYAVD   35 (254)
T ss_dssp             ECSSSHHHHHHHHHHHHHHTTTC--SCEEEEE
T ss_pred             ecCCCCCHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            44679999999988877765443  6777774

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=86.08  E-value=1.8  Score=35.13  Aligned_cols=33  Identities=21%  Similarity=0.219  Sum_probs=20.2

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhccccccEEEEecc
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGW  157 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~T  157 (169)
                      +.|++|+|||-.+-  .....+.+.   .-.+++||.|
T Consensus       255 ~~dlliVDEAAaIp--~pll~~ll~---~~~~v~~~tT  287 (671)
T 2zpa_A          255 QADWLVVDEAAAIP--APLLHQLVS---RFPRTLLTTT  287 (671)
T ss_dssp             CCSEEEEETGGGSC--HHHHHHHHT---TSSEEEEEEE
T ss_pred             cCCEEEEEchhcCC--HHHHHHHHh---hCCeEEEEec
Confidence            57899999999873  333222222   2236777766

>3of5_A Dethiobiotin synthetase; structural genomics, center for structural genomics of infec diseases, csgid, ligase; 1.52A {Francisella tularensis subsp}

Probab=86.07  E-value=0.9  Score=31.47  Aligned_cols=25  Identities=12%  Similarity=-0.004  Sum_probs=20.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQ   28 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~   28 (169)
                      |-+.++|.|||..+++++..+.+++
T Consensus         9 Itgt~t~vGKT~vt~~L~~~l~~~G   33 (228)
T 3of5_A            9 IIGTDTEVGKTYISTKLIEVCEHQN   33 (228)
T ss_dssp             EEESSSSSCHHHHHHHHHHHHHHTT
T ss_pred             EEeCCCCCCHHHHHHHHHHHHHHCC
Confidence            3467899999999999988877665

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=85.93  E-value=0.95  Score=34.75  Aligned_cols=45  Identities=4%  Similarity=-0.119  Sum_probs=32.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+++-.+|+|||.-++.++......  ..+++++.......|....+
T Consensus       200 iiIaG~pG~GKTtlal~ia~~~a~~--g~~vl~fSlEms~~ql~~R~  244 (444)
T 3bgw_A          200 VLIAARPSMGKTAFALKQAKNMSDN--DDVVNLHSLEMGKKENIKRL  244 (444)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHHHT--TCEEEEECSSSCTTHHHHHH
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHc--CCEEEEEECCCCHHHHHHHH
Confidence            4678889999998888887766544  46888888776555555544

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=85.86  E-value=1.3  Score=40.36  Aligned_cols=40  Identities=10%  Similarity=0.036  Sum_probs=30.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNN   44 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~q   44 (169)
                      .+|.-.+|+|||..+++++.....  ...+++++...+.+.+
T Consensus      1430 vll~GppGtGKT~LA~ala~ea~~--~G~~v~Fi~~e~~~~~ 1469 (2050)
T 3cmu_A         1430 VEIYGPESSGKTTLTLQVIAAAQR--EGKTCAFIDAEHALDP 1469 (2050)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHT--TTCCEEEECTTSCCCH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH--cCCcEEEEEcccccCH
Confidence            567789999999999988775443  3467888888776654

>3qxc_A Dethiobiotin synthetase; DTBS, structural genomics, ATP BIND biology, protein structure initiative, midwest center for S genomics, MCSG; HET: ATP; 1.34A {Helicobacter pylori} PDB: 3mle_A* 3qxh_A* 3qxj_A* 3qxs_A* 3qxx_A* 3qy0_A* 2qmo_A

Probab=85.85  E-value=0.96  Score=31.73  Aligned_cols=31  Identities=6%  Similarity=-0.101  Sum_probs=23.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      |-+-++|.|||..+++++..+.+++  .++..+
T Consensus        26 ItgT~t~vGKT~vs~gL~~~L~~~G--~~V~~f   56 (242)
T 3qxc_A           26 ISATNTNAGKTTCARLLAQYCNACG--VKTILL   56 (242)
T ss_dssp             EEESSTTSSHHHHHHHHHHHHHHTT--CCEEEE
T ss_pred             EEeCCCCCcHHHHHHHHHHHHHhCC--CceEEE
Confidence            4567899999999999988877655  334444

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=85.75  E-value=0.86  Score=32.94  Aligned_cols=31  Identities=10%  Similarity=-0.015  Sum_probs=23.3

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .+-..|.|||.+++.+...+...+  +++|+|-
T Consensus       110 ts~kgG~GKTtva~nLA~~lA~~G--~rVLLID  140 (299)
T 3cio_A          110 TGATPDSGKTFVSSTLAAVIAQSD--QKVLFID  140 (299)
T ss_dssp             EESSSSSCHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             ECCCCCCChHHHHHHHHHHHHhCC--CcEEEEE
Confidence            345679999999988887776543  6788775

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=85.66  E-value=0.94  Score=33.87  Aligned_cols=41  Identities=12%  Similarity=0.003  Sum_probs=30.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      +++-++|+|||..++.++......  .++++++.......++.
T Consensus        78 ~I~G~pGsGKTtlal~la~~~~~~--g~~vlyi~~E~s~~~~~  118 (366)
T 1xp8_A           78 EIYGPESGGKTTLALAIVAQAQKA--GGTCAFIDAEHALDPVY  118 (366)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHHH
T ss_pred             EEEcCCCCChHHHHHHHHHHHHHC--CCeEEEEECCCChhHHH
Confidence            456789999999888887665543  35788888877666664

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=85.64  E-value=0.95  Score=32.20  Aligned_cols=31  Identities=16%  Similarity=0.043  Sum_probs=22.8

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      .+-..|.|||..++.+...+...+  +++|+|-
T Consensus        88 ts~kgG~GKTt~a~nLA~~lA~~G--~rVLLID  118 (271)
T 3bfv_A           88 TSEAPGAGKSTIAANLAVAYAQAG--YKTLIVD  118 (271)
T ss_dssp             ECSSTTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             ECCCCCCcHHHHHHHHHHHHHhCC--CeEEEEe
Confidence            345679999999988877776543  5777774

>2xj4_A MIPZ; replication, cell division, ATPase, WACA; 1.60A {Caulobacter vibrioides} PDB: 2xj9_A* 2xit_A

Probab=85.15  E-value=1.1  Score=31.99  Aligned_cols=42  Identities=7%  Similarity=-0.043  Sum_probs=28.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--c-CcchHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--P-LSVLNNWEA   47 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P-~~~l~qW~~   47 (169)
                      +.+-.-|.|||..+..+...+...+  .++|+|=  | ...+..|..
T Consensus         9 v~s~KGGvGKTT~a~nLA~~La~~G--~~VlliD~D~~q~~l~~~l~   53 (286)
T 2xj4_A            9 VGNEKGGAGKSTIAVHLVTALLYGG--AKVAVIDLDLRQRTSARFFE   53 (286)
T ss_dssp             ECCSSSCTTHHHHHHHHHHHHHHTT--CCEEEEECCTTTCHHHHHHH
T ss_pred             EEcCCCCCCHHHHHHHHHHHHHHCC--CcEEEEECCCCCCCHHHHhC
Confidence            4456679999999998887776543  5677764  4 445555553

>1wcv_1 SOJ, segregation protein; ATPase, bacterial, chromosome segregation; 1.6A {Thermus thermophilus} PDB: 2bej_A* 2bek_A*

Probab=84.93  E-value=0.81  Score=32.02  Aligned_cols=32  Identities=13%  Similarity=0.060  Sum_probs=23.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-.-|.|||..++.+...+...+  .++|+|=
T Consensus        11 v~s~kGGvGKTt~a~~LA~~la~~g--~~VlliD   42 (257)
T 1wcv_1           11 LANQKGGVGKTTTAINLAAYLARLG--KRVLLVD   42 (257)
T ss_dssp             ECCSSCCHHHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EEeCCCCchHHHHHHHHHHHHHHCC--CCEEEEE
Confidence            3455679999999998887776543  6788774

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=84.78  E-value=0.75  Score=32.27  Aligned_cols=22  Identities=14%  Similarity=0.039  Sum_probs=17.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      |.+|.-++|+|||..+-++...
T Consensus        46 ~vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           46 GVLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             CCCCBCSSCSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            5678899999999887666543

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=84.73  E-value=0.97  Score=33.42  Aligned_cols=32  Identities=16%  Similarity=-0.007  Sum_probs=23.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +..---|.|||.++.++...+...+  .++|+|-
T Consensus        30 v~sgKGGvGKTTvA~~LA~~lA~~G--~rVLlvD   61 (349)
T 3ug7_A           30 MFGGKGGVGKTTMSAATGVYLAEKG--LKVVIVS   61 (349)
T ss_dssp             EEECSSSTTHHHHHHHHHHHHHHSS--CCEEEEE
T ss_pred             EEeCCCCccHHHHHHHHHHHHHHCC--CeEEEEe
Confidence            3455679999999998887776543  5777776

>3fgn_A Dethiobiotin synthetase; biotin biosynthesis, BIOD, ATP-BIND ligase, magnesium, nucleotide-binding; 1.85A {Mycobacterium tuberculosis} PDB: 3fmf_A* 3fmi_A* 3fpa_A*

Probab=84.19  E-value=1.4  Score=31.15  Aligned_cols=33  Identities=15%  Similarity=-0.015  Sum_probs=23.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      |-+-++|.|||..+++++..+.+++  .++..+=|
T Consensus        31 Itgt~t~vGKT~vt~gL~~~l~~~G--~~V~~fKP   63 (251)
T 3fgn_A           31 VTGTGTGVGKTVVCAALASAARQAG--IDVAVCKP   63 (251)
T ss_dssp             EEESSTTSCHHHHHHHHHHHHHHTT--CCEEEEEE
T ss_pred             EEeCCCCCcHHHHHHHHHHHHHHCC--CeEEEEee
Confidence            3467899999999999988877665  34444433

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=83.94  E-value=0.77  Score=33.86  Aligned_cols=41  Identities=10%  Similarity=0.081  Sum_probs=27.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWE   46 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~   46 (169)
                      +...--|.|||.++.++...+...  .+++|+|-  |...+..|.
T Consensus        20 ~~sgkGGvGKTt~a~~lA~~la~~--g~~vllid~D~~~~l~~~l   62 (334)
T 3iqw_A           20 FVGGKGGVGKTTTSCSLAIQLAKV--RRSVLLLSTDPAHNLSDAF   62 (334)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHTTS--SSCEEEEECCSSCHHHHHH
T ss_pred             EEeCCCCccHHHHHHHHHHHHHhC--CCcEEEEECCCCCChhHHh
Confidence            344567999999998887666543  35777776  445555554

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=83.91  E-value=2.9  Score=30.36  Aligned_cols=32  Identities=6%  Similarity=0.017  Sum_probs=21.4

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +.-..|.|||.++..++..+...  .++++++.-
T Consensus       109 ivG~~GsGKTTl~~~LA~~l~~~--g~kV~lv~~  140 (306)
T 1vma_A          109 VVGVNGTGKTTSCGKLAKMFVDE--GKSVVLAAA  140 (306)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHT--TCCEEEEEE
T ss_pred             EEcCCCChHHHHHHHHHHHHHhc--CCEEEEEcc
Confidence            34469999998887776665443  356666653

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=83.82  E-value=2.1  Score=39.22  Aligned_cols=41  Identities=12%  Similarity=0.028  Sum_probs=32.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      +|+-++|+|||.-++.++......  .++++++.-.....||.
T Consensus       736 lIaG~PG~GKTtLalqlA~~~a~~--g~~VlyiS~Ees~~ql~  776 (2050)
T 3cmu_A          736 EIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY  776 (2050)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHTT--TCCEEEECTTSCCCHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEECCCcHHHHH
Confidence            688999999998888887665432  45788888888888875

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=83.54  E-value=1.1  Score=30.35  Aligned_cols=42  Identities=12%  Similarity=0.165  Sum_probs=29.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNWEAE   48 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW~~e   48 (169)
                      +.+.--|.|||..++.+...+...+   ++++|=  |...+..|...
T Consensus         5 v~s~KGGvGKTT~a~~LA~~la~~g---~VlliD~D~q~~~~~~~~~   48 (209)
T 3cwq_A            5 VASFKGGVGKTTTAVHLSAYLALQG---ETLLIDGDPNRSATGWGKR   48 (209)
T ss_dssp             EEESSTTSSHHHHHHHHHHHHHTTS---CEEEEEECTTCHHHHHHHH
T ss_pred             EEcCCCCCcHHHHHHHHHHHHHhcC---CEEEEECCCCCCHHHHhcC
Confidence            3455679999999988877765443   677754  66666677653

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=83.17  E-value=1.1  Score=32.10  Aligned_cols=32  Identities=6%  Similarity=-0.088  Sum_probs=23.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+-..|.|||..+..+...+...  .+++|+|=
T Consensus        97 vts~kgG~GKTtva~nLA~~lA~~--G~rVLLID  128 (286)
T 3la6_A           97 MTGVSPSIGMTFVCANLAAVISQT--NKRVLLID  128 (286)
T ss_dssp             EEESSSSSSHHHHHHHHHHHHHTT--TCCEEEEE
T ss_pred             EECCCCCCcHHHHHHHHHHHHHhC--CCCEEEEe
Confidence            344567999999998887776644  36787774

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=83.02  E-value=0.94  Score=31.18  Aligned_cols=33  Identities=15%  Similarity=-0.035  Sum_probs=22.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+---|.|||..++.+...+... ...++|+|=
T Consensus         9 v~s~kGGvGKTt~a~~LA~~la~~-~g~~VlliD   41 (245)
T 3ea0_A            9 FVSAKGGDGGSCIAANFAFALSQE-PDIHVLAVD   41 (245)
T ss_dssp             EEESSTTSSHHHHHHHHHHHHTTS-TTCCEEEEE
T ss_pred             EECCCCCcchHHHHHHHHHHHHhC-cCCCEEEEE
Confidence            344567999999998887766543 135677765

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=82.81  E-value=1.4  Score=32.82  Aligned_cols=39  Identities=13%  Similarity=0.104  Sum_probs=28.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLN   43 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~   43 (169)
                      .++.-++|+|||..++.++......+  .+++++.......
T Consensus        66 i~I~G~pGsGKTtLal~la~~~~~~g--~~vlyid~E~s~~  104 (356)
T 1u94_A           66 VEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALD  104 (356)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCcc
Confidence            35677999999999888877655433  5788887765443

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=82.72  E-value=1.1  Score=33.34  Aligned_cols=34  Identities=9%  Similarity=-0.011  Sum_probs=23.4

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      .---|.|||.++.++...+......+++|+|-..
T Consensus        24 sgKGGvGKTTvaanLA~~lA~~~~G~rVLLvD~D   57 (354)
T 2woj_A           24 GGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTD   57 (354)
T ss_dssp             EESTTSSHHHHHHHHHHHHHHHCTTSCEEEEECC
T ss_pred             eCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEECC
Confidence            3457999999998887776521234678887643

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=82.65  E-value=0.71  Score=30.06  Aligned_cols=24  Identities=21%  Similarity=0.189  Sum_probs=18.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      .+|.-+.|+|||..+-+++..+..
T Consensus        46 ~ll~G~~G~GKT~l~~~~~~~~~~   69 (195)
T 1jbk_A           46 PVLIGEPGVGKTAIVEGLAQRIIN   69 (195)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHh
Confidence            567889999999888777665543

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=82.20  E-value=1.2  Score=31.15  Aligned_cols=39  Identities=10%  Similarity=0.086  Sum_probs=25.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe--cCcchHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC--PLSVLNNW   45 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~--P~~~l~qW   45 (169)
                      +.+---|.|||..++.+...+. .  ..++|+|=  |..-...|
T Consensus        32 v~s~kGGvGKTT~a~~LA~~la-~--g~~VlliD~D~~~~~~~~   72 (267)
T 3k9g_A           32 IASIKGGVGKSTSAIILATLLS-K--NNKVLLIDMDTQASITSY   72 (267)
T ss_dssp             ECCSSSSSCHHHHHHHHHHHHT-T--TSCEEEEEECTTCHHHHH
T ss_pred             EEeCCCCchHHHHHHHHHHHHH-C--CCCEEEEECCCCCCHHHH
Confidence            4456679999999988877665 3  36777774  33433344

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=82.14  E-value=3.4  Score=31.65  Aligned_cols=46  Identities=7%  Similarity=-0.002  Sum_probs=31.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+++-.+|+|||.-++.++....... ..+++++.......+....+
T Consensus       206 iiI~G~pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~E~s~~~l~~r~  251 (454)
T 2r6a_A          206 IIVAARPSVGKTAFALNIAQNVATKT-NENVAIFSLEMSAQQLVMRM  251 (454)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHS-SCCEEEEESSSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhC-CCcEEEEECCCCHHHHHHHH
Confidence            46788999999988887776655432 35788888765555555443

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=82.07  E-value=2.9  Score=33.72  Aligned_cols=50  Identities=6%  Similarity=-0.027  Sum_probs=34.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh-C-CCCceEEEecCc-chHHHHHHHHHhC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE-Q-ALEPNLIVCPLS-VLNNWEAEFRKFA   53 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~-~-~~~~~Liv~P~~-~l~qW~~e~~~~~   53 (169)
                      ++.-..|+|||.+.+.-+.++... + ....+|+|+.+. ...+..+.+.+..
T Consensus        19 lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l   71 (673)
T 1uaa_A           19 LVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTL   71 (673)
T ss_dssp             EECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHc
Confidence            445678999999988877777665 2 345789998764 4455666666554

>3pg5_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 3.30A {Corynebacterium diphtheriae}

Probab=81.21  E-value=1.4  Score=32.66  Aligned_cols=32  Identities=9%  Similarity=-0.123  Sum_probs=23.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +...--|.|||.+++.+...+...  ..++|+|=
T Consensus         6 v~s~KGGvGKTT~a~nLA~~LA~~--G~rVLlID   37 (361)
T 3pg5_A            6 FFNNKGGVGKTTLSTNVAHYFALQ--GKRVLYVD   37 (361)
T ss_dssp             BCCSSCCHHHHHHHHHHHHHHHHT--TCCEEEEE
T ss_pred             EEcCCCCCcHHHHHHHHHHHHHhC--CCcEEEEE
Confidence            445567999999998887776553  36787774

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=81.06  E-value=1.6  Score=29.06  Aligned_cols=23  Identities=17%  Similarity=0.283  Sum_probs=16.1

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|.-+.|+|||..+-.+...+.
T Consensus        41 ~ll~G~~G~GKT~l~~~l~~~~~   63 (226)
T 2chg_A           41 LLFSGPPGTGKTATAIALARDLF   63 (226)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            45677889999977766655443

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=81.05  E-value=1.4  Score=32.19  Aligned_cols=32  Identities=6%  Similarity=0.064  Sum_probs=23.3

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +..-.-|.|||..+.++...+...  ..++++|-
T Consensus        23 v~sgkGGvGKTTva~~LA~~lA~~--G~rVllvD   54 (329)
T 2woo_A           23 FVGGKGGVGKTTTSCSLAIQMSKV--RSSVLLIS   54 (329)
T ss_dssp             EEECSSSSSHHHHHHHHHHHHHTS--SSCEEEEE
T ss_pred             EEeCCCCCcHHHHHHHHHHHHHHC--CCeEEEEE
Confidence            445678999999998887776644  35777764

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=80.96  E-value=1.9  Score=31.96  Aligned_cols=42  Identities=12%  Similarity=0.032  Sum_probs=27.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec--CcchHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP--LSVLNNWE   46 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P--~~~l~qW~   46 (169)
                      +..--|.|||.++.++...+......+++|+|--  .+.+..|.
T Consensus        23 ~~gkGGvGKTt~a~~lA~~la~~~~g~~vllid~D~~~~l~~~~   66 (348)
T 3io3_A           23 VGGKGGVGKTTTSSSVAVQLALAQPNEQFLLISTDPAHNLSDAF   66 (348)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHHHCTTSCEEEEECCSSCHHHHHH
T ss_pred             EeCCCCCcHHHHHHHHHHHHHHhcCCCeEEEEECCCCCChHHHh
Confidence            3446799999999888777652133467777763  44455444

>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=80.73  E-value=0.85  Score=31.72  Aligned_cols=21  Identities=14%  Similarity=0.086  Sum_probs=16.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~   23 (169)
                      .+|.-++|+|||..+-++...
T Consensus        42 vll~G~~GtGKT~la~~la~~   62 (262)
T 2qz4_A           42 ALLLGPPGCGKTLLAKAVATE   62 (262)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            478889999999877666543

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=80.14  E-value=2.1  Score=32.71  Aligned_cols=31  Identities=16%  Similarity=0.004  Sum_probs=22.6

Q ss_pred             CCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           7 DPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         7 de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      --.|.|||.++..++..+.... ..++++|.-
T Consensus       107 G~~GvGKTT~a~~LA~~l~~~~-G~kVllvd~  137 (433)
T 2xxa_A          107 GLQGAGKTTSVGKLGKFLREKH-KKKVLVVSA  137 (433)
T ss_dssp             CSTTSSHHHHHHHHHHHHHHTS-CCCEEEEEC
T ss_pred             CCCCCCHHHHHHHHHHHHHHhc-CCeEEEEec
Confidence            4589999999998887776551 356666663

>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=80.07  E-value=1.1  Score=32.21  Aligned_cols=40  Identities=13%  Similarity=0.062  Sum_probs=24.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      |.+|.-++|+|||..+-++....     ..+.+.+-...+...|.
T Consensus        51 ~vLL~Gp~GtGKT~la~ala~~~-----~~~~i~v~~~~l~~~~~   90 (301)
T 3cf0_A           51 GVLFYGPPGCGKTLLAKAIANEC-----QANFISIKGPELLTMWF   90 (301)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHT-----TCEEEEECHHHHHHHHH
T ss_pred             eEEEECCCCcCHHHHHHHHHHHh-----CCCEEEEEhHHHHhhhc
Confidence            35678899999998776655432     23455444444444443

---

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	169
d1z63a1	230	c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 h	0.001
d1z3ix2	298	c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fis	0.001

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]} Length = 230

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]

 Score = 35.8 bits (81), Expect = 0.001
 Identities = 41/144 (28%), Positives = 72/144 (50%), Gaps = 27/144 (18%)

Query: 13  KSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQ 72
           K+ + IA F    +E  L P+L++CPLSVL NWE E  KFAP +R   ++ +  + K   
Sbjct: 44  KTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLED 103

Query: 73  SEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSV 132
            +                          I++TT  ++  D   LK++ W  I++DE  ++
Sbjct: 104 YD--------------------------IILTTYAVLLRDTR-LKEVEWKYIVIDEAQNI 136

Query: 133 KNKKSKLSIKLTALRATFKVLLTG 156
           KN ++K+   +  L++ +++ LTG
Sbjct: 137 KNPQTKIFKAVKELKSKYRIALTG 160

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 298

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]

 Score = 35.8 bits (81), Expect = 0.001
 Identities = 32/164 (19%), Positives = 61/164 (37%), Gaps = 22/164 (13%)

Query: 15  GK---VIAFFCKIIEEQALEPN-----LIVCPLSVLNNWEAEFRKFAPF-VRTVKYYGNA 65
           GK    I     ++++           ++V P S++ NW  E  K+    V+ V   G +
Sbjct: 91  GKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGS 150

Query: 66  IERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCII 125
            +    +                   +Q       IL+ + +        L K     +I
Sbjct: 151 KDEIDSK-------------LVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVI 197

Query: 126 VDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKWSKQCTL 169
            DEGH +KN  ++  + L ++ A  +VL++G    N   +  +L
Sbjct: 198 CDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQNDLLEYFSL 241

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	169
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	100.0
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	100.0
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.89
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.86
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.82
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.77
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.77
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.75
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.69
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.67
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.66
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.52
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.48
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.4
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.39
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.38
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.33
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.27
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.27
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.22
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.21
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.97
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.88
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	97.68
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	97.66
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.68
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.38
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	96.07
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.8
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.63
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	95.49
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	95.4
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.33
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	94.79
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.76
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	94.37
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	94.36
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	94.08
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	94.04
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.0
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.7
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	93.58
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	93.48
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.33
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	93.25
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	92.84
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	92.79
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	92.64
d1okkd2	207	GTPase domain of the signal recognition particle r	92.3
d1vmaa2	213	GTPase domain of the signal recognition particle r	92.14
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	91.5
d1j8yf2	211	GTPase domain of the signal sequence recognition p	90.81
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	90.63
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	90.5
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	90.35
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	89.87
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	89.87
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	88.38
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	87.94
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	87.85
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	87.79
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	86.06
d2b2na1	308	Transcription-repair coupling factor, TRCF {Escher	85.91
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	85.69
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	85.24
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	84.58
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	84.42
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	84.42
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	83.9
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	83.73
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	83.51
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	83.15
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.8
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	82.57
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	82.54
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	82.34
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	81.91
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	81.6
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	81.24
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	80.48

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=100.00  E-value=2.1e-40  Score=242.26  Aligned_cols=155  Identities=20%  Similarity=0.322  Sum_probs=126.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC-----CCceEEEecCcchHHHHHHHHHhCCC-ceEEEEeCCHHHHHHHHHhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA-----LEPNLIVCPLSVLNNWEAEFRKFAPF-VRTVKYYGNAIERKALQSEA   75 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~-----~~~~Liv~P~~~l~qW~~e~~~~~~~-~~~~~~~g~~~~~~~~~~~~   75 (169)
                      |||||||||+|||+++|+++..+.....     .+++|||||.+++.||.+|+.+|++. ...+.+++..+.+.......
T Consensus        81 g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~sl~~qW~~Ei~k~~~~~~~~v~~~~~~~~~~~~~~~~  160 (298)
T d1z3ix2          81 GCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLVN  160 (298)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHHHHHHHHHHHHHHHGGGCCEEEECSSCHHHHHHHHHH
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccchhhHHHHHHHHhhcCCceeEEEEeCchHHHHHHHHHH
Confidence            7999999999999999999988877643     34699999999999999999999863 55666666544433222222


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEe
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLT  155 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT  155 (169)
                      .....            ......++ ++++|+.+.++.+.+...+|+++|+||+|+++|.+++.++++..++++++|+||
T Consensus       161 ~~~~~------------~~~~~~~v-~i~sy~~~~~~~~~l~~~~~~~vI~DEaH~ikn~~s~~~~a~~~l~~~~rllLT  227 (298)
T d1z3ix2         161 FISQQ------------GMRIPTPI-LIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLIS  227 (298)
T ss_dssp             HHCCC------------SSCCSCCE-EEEEHHHHHHHTTTTTTSCCCEEEETTGGGCCTTCHHHHHHHHHHCCSEEEEEC
T ss_pred             hhhcc------------CccccceE-EEEeecccccchhcccccceeeeecccccccccccchhhhhhhccccceeeeec
Confidence            11100            00134456 999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCchhhccC
Q psy1090         156 GWYYPNKWSKQCTL  169 (169)
Q Consensus       156 ~TP~~n~~~el~~l  169 (169)
                      |||++|++.|||++
T Consensus       228 GTPi~N~~~dl~~l  241 (298)
T d1z3ix2         228 GTPIQNDLLEYFSL  241 (298)
T ss_dssp             SSCSGGGGGGCHHH
T ss_pred             chHHhhhhHHHHHH
Confidence            99999999999974

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=100.00  E-value=1.2e-38  Score=224.93  Aligned_cols=142  Identities=30%  Similarity=0.549  Sum_probs=123.1

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .||+||||||+|||+++++++......+...++|||||.+++.||.+|+.+|.+...+..+........           
T Consensus        32 ~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p~~l~~~W~~e~~~~~~~~~~~~~~~~~~~~~-----------  100 (230)
T d1z63a1          32 FGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSVLKNWEEELSKFAPHLRFAVFHEDRSKIK-----------  100 (230)
T ss_dssp             CCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECSTTHHHHHHHHHHHCTTSCEEECSSSTTSCC-----------
T ss_pred             CCEEEEeCCCCChHHHHHHhhhhhhhcccccccceecchhhhhHHHHHHHhhcccccceeeccccchhh-----------
Confidence            379999999999999999999988888888999999999999999999999998777666544322211           


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCC
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                                    ....++ ++++|+.+.+. ..+.+.+|+++|+||||+++|+.++.++++..++++++|+|||||++
T Consensus       101 --------------~~~~~v-vi~~~~~~~~~-~~l~~~~~~~vI~DEah~~k~~~s~~~~~~~~l~a~~r~~LTgTPi~  164 (230)
T d1z63a1         101 --------------LEDYDI-ILTTYAVLLRD-TRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIE  164 (230)
T ss_dssp             --------------GGGSSE-EEEEHHHHTTC-HHHHTCCEEEEEEETGGGGSCTTSHHHHHHHTSCEEEEEEECSSCST
T ss_pred             --------------ccCcCE-EEeeHHHHHhH-HHHhcccceEEEEEhhhcccccchhhhhhhhhhccceEEEEecchHH
Confidence                          144567 99999998765 44677899999999999999999999999999999999999999999


Q ss_pred             CCchhhccC
Q psy1090         161 NKWSKQCTL  169 (169)
Q Consensus       161 n~~~el~~l  169 (169)
                      |++.|||++
T Consensus       165 n~~~dl~~l  173 (230)
T d1z63a1         165 NKVDDLWSI  173 (230)
T ss_dssp             TCHHHHHHH
T ss_pred             hHHHHHHHH
Confidence            999999974

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.89  E-value=1.9e-23  Score=144.27  Aligned_cols=117  Identities=22%  Similarity=0.241  Sum_probs=88.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      +++.++||+|||++++.++...     .+++|||||. .++.||.+++.+|.+ ..+..+.|..+               
T Consensus        88 ~ll~~~tG~GKT~~a~~~~~~~-----~~~~Liv~p~~~L~~q~~~~~~~~~~-~~~~~~~~~~~---------------  146 (206)
T d2fz4a1          88 GCIVLPTGSGKTHVAMAAINEL-----STPTLIVVPTLALAEQWKERLGIFGE-EYVGEFSGRIK---------------  146 (206)
T ss_dssp             EEEEESSSTTHHHHHHHHHHHS-----CSCEEEEESSHHHHHHHHHHHGGGCG-GGEEEESSSCB---------------
T ss_pred             cEEEeCCCCCceehHHhHHHHh-----cCceeEEEcccchHHHHHHHHHhhcc-cchhhcccccc---------------
Confidence            6889999999999988776432     3689999997 678899999999874 33444443211               


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccC
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWY  158 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP  158 (169)
                                    ...++ ++++|+.+......+. -+|++||+||||+++++  ...+.+..++++++++||||+
T Consensus       147 --------------~~~~i-~i~t~~~~~~~~~~~~-~~~~lvIiDEaH~~~a~--~~~~i~~~~~~~~~lgLTATl  205 (206)
T d2fz4a1         147 --------------ELKPL-TVSTYDSAYVNAEKLG-NRFMLLIFDEVHHLPAE--SYVQIAQMSIAPFRLGLTATF  205 (206)
T ss_dssp             --------------CCCSE-EEEEHHHHHHTHHHHT-TTCSEEEEECSSCCCTT--THHHHHHTCCCSEEEEEEESC
T ss_pred             --------------ccccc-ccceehhhhhhhHhhC-CcCCEEEEECCeeCCcH--HHHHHHhccCCCcEEEEecCC
Confidence                          23345 8999999877655443 37999999999999743  456667778899999999997

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.86  E-value=3.7e-22  Score=143.67  Aligned_cols=135  Identities=19%  Similarity=0.185  Sum_probs=90.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCC--ceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPF--VRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~--~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      .|+|..+||+|||+++++++..+.... ..++||+||. .++.||.+++.+|...  ..+....+.....          
T Consensus       130 ~~il~~pTGsGKT~i~~~i~~~~~~~~-~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~~~g~~~~----------  198 (282)
T d1rifa_         130 RRILNLPTSAGRSLIQALLARYYLENY-EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKD----------  198 (282)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHC-SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSST----------
T ss_pred             CceeEEEcccCccHHHHHHHHHhhhcc-cceEEEEEcCchhHHHHHHHHHHhhccccccceeecceeccc----------
Confidence            378999999999999887776655443 4689999997 7889999999988632  2222222111000          


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc-ccccEEEEecc
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL-RATFKVLLTGW  157 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l-~~~~~~~lT~T  157 (169)
                                   .......++ +++|++.+.+....+. .+|+++|+||||+++.  ......+..+ ++++|++||||
T Consensus       199 -------------~~~~~~~~i-~i~t~qs~~~~~~~~~-~~f~~VIvDEaH~~~a--~~~~~il~~~~~~~~rlGlTaT  261 (282)
T d1rifa_         199 -------------DKYKNDAPV-VVGTWQTVVKQPKEWF-SQFGMMMNDECHLATG--KSISSIISGLNNCMFKFGLSGS  261 (282)
T ss_dssp             -------------TCCCTTCSE-EEECHHHHTTSCGGGG-GGEEEEEEETGGGCCH--HHHHHHTTTCTTCCEEEEECSS
T ss_pred             -------------ccccccceE-EEEeeehhhhhccccc-CCCCEEEEECCCCCCc--hhHHHHHHhccCCCeEEEEEee
Confidence                         000134455 9999999876543322 3689999999999863  2233444445 78899999999


Q ss_pred             CCCCCch
Q psy1090         158 YYPNKWS  164 (169)
Q Consensus       158 P~~n~~~  164 (169)
                      |......
T Consensus       262 ~~~~~~~  268 (282)
T d1rifa_         262 LRDGKAN  268 (282)
T ss_dssp             CCTTSTT
T ss_pred             cCCCCcc
Confidence            9765543

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.82  E-value=1.3e-19  Score=124.09  Aligned_cols=136  Identities=19%  Similarity=0.191  Sum_probs=91.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhcC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALSL   78 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~   78 (169)
                      +++++.++|+|||++++.++...... ..+++|+|+|. .++.||.+++.+++.  ...+..+.+.......... .   
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~~~~-~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~-~---   99 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYRLTK-YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKA-W---   99 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHH-SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHH-H---
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHHHHh-cCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeecccchhHHHHh-h---
Confidence            57889999999999877666554443 35789999997 778899999999873  5566666554333221111 1   


Q ss_pred             CCcccccccCCccccccCCCCeEEEecHHHHHhch--hccccccccEEEEeCCcccCCcccHHHHHHh---ccccccEEE
Q psy1090          79 PTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVDEGHSVKNKKSKLSIKLT---ALRATFKVL  153 (169)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~--~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~---~l~~~~~~~  153 (169)
                                       ...++ +++|++.+....  ..+...+++++|+||||++.+..........   .....+.++
T Consensus       100 -----------------~~~~i-~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~  161 (200)
T d1wp9a1         100 -----------------ARAKV-IVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIG  161 (200)
T ss_dssp             -----------------HHCSE-EEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEE
T ss_pred             -----------------hcccc-cccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCCcEEE
Confidence                             22344 899998886542  2233347899999999998875543332221   123456899


Q ss_pred             EeccCCC
Q psy1090         154 LTGWYYP  160 (169)
Q Consensus       154 lT~TP~~  160 (169)
                      |||||-.
T Consensus       162 ~SATp~~  168 (200)
T d1wp9a1         162 LTASPGS  168 (200)
T ss_dssp             EESCSCS
T ss_pred             EEecCCC
Confidence            9999953

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.77  E-value=1.1e-18  Score=123.40  Aligned_cols=137  Identities=13%  Similarity=0.139  Sum_probs=98.0

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhCC--CceEEEEeCCH--HHHHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAP--FVRTVKYYGNA--IERKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~~--~~~~~~~~g~~--~~~~~~~~~~   75 (169)
                      |..+|..++|+|||..++..+......+  ..+++++|..++ .|+.+.+.++++  +..+..++|..  +++.......
T Consensus       105 m~rLL~GdvGSGKT~Va~~a~~~~~~~g--~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~  182 (264)
T d1gm5a3         105 MNRLLQGDVGSGKTVVAQLAILDNYEAG--FQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGL  182 (264)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHHHT--SCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHH
T ss_pred             ceeeeeccccccccHHHHHHHHHHHhcc--cceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHH
Confidence            5679999999999999888777666655  689999998655 699999999886  45677777643  4444444433


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhccccccEEEEe
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLT  155 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT  155 (169)
                      ..                  +..++ ++.|+..+..+..+   .+.+++|+||-|++.-  .++......-+..+.++||
T Consensus       183 ~~------------------g~~~i-iIGThsl~~~~~~f---~~LglviiDEqH~fgv--~Qr~~l~~~~~~~~~l~~S  238 (264)
T d1gm5a3         183 RN------------------GQIDV-VIGTHALIQEDVHF---KNLGLVIIDEQHRFGV--KQREALMNKGKMVDTLVMS  238 (264)
T ss_dssp             HS------------------SCCCE-EEECTTHHHHCCCC---SCCCEEEEESCCCC-------CCCCSSSSCCCEEEEE
T ss_pred             HC------------------CCCCE-EEeehHHhcCCCCc---cccceeeeccccccch--hhHHHHHHhCcCCCEEEEE
Confidence            22                  67788 99999999876553   2568999999998742  2221111222457789999


Q ss_pred             ccCCCCCc
Q psy1090         156 GWYYPNKW  163 (169)
Q Consensus       156 ~TP~~n~~  163 (169)
                      |||.+.++
T Consensus       239 ATPiprtl  246 (264)
T d1gm5a3         239 ATPIPRSM  246 (264)
T ss_dssp             SSCCCHHH
T ss_pred             CCCCHHHH
Confidence            99998765

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.77  E-value=9.1e-19  Score=112.90  Aligned_cols=121  Identities=22%  Similarity=0.117  Sum_probs=76.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI   81 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~   81 (169)
                      ++|...+|+|||..++.++.     ....++||++|. .+.+||.+++.++..........+...               
T Consensus        11 ~ll~apTGsGKT~~~~~~~~-----~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~---------------   70 (136)
T d1a1va1          11 AHLHAPTGSGKSTKVPAAYA-----AQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTI---------------   70 (136)
T ss_dssp             EEEECCTTSCTTTHHHHHHH-----TTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEE---------------
T ss_pred             EEEEeCCCCCHHHHHHHHHH-----HcCCcEEEEcChHHHHHHHHHHHHHHhhcccccccccccc---------------
Confidence            67899999999976644332     234689999998 566799999988764333332222111               


Q ss_pred             ccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHH-HHHhcc---ccccEEEEecc
Q psy1090          82 KVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLS-IKLTAL---RATFKVLLTGW  157 (169)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~-~~~~~l---~~~~~~~lT~T  157 (169)
                                   .....+ .+.++.......... -.+|+++|+||+|++.......+ ..+..+   .....++||||
T Consensus        71 -------------~~~~~~-~~~~~~~~~~~~~~~-~~~~~~vIiDE~H~~~~~~~~~~~~~l~~~~~~~~~~~l~~TAT  135 (136)
T d1a1va1          71 -------------TTGSPI-TYSTYGKFLADGGCS-GGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATAT  135 (136)
T ss_dssp             -------------CCCCSE-EEEEHHHHHHTTGGG-GCCCSEEEEETTTCCSHHHHHHHHHHHHHTTTTTCSEEEEEESS
T ss_pred             -------------ccccce-EEEeeeeeccccchh-hhcCCEEEEecccccCHHHHHHHHHHHHHHHHCCCCcEEEEeCC
Confidence                         133344 677777665443221 23789999999999854332222 333333   23457999999


Q ss_pred             C
Q psy1090         158 Y  158 (169)
Q Consensus       158 P  158 (169)
                      |
T Consensus       136 P  136 (136)
T d1a1va1         136 P  136 (136)
T ss_dssp             C
T ss_pred             C
Confidence            9

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.75  E-value=3.6e-19  Score=114.77  Aligned_cols=126  Identities=13%  Similarity=0.090  Sum_probs=72.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      .++|..+||+|||.+++..+....... ...+++++|...+ .||.+.+.    ............              
T Consensus         9 ~~il~~~tGsGKT~~~~~~~~~~~~~~-~~~vli~~p~~~l~~q~~~~~~----~~~~~~~~~~~~--------------   69 (140)
T d1yksa1           9 TTVLDFHPGAGKTRRFLPQILAECARR-RLRTLVLAPTRVVLSEMKEAFH----GLDVKFHTQAFS--------------   69 (140)
T ss_dssp             EEEECCCTTSSTTTTHHHHHHHHHHHT-TCCEEEEESSHHHHHHHHHHTT----TSCEEEESSCCC--------------
T ss_pred             cEEEEcCCCCChhHHHHHHHHHHhhhc-CceeeeeecchhHHHHHHHHhh----hhhhhhcccccc--------------
Confidence            368999999999998876654433333 4678999998544 45554443    222222111100              


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHh-chhccccccccEEEEeCCcccCCcccHHH----HHHhccccccEEEEe
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIEN-DFGFLKKITWNCIIVDEGHSVKNKKSKLS----IKLTALRATFKVLLT  155 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~-~~~~~~~~~~~~vi~DEah~~k~~~~~~~----~~~~~l~~~~~~~lT  155 (169)
                                 ......... ...++..+.. ........+|+++|+||||++.. .+...    ......+..+.++||
T Consensus        70 -----------~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~lvIiDEaH~~~~-~~~~~~~~~~~~~~~~~~~~l~lT  136 (140)
T d1yksa1          70 -----------AHGSGREVI-DAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDP-ASIAARGWAAHRARANESATILMT  136 (140)
T ss_dssp             -----------CCCCSSCCE-EEEEHHHHHHHHTSSSCCCCCSEEEETTTTCCSH-HHHHHHHHHHHHHHTTSCEEEEEC
T ss_pred             -----------cccccccch-hhhhHHHHHHHHhccccccceeEEEEccccccCh-hhHHHHHHHHHHhhCCCCCEEEEE
Confidence                       000123334 5555555443 33444456899999999998742 22211    112223567889999


Q ss_pred             ccCC
Q psy1090         156 GWYY  159 (169)
Q Consensus       156 ~TP~  159 (169)
                      |||.
T Consensus       137 ATPp  140 (140)
T d1yksa1         137 ATPP  140 (140)
T ss_dssp             SSCT
T ss_pred             cCCC
Confidence            9995

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.69  E-value=3e-16  Score=108.93  Aligned_cols=136  Identities=19%  Similarity=0.238  Sum_probs=96.0

Q ss_pred             CCccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHHHHHhCCC--ceEEEEeCC--HHHHHHHHHhh
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAPF--VRTVKYYGN--AIERKALQSEA   75 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e~~~~~~~--~~~~~~~g~--~~~~~~~~~~~   75 (169)
                      |..+|.-++|+|||..++..+......+  +.+++++|...+ .|+.+.|+++++.  .++..+++.  ..++.......
T Consensus        77 ~~~LL~GdvGsGKT~V~~~a~~~~~~~g--~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~  154 (233)
T d2eyqa3          77 MDRLVCGDVGFGKTEVAMRAAFLAVDNH--KQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEV  154 (233)
T ss_dssp             CEEEEECCCCTTTHHHHHHHHHHHHTTT--CEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHH
T ss_pred             cCeEEEcCCCCCcHHHHHHHHHHHHHcC--CceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHH
Confidence            3468899999999998887776655444  789999999655 6999999988764  466677774  33444444433


Q ss_pred             hcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhc-cccccEEEE
Q psy1090          76 LSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA-LRATFKVLL  154 (169)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~-l~~~~~~~l  154 (169)
                      ..                  +..++ ++-|+..+.....+   .+.+++|+||-|++.   .+.-..++. ....+.+.+
T Consensus       155 ~~------------------g~~~i-viGths~l~~~~~f---~~LgLiIiDEeH~fg---~kQ~~~l~~~~~~~~~l~~  209 (233)
T d2eyqa3         155 AE------------------GKIDI-LIGTHKLLQSDVKF---KDLGLLIVDEEHRFG---VRHKERIKAMRANVDILTL  209 (233)
T ss_dssp             HT------------------TCCSE-EEECTHHHHSCCCC---SSEEEEEEESGGGSC---HHHHHHHHHHHTTSEEEEE
T ss_pred             hC------------------CCCCE-EEeehhhhccCCcc---ccccceeeechhhhh---hHHHHHHHhhCCCCCEEEE
Confidence            32                  66777 99999988764442   367899999999863   222233332 244679999


Q ss_pred             eccCCCCCc
Q psy1090         155 TGWYYPNKW  163 (169)
Q Consensus       155 T~TP~~n~~  163 (169)
                      ||||.+.++
T Consensus       210 SATPiprtl  218 (233)
T d2eyqa3         210 TATPIPRTL  218 (233)
T ss_dssp             ESSCCCHHH
T ss_pred             ecchhHHHH
Confidence            999997654

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.67  E-value=5.4e-17  Score=111.12  Aligned_cols=131  Identities=20%  Similarity=0.164  Sum_probs=82.2

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC-CceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP-FVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      +++++.++|+|||..++..+....  ...+++|+++|. .++.||.++++++.+ ..++..+.+....+.          
T Consensus        42 ~~il~apTGsGKT~~a~l~i~~~~--~~~~~vl~l~P~~~L~~q~~~~~~~~~~~~~~v~~~~~~~~~~~----------  109 (202)
T d2p6ra3          42 NLLLAMPTAAGKTLLAEMAMVREA--IKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRD----------  109 (202)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHH--HTTCCEEEEESSHHHHHHHHHHHTTTTTTTCCEEEECSSCBCCS----------
T ss_pred             CEEEEcCCCCchhHHHHHHHHHHh--hccCcceeecccHHHHHHHHHHHHHHhhccccceeeccCccccc----------
Confidence            478999999999988754443332  234689999997 678899999998875 334444444322110          


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchhcc--ccccccEEEEeCCcccCCccc--HHHHHHh---cc-ccccE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFL--KKITWNCIIVDEGHSVKNKKS--KLSIKLT---AL-RATFK  151 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~--~~~~~~~vi~DEah~~k~~~~--~~~~~~~---~l-~~~~~  151 (169)
                                   ......++ +++++..+.......  ....++++|+||+|.+.++.-  .....+.   .. +...+
T Consensus       110 -------------~~~~~~~i-i~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~  175 (202)
T d2p6ra3         110 -------------EHLGDCDI-IVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRV  175 (202)
T ss_dssp             -------------SCSTTCSE-EEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEE
T ss_pred             -------------ccccccce-eeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHHHHHHHhcCCCCcE
Confidence                         11144566 788877765433211  123678999999999875431  1122222   22 34468


Q ss_pred             EEEeccC
Q psy1090         152 VLLTGWY  158 (169)
Q Consensus       152 ~~lT~TP  158 (169)
                      ++||||.
T Consensus       176 l~lSATl  182 (202)
T d2p6ra3         176 IGLSATA  182 (202)
T ss_dssp             EEEECCC
T ss_pred             EEEcCCC
Confidence            9999994

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.66  E-value=2.1e-16  Score=110.65  Aligned_cols=110  Identities=16%  Similarity=0.172  Sum_probs=71.7

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCce------EEEEeCCHHHHHHHHHh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVR------TVKYYGNAIERKALQSE   74 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~------~~~~~g~~~~~~~~~~~   74 (169)
                      +.++.-++|+|||..++..+.....  ..+++|||+|. .+..||.++++++.....      ...+.+...........
T Consensus        60 ~~~i~apTGsGKT~~~~~~~~~~~~--~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  137 (237)
T d1gkub1          60 SFAATAPTGVGKTSFGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFM  137 (237)
T ss_dssp             CEECCCCBTSCSHHHHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHH
T ss_pred             CEEEEecCCChHHHHHHHHHHHHHH--hcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhh
Confidence            4578889999999876655444333  34689999997 688899999998864321      22333322222111111


Q ss_pred             hhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchhccccccccEEEEeCCcccCC
Q psy1090          75 ALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKN  134 (169)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~~~~~~~~~vi~DEah~~k~  134 (169)
                      ..                  ....++ +++|++.+.+....+.  .++++|+||+|.+-.
T Consensus       138 ~~------------------~~~~~I-lv~Tp~~l~~~~~~~~--~~~~vVvDE~d~~l~  176 (237)
T d1gkub1         138 QN------------------LRNFKI-VITTTQFLSKHYRELG--HFDFIFVDDVDAILK  176 (237)
T ss_dssp             HS------------------GGGCSE-EEEEHHHHHHCSTTSC--CCSEEEESCHHHHHT
T ss_pred             cc------------------ccccce-eccChHHHHHhhhhcC--CCCEEEEEChhhhhh
Confidence            11                  144667 9999998877655443  678999999998643

>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=99.52  E-value=5.5e-14  Score=96.38  Aligned_cols=135  Identities=16%  Similarity=0.163  Sum_probs=87.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhcCC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALSLP   79 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~   79 (169)
                      .++...+|+|||+..+..+......+....+||+||. .+..|..+.+.++.  .+.++..+.|...........     
T Consensus        45 ~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-----  119 (208)
T d1hv8a1          45 IVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL-----  119 (208)
T ss_dssp             EEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH-----
T ss_pred             eeeechhcccccceeecccccccccccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc-----
Confidence            3556799999998876665544444444579999998 66778888888776  356777777765444333211     


Q ss_pred             CcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhccc-cccEEEE
Q psy1090          80 TIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-ATFKVLL  154 (169)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~~~~~~l  154 (169)
                                      ...++ +++|++.+.+...  .+.-....++|+||||++-+.+  ....+.+..++ ....+++
T Consensus       120 ----------------~~~~I-lV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~  182 (208)
T d1hv8a1         120 ----------------KNANI-VVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLF  182 (208)
T ss_dssp             ----------------HTCSE-EEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEE
T ss_pred             ----------------CCCCE-EEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCCChHHHHHHHHhCCCCCeEEEE
Confidence                            33566 9999887754322  2223456799999999864432  22334444554 3457888


Q ss_pred             eccCC
Q psy1090         155 TGWYY  159 (169)
Q Consensus       155 T~TP~  159 (169)
                      |||..
T Consensus       183 SAT~~  187 (208)
T d1hv8a1         183 SATMP  187 (208)
T ss_dssp             CSSCC
T ss_pred             EccCC
Confidence            99953

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.48  E-value=7.8e-14  Score=95.34  Aligned_cols=135  Identities=15%  Similarity=0.044  Sum_probs=82.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      ++++...+|+|||..+...+.     ...+++++++|. .+..|+.++++.+.........................   
T Consensus        42 ~vlv~apTGsGKT~~~~~~~~-----~~~~~~~~v~P~~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  113 (206)
T d1oywa2          42 DCLVVMPTGGGKSLCYQIPAL-----LLNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRT---  113 (206)
T ss_dssp             CEEEECSCHHHHHHHHHHHHH-----HSSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHH---
T ss_pred             CEEEEcCCCCCCcchhhhhhh-----hccCceEEeccchhhhhhHHHHHHhhcccccccccccccccchhHHHHHhc---
Confidence            468889999999976543322     234689999998 66779999998886333322222333333222222221   


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhc--hhccccccccEEEEeCCcccCCcccH---HH----HHHhccccccE
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIEND--FGFLKKITWNCIIVDEGHSVKNKKSK---LS----IKLTALRATFK  151 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~--~~~~~~~~~~~vi~DEah~~k~~~~~---~~----~~~~~l~~~~~  151 (169)
                                     ...++ ++++...+...  ........++++|+||+|.+......   .+    .....+.....
T Consensus       114 ---------------~~~~i-~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~~~~~~~~~~~~l~~~~~~~~i  177 (206)
T d1oywa2         114 ---------------GQIRL-LYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPF  177 (206)
T ss_dssp             ---------------TCCSE-EEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCE
T ss_pred             ---------------CCceE-EEEechhhhchhhcccchhheeeeeeeeeeeeeeccccchHHHHHHHHHHHHhCCCCce
Confidence                           55566 78887766433  22334456889999999987654321   11    11222345568


Q ss_pred             EEEeccCCC
Q psy1090         152 VLLTGWYYP  160 (169)
Q Consensus       152 ~~lT~TP~~  160 (169)
                      ++||||+-.
T Consensus       178 i~lSATl~~  186 (206)
T d1oywa2         178 MALTATADD  186 (206)
T ss_dssp             EEEESCCCH
T ss_pred             EEEEeCCCH
Confidence            999999754

>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=99.40  E-value=3.1e-13  Score=97.21  Aligned_cols=127  Identities=14%  Similarity=0.080  Sum_probs=74.9

Q ss_pred             ccccCCCCCcHHHHHH-HHHHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhcCCC
Q psy1090           3 TVIPDPTRYRKSGKVI-AFFCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPT   80 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i-~~i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~   80 (169)
                      +++...+|+|||...+ +++......  ..++||++|. .+..||.++++............+                 
T Consensus        12 ~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~-----------------   72 (305)
T d2bmfa2          12 TIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRA-----------------   72 (305)
T ss_dssp             EEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBCCC----------------------
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEee-----------------
Confidence            5788999999997654 333333333  3579999998 677899988875532111111000                 


Q ss_pred             cccccccCCccccccCCCCeEEEecHHHHHhchhc-cccccccEEEEeCCcccCCcccHHHHHHhcc---ccccEEEEec
Q psy1090          81 IKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF-LKKITWNCIIVDEGHSVKNKKSKLSIKLTAL---RATFKVLLTG  156 (169)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~-~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l---~~~~~~~lT~  156 (169)
                                  .......+ +++++..+...... ....+++++|+||+|++..........+..+   .....+++||
T Consensus        73 ------------~~~~~~~i-~~~t~~~l~~~~~~~~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~~~~~~~~v~~SA  139 (305)
T d2bmfa2          73 ------------EHTGREIV-DLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTA  139 (305)
T ss_dssp             ---------------CCCSE-EEEEHHHHHHHHTSSSCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEECS
T ss_pred             ------------cccCcccc-ccCCcHHHHHHHhcCccccceeEEEeeeeeecchhhHHHHHHHHHhhccccceEEEeec
Confidence                        00133445 88888887654321 1224689999999998853222111122222   3356789999


Q ss_pred             cCCCC
Q psy1090         157 WYYPN  161 (169)
Q Consensus       157 TP~~n  161 (169)
                      ||...
T Consensus       140 T~~~~  144 (305)
T d2bmfa2         140 TPPGS  144 (305)
T ss_dssp             SCTTC
T ss_pred             CCCcc
Confidence            99654

>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=99.39  E-value=2.1e-12  Score=88.33  Aligned_cols=144  Identities=13%  Similarity=0.129  Sum_probs=87.1

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.++..++|+|||...+--+...... .....++|++|. .+..|..+.+..+.   +........|.............
T Consensus        40 dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~  119 (207)
T d1t6na_          40 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK  119 (207)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHH
T ss_pred             CeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHh
Confidence            46788999999998755433322222 223368999998 56667777777766   34556666665444333332221


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcccH---HHHHHhccc-ccc
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKKSK---LSIKLTALR-ATF  150 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~~~---~~~~~~~l~-~~~  150 (169)
                                         ...++ +++|++.+......  +.-....++|+||||.+-.....   ....++.++ ...
T Consensus       120 -------------------~~~~i-lI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q  179 (207)
T d1t6na_         120 -------------------NCPHI-VVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ  179 (207)
T ss_dssp             -------------------SCCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSE
T ss_pred             -------------------cCCCE-EEeCcchhhhhccCCceeccccceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCE
Confidence                               45677 99999988764432  22234569999999987542111   122333443 345


Q ss_pred             EEEEeccCCCCCchhh
Q psy1090         151 KVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       151 ~~~lT~TP~~n~~~el  166 (169)
                      .+++|||.. +++.++
T Consensus       180 ~il~SAT~~-~~v~~l  194 (207)
T d1t6na_         180 VMMFSATLS-KEIRPV  194 (207)
T ss_dssp             EEEEESCCC-TTTHHH
T ss_pred             EEEEeeeCC-HHHHHH
Confidence            678899964 444443

>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=99.38  E-value=2.1e-12  Score=89.08  Aligned_cols=137  Identities=14%  Similarity=0.091  Sum_probs=87.7

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHhCCCCceEEEecC-cchHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.+..-++|+|||+..+--+. .+.........+|++|. .+..|-.+++.++.  .++++....|............  
T Consensus        56 dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~--  133 (222)
T d2j0sa1          56 DVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD--  133 (222)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH--
T ss_pred             CeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc--
Confidence            356788999999977554333 22222333468999998 56678888888876  3567777776654444333322  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCccc--HHHHHHhccc-cccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKKS--KLSIKLTALR-ATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~~--~~~~~~~~l~-~~~~~  152 (169)
                                        ...++ +++|++.+.....  .+.-....++|+||||++-+.+-  .....+..++ .+..+
T Consensus       134 ------------------~~~~I-lv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~i  194 (222)
T d2j0sa1         134 ------------------YGQHV-VAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV  194 (222)
T ss_dssp             ------------------HCCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEE
T ss_pred             ------------------cCCeE-EeCCCCcHHhcccccccccccceeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEE
Confidence                              44566 9999998865332  12223567999999998876432  2333444553 45578


Q ss_pred             EEeccCC
Q psy1090         153 LLTGWYY  159 (169)
Q Consensus       153 ~lT~TP~  159 (169)
                      ++|||-.
T Consensus       195 lfSAT~~  201 (222)
T d2j0sa1         195 LISATLP  201 (222)
T ss_dssp             EEESCCC
T ss_pred             EEEEeCC
Confidence            8899974

>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=99.33  E-value=8.3e-12  Score=85.19  Aligned_cols=142  Identities=12%  Similarity=0.092  Sum_probs=87.0

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHhCCCCceEEEecC-cchHHHHHHHHHhC---CCceEEEEeCCHHHHHHHHHhhh
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEEQALEPNLIVCPL-SVLNNWEAEFRKFA---PFVRTVKYYGNAIERKALQSEAL   76 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~---~~~~~~~~~g~~~~~~~~~~~~~   76 (169)
                      +.++..++|+|||+..+--+. ..........+||++|. .+..|-.+++.++.   .........|............ 
T Consensus        42 dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~-  120 (206)
T d1veca_          42 DILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-  120 (206)
T ss_dssp             CEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTT-
T ss_pred             CEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHH-
Confidence            467889999999977554433 32233334478999998 45556666666554   4556666666544433332221 


Q ss_pred             cCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-ccccE
Q psy1090          77 SLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RATFK  151 (169)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~~~~  151 (169)
                                         ...++ +++|++.+.....  .+.-....++|+||||.+-+.+  ......+..+ +....
T Consensus       121 -------------------~~~~i-vv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~  180 (206)
T d1veca_         121 -------------------DTVHV-VIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQI  180 (206)
T ss_dssp             -------------------SCCSE-EEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEE
T ss_pred             -------------------hccCe-EEeCCccccccccchhccccccceEEEeccccccccchHHHHHHHHHhCCCCCEE
Confidence                               55677 9999988765432  2223356799999999876543  2233334455 34557


Q ss_pred             EEEeccCCCCCchh
Q psy1090         152 VLLTGWYYPNKWSK  165 (169)
Q Consensus       152 ~~lT~TP~~n~~~e  165 (169)
                      +++|||-. +.+.+
T Consensus       181 ~l~SAT~~-~~v~~  193 (206)
T d1veca_         181 LLYSATFP-LSVQK  193 (206)
T ss_dssp             EEEESCCC-HHHHH
T ss_pred             EEEEecCC-HHHHH
Confidence            88899974 33443

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.27  E-value=1.9e-11  Score=85.11  Aligned_cols=143  Identities=17%  Similarity=0.216  Sum_probs=90.0

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhC---------CCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQ---------ALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIER   68 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~---------~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~   68 (169)
                      +.++..++|+|||+..+-- +..+....         ....+||++|. .+..|..+++..+..  .+++....|.....
T Consensus        60 dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~  139 (238)
T d1wrba1          60 DIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTH  139 (238)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSH
T ss_pred             CEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhh
Confidence            4678899999999885544 44443221         12358999998 677888888887763  46667776654433


Q ss_pred             HHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHh
Q psy1090          69 KALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLT  144 (169)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~  144 (169)
                      .......                    ...++ +++|++.+.....  .+.-....++|+||+|.+-..+  ......++
T Consensus       140 ~~~~~~~--------------------~~~~i-vV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~~f~~~i~~Il~  198 (238)
T d1wrba1         140 SQIREVQ--------------------MGCHL-LVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIE  198 (238)
T ss_dssp             HHHHHHS--------------------SCCSE-EEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHH
T ss_pred             HHHhhcc--------------------cCCce-eecCHHHHHhHHccCceeccccceeeeehhhhhhhhccHHHHHHHHH
Confidence            3322211                    55677 9999999876432  2223466799999999765432  22334444


Q ss_pred             ccc-----cccEEEEeccCCCCCchhh
Q psy1090         145 ALR-----ATFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       145 ~l~-----~~~~~~lT~TP~~n~~~el  166 (169)
                      .++     .+..+++|||. .+++.++
T Consensus       199 ~~~~~~~~~~Q~il~SAT~-~~~v~~l  224 (238)
T d1wrba1         199 ESNMPSGINRQTLMFSATF-PKEIQKL  224 (238)
T ss_dssp             SSCCCCGGGCEEEEEESSC-CHHHHHH
T ss_pred             HhcCCCCCCCEEEEEeeeC-CHHHHHH
Confidence            432     23568999995 4444444

>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=99.27  E-value=2.7e-12  Score=88.39  Aligned_cols=139  Identities=14%  Similarity=0.136  Sum_probs=83.2

Q ss_pred             CccccCCCCCcHHHHHHHHHH-HHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC-KIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~-~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.+++-++|+|||+..+--+. .+........+||++|. .+..|-.+++.++..  ........+........      
T Consensus        51 dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------  124 (218)
T d2g9na1          51 DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEV------  124 (218)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTT------
T ss_pred             CEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHH------
Confidence            357788999999988654433 33223334468999998 566788888887763  33444433322111100      


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcccc-ccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTALRA-TFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~~-~~~~  152 (169)
                                   ........++ +++|++.+.....  ...-....++|+||||.+-+.+  ......+..++. ...+
T Consensus       125 -------------~~~~~~~~~I-vV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~i  190 (218)
T d2g9na1         125 -------------QKLQMEAPHI-IVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV  190 (218)
T ss_dssp             -------------TSSSSCCCSE-EEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEE
T ss_pred             -------------HHHhcCCCEE-EEeCChhHHHHHhcCCcccccceEEEeeecchhhcCchHHHHHHHHHhCCCCCeEE
Confidence                         0011145677 9999988765432  2233456799999999876543  223334455543 5577


Q ss_pred             EEeccCCC
Q psy1090         153 LLTGWYYP  160 (169)
Q Consensus       153 ~lT~TP~~  160 (169)
                      ++|||-..
T Consensus       191 l~SAT~~~  198 (218)
T d2g9na1         191 LLSATMPS  198 (218)
T ss_dssp             EEESCCCH
T ss_pred             EEEecCCH
Confidence            88999854

>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=99.22  E-value=6.5e-11  Score=80.61  Aligned_cols=142  Identities=14%  Similarity=0.108  Sum_probs=85.5

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCCceEEEecCcc-hHHHHHHHHHhC--CCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALEPNLIVCPLSV-LNNWEAEFRKFA--PFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~~~Liv~P~~~-l~qW~~e~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.++..++|+|||...+.- +.....+......++++|... ..+-......+.  .++++....|............  
T Consensus        40 dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~--  117 (206)
T d1s2ma1          40 DILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLN--  117 (206)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTT--
T ss_pred             CEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhc--
Confidence            3578899999999765432 332222333446788888744 434333333333  4778888887655443333221  


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc--cHHHHHHhccc-cccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-ATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~~~~~  152 (169)
                                        ...++ +++|+..+.+....  +.-....++|+||||.+-+.+  ......++.++ .+..+
T Consensus       118 ------------------~~~~I-li~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~i  178 (206)
T d1s2ma1         118 ------------------ETVHI-LVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSL  178 (206)
T ss_dssp             ------------------SCCSE-EEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEE
T ss_pred             ------------------ccceE-EEECCcccccccccceeecccceEEEeechhhhhhhhhHHHHHHHHHhCCCCCEEE
Confidence                              55677 99999988764432  222355789999999987532  22333444554 45578


Q ss_pred             EEeccCCCCCchh
Q psy1090         153 LLTGWYYPNKWSK  165 (169)
Q Consensus       153 ~lT~TP~~n~~~e  165 (169)
                      ++|||- ...+.+
T Consensus       179 l~SATl-~~~v~~  190 (206)
T d1s2ma1         179 LFSATF-PLTVKE  190 (206)
T ss_dssp             EEESCC-CHHHHH
T ss_pred             EEEEeC-CHHHHH
Confidence            889995 334443

>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=99.21  E-value=2.1e-11  Score=83.49  Aligned_cols=142  Identities=15%  Similarity=0.120  Sum_probs=81.0

Q ss_pred             CccccCCCCCcHHHHHHHH-HHHHHHhCCCCceEEEecC-cchHHHHHHHHHhCC--CceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAF-FCKIIEEQALEPNLIVCPL-SVLNNWEAEFRKFAP--FVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~-i~~~~~~~~~~~~Liv~P~-~~l~qW~~e~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      +.++...+|+|||...+-- +..+......-.++|++|. .+..|-...+..+..  ........+..........    
T Consensus        49 dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  124 (212)
T d1qdea_          49 DVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG----  124 (212)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC--------------
T ss_pred             CEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHH----
Confidence            3578899999999875533 3333223333478999998 555666666665553  3344444443322221111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHHHHhchhc--cccccccEEEEeCCcccCCcc--cHHHHHHhccc-cccEE
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFGF--LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALR-ATFKV  152 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~~--~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l~-~~~~~  152 (169)
                                       ....++ +++|++.+......  +.-....++|+||||.+-+.+  ....+.+..++ ....+
T Consensus       125 -----------------~~~~~I-vI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~v  186 (212)
T d1qdea_         125 -----------------LRDAQI-VVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVV  186 (212)
T ss_dssp             -----------------CTTCSE-EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEE
T ss_pred             -----------------hcCCcE-EEECCCccccccccCceecCcceEEeehhhhhhcccchHHHHHHHHHhCCCCCeEE
Confidence                             144577 99999888764322  223357799999999876432  22333344453 45578


Q ss_pred             EEeccCCCCCchhh
Q psy1090         153 LLTGWYYPNKWSKQ  166 (169)
Q Consensus       153 ~lT~TP~~n~~~el  166 (169)
                      ++|||-. +++.++
T Consensus       187 l~SAT~~-~~v~~l  199 (212)
T d1qdea_         187 LLSATMP-NDVLEV  199 (212)
T ss_dssp             EEESSCC-HHHHHH
T ss_pred             EEEeeCC-HHHHHH
Confidence            8999973 334443

>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=98.97  E-value=9.3e-10  Score=74.80  Aligned_cols=143  Identities=17%  Similarity=0.213  Sum_probs=78.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHh-CCCCceEEEecCcch-H---HHHHHHHHhCC---CceEEEEeCCHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEE-QALEPNLIVCPLSVL-N---NWEAEFRKFAP---FVRTVKYYGNAIERKALQS   73 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~-~~~~~~Liv~P~~~l-~---qW~~e~~~~~~---~~~~~~~~g~~~~~~~~~~   73 (169)
                      +.++..++|+|||+..+..+...... ......++++|.... .   ++.....++..   ........+......... 
T Consensus        40 dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  118 (209)
T d1q0ua_          40 SMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALE-  118 (209)
T ss_dssp             CEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTC-
T ss_pred             CeEeecccccccceeeeeeeccccccccccccccccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHH-
Confidence            35788999999998654443332222 333466777776433 2   33333333331   233333343332211100 


Q ss_pred             hhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcccCCcc--cHHHHHHhcc-cc
Q psy1090          74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHSVKNKK--SKLSIKLTAL-RA  148 (169)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~~k~~~--~~~~~~~~~l-~~  148 (169)
                                         ......++ +++|++.+.....  ........++|+||||.+-+.+  ......+..+ +.
T Consensus       119 -------------------~~~~~~~I-lv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~  178 (209)
T d1q0ua_         119 -------------------KLNVQPHI-VIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKD  178 (209)
T ss_dssp             -------------------CCSSCCSE-EEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTT
T ss_pred             -------------------HhccCceE-EEecCchhhhhhhhhccccccceEEEEeecccccccccHHHHHHHHHHCCCC
Confidence                               01155677 9999998865332  2223467789999999876543  2233444555 34


Q ss_pred             ccEEEEeccCCCCCchhh
Q psy1090         149 TFKVLLTGWYYPNKWSKQ  166 (169)
Q Consensus       149 ~~~~~lT~TP~~n~~~el  166 (169)
                      ...+++|||- .+++.++
T Consensus       179 ~Q~il~SATl-~~~v~~l  195 (209)
T d1q0ua_         179 LQMLVFSATI-PEKLKPF  195 (209)
T ss_dssp             CEEEEEESCC-CGGGHHH
T ss_pred             CEEEEEEccC-CHHHHHH
Confidence            5578889996 4455544

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.88  E-value=0.00017  Score=52.24  Aligned_cols=44  Identities=18%  Similarity=0.197  Sum_probs=33.2

Q ss_pred             cccccEEEEeCCcccCCcccHHHHHHhccccccEEEEeccCCCCCc
Q psy1090         118 KITWNCIIVDEGHSVKNKKSKLSIKLTALRATFKVLLTGWYYPNKW  163 (169)
Q Consensus       118 ~~~~~~vi~DEah~~k~~~~~~~~~~~~l~~~~~~~lT~TP~~n~~  163 (169)
                      ..+++++|+||+..+-  .......+..+....+++|.|=|-|-.+
T Consensus       259 ~l~~d~lIIDEaSmv~--~~l~~~ll~~~~~~~~lILvGD~~QLpp  302 (359)
T d1w36d1         259 PLHLDVLVVDEASMID--LPMMSRLIDALPDHARVIFLGDRDQLAS  302 (359)
T ss_dssp             CCSCSEEEECSGGGCB--HHHHHHHHHTCCTTCEEEEEECTTSGGG
T ss_pred             ccccceeeehhhhccC--HHHHHHHHHHhcCCCEEEEECChhhccC
Confidence            4578999999999873  3344566777777889999998876533

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=97.68  E-value=0.0002  Score=49.39  Aligned_cols=132  Identities=8%  Similarity=-0.066  Sum_probs=74.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch----HHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhhhc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL----NNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALS   77 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l----~qW~~e~~~~~~~~~~~~~~g~~~~~~~~~~~~~~   77 (169)
                      |.|.-..+|=|||+++...+......+  +++=||..+.-+    .+|...+-+|+ ++.+...............    
T Consensus        95 G~iaem~TGEGKTL~a~l~a~l~al~g--~~vhvvTvNdyLA~RDae~m~~iy~~l-Glsvg~~~~~~~~~~r~~~----  167 (273)
T d1tf5a3          95 GNIAEMKTGEGKTLTSTLPVYLNALTG--KGVHVVTVNEYLASRDAEQMGKIFEFL-GLTVGLNLNSMSKDEKREA----  167 (273)
T ss_dssp             TSEEECCTTSCHHHHHHHHHHHHHTTS--SCEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTSCHHHHHHH----
T ss_pred             hhheeecCCCcchhHHHHHHHHHHhcC--CCceEEecCccccchhhhHHhHHHHHc-CCCccccccccCHHHHHHH----
Confidence            567778999999987644433322222  456666666444    27999998888 6777665543322221111    


Q ss_pred             CCCcccccccCCccccccCCCCeEEEecHHH-----HHhc----hhccccccccEEEEeCCcccCCcc------------
Q psy1090          78 LPTIKVPAKKGKTKKQISLKLPLILVTTPQI-----IEND----FGFLKKITWNCIIVDEGHSVKNKK------------  136 (169)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~-----~~~~----~~~~~~~~~~~vi~DEah~~k~~~------------  136 (169)
                                        -.+|| +-.|.+.     ++.+    .+...+.++.++|+||+..+--+.            
T Consensus       168 ------------------Y~~di-~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~  228 (273)
T d1tf5a3         168 ------------------YAADI-TYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSM  228 (273)
T ss_dssp             ------------------HHSSE-EEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEE
T ss_pred             ------------------hhCCc-eecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCcc
Confidence                              34566 4444333     3332    223334578899999988543221            


Q ss_pred             ---cHHHHHHhccccccEEEEeccCCC
Q psy1090         137 ---SKLSIKLTALRATFKVLLTGWYYP  160 (169)
Q Consensus       137 ---~~~~~~~~~l~~~~~~~lT~TP~~  160 (169)
                         +..++.+..+ .++.-+||||-..
T Consensus       229 ~~a~it~q~~f~~-y~~l~gmtgta~~  254 (273)
T d1tf5a3         229 TLATITFQNYFRM-YEKLAGMTGTAKT  254 (273)
T ss_dssp             EEEEEEHHHHHTT-SSEEEEEESCCGG
T ss_pred             chhhhhHHHHHHH-HHHHhCCccccHH
Confidence               1123333332 3577899999753

>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=96.68  E-value=0.00073  Score=45.83  Aligned_cols=23  Identities=17%  Similarity=0.297  Sum_probs=18.4

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|-...|+|||..+-+++..+.
T Consensus        36 lll~Gp~G~GKTt~~~~la~~l~   58 (252)
T d1sxje2          36 LLLYGPNGTGKKTRCMALLESIF   58 (252)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhhc
Confidence            46778999999998888776553

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.38  E-value=0.0038  Score=45.74  Aligned_cols=52  Identities=13%  Similarity=0.250  Sum_probs=39.4

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEE
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKY   61 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~   61 (169)
                      |..=+|+|||+.+.+++...     .+|+|||+|+. ...||.+++..|.|+-.+..+
T Consensus        36 l~GltGS~ka~~iA~l~~~~-----~rp~LVVt~n~~~A~qL~~dL~~~l~~~~v~~f   88 (413)
T d1t5la1          36 LLGATGTGKTFTISNVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYF   88 (413)
T ss_dssp             EEECTTSCHHHHHHHHHHHH-----TCCEEEECSSHHHHHHHHHHHHHHCTTSEEEEE
T ss_pred             EeCCCCcHHHHHHHHHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHcCCCceeec
Confidence            44458999998876665432     47999999985 457999999999977666554

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.07  E-value=0.015  Score=35.52  Aligned_cols=35  Identities=17%  Similarity=0.056  Sum_probs=25.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ++.-.|.+|||...|..+..+...  .++++++-|..
T Consensus         6 li~GpMfsGKTt~Li~~~~~~~~~--g~~v~~ikp~~   40 (133)
T d1xbta1           6 VILGPMFSGKSTELMRRVRRFQIA--QYKCLVIKYAK   40 (133)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTT--TCCEEEEEETT
T ss_pred             EEEecccCHHHHHHHHHHHHHHHc--CCcEEEEeccc
Confidence            356789999999888776654433  36788888874

>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=95.80  E-value=0.13  Score=33.82  Aligned_cols=105  Identities=17%  Similarity=0.139  Sum_probs=69.3

Q ss_pred             CCCCceEEEecC-cchHHHHHHHHHhCCCceEEEEeCCHHH--HHHHHHhhhcCCCcccccccCCccccccCCCCeEEEe
Q psy1090          28 QALEPNLIVCPL-SVLNNWEAEFRKFAPFVRTVKYYGNAIE--RKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVT  104 (169)
Q Consensus        28 ~~~~~~Liv~P~-~~l~qW~~e~~~~~~~~~~~~~~g~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~  104 (169)
                      ...+.+.+|||. .-+.+..+.+.+.+|+.++...+|.-..  +...-.....                  ++.++ +++
T Consensus        29 ~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~------------------g~~~I-Lv~   89 (211)
T d2eyqa5          29 LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHH------------------QRFNV-LVC   89 (211)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHT------------------TSCCE-EEE
T ss_pred             HcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHc------------------CCcce-EEE
Confidence            556899999997 5778888999999999999999995433  3333332222                  77888 666


Q ss_pred             cHHHHHhchhccccccccEEEEeCCcccCCcccHHHHHHhcc----ccccEEEEecc
Q psy1090         105 TPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTAL----RATFKVLLTGW  157 (169)
Q Consensus       105 ty~~~~~~~~~~~~~~~~~vi~DEah~~k~~~~~~~~~~~~l----~~~~~~~lT~T  157 (169)
                      |- .+..-.+   --+-..+|+..|+++.  -++.++.-.++    ...+.++++.-
T Consensus        90 Tt-vIEvGiD---vpnA~~iiI~~a~rfG--LaQLhQLRGRVGR~~~~s~c~l~~~~  140 (211)
T d2eyqa5          90 TT-IIETGID---IPTANTIIIERADHFG--LAQLHQLRGRVGRSHHQAYAWLLTPH  140 (211)
T ss_dssp             SS-TTGGGSC---CTTEEEEEETTTTSSC--HHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             eh-hhhhccC---CCCCcEEEEecchhcc--ccccccccceeeecCccceEEEEecC
Confidence            62 1111111   1234589999999984  56667766666    34556777643

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=95.63  E-value=0.0066  Score=41.81  Aligned_cols=38  Identities=16%  Similarity=0.252  Sum_probs=24.4

Q ss_pred             cEEEEeCCcccCCcc------cHHHHHHhcc--ccccEEEEeccCC
Q psy1090         122 NCIIVDEGHSVKNKK------SKLSIKLTAL--RATFKVLLTGWYY  159 (169)
Q Consensus       122 ~~vi~DEah~~k~~~------~~~~~~~~~l--~~~~~~~lT~TP~  159 (169)
                      -++++||.|.+-+.+      ......++..  +...+++.+.||-
T Consensus       112 iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~e  157 (268)
T d1r6bx2         112 SILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQ  157 (268)
T ss_dssp             EEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHH
T ss_pred             ceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHH
Confidence            468899999884321      1234455533  5667888888873

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=95.49  E-value=0.049  Score=36.37  Aligned_cols=23  Identities=4%  Similarity=-0.107  Sum_probs=17.7

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      +|..++|+|||..+..++..+..
T Consensus        38 Ll~Gp~G~GKtt~a~~~~~~l~~   60 (239)
T d1njfa_          38 LFSGTRGVGKTSIARLLAKGLNC   60 (239)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHC
T ss_pred             EEECCCCCcHHHHHHHHHHHhcC
Confidence            56788999999888877666543

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=95.40  E-value=0.0092  Score=39.32  Aligned_cols=24  Identities=8%  Similarity=0.062  Sum_probs=19.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEE   27 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~   27 (169)
                      +|..+.|+|||..+..++..+...
T Consensus        28 Ll~Gp~G~GKtt~a~~~a~~l~~~   51 (207)
T d1a5ta2          28 LIQALPGMGDDALIYALSRYLLCQ   51 (207)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHTCS
T ss_pred             EEECCCCCcHHHHHHHHHHhcccc
Confidence            568889999999998888776533

>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=95.33  E-value=0.0096  Score=39.49  Aligned_cols=58  Identities=2%  Similarity=-0.013  Sum_probs=32.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHhCC--CceEEEEeC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAP--FVRTVKYYG   63 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~~~--~~~~~~~~g   63 (169)
                      .|.-.+|+|||.+..-++..+..++  .++.+++-..-=..=.++++.|..  ++.+.....
T Consensus        13 ~lvGptGvGKTTTiAKLA~~~~~~g--~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~   72 (211)
T d2qy9a2          13 LMVGVNGVGKTTTIGKLARQFEQQG--KSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHT   72 (211)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTTT--CCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCST
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEecccccccchhhhhhhhhhcCCccccccc
Confidence            3578899999999988866554332  455555543221122344544442  444443333

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.79  E-value=0.077  Score=34.50  Aligned_cols=22  Identities=5%  Similarity=-0.140  Sum_probs=15.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      ++..+.|+|||..++.+...+.
T Consensus        19 l~~G~~g~gk~~~a~~l~~~i~   40 (198)
T d2gnoa2          19 LINGEDLSYPREVSLELPEYVE   40 (198)
T ss_dssp             EEECSSSSHHHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHh
Confidence            4566788888877777765543

>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=94.76  E-value=0.026  Score=38.81  Aligned_cols=50  Identities=6%  Similarity=-0.044  Sum_probs=33.6

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC--CCCceEEEecCcc-hHHHHHHHHHh
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ--ALEPNLIVCPLSV-LNNWEAEFRKF   52 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~--~~~~~Liv~P~~~-l~qW~~e~~~~   52 (169)
                      .++.-..|+|||.+++.-+.++....  ..+.+|+++++.. ...-.+.+.+.
T Consensus        17 ~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~   69 (306)
T d1uaaa1          17 CLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQT   69 (306)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             EEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHh
Confidence            34556799999999887776665542  3457999999854 44444555444

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.37  E-value=0.028  Score=37.11  Aligned_cols=23  Identities=13%  Similarity=0.184  Sum_probs=17.3

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      .+|...+|+|||..+-.++..+.
T Consensus        39 ~ll~Gp~G~GKTt~a~~la~~l~   61 (224)
T d1sxjb2          39 MIISGMPGIGKTTSVHCLAHELL   61 (224)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCchhhHHHHHHHHh
Confidence            46778899999988877766544

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.36  E-value=0.18  Score=33.05  Aligned_cols=41  Identities=10%  Similarity=0.097  Sum_probs=24.4

Q ss_pred             cccEEEEeCCcccCCcccHHHHHHhc----cccccEEEEeccCCC
Q psy1090         120 TWNCIIVDEGHSVKNKKSKLSIKLTA----LRATFKVLLTGWYYP  160 (169)
Q Consensus       120 ~~~~vi~DEah~~k~~~~~~~~~~~~----l~~~~~~~lT~TP~~  160 (169)
                      ..+++++|+.|.+.+........+..    ......+++|+.-.+
T Consensus        97 ~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence            56899999999986532221112222    245667777776443

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=94.08  E-value=0.053  Score=39.43  Aligned_cols=52  Identities=19%  Similarity=0.259  Sum_probs=38.6

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEE
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKY   61 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~   61 (169)
                      |..-.|++|++.+.+++...     .+|+|||||.. ...+|.+++..|.++..+..+
T Consensus        33 L~GlsgS~ka~~~A~l~~~~-----~rp~LvVt~~~~~A~~l~~dL~~~l~~~~v~~f   85 (408)
T d1c4oa1          33 LLGATGTGKTVTMAKVIEAL-----GRPALVLAPNKILAAQLAAEFRELFPENAVEYF   85 (408)
T ss_dssp             EEECTTSCHHHHHHHHHHHH-----TCCEEEEESSHHHHHHHHHHHHHHCTTSEEEEC
T ss_pred             EecCCCCHHHHHHHHHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHhcCccceeeC
Confidence            44568999998776655432     36999999985 557999999999876665553

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=94.04  E-value=0.26  Score=31.89  Aligned_cols=110  Identities=11%  Similarity=0.074  Sum_probs=61.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCC----CCceEEEe-cCcch------HHHHHHHHHhC-----CCceEEEEeCCH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQA----LEPNLIVC-PLSVL------NNWEAEFRKFA-----PFVRTVKYYGNA   65 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~----~~~~Liv~-P~~~l------~qW~~e~~~~~-----~~~~~~~~~g~~   65 (169)
                      +.+|.-|+|.|||..+=+++..+.....    .++.++.. +..++      .+|.+.+....     ..-+++.|...-
T Consensus        45 n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDei  124 (195)
T d1jbka_          45 NPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDEL  124 (195)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETG
T ss_pred             CeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchH
Confidence            3678899999999877777666655332    12444444 45554      47887765433     122444444221


Q ss_pred             H-------------HHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCC
Q psy1090          66 I-------------ERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEG  129 (169)
Q Consensus        66 ~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEa  129 (169)
                      .             ..+.+...-                  ..+...+|..+|++.+.+...  .-....|..+-++|-
T Consensus       125 h~l~~~g~~~g~~d~~~~Lkp~L------------------~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep  185 (195)
T d1jbka_         125 HTMVGAGKADGAMDAGNMLKPAL------------------ARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEP  185 (195)
T ss_dssp             GGGTT------CCCCHHHHHHHH------------------HTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCC
T ss_pred             HHHhcCCCCCCcccHHHHHHHHH------------------hCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCC
Confidence            1             112222211                  126777777888888765332  222346778888884

>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=94.00  E-value=0.073  Score=34.92  Aligned_cols=34  Identities=9%  Similarity=-0.038  Sum_probs=23.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecC
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPL   39 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~   39 (169)
                      +|.-.+|.|||.++.-++.++..++  .++.+++..
T Consensus        14 ~lvGp~GvGKTTTiaKLA~~~~~~g--~kV~lit~D   47 (207)
T d1ls1a2          14 FLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAAD   47 (207)
T ss_dssp             EEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEecc
Confidence            4578899999999888876665443  456655554

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=93.70  E-value=0.035  Score=36.09  Aligned_cols=31  Identities=13%  Similarity=-0.083  Sum_probs=24.0

Q ss_pred             cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           6 PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         6 ~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      +-.+|.|||..++.++..+.+++  .+++++=|
T Consensus         8 gt~~GVGKTtvs~~La~aLa~~G--~rVl~id~   38 (224)
T d1byia_           8 GTDTEVGKTVASCALLQAAKAAG--YRTAGYKP   38 (224)
T ss_dssp             ESSTTSCHHHHHHHHHHHHHHTT--CCEEEECS
T ss_pred             ECCCCccHHHHHHHHHHHHHHCC--CeEEEECc
Confidence            44579999999999988877765  56777643

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.58  E-value=0.025  Score=37.42  Aligned_cols=21  Identities=14%  Similarity=0.289  Sum_probs=16.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~   24 (169)
                      +|..++|+|||..+-+++..+
T Consensus        37 ll~Gp~G~GKTtl~~~i~~~l   57 (237)
T d1sxjd2          37 LFYGPPGTGKTSTILALTKEL   57 (237)
T ss_dssp             EEECSTTSSHHHHHHHHHHHH
T ss_pred             EEECCCCCChHHHHHHHHHHH
Confidence            677889999998887777654

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=93.48  E-value=0.063  Score=35.54  Aligned_cols=47  Identities=11%  Similarity=-0.023  Sum_probs=34.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHHh
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRKF   52 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~~   52 (169)
                      ++.-++|+|||..++.++.....  ...+++.++......++.+....+
T Consensus        30 li~G~pGsGKT~l~~qia~~~~~--~~~~~~~is~e~~~~~~~~~~~~~   76 (242)
T d1tf7a2          30 LATGATGTGKTLLVSRFVENACA--NKERAILFAYEESRAQLLRNAYSW   76 (242)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHT--TTCCEEEEESSSCHHHHHHHHHTT
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHH--hccccceeeccCCHHHHHHHHHHc
Confidence            56779999999998888776543  346788888776666776666654

>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=93.33  E-value=0.033  Score=38.61  Aligned_cols=38  Identities=11%  Similarity=-0.032  Sum_probs=27.5

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCC--CCceEEEecCcc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQA--LEPNLIVCPLSV   41 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~--~~~~Liv~P~~~   41 (169)
                      ++.-..|+|||.+++.-+.++...+.  ...+|+++++..
T Consensus        28 lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~   67 (318)
T d1pjra1          28 LIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNK   67 (318)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHH
T ss_pred             EEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHH
Confidence            34456899999999887776665542  347899998853

>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=93.25  E-value=0.13  Score=34.10  Aligned_cols=20  Identities=10%  Similarity=0.041  Sum_probs=15.5

Q ss_pred             ccccCCCCCcHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFC   22 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~   22 (169)
                      .+|...+|+|||..+-+++.
T Consensus        55 lll~GPpG~GKTt~a~~la~   74 (253)
T d1sxja2          55 AMLYGPPGIGKTTAAHLVAQ   74 (253)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56778999999987766553

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=92.84  E-value=0.64  Score=33.29  Aligned_cols=124  Identities=14%  Similarity=0.060  Sum_probs=57.9

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCC----CceEEEe-cCcch------HHHHHHHHHhC-----CCceEEEEeCCH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQAL----EPNLIVC-PLSVL------NNWEAEFRKFA-----PFVRTVKYYGNA   65 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~----~~~Liv~-P~~~l------~qW~~e~~~~~-----~~~~~~~~~g~~   65 (169)
                      +.+|..|+|.|||..+=+++..+......    ++.++.. +..++      .+|.+.+....     ..-+++.|...-
T Consensus        45 n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~  124 (387)
T d1qvra2          45 NPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDEL  124 (387)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC
T ss_pred             CCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccH
Confidence            46788999999998776676666554322    2334444 44544      36776664432     123454443221


Q ss_pred             HHHHHHHHhhhcCCCcccccccCCccccccCCCCeEEEecHHHHHhchh--ccccccccEEEEeCCcc
Q psy1090          66 IERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDFG--FLKKITWNCIIVDEGHS  131 (169)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~ty~~~~~~~~--~~~~~~~~~vi~DEah~  131 (169)
                      ..-.......     ...+...-..+.-..+...+|..||++.++. ..  .-..-.|..|-++|-..
T Consensus       125 h~l~~~g~~~-----g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         125 HTVVGAGKAE-----GAVDAGNMLKPALARGELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             ------------------------HHHHHTTCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCH
T ss_pred             HHHhcCCCCC-----CcccHHHHHHHHHhCCCcceeeecCHHHHHH-hcccHHHHHhcccccCCCCcH
Confidence            1100000000     0000000001111227777778888887753 22  12234678888988653

>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=92.79  E-value=0.056  Score=33.80  Aligned_cols=38  Identities=5%  Similarity=-0.060  Sum_probs=26.3

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +.+|.-+.|+|||..+-.++..+...+ ..-..+.|+..
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~~~-~~v~~~~~~~~   40 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKSSG-VPVDGFYTEEV   40 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHTT-CCCEEEECCEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCC-CEEEEEEeccc
Confidence            457788999999998888887766554 23345555543

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=92.64  E-value=0.056  Score=36.89  Aligned_cols=28  Identities=18%  Similarity=0.125  Sum_probs=21.7

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      -=|.|||.++.++...+.+.+  +++|+|-
T Consensus        16 KGGVGKTTvaa~lA~~lA~~G--~rVLlvD   43 (296)
T d1ihua1          16 KGGVGKTSISCATAIRLAEQG--KRVLLVS   43 (296)
T ss_dssp             STTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             CCcChHHHHHHHHHHHHHHCC--CCEEEEe
Confidence            349999999988877776654  6788776

>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=92.30  E-value=0.068  Score=35.08  Aligned_cols=33  Identities=3%  Similarity=-0.073  Sum_probs=23.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      .|.-.+|+|||.++.-+..++...+  +++.+|+-
T Consensus        10 ~lvGptGvGKTTTiaKLA~~~~~~g--~kV~lit~   42 (207)
T d1okkd2          10 LVVGVNGVGKTTTIAKLGRYYQNLG--KKVMFCAG   42 (207)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHTTT--CCEEEECC
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEEe
Confidence            4578899999999988876554333  45555554

>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=92.14  E-value=0.094  Score=34.56  Aligned_cols=36  Identities=8%  Similarity=-0.047  Sum_probs=23.4

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      +|.-.+|.|||.+..-++..+..++ .+..||-+-..
T Consensus        15 ~lvGptGvGKTTTiAKLAa~~~~~~-~kV~lit~Dt~   50 (213)
T d1vmaa2          15 MVVGVNGTGKTTSCGKLAKMFVDEG-KSVVLAAADTF   50 (213)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTT-CCEEEEEECTT
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC-CceEEEeeccc
Confidence            4677899999999888876654433 33344444443

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=91.50  E-value=0.093  Score=35.53  Aligned_cols=31  Identities=6%  Similarity=-0.037  Sum_probs=22.4

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.--=|.|||.++..+...+.+.+  +++|+|-
T Consensus        25 ~sGKGGVGKTT~a~nLA~~lA~~G--~rVllvD   55 (279)
T d1ihua2          25 LMGKGGVGKTTMAAAIAVRLADMG--FDVHLTT   55 (279)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCC--CcEEEEe
Confidence            344569999999988877776654  5666665

>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=90.81  E-value=0.12  Score=33.97  Aligned_cols=36  Identities=6%  Similarity=-0.041  Sum_probs=18.9

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      .|.-.+|+|||.+..-++..+..++ .+..||-+-..
T Consensus        16 ~lvGptGvGKTTTiAKLA~~~~~~g-~kV~lit~Dt~   51 (211)
T d1j8yf2          16 MLVGVQGTGKATTAGKLAYFYKKKG-FKVGLVGADVY   51 (211)
T ss_dssp             EEECSCCC----HHHHHHHHHHHTT-CCEEEEECCCS
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC-CceEEEEeecc
Confidence            3568899999999888876655433 33334444333

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=90.63  E-value=0.13  Score=35.19  Aligned_cols=27  Identities=19%  Similarity=0.123  Sum_probs=19.7

Q ss_pred             CCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           9 TRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         9 ~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      =|.|||.+++.+...+.+.+  +++|+|=
T Consensus        11 GGVGKTT~a~NLA~~LA~~G--~rVLlID   37 (289)
T d2afhe1          11 GGIGKSTTTQNLVAALAEMG--KKVMIVG   37 (289)
T ss_dssp             TTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             CCCCHHHHHHHHHHHHHHCC--CCEEEEe
Confidence            49999999988877665544  5677664

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=90.50  E-value=0.24  Score=32.07  Aligned_cols=47  Identities=19%  Similarity=0.116  Sum_probs=30.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEFRK   51 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~~~   51 (169)
                      ++.-++|+|||..++.++......+ ..+++++............+..
T Consensus        30 ~I~G~~G~GKT~la~~~~~~~~~~~-~~~~~~~s~e~~~~~~~~~~~~   76 (242)
T d1tf7a1          30 LVSGTSGTGKTLFSIQFLYNGIIEF-DEPGVFVTFEETPQDIIKNARS   76 (242)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHHH-CCCEEEEESSSCHHHHHHHHGG
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHhc-CCCcccccccCCHHHHHHHHHH
Confidence            5677899999988887765443333 3467887776655554444443

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.35  E-value=0.14  Score=33.44  Aligned_cols=32  Identities=9%  Similarity=0.024  Sum_probs=24.1

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      +.+---|.|||..++.+...+...+  .++++|=
T Consensus         7 v~~~kGGvGKTtia~nLA~~la~~g--~~VlliD   38 (237)
T d1g3qa_           7 IVSGKGGTGKTTVTANLSVALGDRG--RKVLAVD   38 (237)
T ss_dssp             EECSSTTSSHHHHHHHHHHHHHHTT--CCEEEEE
T ss_pred             EECCCCCCcHHHHHHHHHHHHHhCC--CCEEEEe
Confidence            4455679999999999888776544  5787773

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=89.87  E-value=0.25  Score=30.19  Aligned_cols=35  Identities=20%  Similarity=0.129  Sum_probs=25.6

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ++.-.|.+|||...+..+..+...+  .+++++-|..
T Consensus        11 lI~GpMfSGKTteLi~~~~~~~~~g--~~vl~i~~~~   45 (141)
T d1xx6a1          11 VIVGPMYSGKSEELIRRIRRAKIAK--QKIQVFKPEI   45 (141)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEEEC-
T ss_pred             EEEeccccHHHHHHHHHHHHhhhcC--CcEEEEEecc
Confidence            4567899999999888776555443  5788888864

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=89.87  E-value=0.14  Score=34.48  Aligned_cols=28  Identities=11%  Similarity=0.003  Sum_probs=20.3

Q ss_pred             CCCCcHHHHHHHHHHHHHHhCCCCceEEEe
Q psy1090           8 PTRYRKSGKVIAFFCKIIEEQALEPNLIVC   37 (169)
Q Consensus         8 e~G~GKT~~~i~~i~~~~~~~~~~~~Liv~   37 (169)
                      -=|.|||.+++.+...+.+.+  .++|+|=
T Consensus         9 KGGvGKTT~a~nLA~~LA~~G--~rVllID   36 (269)
T d1cp2a_           9 KGGIGKSTTTQNLTSGLHAMG--KTIMVVG   36 (269)
T ss_dssp             CTTSSHHHHHHHHHHHHHTTT--CCEEEEE
T ss_pred             CCcCCHHHHHHHHHHHHHhCC--CcEEEEe
Confidence            349999999988877776543  5666664

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=88.38  E-value=0.37  Score=29.28  Aligned_cols=35  Identities=17%  Similarity=0.185  Sum_probs=25.2

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      ++.-.|.+|||...+-.+..+...+  ++++++-|..
T Consensus         6 ~i~GpMfsGKTteLi~~~~~~~~~~--~kv~~ikp~~   40 (139)
T d2b8ta1           6 FITGPMFAGKTAELIRRLHRLEYAD--VKYLVFKPKI   40 (139)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTT--CCEEEEEECC
T ss_pred             EEEccccCHHHHHHHHHHHHHHHCC--CcEEEEEEcc
Confidence            4567899999988887765554333  5788888864

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=87.94  E-value=0.49  Score=31.59  Aligned_cols=51  Identities=10%  Similarity=0.066  Sum_probs=33.9

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhC--------CCCceEEEecCcchHHHHHHHHHhC
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQ--------ALEPNLIVCPLSVLNNWEAEFRKFA   53 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~--------~~~~~Liv~P~~~l~qW~~e~~~~~   53 (169)
                      .+|+-+.|+|||.-++.++..+....        ..++++++.-.....++.+.+....
T Consensus        32 ~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          32 GALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALG   90 (274)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSCHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccchHHHHHHHHHHHh
Confidence            35788999999988888776544221        2246777776666666666655443

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.85  E-value=0.28  Score=31.87  Aligned_cols=30  Identities=10%  Similarity=-0.059  Sum_probs=21.7

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEE
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIV   36 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv   36 (169)
                      .+--=|.|||..+..+...+...+  .++++|
T Consensus         7 ~s~KGGvGKTtia~nlA~~la~~g--~~Vlli   36 (232)
T d1hyqa_           7 ASGKGGTGKTTITANLGVALAQLG--HDVTIV   36 (232)
T ss_dssp             EESSSCSCHHHHHHHHHHHHHHTT--CCEEEE
T ss_pred             ECCCCCChHHHHHHHHHHHHHhCC--CCEEEE
Confidence            334569999999998887776543  567766

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=87.79  E-value=0.67  Score=31.02  Aligned_cols=46  Identities=7%  Similarity=-0.124  Sum_probs=31.2

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWEAEF   49 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~~e~   49 (169)
                      .+++-.+|.|||..++.++.... .....+++++.......+....+
T Consensus        38 ~vi~G~~G~GKT~~~~~la~~~a-~~~g~~v~~~s~E~~~~~~~~r~   83 (277)
T d1cr2a_          38 IMVTSGSGMGKSTFVRQQALQWG-TAMGKKVGLAMLEESVEETAEDL   83 (277)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH-HTSCCCEEEEESSSCHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHhhh-hhcccceeEeeeccchhhHHhHH
Confidence            46788999999977776654432 23346899998876655554444

>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=86.06  E-value=0.21  Score=32.85  Aligned_cols=22  Identities=9%  Similarity=0.149  Sum_probs=16.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      +.+|.-++|+|||..|=+++..
T Consensus        37 ~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2          37 HVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             CEEEESSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHhc
Confidence            3577889999999877655543

>d2b2na1 c.37.1.19 (A:26-333) 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=85.91  E-value=1.2  Score=30.76  Aligned_cols=42  Identities=17%  Similarity=0.212  Sum_probs=28.3

Q ss_pred             HHHHHHHHhCCCCceEEEecCc-chHHHHHHHHHhCCCceEEEE
Q psy1090          19 AFFCKIIEEQALEPNLIVCPLS-VLNNWEAEFRKFAPFVRTVKY   61 (169)
Q Consensus        19 ~~i~~~~~~~~~~~~Liv~P~~-~l~qW~~e~~~~~~~~~~~~~   61 (169)
                      |++.........+|+|||||.. ...++.+++..|.+ ..+..+
T Consensus         3 a~~~a~~~~~~~~p~lvv~~~~~~A~~l~~~L~~~~~-~~v~~f   45 (308)
T d2b2na1           3 ATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTD-QMVMNL   45 (308)
T ss_dssp             HHHHHHHHHHCSSCEEEEESSHHHHHHHHHHHHTTCS-SCEEEC
T ss_pred             HHHHHHHHHhhCCCEEEEcCCHHHHHHHHHHHHhcCC-CceEEc
Confidence            4444444445568999999984 56789999987764 344443

>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=85.69  E-value=0.23  Score=32.65  Aligned_cols=56  Identities=5%  Similarity=-0.136  Sum_probs=31.0

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc--chHHHHHHHHHhCCCceEEEEe
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS--VLNNWEAEFRKFAPFVRTVKYY   62 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~--~l~qW~~e~~~~~~~~~~~~~~   62 (169)
                      +.+|.-.+|+|||..+-+++..+.     .+...+.-..  ....+...+.+......+....
T Consensus        37 ~~Ll~GPpG~GKTtla~~la~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iD   94 (239)
T d1ixsb2          37 HLLLFGPPGLGKTTLAHVIAHELG-----VNLRVTSGPAIEKPGDLAAILANSLEEGDILFID   94 (239)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHT-----CCEEEEETTTCCSHHHHHHHHHTTCCTTCEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC-----CCeEeccCCccccchhhHHHHHhhccCCCeeeee
Confidence            457888999999987766654321     2333333222  2335555565555344444444

>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=85.24  E-value=0.32  Score=32.39  Aligned_cols=23  Identities=9%  Similarity=-0.161  Sum_probs=18.0

Q ss_pred             cccCCCCCcHHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKIIE   26 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~~   26 (169)
                      ++.-++|+|||..+-+++..+.+
T Consensus        50 ~l~GppGtGKT~l~~~l~~~l~~   72 (287)
T d1w5sa2          50 GSIGRVGIGKTTLAKFTVKRVSE   72 (287)
T ss_dssp             ECTTCCSSSHHHHHHHHHHHHHH
T ss_pred             EeECCCCCCHHHHHHHHHHHHHh
Confidence            35689999999988888766543

>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=84.58  E-value=0.27  Score=32.56  Aligned_cols=22  Identities=5%  Similarity=-0.046  Sum_probs=16.7

Q ss_pred             ccccCCCCCcHHHHHHHHHHHH
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKI   24 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~   24 (169)
                      .+|..++|+|||..+=+++..+
T Consensus        46 lll~GppGtGKT~l~~~l~~~l   67 (276)
T d1fnna2          46 ATLLGRPGTGKTVTLRKLWELY   67 (276)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEECCCCCCHHHHHHHHHHHH
Confidence            5788899999997776655544

>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=84.42  E-value=0.28  Score=33.95  Aligned_cols=22  Identities=14%  Similarity=0.064  Sum_probs=17.5

Q ss_pred             CccccCCCCCcHHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      |.+|.-.+|+|||..|=+++..
T Consensus        51 ~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          51 NILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHhhc
Confidence            5678899999999888666543

>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=84.42  E-value=0.18  Score=33.71  Aligned_cols=21  Identities=14%  Similarity=0.053  Sum_probs=16.3

Q ss_pred             CccccCCCCCcHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC   22 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~   22 (169)
                      |.+|.-.+|+|||..+-+++.
T Consensus        34 ~ilL~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             EEEEECCTTSCTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            457899999999987755543

>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=83.73  E-value=0.31  Score=31.81  Aligned_cols=22  Identities=14%  Similarity=0.286  Sum_probs=17.8

Q ss_pred             cccCCCCCcHHHHHHHHHHHHH
Q psy1090           4 VIPDPTRYRKSGKVIAFFCKII   25 (169)
Q Consensus         4 iL~de~G~GKT~~~i~~i~~~~   25 (169)
                      +|..++|+|||..+-+++..+.
T Consensus        49 ll~Gp~G~GKTtla~~iak~l~   70 (231)
T d1iqpa2          49 LFAGPPGVGKTTAALALARELF   70 (231)
T ss_dssp             EEESCTTSSHHHHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHHHHH
Confidence            6788999999988887776554

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=83.51  E-value=0.53  Score=33.75  Aligned_cols=36  Identities=17%  Similarity=0.057  Sum_probs=24.5

Q ss_pred             ccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCc
Q psy1090           3 TVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLS   40 (169)
Q Consensus         3 ~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~   40 (169)
                      .++.-.+|+|||.....++......+  .+++|+=|+.
T Consensus        53 ~~I~G~tGsGKT~~l~~li~~~~~~g--~~~iiiD~kg   88 (433)
T d1e9ra_          53 LLVNGATGTGKSVLLRELAYTGLLRG--DRMVIVDPNG   88 (433)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTT--CEEEEEEETT
T ss_pred             EEEEeCCCCcHHHHHHHHHHHHHhCC--CCEEEEeCCh
Confidence            35566899999987655555554433  5677777875

>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=83.15  E-value=0.39  Score=29.37  Aligned_cols=20  Identities=5%  Similarity=-0.009  Sum_probs=14.7

Q ss_pred             CccccCCCCCcHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFF   21 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i   21 (169)
                      .-+|.-.+|+|||..+=.+.
T Consensus         6 ~I~i~G~pGsGKTTia~~La   25 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELA   25 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            45677889999997664443

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.80  E-value=0.14  Score=34.55  Aligned_cols=36  Identities=8%  Similarity=-0.016  Sum_probs=23.6

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL   42 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l   42 (169)
                      |.+|.-++|+|||..+=+++..     ...+.+.+.+..+.
T Consensus        40 giLL~GppGtGKT~l~~ala~~-----~~~~~~~i~~~~l~   75 (258)
T d1e32a2          40 GILLYGPPGTGKTLIARAVANE-----TGAFFFLINGPEIM   75 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH-----TTCEEEEECHHHHT
T ss_pred             eeEEecCCCCCchHHHHHHHHH-----hCCeEEEEEchhhc
Confidence            5678889999999765444332     23567777765543

>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=82.57  E-value=0.32  Score=32.52  Aligned_cols=21  Identities=10%  Similarity=0.126  Sum_probs=16.6

Q ss_pred             CccccCCCCCcHHHHHHHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFC   22 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~   22 (169)
                      |.+|.-++|+|||..+=+++.
T Consensus        42 ~vLL~GppGtGKT~la~alA~   62 (246)
T d1d2na_          42 SVLLEGPPHSGKTALAAKIAE   62 (246)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHhh
Confidence            568899999999987766543

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=82.54  E-value=0.18  Score=35.36  Aligned_cols=39  Identities=18%  Similarity=-0.017  Sum_probs=25.0

Q ss_pred             cc-cCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHH
Q psy1090           4 VI-PDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNW   45 (169)
Q Consensus         4 iL-~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW   45 (169)
                      +| .-++|+|||..+=++...+-   ...+.+.+-++.++..|
T Consensus       126 ~l~~G~pG~GKT~la~ala~~~~---~~~~~~~~~~~~~~~~~  165 (321)
T d1w44a_         126 VIVTGKGNSGKTPLVHALGEALG---GKDKYATVRFGEPLSGY  165 (321)
T ss_dssp             EEEECSSSSCHHHHHHHHHHHHH---TTSCCEEEEBSCSSTTC
T ss_pred             EEEECCCCccHHHHHHHHHHHhc---CCCCeEEEEhhHhhhcc
Confidence            44 59999999988877665432   12245556666666533

>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=82.34  E-value=0.37  Score=30.13  Aligned_cols=23  Identities=17%  Similarity=0.242  Sum_probs=17.1

Q ss_pred             CCccccCCCCCcHHHHHHHHHHH
Q psy1090           1 MDTVIPDPTRYRKSGKVIAFFCK   23 (169)
Q Consensus         1 ~g~iL~de~G~GKT~~~i~~i~~   23 (169)
                      |.-+|.-.+|+|||.++=.+...
T Consensus         1 m~I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           1 MRVLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            45678889999999877555443

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=81.91  E-value=0.39  Score=32.32  Aligned_cols=36  Identities=11%  Similarity=0.058  Sum_probs=24.4

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL   42 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l   42 (169)
                      |.+|--.+|+|||..+=+++..+     ..+.+.|-+..++
T Consensus        47 ~iLL~GppGtGKT~la~~iA~~~-----~~~~~~i~~~~l~   82 (256)
T d1lv7a_          47 GVLMVGPPGTGKTLLAKAIAGEA-----KVPFFTISGSDFV   82 (256)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH-----TCCEEEECSCSST
T ss_pred             eEEeeCCCCCCccHHHHHHHHHc-----CCCEEEEEhHHhh
Confidence            46788899999998776555432     2456666666554

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=81.60  E-value=0.24  Score=33.19  Aligned_cols=40  Identities=10%  Similarity=0.061  Sum_probs=27.8

Q ss_pred             CccccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcchHHHH
Q psy1090           2 DTVIPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVLNNWE   46 (169)
Q Consensus         2 g~iL~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l~qW~   46 (169)
                      |.+|.-.+|+|||..+=+++...     ..+.+.+-+..++..|.
T Consensus        44 giLl~GppGtGKT~la~aia~~~-----~~~~~~i~~~~l~~~~~   83 (247)
T d1ixza_          44 GVLLVGPPGVGKTHLARAVAGEA-----RVPFITASGSDFVEMFV   83 (247)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT-----TCCEEEEEHHHHHHSCT
T ss_pred             eEEEecCCCCChhHHHHHHHHHc-----CCCEEEEEhHHhhhccc
Confidence            46788999999998776665421     35677777777666544

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=81.24  E-value=1  Score=30.29  Aligned_cols=42  Identities=12%  Similarity=0.075  Sum_probs=28.0

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEecCcch-HHHHHH
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAE   48 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P~~~l-~qW~~e   48 (169)
                      +.-+.|+|||..++.++......  .+.++++.-.... .+|.+.
T Consensus        59 i~G~~gsGKTtl~l~~~~~~q~~--g~~~vyidtE~~~~~~~a~~  101 (263)
T d1u94a1          59 IYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIYARK  101 (263)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHHHHHH
T ss_pred             EecCCCcHHHHHHHHHHHHHHcC--CCEEEEEccccccCHHHHHH
Confidence            56799999999888877665443  3566666666444 445433

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.48  E-value=0.62  Score=31.90  Aligned_cols=34  Identities=18%  Similarity=0.195  Sum_probs=20.4

Q ss_pred             ccCCCCCcHHHHHHHHHHHHHHhCCCCceEEEec
Q psy1090           5 IPDPTRYRKSGKVIAFFCKIIEEQALEPNLIVCP   38 (169)
Q Consensus         5 L~de~G~GKT~~~i~~i~~~~~~~~~~~~Liv~P   38 (169)
                      ++-.+|+|||..+-.+...+.+.....+.+++++
T Consensus        32 i~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS   65 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYAS   65 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEE
T ss_pred             eECCCCCCHHHHHHHHHHHHHHHhCCCcceEeec
Confidence            5778999999766555555544322233444444