Psyllid ID: psy3307

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130
Protein Sequence
MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHHHcccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHHHcccccccEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHHcccccccccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccEEEEc
Coil and Loop (DISEMBL)
MQECLVSLkkqgfddiqMTEIITNNialarydkptpvqkyaIPVIIsgrdvmacaqtgsgktaAFLVPILNQmyergplptppagrgypsrkkvfplglvlapTRELATQIYDEAKKFayrsqlrpcvvl
Flexible Loop (DISEMBL)
MQECLVSLkkqgfddiqMTEIITNNialarydkptpVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKfayrsqlrpcvvl
Low Complexity Region (SEG)
MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL
Disordered region (IsUnstruct)
****LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYER***************KKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPC***
Disordered Region (DISOPRED)
****LVS*KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMY*******************VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL
Disordered Region (DISEMBL)
MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL
Disordered Region (DISPRO)
*********KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG***************KVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL
Positional Conservation
no confident homologs detected

---

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	130	2.2.26 [Sep-21-2011]
Q9VHP0	798	ATP-dependent RNA helicas	yes	N/A	0.892	0.145	0.777	8e-50
P24346	697	Putative ATP-dependent RN	N/A	N/A	0.915	0.170	0.644	3e-40
Q62095	658	ATP-dependent RNA helicas	yes	N/A	0.915	0.180	0.628	7e-40
O00571	662	ATP-dependent RNA helicas	yes	N/A	0.915	0.179	0.619	1e-39
Q62167	662	ATP-dependent RNA helicas	no	N/A	0.915	0.179	0.619	1e-39
Q5RF43	658	ATP-dependent RNA helicas	no	N/A	0.915	0.180	0.628	2e-39
P16381	660	Putative ATP-dependent RN	no	N/A	0.915	0.180	0.619	2e-39
O15523	660	ATP-dependent RNA helicas	no	N/A	0.915	0.180	0.628	2e-39
Q6GVM6	660	ATP-dependent RNA helicas	yes	N/A	0.915	0.180	0.628	3e-39
Q0CLJ6	674	ATP-dependent RNA helicas	N/A	N/A	0.907	0.175	0.603	4e-37

>sp|Q9VHP0|DDX3_DROME ATP-dependent RNA helicase bel OS=Drosophila melanogaster GN=bel PE=1 SV=1

 Score =  195 bits (495), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 297 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 356

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 357 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 412

ATP-dependent RNA helicase that is essential and required for cellular function, larval growth, and for male and female fertility. Also required for RNA interference (RNAi), double-stranded RNA induces potent and specific gene silencing, by acting downstream of dsRNA internalization. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys or silences messenger RNAs homologous to the silencing trigger.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|P24346|DDX3_XENLA Putative ATP-dependent RNA helicase an3 OS=Xenopus laevis GN=an3 PE=2 SV=1

 Score =  163 bits (413), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 78/121 (64%), Positives = 92/121 (76%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F D+ M EII  NI L RY +PTPVQK+AIP+II  RD+MACAQTGSGKTAAFL+PIL
Sbjct: 221 ESFHDVTMGEIIMGNIQLTRYTRPTPVQKHAIPIIIEKRDLMACAQTGSGKTAAFLLPIL 280

Query: 71  NQMYERGPLPTPP--AGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP          G   R+K FPL LVLAPTRELA QIY+EA+KFAYRS++RPCV
Sbjct: 281 SQIYADGPGDAMKHLQENGRYGRRKQFPLSLVLAPTRELAVQIYEEARKFAYRSRVRPCV 340

Query: 129 V 129
           V
Sbjct: 341 V 341

Putative ATP-dependent RNA helicase.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62095|DDX3Y_MOUSE ATP-dependent RNA helicase DDX3Y OS=Mus musculus GN=Ddx3y PE=1 SV=2

 Score =  162 bits (409), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 76/121 (62%), Positives = 94/121 (77%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F DI+M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 179 ENFSDIEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 238

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 239 SQIYTDGPGEALKAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 298

Query: 129 V 129
           V
Sbjct: 299 V 299

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O00571|DDX3X_HUMAN ATP-dependent RNA helicase DDX3X OS=Homo sapiens GN=DDX3X PE=1 SV=3

 Score =  161 bits (407), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 75/121 (61%), Positives = 94/121 (77%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 180 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 239

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 240 SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 299

Query: 129 V 129
           V
Sbjct: 300 V 300

ATP-dependent RNA helicase. Acts as a cofactor for XPO1-mediated nuclear export of incompletely spliced HIV-1 Rev RNAs. Also involved in HIV-1 replication. Interacts specifically with hepatitis C virus core protein resulting in a change in intracellular location.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62167|DDX3X_MOUSE ATP-dependent RNA helicase DDX3X OS=Mus musculus GN=Ddx3x PE=1 SV=3

 Score =  160 bits (406), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 75/121 (61%), Positives = 94/121 (77%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 180 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 239

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 240 SQIYADGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 299

Query: 129 V 129
           V
Sbjct: 300 V 300

Putative ATP-dependent RNA helicase. It may play a role in translational activation of mRNA in the oocyte and early embryo.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RF43|DDX3Y_PONAB ATP-dependent RNA helicase DDX3Y OS=Pongo abelii GN=DDX3Y PE=2 SV=1

 Score =  160 bits (406), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 76/121 (62%), Positives = 93/121 (76%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F DI M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 178 ENFSDIDMGEIIMGNIELTRYTRPTPVQKHAIPIIKGKRDLMACAQTGSGKTAAFLLPIL 237

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 238 SQIYTDGPGEALKAVKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 297

Query: 129 V 129
           V
Sbjct: 298 V 298

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P16381|DDX3L_MOUSE Putative ATP-dependent RNA helicase Pl10 OS=Mus musculus GN=D1Pas1 PE=1 SV=1

 Score =  160 bits (406), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 75/121 (61%), Positives = 94/121 (77%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 179 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 238

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 239 SQIYTDGPGEALRAMKENGKYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 298

Query: 129 V 129
           V
Sbjct: 299 V 299

Putative ATP-dependent RNA helicase. Possible role in a key step of the spermatogenic process.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O15523|DDX3Y_HUMAN ATP-dependent RNA helicase DDX3Y OS=Homo sapiens GN=DDX3Y PE=1 SV=2

 Score =  160 bits (406), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 76/121 (62%), Positives = 93/121 (76%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F DI M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 178 ENFSDIDMGEIIMGNIELTRYTRPTPVQKHAIPIIKGKRDLMACAQTGSGKTAAFLLPIL 237

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 238 SQIYTDGPGEALKAVKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 297

Query: 129 V 129
           V
Sbjct: 298 V 298

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6GVM6|DDX3Y_PANTR ATP-dependent RNA helicase DDX3Y OS=Pan troglodytes GN=DDX3Y PE=2 SV=1

 Score =  160 bits (404), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 76/121 (62%), Positives = 93/121 (76%), Gaps = 2/121 (1%)

Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F DI M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 178 ENFGDIDMGEIIMGNIQLTRYTRPTPVQKHAIPIIKGKRDLMACAQTGSGKTAAFLLPIL 237

Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 238 SQIYTDGPGEALKAVKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 297

Query: 129 V 129
           V
Sbjct: 298 V 298

Probable ATP-dependent RNA helicase. May play a role in spermatogenesis.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0CLJ6|DED1_ASPTN ATP-dependent RNA helicase ded1 OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) GN=ded1 PE=3 SV=1

 Score =  152 bits (385), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 73/121 (60%), Positives = 95/121 (78%), Gaps = 3/121 (2%)

Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
            F +  + + + +NIALARY  PTPVQKY+IP++++GRD+MACAQTGSGKT  FL PIL+
Sbjct: 187 AFTNPPLDDHLISNIALARYLTPTPVQKYSIPIVMNGRDLMACAQTGSGKTGGFLFPILS 246

Query: 72  QMYERGPLPTP-PAG--RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           Q ++ GP PTP PAG   GY  ++K +P  L+LAPTREL +QI+DEA+KFAYRS +RPCV
Sbjct: 247 QAFQNGPSPTPAPAGGQLGYGRQRKAYPTSLILAPTRELVSQIFDEARKFAYRSWVRPCV 306

Query: 129 V 129
           V
Sbjct: 307 V 307

ATP-binding RNA helicase involved in translation initiation. Remodels RNA in response to ADP and ATP concentrations by facilitating disruption, but also formation of RNA duplexes.

Aspergillus terreus (strain NIH 2624 / FGSC A1156) (taxid: 341663)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	130
195499159	792	bel [Drosophila yakuba] gi|194182931|gb|	0.892	0.146	0.786	2e-48
442618017	801	belle, isoform B [Drosophila melanogaste	0.892	0.144	0.777	4e-48
195330652	797	GM26328 [Drosophila sechellia] gi|194120	0.892	0.145	0.777	5e-48
17985987	798	belle, isoform A [Drosophila melanogaste	0.892	0.145	0.777	6e-48
19528473	798	RE28061p [Drosophila melanogaster]	0.892	0.145	0.777	6e-48
194745552	784	GF16329 [Drosophila ananassae] gi|190628	0.892	0.147	0.777	7e-48
194903791	793	GG17436 [Drosophila erecta] gi|190652642	0.892	0.146	0.777	7e-48
195395963	817	GJ11034 [Drosophila virilis] gi|19414331	0.892	0.141	0.786	1e-47
195452372	802	GK14071 [Drosophila willistoni] gi|19416	0.892	0.144	0.769	2e-47
195054323	799	GH22875 [Drosophila grimshawi] gi|193895	0.892	0.145	0.786	2e-47

>gi|195499159|ref|XP_002096830.1| bel [Drosophila yakuba] gi|194182931|gb|EDW96542.1| bel [Drosophila yakuba]

 Score =  196 bits (498), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 92/117 (78%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQKYAIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 292 FDDVQLTEIIRNNVALARYDKPTPVQKYAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 351

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 352 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 407

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442618017|ref|NP_001262379.1| belle, isoform B [Drosophila melanogaster] gi|440217205|gb|AGB95761.1| belle, isoform B [Drosophila melanogaster]

 Score =  195 bits (496), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 297 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 356

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 357 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 412

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195330652|ref|XP_002032017.1| GM26328 [Drosophila sechellia] gi|194120960|gb|EDW43003.1| GM26328 [Drosophila sechellia]

 Score =  195 bits (496), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 296 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 355

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 356 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 411

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17985987|ref|NP_536783.1| belle, isoform A [Drosophila melanogaster] gi|74947986|sp|Q9VHP0.1|DDX3_DROME RecName: Full=ATP-dependent RNA helicase bel; AltName: Full=Protein belle gi|7299061|gb|AAF54262.1| belle, isoform A [Drosophila melanogaster]

 Score =  195 bits (495), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 297 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 356

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 357 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 412

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|19528473|gb|AAL90351.1| RE28061p [Drosophila melanogaster]

 Score =  195 bits (495), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 297 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 356

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 357 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 412

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194745552|ref|XP_001955251.1| GF16329 [Drosophila ananassae] gi|190628288|gb|EDV43812.1| GF16329 [Drosophila ananassae]

 Score =  194 bits (494), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 104/117 (88%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ LARYDKPTPVQKYAIP+IISGRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 287 FDDVQLTEIIRNNVNLARYDKPTPVQKYAIPIIISGRDLMACAQTGSGKTAAFLVPILNQ 346

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G    P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 347 MYEHGHSAPPQSNRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 402

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194903791|ref|XP_001980939.1| GG17436 [Drosophila erecta] gi|190652642|gb|EDV49897.1| GG17436 [Drosophila erecta]

 Score =  194 bits (494), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 91/117 (77%), Positives = 107/117 (91%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 292 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 351

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 352 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 407

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195395963|ref|XP_002056603.1| GJ11034 [Drosophila virilis] gi|194143312|gb|EDW59715.1| GJ11034 [Drosophila virilis]

 Score =  194 bits (492), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 92/117 (78%), Positives = 104/117 (88%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ LARYDKPTPVQKYAIP+IISGRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 306 FDDVQLTEIIRNNVNLARYDKPTPVQKYAIPIIISGRDLMACAQTGSGKTAAFLVPILNQ 365

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G    P + R Y SR+K FPLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 366 MYEHGLSAPPQSNRQY-SRRKQFPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 421

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195452372|ref|XP_002073325.1| GK14071 [Drosophila willistoni] gi|194169410|gb|EDW84311.1| GK14071 [Drosophila willistoni]

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 90/117 (76%), Positives = 104/117 (88%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ LARYDKPTPVQKYAIP+IISGRD+MACAQTGSGKTAAFL+PILNQ
Sbjct: 298 FDDVQLTEIIRNNVNLARYDKPTPVQKYAIPIIISGRDLMACAQTGSGKTAAFLLPILNQ 357

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G    P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 358 MYEHGISSPPQSNRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 413

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195054323|ref|XP_001994075.1| GH22875 [Drosophila grimshawi] gi|193895945|gb|EDV94811.1| GH22875 [Drosophila grimshawi]

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 92/117 (78%), Positives = 103/117 (88%), Gaps = 1/117 (0%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+Q+TEII NN+ LARYDKPTPVQKYAIP+IISGRD+MACAQTGSGKTAAFLVPILNQ
Sbjct: 295 FDDVQLTEIIRNNVNLARYDKPTPVQKYAIPIIISGRDLMACAQTGSGKTAAFLVPILNQ 354

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           MYE G L  PP      SR+K FPLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct: 355 MYEHG-LSAPPQNNRQYSRRKQFPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 410

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	130
FB|FBgn0263231	798	bel "belle" [Drosophila melano	0.892	0.145	0.777	9.5e-45
UNIPROTKB|F1NIX2	636	DDX3X "Uncharacterized protein	0.915	0.187	0.631	3.1e-35
ZFIN|ZDB-GENE-030131-1565	709	ddx3 "DEAD (Asp-Glu-Ala-Asp) b	0.915	0.167	0.619	6.6e-35
MGI|MGI:1349406	658	Ddx3y "DEAD (Asp-Glu-Ala-Asp)	0.915	0.180	0.628	1.3e-34
UNIPROTKB|F1NIX1	638	DDX3X "Uncharacterized protein	0.915	0.186	0.628	1.5e-34
UNIPROTKB|G5E631	661	DDX3X "Uncharacterized protein	0.915	0.180	0.619	1.7e-34
UNIPROTKB|F1RX16	661	DDX3X "Uncharacterized protein	0.915	0.180	0.619	1.7e-34
UNIPROTKB|J9P0V9	662	DDX3X "Uncharacterized protein	0.915	0.179	0.619	1.7e-34
UNIPROTKB|O00571	662	DDX3X "ATP-dependent RNA helic	0.915	0.179	0.619	1.7e-34
UNIPROTKB|I3LDV0	667	DDX3Y "Uncharacterized protein	0.915	0.178	0.619	1.8e-34

FB|FBgn0263231 bel "belle" [Drosophila melanogaster (taxid:7227)]

 Score = 477 (173.0 bits), Expect = 9.5e-45, P = 9.5e-45
 Identities = 91/117 (77%), Positives = 107/117 (91%)

Query:    13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
             FDD+Q+TEII NN+ALARYDKPTPVQK+AIP+II+GRD+MACAQTGSGKTAAFLVPILNQ
Sbjct:   297 FDDVQLTEIIRNNVALARYDKPTPVQKHAIPIIINGRDLMACAQTGSGKTAAFLVPILNQ 356

Query:    73 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
             MYE G +P P + R Y SR+K +PLGLVLAPTRELATQI++EAKKFAYRS++RP V+
Sbjct:   357 MYELGHVPPPQSTRQY-SRRKQYPLGLVLAPTRELATQIFEEAKKFAYRSRMRPAVL 412

GO:0007286 "spermatid development" evidence=IMP

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

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0043186 "P granule" evidence=IDA

GO:0007283 "spermatogenesis" evidence=IMP

GO:0002168 "instar larval development" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP

GO:0016442 "RNA-induced silencing complex" evidence=IDA

GO:0016246 "RNA interference" evidence=IMP

GO:0005811 "lipid particle" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0043025 "neuronal cell body" evidence=IDA

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0000070 "mitotic sister chromatid segregation" evidence=IMP

UNIPROTKB|F1NIX2 DDX3X "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 386 (140.9 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 77/122 (63%), Positives = 93/122 (76%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D+ M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   156 ESFSDVDMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 215

Query:    71 NQMYERGP---LPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPC 127
             +Q+Y  GP   L    A  G   R+K +P+ LVLAPTRELA QIY+EA+KFAYRS++RPC
Sbjct:   216 SQIYADGPGDALRAMKATNGRYGRRKQYPISLVLAPTRELAVQIYEEARKFAYRSRVRPC 275

Query:   128 VV 129
             VV
Sbjct:   276 VV 277

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

ZFIN|ZDB-GENE-030131-1565 ddx3 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3" [Danio rerio (taxid:7955)]

 Score = 385 (140.6 bits), Expect = 6.6e-35, P = 6.6e-35
 Identities = 78/126 (61%), Positives = 95/126 (75%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D+ M EII  NI L+RY +PTPVQKYAIP+I + RD+MACAQTGSGKTAAFL+P+L
Sbjct:   223 ESFHDVDMGEIIMGNITLSRYTRPTPVQKYAIPIIKTKRDLMACAQTGSGKTAAFLLPVL 282

Query:    71 NQMYERGP---LPTPPAG----RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ 123
             +Q+Y  GP   L    A      G   R+K +P+ LVLAPTRELA QIYDEA+KFAYRS+
Sbjct:   283 SQIYSEGPGEALQATKASTQQENGKYVRRKQYPISLVLAPTRELALQIYDEARKFAYRSR 342

Query:   124 LRPCVV 129
             +RPCVV
Sbjct:   343 VRPCVV 348

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:1349406 Ddx3y "DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked" [Mus musculus (taxid:10090)]

 Score = 381 (139.2 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 76/121 (62%), Positives = 94/121 (77%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F DI+M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   179 ENFSDIEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 238

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct:   239 SQIYTDGPGEALKAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 298

Query:   129 V 129
             V
Sbjct:   299 V 299

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|F1NIX1 DDX3X "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 380 (138.8 bits), Expect = 1.5e-34, P = 1.5e-34
 Identities = 76/121 (62%), Positives = 93/121 (76%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D+ M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   158 ESFSDVDMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 217

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KFAYRS++RPCV
Sbjct:   218 SQIYADGPGDALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFAYRSRVRPCV 277

Query:   129 V 129
             V
Sbjct:   278 V 278

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|G5E631 DDX3X "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 380 (138.8 bits), Expect = 1.7e-34, P = 1.7e-34
 Identities = 75/121 (61%), Positives = 94/121 (77%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   179 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 238

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct:   239 SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 298

Query:   129 V 129
             V
Sbjct:   299 V 299

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IEA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IEA

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0045948 "positive regulation of translational initiation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043024 "ribosomal small subunit binding" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=IEA

GO:0035613 "RNA stem-loop binding" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0031333 "negative regulation of protein complex assembly" evidence=IEA

GO:0030308 "negative regulation of cell growth" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1RX16 DDX3X "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 380 (138.8 bits), Expect = 1.7e-34, P = 1.7e-34
 Identities = 75/121 (61%), Positives = 94/121 (77%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   180 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 239

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct:   240 SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 299

Query:   129 V 129
             V
Sbjct:   300 V 300

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IEA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IEA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IEA

GO:0071470 "cellular response to osmotic stress" evidence=IEA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IEA

GO:0048027 "mRNA 5'-UTR binding" evidence=IEA

GO:0045948 "positive regulation of translational initiation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043024 "ribosomal small subunit binding" evidence=IEA

GO:0042256 "mature ribosome assembly" evidence=IEA

GO:0035613 "RNA stem-loop binding" evidence=IEA

GO:0034063 "stress granule assembly" evidence=IEA

GO:0031333 "negative regulation of protein complex assembly" evidence=IEA

GO:0030308 "negative regulation of cell growth" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0009615 "response to virus" evidence=IEA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IEA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0007243 "intracellular protein kinase cascade" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|J9P0V9 DDX3X "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 380 (138.8 bits), Expect = 1.7e-34, P = 1.7e-34
 Identities = 75/121 (61%), Positives = 94/121 (77%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   180 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 239

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct:   240 SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 299

Query:   129 V 129
             V
Sbjct:   300 V 300

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|O00571 DDX3X "ATP-dependent RNA helicase DDX3X" [Homo sapiens (taxid:9606)]

 Score = 380 (138.8 bits), Expect = 1.7e-34, P = 1.7e-34
 Identities = 75/121 (61%), Positives = 94/121 (77%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   180 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 239

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct:   240 SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 299

Query:   129 V 129
             V
Sbjct:   300 V 300

GO:0005524 "ATP binding" evidence=IEA

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

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005741 "mitochondrial outer membrane" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0030307 "positive regulation of cell growth" evidence=IMP

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IDA

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=IMP

GO:0045948 "positive regulation of translational initiation" evidence=IMP

GO:0031333 "negative regulation of protein complex assembly" evidence=IDA

GO:0008190 "eukaryotic initiation factor 4E binding" evidence=IDA

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0034063 "stress granule assembly" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0071470 "cellular response to osmotic stress" evidence=IDA

GO:0071243 "cellular response to arsenic-containing substance" evidence=IDA

GO:2001243 "negative regulation of intrinsic apoptotic signaling pathway" evidence=IMP

GO:0007059 "chromosome segregation" evidence=IMP

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0031369 "translation initiation factor binding" evidence=IDA

GO:0042256 "mature ribosome assembly" evidence=IMP

GO:0043024 "ribosomal small subunit binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0016887 "ATPase activity" evidence=IDA

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

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA

GO:0009615 "response to virus" evidence=IDA

GO:0007243 "intracellular protein kinase cascade" evidence=IDA

GO:0032728 "positive regulation of interferon-beta production" evidence=TAS

GO:0045087 "innate immune response" evidence=IMP

GO:0071651 "positive regulation of chemokine (C-C motif) ligand 5 production" evidence=TAS

GO:0035613 "RNA stem-loop binding" evidence=IDA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

GO:0048027 "mRNA 5'-UTR binding" evidence=IDA

GO:0008134 "transcription factor binding" evidence=IDA

GO:0030308 "negative regulation of cell growth" evidence=IDA

GO:0008625 "extrinsic apoptotic signaling pathway via death domain receptors" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0043154 "negative regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IMP

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IMP

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IMP

GO:0043065 "positive regulation of apoptotic process" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006200 "ATP catabolic process" evidence=IDA

UNIPROTKB|I3LDV0 DDX3Y "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 380 (138.8 bits), Expect = 1.8e-34, P = 1.8e-34
 Identities = 75/121 (61%), Positives = 94/121 (77%)

Query:    11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
             + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct:   181 ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 240

Query:    71 NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
             +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct:   241 SQIYTDGPGEALKAVKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 300

Query:   129 V 129
             V
Sbjct:   301 V 301

GO:0005737 "cytoplasm" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6GVM6	DDX3Y_PANTR	3, ., 6, ., 4, ., 1, 3	0.6280	0.9153	0.1803	yes	N/A
Q6CLR3	DED1_KLULA	3, ., 6, ., 4, ., 1, 3	0.5726	0.8923	0.1850	yes	N/A
P0CQ74	DED1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.5929	0.8307	0.1695	yes	N/A
Q9VHP0	DDX3_DROME	3, ., 6, ., 4, ., 1, 3	0.7777	0.8923	0.1453	yes	N/A
Q6BU54	DED1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.5688	0.8307	0.1714	yes	N/A
Q75B50	DED1_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5897	0.8846	0.1845	yes	N/A
A2QI25	DED1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5537	0.9076	0.1740	yes	N/A
Q6CB69	DED1_YARLI	3, ., 6, ., 4, ., 1, 3	0.6016	0.9076	0.1909	yes	N/A
Q2UGK3	DED1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.5619	0.9076	0.1748	yes	N/A
Q8TFK8	DED1_CANGA	3, ., 6, ., 4, ., 1, 3	0.5555	0.8923	0.1880	yes	N/A
A3LQ01	DED1_PICST	3, ., 6, ., 4, ., 1, 3	0.5625	0.8538	0.1715	yes	N/A
O00571	DDX3X_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6198	0.9153	0.1797	yes	N/A
Q4I7K4	DED1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.5663	0.8615	0.1659	yes	N/A
O13370	DED1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5675	0.8230	0.1682	yes	N/A
Q54QS3	DDX3_DICDI	3, ., 6, ., 4, ., 1, 3	0.5254	0.8846	0.1615	yes	N/A
P24784	DBP1_YEAST	3, ., 6, ., 4, ., 1, 3	0.5641	0.8923	0.1880	yes	N/A
Q4WP13	DED1_ASPFU	3, ., 6, ., 4, ., 1, 3	0.5619	0.9076	0.1750	yes	N/A
Q62095	DDX3Y_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6280	0.9153	0.1808	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	130
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-41
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	5e-34
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	3e-26
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-23
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-23
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-21
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-21
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-19
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	5e-19
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-18
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-17
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-15
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	1e-14
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	4e-14
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-14
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	3e-11
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-10
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	2e-08
COG1205	851	COG1205, COG1205, Distinct helicase family with a	9e-07
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	0.002
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	0.002

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

 Score =  136 bits (345), Expect = 1e-41
 Identities = 47/117 (40%), Positives = 68/117 (58%), Gaps = 14/117 (11%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F+++ ++  +   I    ++KPTP+Q  AIP ++SGRDV+  AQTGSGKTAAFL+PIL +
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +        P A              L+LAPTRELA QI + A+K    + L+  V+
Sbjct: 61  LDPSPKKDGPQA--------------LILAPTRELALQIAEVARKLGKHTNLKVVVI 103

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

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

 Score =  122 bits (309), Expect = 5e-34
 Identities = 44/122 (36%), Positives = 66/122 (54%), Gaps = 15/122 (12%)

Query: 9   KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
               F  + ++  +   +    +++PTP+Q  AIP+I++GRDV+  AQTG+GKTAAFL+P
Sbjct: 27  TPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLP 86

Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA-YRSQLRPC 127
           +L ++ +        A              L+LAPTRELA QI +E +K       LR  
Sbjct: 87  LLQKILKSVERKYVSA--------------LILAPTRELAVQIAEELRKLGKNLGGLRVA 132

Query: 128 VV 129
           VV
Sbjct: 133 VV 134

Length = 513

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

 Score = 96.2 bits (240), Expect = 3e-26
 Identities = 45/95 (47%), Positives = 54/95 (56%), Gaps = 16/95 (16%)

Query: 35  TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 94
           TP+Q  AIP I+SG+DV+  A TGSGKT AFL+PIL  +                  KK 
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLP----------------KKG 44

Query: 95  FPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
            P  LVLAPTRELA QIY+E KK      LR  ++
Sbjct: 45  GPQALVLAPTRELAEQIYEELKKLFKILGLRVALL 79

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

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

 Score = 92.9 bits (231), Expect = 2e-23
 Identities = 47/117 (40%), Positives = 67/117 (57%), Gaps = 10/117 (8%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD + ++  I   +A   Y +PTP+Q+ AIP ++ GRD+MA AQTG+GKTA F +P+L  
Sbjct: 3   FDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQH 62

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +  R P      GR  P R       L+L PTRELA QI +  + ++    +R  VV
Sbjct: 63  LITRQP---HAKGR-RPVR------ALILTPTRELAAQIGENVRDYSKYLNIRSLVV 109

Length = 456

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

 Score = 91.9 bits (229), Expect = 6e-23
 Identities = 42/112 (37%), Positives = 63/112 (56%), Gaps = 12/112 (10%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F ++++ E +   +    Y +PT +Q  AIP  + GRDV+  A TG+GKTAAFL+P L  
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL 124
           + +            +P RK   P  L+L PTRELA Q+ D+A++ A  + L
Sbjct: 63  LLD------------FPRRKSGPPRILILTPTRELAMQVADQARELAKHTHL 102

Length = 434

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

 Score = 88.7 bits (220), Expect = 1e-21
 Identities = 41/109 (37%), Positives = 58/109 (53%), Gaps = 13/109 (11%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F    +   +  N+  A Y+ PTP+Q  AIP  +SGR ++  A TGSGKTA+FLVPI+++
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182

Query: 73  --MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
                 G             ++   PL +VL PTREL  Q+ D+AK   
Sbjct: 183 CCTIRSG---------HPSEQRN--PLAMVLTPTRELCVQVEDQAKVLG 220

Length = 518

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

 Score = 84.5 bits (209), Expect = 2e-21
 Identities = 36/106 (33%), Positives = 46/106 (43%), Gaps = 18/106 (16%)

Query: 26  IALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA 84
           I    ++   P QK AI  ++SG RDV+  A TGSGKT A L+P L  +           
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRV--- 57

Query: 85  GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL 130
                         LVL PTRELA Q  +E KK      L+   + 
Sbjct: 58  --------------LVLVPTRELAEQWAEELKKLGPSLGLKVVGLY 89

Length = 201

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

 Score = 82.9 bits (205), Expect = 1e-19
 Identities = 47/129 (36%), Positives = 64/129 (49%), Gaps = 24/129 (18%)

Query: 5   LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA 64
           +VS +   F D  +  +           +PTP+Q    P+ +SGRD++  A+TGSGKT A
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFT-----EPTPIQVQGWPIALSGRDMIGIAETGSGKTLA 183

Query: 65  FLVP----ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY 120
           FL+P    I  Q     PL     G          P+ LVLAPTRELA QI ++  KF  
Sbjct: 184 FLLPAIVHINAQ-----PLLRYGDG----------PIVLVLAPTRELAEQIREQCNKFGA 228

Query: 121 RSQLRPCVV 129
            S++R  V 
Sbjct: 229 SSKIRNTVA 237

Length = 545

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

 Score = 80.8 bits (200), Expect = 5e-19
 Identities = 42/118 (35%), Positives = 62/118 (52%), Gaps = 9/118 (7%)

Query: 8   LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLV 67
           L +Q F D  +   +   +    +   TP+Q  A+P+ ++GRDV   AQTG+GKT AFL 
Sbjct: 5   LTEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLT 64

Query: 68  PILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
              +       L + PA      RK   P  L++APTRELA QI+ +A+  A  + L+
Sbjct: 65  ATFHY------LLSHPAPED---RKVNQPRALIMAPTRELAVQIHADAEPLAQATGLK 113

Length = 423

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

 Score = 79.1 bits (195), Expect = 3e-18
 Identities = 42/107 (39%), Positives = 59/107 (55%), Gaps = 16/107 (14%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F D+ +   I   +    Y+KP+P+Q   IP +++GRDV+  AQTGSGKTAAF +P+L+ 
Sbjct: 8   FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +               P  K   P  LVLAPTRELA Q+ +    F+
Sbjct: 68  L--------------DPELKA--PQILVLAPTRELAVQVAEAMTDFS 98

Length = 629

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

 Score = 77.3 bits (190), Expect = 1e-17
 Identities = 42/97 (43%), Positives = 55/97 (56%), Gaps = 9/97 (9%)

Query: 29  ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY 88
           A + + TP+Q   +PV + G DV   AQTG+GKT AFLV ++N++  R  L         
Sbjct: 27  AGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPAL--------- 77

Query: 89  PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
             RK   P  L+LAPTRELA QI+ +A KF     LR
Sbjct: 78  ADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLR 114

Length = 572

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

 Score = 71.4 bits (176), Expect = 1e-15
 Identities = 35/89 (39%), Positives = 52/89 (58%), Gaps = 16/89 (17%)

Query: 31  YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS 90
           Y + TP+Q  ++P I++G+DV+A A+TGSGKTAAF + +L ++                 
Sbjct: 24  YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKL--------------DVK 69

Query: 91  RKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           R +V    LVL PTRELA Q+  E ++ A
Sbjct: 70  RFRV--QALVLCPTRELADQVAKEIRRLA 96

Length = 460

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

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 30 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERGPLPTPPA 84
          ++   TP Q+YAIP I SG +V+  A TGSGKT AAFL P++N++   G       
Sbjct: 19 KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFL-PVINELLSLGKGKLEDG 73

Length = 814

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

 Score = 64.3 bits (157), Expect = 4e-14
 Identities = 27/70 (38%), Positives = 33/70 (47%), Gaps = 17/70 (24%)

Query: 49  RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA 108
           RDV+  A TGSGKT A L+PIL  +                         LVLAPTRELA
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQV-----------------LVLAPTRELA 43

Query: 109 TQIYDEAKKF 118
            Q+ +  K+ 
Sbjct: 44  NQVAERLKEL 53

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

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

 Score = 66.1 bits (161), Expect = 9e-14
 Identities = 39/107 (36%), Positives = 55/107 (51%), Gaps = 9/107 (8%)

Query: 10  KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPI 69
           K  F D  +   + + I    +   TP+Q   +   ++G D +  AQTG+GKTAAFL+ I
Sbjct: 86  KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISI 145

Query: 70  LNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK 116
           +NQ+     L TPP    Y       P  L++APTREL  QI  +A 
Sbjct: 146 INQL-----LQTPPPKERYMGE----PRALIIAPTRELVVQIAKDAA 183

Length = 475

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

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 22/49 (44%), Positives = 35/49 (71%), Gaps = 2/49 (4%)

Query: 30 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERG 77
          ++   TP Q+YAIP+I  G++V+  + TGSGKT AAFL  I+++++  G
Sbjct: 29 KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA-IIDELFRLG 76

Length = 876

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

 Score = 56.0 bits (135), Expect = 3e-10
 Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 16/99 (16%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD +++ E +   I    ++KP+ +Q+  I  I+ G D +  AQ+G+GKTA F++  L  
Sbjct: 30  FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
           +                         L+LAPTRELA QI
Sbjct: 90  I----------------DYDLNACQALILAPTRELAQQI 112

Length = 401

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 18/84 (21%)

Query: 36  PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF 95
           P Q+     ++S  +V+  A TGSGKT   L+ IL+ + E G              K V+
Sbjct: 35  PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGG-------------GKVVY 81

Query: 96  PLGLVLAPTRELATQIYDEAKKFA 119
                + P + LA + Y+E  +  
Sbjct: 82  -----IVPLKALAEEKYEEFSRLE 100

Length = 766

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

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 17/84 (20%)

Query: 38  QKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 97
           Q  A+ +I  GR+V+    TGSGKT +FL+PIL+ +               PS +     
Sbjct: 75  QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRD------------PSAR----- 117

Query: 98  GLVLAPTRELATQIYDEAKKFAYR 121
            L+L PT  LA    +  ++    
Sbjct: 118 ALLLYPTNALANDQAERLRELISD 141

Length = 851

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 27/94 (28%)

Query: 33  KPTPVQKYAIPVIISGRDVMACAQTGSGKT--AAFLVPILNQMYERGPLPTPPAGRGYPS 90
           +  P Q+ AI  ++  +  +    TGSGKT  AA L+  L +                  
Sbjct: 3   ELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAK-----------------G 45

Query: 91  RKKVFPLGLVLAPTRELATQ----IYDEAKKFAY 120
           +KKV    L + P ++L  Q    I DEA   + 
Sbjct: 46  KKKV----LFVVPRKDLLEQALVIIIDEAHHSSA 75

Length = 100

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 26/112 (23%), Positives = 42/112 (37%), Gaps = 30/112 (26%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIIS----GRDVMACAQTGSGKT--AAFL 66
             D  + E +   + +A   +  P Q+ A+  ++      R  +    TG+GKT  AA  
Sbjct: 16  LADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEA 75

Query: 67  VPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF 118
                 + E               ++      LVL PT+EL  Q  +  KKF
Sbjct: 76  ------IAEL--------------KRST----LVLVPTKELLDQWAEALKKF 103

Length = 442

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	130
PTZ00110	545	helicase; Provisional	99.95
KOG0330|consensus	476		99.95
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
KOG0331|consensus	519		99.94
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.94
KOG0340|consensus	442		99.93
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.93
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.93
KOG0346|consensus	569		99.93
KOG0338|consensus	691		99.93
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.92
KOG0334|consensus	997		99.92
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.92
KOG0348|consensus	708		99.92
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.92
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.91
KOG0345|consensus	567		99.91
KOG0343|consensus	758		99.9
PTZ00424	401	helicase 45; Provisional	99.9
KOG0347|consensus	731		99.9
KOG0335|consensus	482		99.9
KOG0333|consensus	673		99.89
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.89
KOG0342|consensus	543		99.89
KOG0339|consensus	731		99.88
KOG0326|consensus	459		99.88
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.88
KOG0328|consensus	400		99.87
KOG0341|consensus	610		99.87
KOG0337|consensus	529		99.86
KOG0344|consensus	593		99.85
PRK02362	737	ski2-like helicase; Provisional	99.83
KOG0350|consensus	620		99.82
PRK00254	720	ski2-like helicase; Provisional	99.82
KOG0336|consensus	629		99.8
KOG0327|consensus	397		99.79
KOG0329|consensus	387		99.78
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.77
PRK01172	674	ski2-like helicase; Provisional	99.76
PRK13767	876	ATP-dependent helicase; Provisional	99.74
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.73
KOG0332|consensus	477		99.73
KOG4284|consensus	980		99.71
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.69
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.67
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.66
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.66
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.66
PRK09401	1176	reverse gyrase; Reviewed	99.65
COG1205	851	Distinct helicase family with a unique C-terminal	99.65
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.65
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.64
PRK14701	1638	reverse gyrase; Provisional	99.63
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.63
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.59
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.58
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.58
PRK10689	1147	transcription-repair coupling factor; Provisional	99.57
COG1204	766	Superfamily II helicase [General function predicti	99.47
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.45
PHA02558	501	uvsW UvsW helicase; Provisional	99.4
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.39
KOG0952|consensus	1230		99.38
COG1202	830	Superfamily II helicase, archaea-specific [General	99.36
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.36
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.35
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.32
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.3
PRK05580	679	primosome assembly protein PriA; Validated	99.3
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.28
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.27
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.27
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.24
PHA02653	675	RNA helicase NPH-II; Provisional	99.22
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.16
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.13
PRK13766	773	Hef nuclease; Provisional	99.12
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.09
KOG0349|consensus	725		99.08
KOG0353|consensus	695		99.04
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.03
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.02
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.98
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.98
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.95
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.94
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.94
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.94
KOG0354|consensus	746		98.91
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.89
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.89
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.86
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.85
KOG0951|consensus	1674		98.84
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.83
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.8
KOG0352|consensus	641		98.8
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.75
PRK09694	878	helicase Cas3; Provisional	98.74
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.74
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.66
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.56
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.53
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.48
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.46
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.42
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.41
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.4
KOG0351|consensus	941		98.4
PF13245	76	AAA_19: Part of AAA domain	98.35
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.28
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.18
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.16
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.11
KOG1132|consensus	945		98.1
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.1
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.08
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.05
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.04
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.0
KOG0947|consensus	1248		97.99
KOG0948|consensus	1041		97.91
COG4096	875	HsdR Type I site-specific restriction-modification	97.82
KOG1802|consensus	935		97.82
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.79
KOG0951|consensus	1674		97.79
PRK15483	986	type III restriction-modification system StyLTI en	97.74
KOG1803|consensus	649		97.69
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.63
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.55
KOG0949|consensus	1330		97.55
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.52
KOG0950|consensus	1008		97.5
KOG1133|consensus	821		97.46
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.44
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	97.43
PRK11054	684	helD DNA helicase IV; Provisional	97.42
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.24
PRK10536	262	hypothetical protein; Provisional	97.21
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	97.15
COG4889	1518	Predicted helicase [General function prediction on	97.15
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.11
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.1
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.08
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.07
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.07
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	97.05
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.97
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.94
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.94
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	96.93
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.93
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.88
PRK04914	956	ATP-dependent helicase HepA; Validated	96.88
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.84
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.8
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	96.79
PRK05298	652	excinuclease ABC subunit B; Provisional	96.79
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.65
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.6
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.57
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.55
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	96.48
COG3587	985	Restriction endonuclease [Defense mechanisms]	96.45
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	96.39
KOG1131|consensus	755		96.38
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.32
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	96.32
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.25
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.24
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	96.06
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.04
KOG2340|consensus	698		96.0
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	95.98
PRK08181	269	transposase; Validated	95.97
PRK13851	344	type IV secretion system protein VirB11; Provision	95.96
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	95.94
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	95.88
PRK05973	237	replicative DNA helicase; Provisional	95.85
PRK13826	1102	Dtr system oriT relaxase; Provisional	95.84
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.84
PRK13764	602	ATPase; Provisional	95.84
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.83
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	95.83
PRK14873	665	primosome assembly protein PriA; Provisional	95.79
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	95.72
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.72
PRK06921	266	hypothetical protein; Provisional	95.71
PRK06526	254	transposase; Provisional	95.64
KOG0952|consensus	1230		95.62
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	95.53
PRK13897	606	type IV secretion system component VirD4; Provisio	95.53
PF12846	304	AAA_10: AAA-like domain	95.51
PRK06835	329	DNA replication protein DnaC; Validated	95.45
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.43
PHA02533	534	17 large terminase protein; Provisional	95.41
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.41
KOG0744|consensus	423		95.37
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	95.35
smart00382	148	AAA ATPases associated with a variety of cellular	95.28
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.25
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	95.24
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.23
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.23
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	95.18
PRK12377	248	putative replication protein; Provisional	95.14
COG0610	962	Type I site-specific restriction-modification syst	95.13
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.1
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.02
PRK13850	670	type IV secretion system protein VirD4; Provisiona	95.0
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.94
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.92
PRK10436	462	hypothetical protein; Provisional	94.9
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.84
KOG0745|consensus	564		94.82
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	94.79
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	94.72
TIGR02533	486	type_II_gspE general secretory pathway protein E.	94.7
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	94.69
PRK09183	259	transposase/IS protein; Provisional	94.67
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.63
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	94.57
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	94.5
KOG0953|consensus	700		94.5
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	94.48
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	94.47
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	94.46
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	94.44
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	94.41
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.38
PF13555	62	AAA_29: P-loop containing region of AAA domain	94.38
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.32
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.32
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	94.3
PRK07952	244	DNA replication protein DnaC; Validated	94.28
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	94.24
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.22
PHA02535	581	P terminase ATPase subunit; Provisional	94.21
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.21
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	94.19
KOG0925|consensus	699		94.12
PRK13822	641	conjugal transfer coupling protein TraG; Provision	94.12
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	94.11
PRK13876	663	conjugal transfer coupling protein TraG; Provision	94.09
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.09
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	94.05
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	94.04
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	93.98
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	93.96
KOG1805|consensus	1100		93.96
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	93.85
KOG0390|consensus	776		93.83
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	93.83
PF00004	132	AAA: ATPase family associated with various cellula	93.79
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	93.7
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.7
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	93.67
PRK03992	389	proteasome-activating nucleotidase; Provisional	93.65
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.65
KOG0989|consensus	346		93.64
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.52
PRK04328	249	hypothetical protein; Provisional	93.45
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	93.43
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.37
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	93.36
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	93.34
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	93.3
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.28
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	93.19
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	93.17
PRK08699	325	DNA polymerase III subunit delta'; Validated	93.16
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	93.13
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.11
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	93.1
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.08
PRK13880	636	conjugal transfer coupling protein TraG; Provision	93.02
KOG0733|consensus	802		93.01
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	93.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.99
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	92.96
PRK08769	319	DNA polymerase III subunit delta'; Validated	92.96
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.95
KOG0738|consensus	491		92.95
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	92.95
KOG0920|consensus	924		92.92
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	92.89
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	92.88
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	92.79
KOG1533|consensus	290		92.76
PRK13700	732	conjugal transfer protein TraD; Provisional	92.66
PF09439	181	SRPRB: Signal recognition particle receptor beta s	92.59
PRK08116	268	hypothetical protein; Validated	92.59
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	92.54
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	92.53
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	92.42
PRK13531	498	regulatory ATPase RavA; Provisional	92.37
KOG0730|consensus	693		92.34
KOG0733|consensus	802		92.29
PRK06871	325	DNA polymerase III subunit delta'; Validated	92.24
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	92.21
PRK08939	306	primosomal protein DnaI; Reviewed	92.2
KOG4150|consensus	1034		92.15
KOG0387|consensus	923		92.14
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	92.1
COG4133	209	CcmA ABC-type transport system involved in cytochr	92.09
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	92.05
PRK08903	227	DnaA regulatory inactivator Hda; Validated	92.05
KOG1123|consensus	776		92.02
PRK06067	234	flagellar accessory protein FlaH; Validated	91.93
PRK08727	233	hypothetical protein; Validated	91.92
COG0606	490	Predicted ATPase with chaperone activity [Posttran	91.9
KOG0729|consensus	435		91.89
KOG0926|consensus	1172		91.87
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	91.87
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	91.81
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	91.77
CHL00181	287	cbbX CbbX; Provisional	91.75
PHA02244	383	ATPase-like protein	91.73
PRK04296	190	thymidine kinase; Provisional	91.64
KOG1807|consensus	1025		91.54
PRK12402	337	replication factor C small subunit 2; Reviewed	91.51
PRK05642	234	DNA replication initiation factor; Validated	91.43
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	91.4
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	91.39
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	91.35
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	91.23
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	91.23
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	91.21
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	91.18
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	91.16
PRK06090	319	DNA polymerase III subunit delta'; Validated	91.14
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	91.09
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	91.05
PRK11823	446	DNA repair protein RadA; Provisional	90.93
PRK14974	336	cell division protein FtsY; Provisional	90.85
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	90.78
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	90.76
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	90.74
KOG1806|consensus	1320		90.69
PRK10867	433	signal recognition particle protein; Provisional	90.68
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	90.6
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	90.58
COG0714	329	MoxR-like ATPases [General function prediction onl	90.51
PRK14530	215	adenylate kinase; Provisional	90.46
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	90.44
PHA03333	752	putative ATPase subunit of terminase; Provisional	90.37
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	90.34
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	90.33
TIGR00609	1087	recB exodeoxyribonuclease V, beta subunit. All pro	90.33
TIGR02237	209	recomb_radB DNA repair and recombination protein R	90.19
KOG0060|consensus	659		90.13
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	90.11
PRK08084	235	DNA replication initiation factor; Provisional	90.09
PRK13909	910	putative recombination protein RecB; Provisional	90.06
PLN02796	347	D-glycerate 3-kinase	89.99
KOG0924|consensus	1042		89.96
PRK00131	175	aroK shikimate kinase; Reviewed	89.96
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	89.93
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	89.93
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	89.85
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	89.84
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	89.83
PRK08118	167	topology modulation protein; Reviewed	89.82
PLN02165	334	adenylate isopentenyltransferase	89.79
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	89.75
KOG0731|consensus	774		89.63
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	89.51
PRK00300	205	gmk guanylate kinase; Provisional	89.46
PF13654	509	AAA_32: AAA domain; PDB: 3K1J_B.	89.45
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	89.39
cd03115	173	SRP The signal recognition particle (SRP) mediates	89.36
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	89.35
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	89.33
PRK07261	171	topology modulation protein; Provisional	89.31
PRK06620	214	hypothetical protein; Validated	89.27
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	89.26
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	89.22
TIGR00959	428	ffh signal recognition particle protein. This mode	89.22
KOG0652|consensus	424		89.2
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	89.18
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	89.13
PRK07993	334	DNA polymerase III subunit delta'; Validated	89.03
PF00005	137	ABC_tran: ABC transporter This structure is on hol	89.01
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	88.91
KOG0736|consensus	953		88.9
PRK14087	450	dnaA chromosomal replication initiation protein; P	88.89
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	88.76
PLN03025	319	replication factor C subunit; Provisional	88.72
COG4604	252	CeuD ABC-type enterochelin transport system, ATPas	88.62
PRK00771	437	signal recognition particle protein Srp54; Provisi	88.61
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	88.61
PF05729	166	NACHT: NACHT domain	88.58
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	88.47
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	88.47
PRK00411	394	cdc6 cell division control protein 6; Reviewed	88.45
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	88.39
PRK09302	509	circadian clock protein KaiC; Reviewed	88.35
cd01394	218	radB RadB. The archaeal protein radB shares simila	88.32
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	88.27
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	88.25
KOG0991|consensus	333		88.23
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	88.22
PRK09302	509	circadian clock protein KaiC; Reviewed	88.09
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	88.08
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	88.04
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	88.04
PRK14088	440	dnaA chromosomal replication initiation protein; P	87.92
KOG0726|consensus	440		87.91
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	87.9
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	87.78
KOG0741|consensus	744		87.78
PRK14531	183	adenylate kinase; Provisional	87.72
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	87.64
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	87.63
PRK00149	450	dnaA chromosomal replication initiation protein; R	87.52
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	87.48
COG1855	604	ATPase (PilT family) [General function prediction	87.41
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	87.38
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	87.25
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	87.18
PRK10876	1181	recB exonuclease V subunit beta; Provisional	87.17
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	87.14
PRK06893	229	DNA replication initiation factor; Validated	87.08
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	86.98
CHL00195	489	ycf46 Ycf46; Provisional	86.95
PF14516	331	AAA_35: AAA-like domain	86.95
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	86.93
PRK07399	314	DNA polymerase III subunit delta'; Validated	86.86
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	86.83
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	86.83
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	86.71
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	86.68
PRK04220	301	2-phosphoglycerate kinase; Provisional	86.68
PRK08233	182	hypothetical protein; Provisional	86.66
PRK06762	166	hypothetical protein; Provisional	86.64
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	86.64
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	86.58
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	86.52
PRK09825	176	idnK D-gluconate kinase; Provisional	86.46
PRK10416	318	signal recognition particle-docking protein FtsY;	86.46
TIGR00064	272	ftsY signal recognition particle-docking protein F	86.45
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	86.43
PRK11608	326	pspF phage shock protein operon transcriptional ac	86.42
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	86.4
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	86.37
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	86.37
KOG2373|consensus	514		86.32
PRK05748	448	replicative DNA helicase; Provisional	86.31
KOG0737|consensus	386		86.24
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	86.16
PF00225	335	Kinesin: Kinesin motor domain; InterPro: IPR001752	86.15
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	86.11
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	86.1
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	86.09
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	86.07
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	86.06
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	86.02
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	86.02
PRK13891	852	conjugal transfer protein TrbE; Provisional	85.98
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	85.98
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	85.96
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	85.95
KOG0349|consensus	725		85.91
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	85.86
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	85.82
PRK05541	176	adenylylsulfate kinase; Provisional	85.8
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	85.78
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	85.75
PRK14532	188	adenylate kinase; Provisional	85.72
PHA00729	226	NTP-binding motif containing protein	85.69
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	85.66
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	85.64
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	85.59
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	85.57
cd03269	210	ABC_putative_ATPase This subfamily is involved in	85.56
PF10609	81	ParA: ParA/MinD ATPase like; InterPro: IPR019591 T	85.53
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	85.52
KOG0732|consensus	1080		85.4
PRK14737	186	gmk guanylate kinase; Provisional	85.38
KOG1942|consensus	456		85.38
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	85.34
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	85.34
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	85.31
PRK08356	195	hypothetical protein; Provisional	85.21
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	85.17
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	85.15
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	85.14
PRK01184	184	hypothetical protein; Provisional	85.14
PRK06547	172	hypothetical protein; Provisional	85.1
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	85.09
cd00983	325	recA RecA is a bacterial enzyme which has roles in	85.08
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	85.08
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	85.04
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	85.04
PTZ00301	210	uridine kinase; Provisional	85.01
cd03114	148	ArgK-like The function of this protein family is u	85.0
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	84.96
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	84.95
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	84.95

>PTZ00110 helicase; Provisional

Probab=99.95  E-value=3.6e-27  Score=184.25  Aligned_cols=118  Identities=37%  Similarity=0.539  Sum_probs=104.8

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      ++..+|.|..+|+++++++.++++|.+.||+.||++|.++||.+++|+|++++||||||||++|++|++..+......  
T Consensus       121 ~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~--  198 (545)
T PTZ00110        121 AGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLL--  198 (545)
T ss_pred             cCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccc--
Confidence            456789999999999999999999999999999999999999999999999999999999999999999988653211  


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                               ....++++|||+||||||.|+.+.+++++...+++++++|
T Consensus       199 ---------~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~  238 (545)
T PTZ00110        199 ---------RYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAY  238 (545)
T ss_pred             ---------cCCCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEe
Confidence                     1122478999999999999999999999999888887764

>KOG0330|consensus

Probab=99.95  E-value=1.6e-27  Score=175.25  Aligned_cols=106  Identities=39%  Similarity=0.579  Sum_probs=99.7

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ...+|.+|++++++++++.+++|+.||++|.++||.++.|+|+++.|.||||||.+|++|+++++......         
T Consensus        59 ~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~---------  129 (476)
T KOG0330|consen   59 SFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKL---------  129 (476)
T ss_pred             hhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCC---------
Confidence            34579999999999999999999999999999999999999999999999999999999999999975432         


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                             ++++|++||||||.|+...++.++..+|+++++++
T Consensus       130 -------~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lv  164 (476)
T KOG0330|consen  130 -------FFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLV  164 (476)
T ss_pred             -------ceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEe
Confidence                   89999999999999999999999999999999874

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=2e-26  Score=175.42  Aligned_cols=112  Identities=34%  Similarity=0.523  Sum_probs=98.8

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ...+|++++|++.+++++.+.||+.|||+|.++||.+++|+|++++||||||||++|++|+++.+.......        
T Consensus         6 ~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~--------   77 (423)
T PRK04837          6 TEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPE--------   77 (423)
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhccccc--------
Confidence            446899999999999999999999999999999999999999999999999999999999999987643211        


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                       .....++++||++||++||.|+++.++.+.+..++++..+
T Consensus        78 -~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~  117 (423)
T PRK04837         78 -DRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLA  117 (423)
T ss_pred             -ccccCCceEEEECCcHHHHHHHHHHHHHHhccCCceEEEE
Confidence             0112347899999999999999999999999999887765

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

Probab=99.94  E-value=1.3e-26  Score=180.36  Aligned_cols=119  Identities=35%  Similarity=0.517  Sum_probs=104.1

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      .+...|.|+.+|++++|++.++++|.+.||..|||+|.++||.+++|+|++++||||||||++|++|++.++....... 
T Consensus       112 ~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~-  190 (518)
T PLN00206        112 KGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGH-  190 (518)
T ss_pred             cCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcccc-
Confidence            3567899999999999999999999999999999999999999999999999999999999999999999887532110 


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                              .....++++||++|||+||.|+.+.++.+.+.++++++++
T Consensus       191 --------~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~  230 (518)
T PLN00206        191 --------PSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALV  230 (518)
T ss_pred             --------ccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEE
Confidence                    0112348999999999999999999999999988887655

>KOG0331|consensus

Probab=99.94  E-value=1.2e-26  Score=177.38  Aligned_cols=113  Identities=35%  Similarity=0.575  Sum_probs=101.5

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      .+...|+++++++++..+++..||..|||||.++||.+++|+|++..|.||||||++|++|++.++.....         
T Consensus        88 ~~~~~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~---------  158 (519)
T KOG0331|consen   88 DSSAAFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQG---------  158 (519)
T ss_pred             CcchhhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccc---------
Confidence            34447999999999999999999999999999999999999999999999999999999999999987421         


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                       ......+|.+||++||||||.|+.+++..+++.+++++.|+|
T Consensus       159 -~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvy  200 (519)
T KOG0331|consen  159 -KLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVY  200 (519)
T ss_pred             -cccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEe
Confidence             122334599999999999999999999999999999999886

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

Probab=99.94  E-value=9.2e-26  Score=175.25  Aligned_cols=107  Identities=41%  Similarity=0.647  Sum_probs=95.2

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ...|+++++++.+++++.+.||..|||+|.++||.++.|+|++++|+||||||++|++|+++++.....           
T Consensus        28 ~~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~-----------   96 (513)
T COG0513          28 PPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE-----------   96 (513)
T ss_pred             cCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccc-----------
Confidence            367999999999999999999999999999999999999999999999999999999999999764211           


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEeC
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVVL  130 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~~  130 (130)
                        ... ..+||++||||||.|+++.++.++++. +++++++|
T Consensus        97 --~~~-~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~  135 (513)
T COG0513          97 --RKY-VSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVY  135 (513)
T ss_pred             --cCC-CceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEE
Confidence              000 119999999999999999999999999 78887764

>KOG0340|consensus

Probab=99.93  E-value=6.1e-26  Score=165.38  Aligned_cols=107  Identities=38%  Similarity=0.582  Sum_probs=100.9

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      .....|++|||++|+.+.++.+|++.|||+|..+||.++.|+|++.+|.||||||.+|.+|+++++.+...         
T Consensus         4 ~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~---------   74 (442)
T KOG0340|consen    4 KTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPY---------   74 (442)
T ss_pred             cccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCC---------
Confidence            46788999999999999999999999999999999999999999999999999999999999999987543         


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                             +..++|++||||||.|+.+.|..+++.++++++++|
T Consensus        75 -------giFalvlTPTrELA~QiaEQF~alGk~l~lK~~viv  110 (442)
T KOG0340|consen   75 -------GIFALVLTPTRELALQIAEQFIALGKLLNLKVSVIV  110 (442)
T ss_pred             -------cceEEEecchHHHHHHHHHHHHHhcccccceEEEEE
Confidence                   278999999999999999999999999999999875

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.93  E-value=3.2e-25  Score=174.14  Aligned_cols=113  Identities=39%  Similarity=0.578  Sum_probs=97.9

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ...+|++|+|++.++++|.+.||..|||+|.++||.+++|+|++++||||||||++|++|+++++.......        
T Consensus         7 ~~~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~--------   78 (572)
T PRK04537          7 TDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALA--------   78 (572)
T ss_pred             CCCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccc--------
Confidence            345799999999999999999999999999999999999999999999999999999999999987542110        


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                       ......+++|||+||++|+.|+++.+++++..+++++..++
T Consensus        79 -~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~  119 (572)
T PRK04537         79 -DRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVY  119 (572)
T ss_pred             -ccccCCceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEE
Confidence             01112378999999999999999999999999998887653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.93  E-value=4.8e-25  Score=169.32  Aligned_cols=108  Identities=40%  Similarity=0.672  Sum_probs=95.0

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSR   91 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~   91 (130)
                      +|++|+|+++++++|.+.||..||++|.++|+.+++|+|++++||||||||++|++|+++.+.......          .
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~----------~   71 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHA----------K   71 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhccccc----------c
Confidence            699999999999999999999999999999999999999999999999999999999999987543210          0


Q ss_pred             CCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          92 KKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        92 ~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ....+++||++||++||.|+.+.++.+....++++..+
T Consensus        72 ~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~  109 (456)
T PRK10590         72 GRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVV  109 (456)
T ss_pred             cCCCceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEE
Confidence            11236899999999999999999999999888876654

>KOG0346|consensus

Probab=99.93  E-value=1.3e-25  Score=167.33  Aligned_cols=103  Identities=34%  Similarity=0.582  Sum_probs=94.1

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      .+|++++|++.+++++.++||+.||-+|..+||.++.|+|++..|.||||||.+|++|+++.+...+...          
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~----------   88 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTN----------   88 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcc----------
Confidence            6899999999999999999999999999999999999999999999999999999999999998766431          


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCC
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ  123 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~  123 (130)
                      ....++.++|++||||||.|+++++.++....+
T Consensus        89 ~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~  121 (569)
T KOG0346|consen   89 DGEQGPSAVILVPTKELAQQVYKVIEKLVEYCS  121 (569)
T ss_pred             cccccceeEEEechHHHHHHHHHHHHHHHHHHH
Confidence            244468999999999999999999999887654

>KOG0338|consensus

Probab=99.93  E-value=7.7e-26  Score=171.12  Aligned_cols=108  Identities=37%  Similarity=0.577  Sum_probs=99.2

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ..+|.+++|+-++++++..+||..|||+|..+||..+-|+|++.||.||||||.+|++|+|.++......          
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~----------  249 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK----------  249 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc----------
Confidence            3589999999999999999999999999999999999999999999999999999999999999876432          


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                         ....|+||++|||||+.|++++.++++.++.+.|++++
T Consensus       250 ---~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~v  287 (691)
T KOG0338|consen  250 ---VAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAV  287 (691)
T ss_pred             ---CcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeee
Confidence               22268999999999999999999999999999988763

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.92  E-value=1.2e-24  Score=167.24  Aligned_cols=104  Identities=34%  Similarity=0.508  Sum_probs=93.1

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      +.+|++++|++.+++++.++||..|||+|.++|+.+++|+|++++||||||||++|++|+++++.....           
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~-----------   71 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRF-----------   71 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccC-----------
Confidence            468999999999999999999999999999999999999999999999999999999999998864321           


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                           .++++|++||++||.|+.+.++.+++.. ++++..+
T Consensus        72 -----~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~  107 (460)
T PRK11776         72 -----RVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTL  107 (460)
T ss_pred             -----CceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEE
Confidence                 2679999999999999999999998764 5666554

>KOG0334|consensus

Probab=99.92  E-value=4.5e-25  Score=176.96  Aligned_cols=118  Identities=38%  Similarity=0.583  Sum_probs=106.7

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      .+...|.|..+|.+.+++..+++.++++||..|++||.+|||+|++|+|+|.+|.||||||++|++|++.++.....   
T Consensus       356 ~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~---  432 (997)
T KOG0334|consen  356 KGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRP---  432 (997)
T ss_pred             ccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCC---
Confidence            35678999999999999999999999999999999999999999999999999999999999999999966654332   


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                              .....||-++|++|||+|+.|+++++++|.+.++++++++|
T Consensus       433 --------~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vy  473 (997)
T KOG0334|consen  433 --------LEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVY  473 (997)
T ss_pred             --------hhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEec
Confidence                    12333699999999999999999999999999999999987

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.92  E-value=3.1e-24  Score=163.76  Aligned_cols=106  Identities=38%  Similarity=0.602  Sum_probs=95.1

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSR   91 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~   91 (130)
                      +|+++++++.+++++++.||..|+++|.++|+.+++|+|++++||||+|||++|++|+++.+......            
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~------------   69 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRR------------   69 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhcccc------------
Confidence            69999999999999999999999999999999999999999999999999999999999998753211            


Q ss_pred             CCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          92 KKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        92 ~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ....+++||++||++|+.|+.+.+..+++..++++..+
T Consensus        70 ~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~  107 (434)
T PRK11192         70 KSGPPRILILTPTRELAMQVADQARELAKHTHLDIATI  107 (434)
T ss_pred             CCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEE
Confidence            11136899999999999999999999999998887765

>KOG0348|consensus

Probab=99.92  E-value=1.6e-24  Score=164.75  Aligned_cols=110  Identities=35%  Similarity=0.562  Sum_probs=96.7

Q ss_pred             ccccCCCcCCCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy3307           7 SLKKQGFDDIQMTEIITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAG   85 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~   85 (130)
                      |.....|..|||++.++..|++ +++..||.+|.++||.+++|+|+++.|+||||||++|++|+++.+......-     
T Consensus       132 ~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki-----  206 (708)
T KOG0348|consen  132 PFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKI-----  206 (708)
T ss_pred             ccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccc-----
Confidence            4556779999999999999966 7999999999999999999999999999999999999999999998765331     


Q ss_pred             CCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCce
Q psy3307          86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRP  126 (130)
Q Consensus        86 ~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~  126 (130)
                           ....|+.+|||+||||||.|+++.+.++.+..-+-|
T Consensus       207 -----~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIV  242 (708)
T KOG0348|consen  207 -----QRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIV  242 (708)
T ss_pred             -----cccCCceEEEEechHHHHHHHHHHHHHHhcCceEEe
Confidence                 244569999999999999999999999998865543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.92  E-value=3.9e-24  Score=169.35  Aligned_cols=105  Identities=38%  Similarity=0.582  Sum_probs=93.8

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ...+|++++|++.++++|.++||..|||+|.++|+.++.|+|++++||||||||++|++|+++.+.....          
T Consensus         4 ~~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~----------   73 (629)
T PRK11634          4 FETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELK----------   73 (629)
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccC----------
Confidence            3457999999999999999999999999999999999999999999999999999999999998864322          


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                            .+++||++||++||.|+.+.++++...+ +++++.+
T Consensus        74 ------~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~  109 (629)
T PRK11634         74 ------APQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVAL  109 (629)
T ss_pred             ------CCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEE
Confidence                  2789999999999999999999998765 6766654

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.91  E-value=1.3e-23  Score=162.15  Aligned_cols=112  Identities=33%  Similarity=0.469  Sum_probs=97.0

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ....|.+++|++.++++|.+.||..+|++|.++|+.+++|+|+++.+|||||||++|++|+++.+........       
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~-------  157 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKE-------  157 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccc-------
Confidence            3457999999999999999999999999999999999999999999999999999999999999876532110       


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                        .....+++|||+||++|+.|+.+.++.+.+.+++++..+
T Consensus       158 --~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~  196 (475)
T PRK01297        158 --RYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTF  196 (475)
T ss_pred             --cccCCceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEE
Confidence              011137899999999999999999999999888877654

>KOG0345|consensus

Probab=99.91  E-value=1.3e-23  Score=157.65  Aligned_cols=108  Identities=34%  Similarity=0.545  Sum_probs=93.1

Q ss_pred             CCCcCCCC--CHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307          11 QGFDDIQM--TEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus        11 ~~f~~l~l--~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      .+|++++.  ++++++++.+.||+.+||+|..+||.+++++|+++.|+||||||+||++|+++.++.+....++.     
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~-----   78 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPG-----   78 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCcc-----
Confidence            47888875  59999999999999999999999999999999999999999999999999999997665432211     


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhc-CCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR-SQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~-~~~~~~~~  129 (130)
                            ..-+|||+|||||+.|+.+++..|.++ .++++.++
T Consensus        79 ------~vgalIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~  114 (567)
T KOG0345|consen   79 ------QVGALIISPTRELARQIREVAQPFLEHLPNLNCELL  114 (567)
T ss_pred             ------ceeEEEecCcHHHHHHHHHHHHHHHHhhhccceEEE
Confidence                  145999999999999999999999888 56666554

>KOG0343|consensus

Probab=99.90  E-value=4e-24  Score=163.09  Aligned_cols=111  Identities=32%  Similarity=0.510  Sum_probs=100.7

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGR   86 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~   86 (130)
                      ......|++|+|+..+.++|++.+|..+|++|..+||..+.|+|++..|.||||||++|++|+|++++......      
T Consensus        65 ~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~------  138 (758)
T KOG0343|consen   65 STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSP------  138 (758)
T ss_pred             hhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCC------
Confidence            44566899999999999999999999999999999999999999999999999999999999999999876542      


Q ss_pred             CCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        87 ~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                            ..|.-+|||+||||||.|++.++.+++++.++++-++
T Consensus       139 ------~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLi  175 (758)
T KOG0343|consen  139 ------TDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLI  175 (758)
T ss_pred             ------CCCceeEEecchHHHHHHHHHHHHHHhhcccccccee
Confidence                  2235599999999999999999999999999887665

>PTZ00424 helicase 45; Provisional

Probab=99.90  E-value=7.4e-23  Score=154.46  Aligned_cols=105  Identities=30%  Similarity=0.401  Sum_probs=93.2

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ....+|+++++++.+++++.+.||..|+++|.++|+.+++|+|++++||||||||++|++|++..+.....         
T Consensus        25 ~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~---------   95 (401)
T PTZ00424         25 EIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLN---------   95 (401)
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCC---------
Confidence            34578999999999999999999999999999999999999999999999999999999999988753221         


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                             +.++||++|+++|+.|+.+.++.++...++.+..
T Consensus        96 -------~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~  129 (401)
T PTZ00424         96 -------ACQALILAPTRELAQQIQKVVLALGDYLKVRCHA  129 (401)
T ss_pred             -------CceEEEECCCHHHHHHHHHHHHHHhhhcCceEEE
Confidence                   2679999999999999999999998877666543

>KOG0347|consensus

Probab=99.90  E-value=3.1e-24  Score=163.60  Aligned_cols=118  Identities=28%  Similarity=0.474  Sum_probs=102.5

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGR   86 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~   86 (130)
                      -.++.|.+|+++.+++++|.++||..||++|..++|++..| .|++..|.||||||+||-+|+++++...++.+.+....
T Consensus       178 ~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~  257 (731)
T KOG0347|consen  178 VDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNT  257 (731)
T ss_pred             cChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhH
Confidence            34567999999999999999999999999999999999999 79999999999999999999999887766544443331


Q ss_pred             CCCCCCCCCce--EEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          87 GYPSRKKVFPL--GLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        87 ~~~~~~~~~~~--~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                           ...+++  +||++||||||.|+.++++.+.+.++++++.|+
T Consensus       258 -----~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~  298 (731)
T KOG0347|consen  258 -----SAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASIT  298 (731)
T ss_pred             -----HhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEee
Confidence                 122344  999999999999999999999999999998874

>KOG0335|consensus

Probab=99.90  E-value=1.2e-23  Score=159.18  Aligned_cols=123  Identities=50%  Similarity=0.826  Sum_probs=108.5

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      .+..+|.++.+|.+-.+.+.+..+++..++..|||+|+.+||.+.+|+|+++||+||||||.+|++|++.++........
T Consensus        65 ~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~  144 (482)
T KOG0335|consen   65 SGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDR  144 (482)
T ss_pred             cCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccC
Confidence            35678888999999999999999999999999999999999999999999999999999999999999999998765433


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      ....      ....|+++|++||||||.|++++++++.-..+++++.+|
T Consensus       145 ~~~~------~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~y  187 (482)
T KOG0335|consen  145 GESG------GGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVY  187 (482)
T ss_pred             cccC------CCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeee
Confidence            2222      113589999999999999999999999999999888765

>KOG0333|consensus

Probab=99.89  E-value=3.2e-23  Score=157.33  Aligned_cols=121  Identities=34%  Similarity=0.505  Sum_probs=108.0

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      +.-+|.|+.+|++.+++.++++.+.+.||..|+|+|..+||..+..+|+|..|.||||||.+|++|++.++.+.......
T Consensus       237 g~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~  316 (673)
T KOG0333|consen  237 GGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARL  316 (673)
T ss_pred             CCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchh
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999876432211


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                             .+...+|+++|+.|||+|++|+..+-.+|++.++++++.++
T Consensus       317 -------en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvi  357 (673)
T KOG0333|consen  317 -------ENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVI  357 (673)
T ss_pred             -------hhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEe
Confidence                   12334699999999999999999999999999999988763

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

Probab=99.89  E-value=2.8e-22  Score=161.29  Aligned_cols=109  Identities=21%  Similarity=0.292  Sum_probs=95.8

Q ss_pred             cccccccccCCCcCCC--CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCC
Q psy3307           2 QECLVSLKKQGFDDIQ--MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPL   79 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~--l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~   79 (130)
                      +.+.+|.....|.+++  +++++.++|++.||+.||++|.++|+.+++|+|+++.+|||||||++|++|+++.+....  
T Consensus         3 ~~~~~p~~~a~~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~--   80 (742)
T TIGR03817         3 HVEHLPARAGRTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP--   80 (742)
T ss_pred             ceeecCCCCcccCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCC--
Confidence            5566777777888775  899999999999999999999999999999999999999999999999999999987532  


Q ss_pred             CCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          80 PTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                                     ++++|||+|||+|+.|+.+.+++++ ..++++..
T Consensus        81 ---------------~~~aL~l~PtraLa~q~~~~l~~l~-~~~i~v~~  113 (742)
T TIGR03817        81 ---------------RATALYLAPTKALAADQLRAVRELT-LRGVRPAT  113 (742)
T ss_pred             ---------------CcEEEEEcChHHHHHHHHHHHHHhc-cCCeEEEE
Confidence                           1689999999999999999999997 44566543

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

>KOG0342|consensus

Probab=99.89  E-value=5.5e-23  Score=154.77  Aligned_cols=108  Identities=33%  Similarity=0.513  Sum_probs=96.9

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ...|+++.|++..+++++++||..+|++|..+++.++.|+|+++.|.||||||++|++|.++.+.+....+         
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~---------  151 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKP---------  151 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCC---------
Confidence            45688999999999999999999999999999999999999999999999999999999999999876432         


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                         ..+..++|+|||||||.|++.+++++.++. ++.+..+
T Consensus       152 ---r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~v  189 (543)
T KOG0342|consen  152 ---RNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIV  189 (543)
T ss_pred             ---CCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEE
Confidence               134679999999999999999999999988 6665544

>KOG0339|consensus

Probab=99.88  E-value=7.1e-23  Score=155.22  Aligned_cols=118  Identities=39%  Similarity=0.628  Sum_probs=107.7

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      .|--+|+|..+|+.+++++.+..++++..|+.|||+|.+++|..+.|+|++..|.||||||-+|+.|++.++......  
T Consensus       214 ~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL--  291 (731)
T KOG0339|consen  214 SGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPEL--  291 (731)
T ss_pred             ccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhh--
Confidence            355689999999999999999999999999999999999999999999999999999999999999999998765432  


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                               ....+|-+||++||||||.|++.++++|++..+++++++|
T Consensus       292 ---------~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~y  331 (731)
T KOG0339|consen  292 ---------KPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVY  331 (731)
T ss_pred             ---------cCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEee
Confidence                     1223489999999999999999999999999999999987

>KOG0326|consensus

Probab=99.88  E-value=1.2e-23  Score=152.07  Aligned_cols=110  Identities=31%  Similarity=0.547  Sum_probs=100.3

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      |++..-....|+|+.|..+++..+.+.||+.|+|+|.++||.++.|+|+++.|.+|+|||-+|++|+|+++......   
T Consensus        77 ~DVt~TkG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~---  153 (459)
T KOG0326|consen   77 EDVTATKGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNV---  153 (459)
T ss_pred             cccccccCccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccc---
Confidence            44455556779999999999999999999999999999999999999999999999999999999999999765443   


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                                   .+++|++||||||.|+.+.++++++++++++..
T Consensus       154 -------------IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmv  186 (459)
T KOG0326|consen  154 -------------IQAIILVPTRELALQTSQVCKELSKHLGIKVMV  186 (459)
T ss_pred             -------------eeEEEEeecchhhHHHHHHHHHHhcccCeEEEE
Confidence                         789999999999999999999999999988754

>cd00268 DEADc DEAD-box helicases

Probab=99.88  E-value=2.4e-21  Score=134.01  Aligned_cols=103  Identities=46%  Similarity=0.705  Sum_probs=92.6

Q ss_pred             CcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q psy3307          13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK   92 (130)
Q Consensus        13 f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~   92 (130)
                      |+++++++.+.+.+.+.|++.|+++|.++++.+.+|+|+++.+|||+|||++|++|++..+.....              
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~--------------   66 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPK--------------   66 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcc--------------
Confidence            789999999999999999999999999999999999999999999999999999999999887520              


Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          93 KVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        93 ~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ..+++++|++|+++|+.|+.+.++.+....++++..+
T Consensus        67 ~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~  103 (203)
T cd00268          67 KDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVI  103 (203)
T ss_pred             cCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEE
Confidence            1127899999999999999999999988777776543

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.

>KOG0328|consensus

Probab=99.87  E-value=7.1e-23  Score=146.06  Aligned_cols=106  Identities=34%  Similarity=0.470  Sum_probs=98.5

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ....+|++++|.+++++.+-..||+.|+.+|++|+++++.|+|++++|..|+|||.+|.+.+++.+......        
T Consensus        24 ~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~--------   95 (400)
T KOG0328|consen   24 KVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRE--------   95 (400)
T ss_pred             ccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccce--------
Confidence            567899999999999999999999999999999999999999999999999999999999999877654432        


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                              .+++|++||||||.|+.+.+..++.++++.+..+
T Consensus        96 --------tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hac  129 (400)
T KOG0328|consen   96 --------TQALILSPTRELAVQIQKVILALGDYMNVQCHAC  129 (400)
T ss_pred             --------eeEEEecChHHHHHHHHHHHHHhcccccceEEEE
Confidence                    6899999999999999999999999999998876

>KOG0341|consensus

Probab=99.87  E-value=7.8e-23  Score=151.21  Aligned_cols=114  Identities=28%  Similarity=0.480  Sum_probs=101.2

Q ss_pred             CcccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCC
Q psy3307           1 MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLP   80 (130)
Q Consensus         1 ~~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~   80 (130)
                      |+++.+|+|+.+|.++.++..+++.|++.|+.+|||+|-+.+|.+++|||.+..|-||||||+.|.+|++-...+.....
T Consensus       160 veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~l  239 (610)
T KOG0341|consen  160 VEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMML  239 (610)
T ss_pred             eeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999888765443


Q ss_pred             CCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC
Q psy3307          81 TPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS  122 (130)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~  122 (130)
                      +..+..        +|..||+||+||||.|.++.+..+...+
T Consensus       240 Pf~~~E--------GP~gLiicPSRELArQt~~iie~~~~~L  273 (610)
T KOG0341|consen  240 PFARGE--------GPYGLIICPSRELARQTHDIIEQYVAAL  273 (610)
T ss_pred             ccccCC--------CCeeEEEcCcHHHHHHHHHHHHHHHHHH
Confidence            333333        4899999999999999999988876543

>KOG0337|consensus

Probab=99.86  E-value=6.6e-22  Score=147.01  Aligned_cols=106  Identities=36%  Similarity=0.627  Sum_probs=99.0

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      .-+|..+||+..+++++.+.||+.|||+|+.+||.+++|+|++..|.||||||.||++|+++++.....           
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~-----------   88 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQ-----------   88 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccc-----------
Confidence            467999999999999999999999999999999999999999999999999999999999999987652           


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                          .+.+++|++|||+|+.|..+..+.+++.++++++++|
T Consensus        89 ----~g~RalilsptreLa~qtlkvvkdlgrgt~lr~s~~~  125 (529)
T KOG0337|consen   89 ----TGLRALILSPTRELALQTLKVVKDLGRGTKLRQSLLV  125 (529)
T ss_pred             ----cccceeeccCcHHHHHHHHHHHHHhccccchhhhhhc
Confidence                2478999999999999999999999999999988765

>KOG0344|consensus

Probab=99.85  E-value=3.9e-21  Score=147.20  Aligned_cols=115  Identities=42%  Similarity=0.648  Sum_probs=100.8

Q ss_pred             CcccccccccCCCcC----CCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307           1 MQECLVSLKKQGFDD----IQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus         1 ~~~~~~~~~~~~f~~----l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      +.+..+|++..+|++    ...+..+++.+...+|..|+|+|.+++|.++.++|++.|+|||||||++|++|+++++...
T Consensus       122 v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~  201 (593)
T KOG0344|consen  122 VDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDL  201 (593)
T ss_pred             ccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHh
Confidence            346778999999998    5689999999999999999999999999999999999999999999999999999999876


Q ss_pred             CCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH--hcCCCce
Q psy3307          77 GPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA--YRSQLRP  126 (130)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~--~~~~~~~  126 (130)
                      ...           +...+.+++|+.|||+|+.|+++++.++.  +.++.+.
T Consensus       202 ~~~-----------~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a  242 (593)
T KOG0344|consen  202 SQE-----------KHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRA  242 (593)
T ss_pred             hcc-----------cCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhh
Confidence            531           23345899999999999999999999998  5555543

>PRK02362 ski2-like helicase; Provisional

Probab=99.83  E-value=7.3e-20  Score=147.59  Aligned_cols=97  Identities=21%  Similarity=0.339  Sum_probs=87.2

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      .|++++|++.+++++++.|+..++|+|.++++. +.+|+|++++||||||||++|.+|+++.+...              
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~--------------   67 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARG--------------   67 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcC--------------
Confidence            589999999999999999999999999999998 77999999999999999999999999988531              


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                           .++||++|+++|+.|.++.++++.. .|+++..
T Consensus        68 -----~kal~i~P~raLa~q~~~~~~~~~~-~g~~v~~   99 (737)
T PRK02362         68 -----GKALYIVPLRALASEKFEEFERFEE-LGVRVGI   99 (737)
T ss_pred             -----CcEEEEeChHHHHHHHHHHHHHhhc-CCCEEEE
Confidence                 4799999999999999999998754 4666654

>KOG0350|consensus

Probab=99.82  E-value=3.6e-20  Score=140.14  Aligned_cols=112  Identities=30%  Similarity=0.427  Sum_probs=95.3

Q ss_pred             ccccccccCCCcCCCCCHHHHHH----------HHHCCCCCCcHHHHHHHhHHh---------cCCcEEEEccCCchHHH
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNN----------IALARYDKPTPVQKYAIPVII---------SGRDVMACAQTGSGKTA   63 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~----------l~~~~~~~~t~~Q~~~i~~~~---------~g~~~l~~aptGsGKT~   63 (130)
                      +..-++..+.|+.+++++.+...          +.++++....|+|..++|.++         .++|+++.||||||||+
T Consensus       119 ~t~~~nslq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTL  198 (620)
T KOG0350|consen  119 ETAQNNSLQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTL  198 (620)
T ss_pred             eecCCCceeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCcee
Confidence            34455666778888877766555          888999999999999999885         46899999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          64 AFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        64 ~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ||.+|+++.+.++..               ...|+|||+||++|+.|+++.|+++..++|+.|+.+
T Consensus       199 aY~iPIVQ~L~~R~v---------------~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~  249 (620)
T KOG0350|consen  199 AYVIPIVQLLSSRPV---------------KRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSL  249 (620)
T ss_pred             eehhHHHHHHccCCc---------------cceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEec
Confidence            999999999876532               237899999999999999999999999999998764

>PRK00254 ski2-like helicase; Provisional

Probab=99.82  E-value=1.9e-19  Score=144.87  Aligned_cols=99  Identities=23%  Similarity=0.387  Sum_probs=88.1

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      .|+++++++.+.+.+++.||+.++|+|.++++. +.+|+|+++++|||||||++|.+|+++.+....             
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~-------------   68 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREG-------------   68 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcC-------------
Confidence            688999999999999999999999999999986 789999999999999999999999999876432             


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                           .++|+++|+++|+.|.++.++.+. ..++++..+
T Consensus        69 -----~~~l~l~P~~aLa~q~~~~~~~~~-~~g~~v~~~  101 (720)
T PRK00254         69 -----GKAVYLVPLKALAEEKYREFKDWE-KLGLRVAMT  101 (720)
T ss_pred             -----CeEEEEeChHHHHHHHHHHHHHHh-hcCCEEEEE
Confidence                 579999999999999999998864 457766543

>KOG0336|consensus

Probab=99.80  E-value=5.4e-20  Score=136.95  Aligned_cols=116  Identities=37%  Similarity=0.516  Sum_probs=96.3

Q ss_pred             cccccccCCCcCCC-CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           4 CLVSLKKQGFDDIQ-MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         4 ~~~~~~~~~f~~l~-l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      .-+|+|.-+|+|.. -.+++++++++.||..|||+|.++||.++.|.|++..|.||+|||++|++|.+.++......-  
T Consensus       212 rpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~--  289 (629)
T KOG0336|consen  212 RPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRR--  289 (629)
T ss_pred             ccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhh--
Confidence            34788888898754 579999999999999999999999999999999999999999999999999988876543210  


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                              ....+|.+|+++|||||+.|+.-+++++..+ |.+..|+|
T Consensus       290 --------~qr~~p~~lvl~ptreLalqie~e~~kysyn-g~ksvc~y  328 (629)
T KOG0336|consen  290 --------EQRNGPGVLVLTPTRELALQIEGEVKKYSYN-GLKSVCVY  328 (629)
T ss_pred             --------hccCCCceEEEeccHHHHHHHHhHHhHhhhc-CcceEEEe
Confidence                    1233588999999999999999999888654 45555554

>KOG0327|consensus

Probab=99.79  E-value=5.7e-20  Score=135.09  Aligned_cols=105  Identities=37%  Similarity=0.512  Sum_probs=96.4

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      -..+|+|++|.+.+++.+-..||+.|+.+|++||.++..|.|+.+++++|+|||.+|++++++.+.-....         
T Consensus        24 vvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke---------   94 (397)
T KOG0327|consen   24 VVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKE---------   94 (397)
T ss_pred             HhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHH---------
Confidence            34589999999999999999999999999999999999999999999999999999999999998543322         


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                             .++++++|||+||.|.....+.++..+++++..+
T Consensus        95 -------~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~  128 (397)
T KOG0327|consen   95 -------TQALILAPTRELAQQIQKVVRALGDHMDVSVHAC  128 (397)
T ss_pred             -------HHHHHhcchHHHHHHHHHHHHhhhcccceeeeee
Confidence                   6899999999999999999999999999988754

>KOG0329|consensus

Probab=99.78  E-value=2.7e-19  Score=126.55  Aligned_cols=112  Identities=32%  Similarity=0.446  Sum_probs=100.7

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      +.++..+.+.|.|+-|.+++++++-+.||++|+++|+++||...-|.|++++|..|.|||..|.++.++.+..-...   
T Consensus        34 gsyv~ihssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~---  110 (387)
T KOG0329|consen   34 GSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQ---  110 (387)
T ss_pred             CcEEEEeccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCe---
Confidence            56788889999999999999999999999999999999999999999999999999999999999999988654332   


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCC-CceEEeC
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ-LRPCVVL  130 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~-~~~~~~~  130 (130)
                                   ..++++|.|||||-|+.++..+++++++ +++++.|
T Consensus       111 -------------vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFf  146 (387)
T KOG0329|consen  111 -------------VSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFF  146 (387)
T ss_pred             -------------EEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEE
Confidence                         6799999999999999999999999865 5666543

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

Probab=99.77  E-value=3.7e-18  Score=137.00  Aligned_cols=98  Identities=27%  Similarity=0.397  Sum_probs=88.1

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCce
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL   97 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (130)
                      |++.+.+++++. |..|||.|.++||.+.+|+|+++.||||||||++.++|++..+.+...           .....+..
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~-----------~~~~~~i~   75 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGK-----------GKLEDGIY   75 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccC-----------CCCCCceE
Confidence            789999999888 899999999999999999999999999999999999999999998741           11233478


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhcCCCceE
Q psy3307          98 GLVLAPTRELATQIYDEAKKFAYRSQLRPC  127 (130)
Q Consensus        98 ~lil~Pt~~La~q~~~~~~~l~~~~~~~~~  127 (130)
                      +|||+|.|+|..++.+.++..++.+|+.+.
T Consensus        76 ~lYIsPLkALn~Di~~rL~~~~~~~G~~v~  105 (814)
T COG1201          76 ALYISPLKALNNDIRRRLEEPLRELGIEVA  105 (814)
T ss_pred             EEEeCcHHHHHHHHHHHHHHHHHHcCCccc
Confidence            999999999999999999999999998763

>PRK01172 ski2-like helicase; Provisional

Probab=99.76  E-value=7.4e-18  Score=134.92  Aligned_cols=96  Identities=20%  Similarity=0.293  Sum_probs=84.9

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSR   91 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~   91 (130)
                      .|++++|++.+++.+.+.+++ ++++|.++++.+.+|+|++++||||||||+++.++++..+...               
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~---------------   65 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAG---------------   65 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhC---------------
Confidence            588999999999999999985 9999999999999999999999999999999999999877542               


Q ss_pred             CCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          92 KKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        92 ~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                          .++|+++|+++||.|.++.++++. ..|+++..
T Consensus        66 ----~k~v~i~P~raLa~q~~~~~~~l~-~~g~~v~~   97 (674)
T PRK01172         66 ----LKSIYIVPLRSLAMEKYEELSRLR-SLGMRVKI   97 (674)
T ss_pred             ----CcEEEEechHHHHHHHHHHHHHHh-hcCCeEEE
Confidence                469999999999999999998864 45665543

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.74  E-value=3.1e-17  Score=134.33  Aligned_cols=88  Identities=27%  Similarity=0.460  Sum_probs=73.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCce
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL   97 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (130)
                      +++.+.+++++ +|..|||+|.++|+.+++|+|++++||||||||++|++|+++.+......          .....+++
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~----------~~~~~~~~   86 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGRE----------GELEDKVY   86 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccc----------cCCCCCeE
Confidence            66777777665 78899999999999999999999999999999999999999988753211          00122478


Q ss_pred             EEEEcCcHHHHHHHHHHHH
Q psy3307          98 GLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        98 ~lil~Pt~~La~q~~~~~~  116 (130)
                      +||++|+|+|+.|+++.+.
T Consensus        87 ~LyIsPtraLa~di~~~L~  105 (876)
T PRK13767         87 CLYVSPLRALNNDIHRNLE  105 (876)
T ss_pred             EEEEcCHHHHHHHHHHHHH
Confidence            9999999999999988665

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

Probab=99.73  E-value=4.7e-17  Score=109.14  Aligned_cols=78  Identities=41%  Similarity=0.646  Sum_probs=69.7

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE  114 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~  114 (130)
                      ||+|.++|+.+.+|+|+++.||||+|||++|+++++..+.+.. .                .++++++|+++|+.|+.+.
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~-~----------------~~~lii~P~~~l~~q~~~~   63 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGK-D----------------ARVLIIVPTRALAEQQFER   63 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTS-S----------------SEEEEEESSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCC-C----------------ceEEEEeeccccccccccc
Confidence            7999999999999999999999999999999999999888752 1                4799999999999999999


Q ss_pred             HHHHHhcCCCceEEe
Q psy3307         115 AKKFAYRSQLRPCVV  129 (130)
Q Consensus       115 ~~~l~~~~~~~~~~~  129 (130)
                      +.++....++++..+
T Consensus        64 ~~~~~~~~~~~~~~~   78 (169)
T PF00270_consen   64 LRKFFSNTNVRVVLL   78 (169)
T ss_dssp             HHHHTTTTTSSEEEE
T ss_pred             ccccccccccccccc
Confidence            999998877777654

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 ....

>KOG0332|consensus

Probab=99.73  E-value=5e-18  Score=124.99  Aligned_cols=103  Identities=26%  Similarity=0.521  Sum_probs=94.2

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ..+|++|+|.+++++.+-.++|..|+.+|..++|.++..  ++++.++.+|+|||.||.+.+|.++.-....        
T Consensus        89 ~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~--------  160 (477)
T KOG0332|consen   89 AKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVV--------  160 (477)
T ss_pred             cccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccC--------
Confidence            568999999999999999999999999999999999977  7999999999999999999999998754432        


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                              |+++-|+||||||.|+.+.+.+.+++.+++...
T Consensus       161 --------PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~y  193 (477)
T KOG0332|consen  161 --------PQCICLAPTRELAPQTGEVVEEMGKFTELTASY  193 (477)
T ss_pred             --------CCceeeCchHHHHHHHHHHHHHhcCceeeeEEE
Confidence                    889999999999999999999999999877654

>KOG4284|consensus

Probab=99.71  E-value=4.7e-18  Score=132.26  Aligned_cols=110  Identities=28%  Similarity=0.381  Sum_probs=98.2

Q ss_pred             cccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCC
Q psy3307           4 CLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPP   83 (130)
Q Consensus         4 ~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~   83 (130)
                      ++.+.-..+|++|.|..+++..|+..+|..||++|..|||.++.+.|+|++|..|+|||+.|.+.+++.+..+...    
T Consensus        18 DV~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~----   93 (980)
T KOG4284|consen   18 DVQSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSH----   93 (980)
T ss_pred             ccccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCc----
Confidence            4556777889999999999999999999999999999999999999999999999999999999888877665433    


Q ss_pred             CCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh-cCCCceEEe
Q psy3307          84 AGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY-RSQLRPCVV  129 (130)
Q Consensus        84 ~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~-~~~~~~~~~  129 (130)
                                  ++++|++||||+|.|+.+.+.+++. ..|.+|.+.
T Consensus        94 ------------~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvf  128 (980)
T KOG4284|consen   94 ------------IQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVF  128 (980)
T ss_pred             ------------ceeEEEecchhhhhHHHHHHHHhcccccCcceEEE
Confidence                        8899999999999999999999887 467777653

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=2.9e-16  Score=127.06  Aligned_cols=98  Identities=15%  Similarity=0.181  Sum_probs=85.6

Q ss_pred             cCCCCCHHHHHHHH-----HCCCCCC---cHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy3307          14 DDIQMTEIITNNIA-----LARYDKP---TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAG   85 (130)
Q Consensus        14 ~~l~l~~~i~~~l~-----~~~~~~~---t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~   85 (130)
                      +.|.+..++.+.+.     ..||..|   +|+|.++++.+..++|++++++||+|||++|++|++..+....        
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~--------  136 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK--------  136 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC--------
Confidence            35667777777765     5788887   9999999999999999999999999999999999998876421        


Q ss_pred             CCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        86 ~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                                 .++|++||++||.|..+++..+.+.+|+++.+++
T Consensus       137 -----------~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~  170 (970)
T PRK12899        137 -----------PVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLV  170 (970)
T ss_pred             -----------CeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEe
Confidence                       2889999999999999999999999999988764

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.67  E-value=6.1e-16  Score=124.04  Aligned_cols=90  Identities=23%  Similarity=0.285  Sum_probs=77.7

Q ss_pred             HHHHHH-HHHCCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q psy3307          20 EIITNN-IALARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK   92 (130)
Q Consensus        20 ~~i~~~-l~~~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~   92 (130)
                      ..+.+. ...++| .||++|.++++.+.++      .+++++||||||||++|++|++..+...                
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g----------------  310 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG----------------  310 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcC----------------
Confidence            344444 466788 6999999999999877      4899999999999999999999877532                


Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          93 KVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        93 ~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                         .+++|++||++||.|+++.++++...+++++.++
T Consensus       311 ---~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll  344 (681)
T PRK10917        311 ---YQAALMAPTEILAEQHYENLKKLLEPLGIRVALL  344 (681)
T ss_pred             ---CeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEE
Confidence               6799999999999999999999999999888765

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.66  E-value=7.8e-16  Score=122.53  Aligned_cols=90  Identities=23%  Similarity=0.289  Sum_probs=78.0

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKK   93 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~   93 (130)
                      +.+.+.++.++| .+|+.|.++|+.++++      .+.+++||||||||++|++|++..+...                 
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g-----------------  284 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAG-----------------  284 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcC-----------------
Confidence            334556688899 7999999999999876      3689999999999999999999887532                 


Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          94 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        94 ~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                        .+++|++||++||.|+++.++++...++++++++
T Consensus       285 --~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~ll  318 (630)
T TIGR00643       285 --YQVALMAPTEILAEQHYNSLRNLLAPLGIEVALL  318 (630)
T ss_pred             --CcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEE
Confidence              5799999999999999999999999888888765

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.66  E-value=4.4e-16  Score=120.27  Aligned_cols=69  Identities=26%  Similarity=0.367  Sum_probs=61.9

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .+||+.++|+|.++|+.+++|+|+++.+|||||||++|++|++..    .                  ..+||++|+++|
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~----~------------------~~~lVi~P~~~L   63 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS----D------------------GITLVISPLISL   63 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc----C------------------CcEEEEecHHHH
Confidence            479999999999999999999999999999999999999998742    1                  359999999999


Q ss_pred             HHHHHHHHHHH
Q psy3307         108 ATQIYDEAKKF  118 (130)
Q Consensus       108 a~q~~~~~~~l  118 (130)
                      +.|..+.++.+
T Consensus        64 ~~dq~~~l~~~   74 (470)
T TIGR00614        64 MEDQVLQLKAS   74 (470)
T ss_pred             HHHHHHHHHHc
Confidence            99988887654

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

>TIGR01054 rgy reverse gyrase

Probab=99.66  E-value=1e-15  Score=128.05  Aligned_cols=88  Identities=20%  Similarity=0.250  Sum_probs=72.3

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEE
Q psy3307          21 IITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLV  100 (130)
Q Consensus        21 ~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~li  100 (130)
                      ++.+.+++.....|+++|..+++.++.|+|++++||||||||+ |.+|++..+....                  ++++|
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~g------------------~~vLI  126 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKKG------------------KRCYI  126 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhcC------------------CeEEE
Confidence            3444455434448999999999999999999999999999997 6677776654321                  68999


Q ss_pred             EcCcHHHHHHHHHHHHHHHhcCCCceE
Q psy3307         101 LAPTRELATQIYDEAKKFAYRSQLRPC  127 (130)
Q Consensus       101 l~Pt~~La~q~~~~~~~l~~~~~~~~~  127 (130)
                      ++||++||.|+++.++.++..+++.+.
T Consensus       127 L~PTreLa~Qi~~~l~~l~~~~~i~~~  153 (1171)
T TIGR01054       127 ILPTTLLVIQVAEKISSLAEKAGVGTV  153 (1171)
T ss_pred             EeCHHHHHHHHHHHHHHHHHhcCCcee
Confidence            999999999999999999998887654

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.65  E-value=1.5e-15  Score=127.00  Aligned_cols=81  Identities=22%  Similarity=0.271  Sum_probs=69.0

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .|+ .|+++|..+++.++.|+|++++||||||||. |.++++..+...                  +.+++|++||++|+
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~~------------------g~~alIL~PTreLa  136 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAKK------------------GKKSYIIFPTRLLV  136 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHhc------------------CCeEEEEeccHHHH
Confidence            476 8999999999999999999999999999996 556655554332                  16899999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|+.+.+++++...++.+.++
T Consensus       137 ~Qi~~~l~~l~~~~~~~~~~~  157 (1176)
T PRK09401        137 EQVVEKLEKFGEKVGCGVKIL  157 (1176)
T ss_pred             HHHHHHHHHHhhhcCceEEEE
Confidence            999999999999888876554

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

Probab=99.65  E-value=1.7e-15  Score=123.51  Aligned_cols=89  Identities=28%  Similarity=0.411  Sum_probs=81.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCce
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL   97 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (130)
                      ..+.+..++.+.|...++..|.+|+..+.+|+|+++.++||||||.+|++|+++.+.....                 -+
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~-----------------a~  117 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPS-----------------AR  117 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcC-----------------cc
Confidence            3445677888889999999999999999999999999999999999999999999987654                 36


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhcCC
Q psy3307          98 GLVLAPTRELATQIYDEAKKFAYRSQ  123 (130)
Q Consensus        98 ~lil~Pt~~La~q~~~~~~~l~~~~~  123 (130)
                      +|+|.||++||++..+.++++...++
T Consensus       118 AL~lYPtnALa~DQ~~rl~~~~~~~~  143 (851)
T COG1205         118 ALLLYPTNALANDQAERLRELISDLP  143 (851)
T ss_pred             EEEEechhhhHhhHHHHHHHHHHhCC
Confidence            99999999999999999999999888

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.65  E-value=2.3e-15  Score=123.46  Aligned_cols=93  Identities=22%  Similarity=0.198  Sum_probs=78.9

Q ss_pred             CCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          17 QMTEIITNNIAL-ARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        17 ~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ..+...++.+.+ ++| .||+.|.++|+.+.++      +|++++|+||||||.+|++|++..+...             
T Consensus       435 ~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g-------------  500 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG-------------  500 (926)
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhC-------------
Confidence            345566666544 688 5999999999999875      7999999999999999999999887542             


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                            .+++|++||++||.|+++.++++...+++++..+
T Consensus       501 ------~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~L  534 (926)
T TIGR00580       501 ------KQVAVLVPTTLLAQQHFETFKERFANFPVTIELL  534 (926)
T ss_pred             ------CeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEE
Confidence                  5799999999999999999999888888887654

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.64  E-value=2.3e-15  Score=119.44  Aligned_cols=81  Identities=25%  Similarity=0.391  Sum_probs=68.5

Q ss_pred             CCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q psy3307          16 IQMTEIITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV   94 (130)
Q Consensus        16 l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~   94 (130)
                      ++.++...+.|++ +||+.++|+|.++|+.+++|+|+++.+|||+|||++|++|++..    .                 
T Consensus         7 ~~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~----~-----------------   65 (607)
T PRK11057          7 LNLESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL----D-----------------   65 (607)
T ss_pred             CCchhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc----C-----------------
Confidence            3445555556655 79999999999999999999999999999999999999999842    1                 


Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          95 FPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        95 ~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                       ..+||++|+++|+.|..+.++.+
T Consensus        66 -g~tlVisPl~sL~~dqv~~l~~~   88 (607)
T PRK11057         66 -GLTLVVSPLISLMKDQVDQLLAN   88 (607)
T ss_pred             -CCEEEEecHHHHHHHHHHHHHHc
Confidence             35899999999999998888764

>PRK14701 reverse gyrase; Provisional

Probab=99.63  E-value=2.9e-15  Score=127.99  Aligned_cols=85  Identities=19%  Similarity=0.174  Sum_probs=69.8

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEE
Q psy3307          21 IITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGL   99 (130)
Q Consensus        21 ~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   99 (130)
                      ++.+.+++ .|| .|+++|..+|+.++.|+|+++.||||||||++++++.+.... .                  +.+++
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~-~------------------g~~aL  126 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL-K------------------GKKCY  126 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh-c------------------CCeEE
Confidence            34445555 799 699999999999999999999999999999976665554321 1                  15799


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhcCCCc
Q psy3307         100 VLAPTRELATQIYDEAKKFAYRSQLR  125 (130)
Q Consensus       100 il~Pt~~La~q~~~~~~~l~~~~~~~  125 (130)
                      |++||++|+.|+.+.++.+++.+++.
T Consensus       127 Vl~PTreLa~Qi~~~l~~l~~~~~~~  152 (1638)
T PRK14701        127 IILPTTLLVKQTVEKIESFCEKANLD  152 (1638)
T ss_pred             EEECHHHHHHHHHHHHHHHHhhcCCc
Confidence            99999999999999999999886543

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

Probab=99.63  E-value=3.6e-15  Score=122.90  Aligned_cols=84  Identities=23%  Similarity=0.268  Sum_probs=68.6

Q ss_pred             CCCc--CCCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307          11 QGFD--DIQMTEIITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus        11 ~~f~--~l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ..|.  +++....+...+++ +|+..++|+|.++|+.++.|+|+++.+|||+|||+||.+|++..    .          
T Consensus       435 ~~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~----~----------  500 (1195)
T PLN03137        435 KKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC----P----------  500 (1195)
T ss_pred             ccccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc----C----------
Confidence            3466  45566667666654 79999999999999999999999999999999999999999852    1          


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                              ..+|||+|+++|+.+....+.
T Consensus       501 --------GiTLVISPLiSLmqDQV~~L~  521 (1195)
T PLN03137        501 --------GITLVISPLVSLIQDQIMNLL  521 (1195)
T ss_pred             --------CcEEEEeCHHHHHHHHHHHHH
Confidence                    359999999999985544443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.59  E-value=8.5e-15  Score=115.91  Aligned_cols=72  Identities=29%  Similarity=0.426  Sum_probs=63.4

Q ss_pred             HHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcC
Q psy3307          25 NIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAP  103 (130)
Q Consensus        25 ~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~P  103 (130)
                      .|++ +||..++|+|.++|+.+++|+|+++++|||+|||++|.+|++..    .                  ..++|++|
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~----~------------------g~~lVisP   61 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL----K------------------GLTVVISP   61 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc----C------------------CcEEEEcC
Confidence            4444 89999999999999999999999999999999999999998741    1                  34899999


Q ss_pred             cHHHHHHHHHHHHHH
Q psy3307         104 TRELATQIYDEAKKF  118 (130)
Q Consensus       104 t~~La~q~~~~~~~l  118 (130)
                      +++|+.|..+.++.+
T Consensus        62 l~sL~~dq~~~l~~~   76 (591)
T TIGR01389        62 LISLMKDQVDQLRAA   76 (591)
T ss_pred             CHHHHHHHHHHHHHc
Confidence            999999998888775

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.58  E-value=1.3e-14  Score=115.00  Aligned_cols=81  Identities=22%  Similarity=0.134  Sum_probs=73.3

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .+|. .|+++|..+++.++.|+  ++++.||+|||++|.+|++......                   ++++|++||++|
T Consensus        99 ~lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G-------------------~~v~VvTptreL  156 (656)
T PRK12898         99 VLGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAG-------------------LPVHVITVNDYL  156 (656)
T ss_pred             HhCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcC-------------------CeEEEEcCcHHH
Confidence            3576 79999999999999999  9999999999999999999865432                   579999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      |.|.++++..+.+.+|+++.+++
T Consensus       157 A~qdae~~~~l~~~lGlsv~~i~  179 (656)
T PRK12898        157 AERDAELMRPLYEALGLTVGCVV  179 (656)
T ss_pred             HHHHHHHHHHHHhhcCCEEEEEe
Confidence            99999999999999999998874

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

Probab=99.58  E-value=8.6e-15  Score=118.34  Aligned_cols=76  Identities=26%  Similarity=0.312  Sum_probs=60.1

Q ss_pred             CCCCCCcHHHHHHHhHHhcCC-cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEE-EcCcHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGR-DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLV-LAPTRE  106 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~-~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~li-l~Pt~~  106 (130)
                      .||+ |||+|.++++.++.|+ ++++++|||||||.++.++.+.. ....                ..++.|| ++|||+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~----------------~~~~rLv~~vPtRe   73 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGA----------------KVPRRLVYVVNRRT   73 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccc----------------cccceEEEeCchHH
Confidence            4886 9999999999999998 68888999999999765555422 1111                1255665 669999


Q ss_pred             HHHHHHHHHHHHHhcC
Q psy3307         107 LATQIYDEAKKFAYRS  122 (130)
Q Consensus       107 La~q~~~~~~~l~~~~  122 (130)
                      |+.|+++.++++++.+
T Consensus        74 La~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        74 VVDQVTEEAEKIGERL   89 (844)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999876

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.57  E-value=2.7e-14  Score=119.35  Aligned_cols=90  Identities=26%  Similarity=0.254  Sum_probs=74.8

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKK   93 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~   93 (130)
                      ++..+....++| .+|+.|.++|+.++++      +|++++|+||+|||.+|+.++...+..                  
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~------------------  648 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN------------------  648 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc------------------
Confidence            344455677888 7999999999999987      899999999999999998888766532                  


Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          94 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        94 ~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                       +.+++|++||++||.|+++.+++.....++++.++
T Consensus       649 -g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l  683 (1147)
T PRK10689        649 -HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEML  683 (1147)
T ss_pred             -CCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEE
Confidence             16799999999999999999998777777766543

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.47  E-value=4e-13  Score=108.65  Aligned_cols=96  Identities=24%  Similarity=0.345  Sum_probs=79.7

Q ss_pred             cCCCCCHHHHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q psy3307          14 DDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK   92 (130)
Q Consensus        14 ~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~   92 (130)
                      +...+++.+.+.++..++.+..+-|+.++.. +.+|+|+++++|||||||+..++.+++.+.+..               
T Consensus        12 ~~~~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~---------------   76 (766)
T COG1204          12 SKVKLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGG---------------   76 (766)
T ss_pred             ccccccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcC---------------
Confidence            3445788889889888997777777776654 556799999999999999999999999998763               


Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          93 KVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        93 ~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                         .++|+++|+|+||.+.++.+.+ .+.+|++|..
T Consensus        77 ---~k~vYivPlkALa~Ek~~~~~~-~~~~GirV~~  108 (766)
T COG1204          77 ---GKVVYIVPLKALAEEKYEEFSR-LEELGIRVGI  108 (766)
T ss_pred             ---CcEEEEeChHHHHHHHHHHhhh-HHhcCCEEEE
Confidence               4699999999999999999994 4667777764

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

Probab=99.45  E-value=7.6e-13  Score=108.60  Aligned_cols=92  Identities=17%  Similarity=0.255  Sum_probs=73.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHh----HHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIP----VIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKK   93 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~----~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~   93 (130)
                      +++...+.+...|| ++++.|.+.+.    .+.+|+++++.||||+|||++|++|++.... ..                
T Consensus       231 ~~~~~~~~~~~~~~-~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~~----------------  292 (850)
T TIGR01407       231 LSSLFSKNIDRLGL-EYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-TE----------------  292 (850)
T ss_pred             ccHHHHHhhhhcCC-ccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-CC----------------
Confidence            34466777778888 48999998666    4558899999999999999999999988665 21                


Q ss_pred             CCceEEEEcCcHHHHHHHHH-HHHHHHhcCC--CceEEe
Q psy3307          94 VFPLGLVLAPTRELATQIYD-EAKKFAYRSQ--LRPCVV  129 (130)
Q Consensus        94 ~~~~~lil~Pt~~La~q~~~-~~~~l~~~~~--~~~~~~  129 (130)
                        .+++|.+||++|+.|+.. .+..+.+.++  ++++++
T Consensus       293 --~~vvi~t~t~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~  329 (850)
T TIGR01407       293 --KPVVISTNTKVLQSQLLEKDIPLLNEILNFKINAALI  329 (850)
T ss_pred             --CeEEEEeCcHHHHHHHHHHHHHHHHHHcCCCceEEEE
Confidence              369999999999999954 7888877766  666554

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.40  E-value=2e-12  Score=100.74  Aligned_cols=72  Identities=19%  Similarity=0.152  Sum_probs=58.2

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..|+++|.++++.++.+++.++++|||+|||+.+.. +...+.....                 .++||++||++|+.|+
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~-l~~~~~~~~~-----------------~~vLilvpt~eL~~Q~  174 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYL-LSRYYLENYE-----------------GKVLIIVPTTSLVTQM  174 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHH-HHHHHHhcCC-----------------CeEEEEECcHHHHHHH
Confidence            489999999999999999999999999999997643 2222222211                 4799999999999999


Q ss_pred             HHHHHHHHhc
Q psy3307         112 YDEAKKFAYR  121 (130)
Q Consensus       112 ~~~~~~l~~~  121 (130)
                      .+.++++...
T Consensus       175 ~~~l~~~~~~  184 (501)
T PHA02558        175 IDDFVDYRLF  184 (501)
T ss_pred             HHHHHHhccc
Confidence            9999987653

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.39  E-value=2.4e-12  Score=104.01  Aligned_cols=80  Identities=23%  Similarity=0.165  Sum_probs=71.5

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|..+++.+.+|+  ++.+.||+|||+++++|++......                   ..++|++||++||
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G-------------------~~v~VvTpt~~LA  132 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEG-------------------KGVHLITVNDYLA  132 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcC-------------------CCeEEEeCCHHHH
Confidence            576 89999999999888887  9999999999999999998665532                   5699999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|.+.++..+.+.+|+++.+++
T Consensus       133 ~qd~e~~~~l~~~lGl~v~~i~  154 (790)
T PRK09200        133 KRDAEEMGQVYEFLGLTVGLNF  154 (790)
T ss_pred             HHHHHHHHHHHhhcCCeEEEEe
Confidence            9999999999999999998763

>KOG0952|consensus

Probab=99.38  E-value=2.2e-12  Score=105.03  Aligned_cols=91  Identities=24%  Similarity=0.253  Sum_probs=74.1

Q ss_pred             HCCCCCCcHHHHHHHhHHh-cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHH
Q psy3307          28 LARYDKPTPVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRE  106 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  106 (130)
                      -++|++++.+|++++|.+. ...|.++|||||||||..++|.+|+.+.+....         ..-..+..++++|+|+++
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~---------~~i~k~~fKiVYIaPmKA  175 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQ---------GDIAKDDFKIVYIAPMKA  175 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccc---------cccccCCceEEEEechHH
Confidence            4577889999999999887 557999999999999999999999999873221         112333489999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCceE
Q psy3307         107 LATQIYDEAKKFAYRSQLRPC  127 (130)
Q Consensus       107 La~q~~~~~~~l~~~~~~~~~  127 (130)
                      ||.++.+.+.+-...+|++|.
T Consensus       176 La~Em~~~~~kkl~~~gi~v~  196 (1230)
T KOG0952|consen  176 LAAEMVDKFSKKLAPLGISVR  196 (1230)
T ss_pred             HHHHHHHHHhhhcccccceEE
Confidence            999999988776676777764

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

Probab=99.36  E-value=3.6e-12  Score=98.89  Aligned_cols=101  Identities=22%  Similarity=0.324  Sum_probs=90.5

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ....++|++++++.+.++..|++++.|+|..++.. ++.|+|.++.++|+||||+.--++-+.++....           
T Consensus       193 r~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g-----------  261 (830)
T COG1202         193 RVPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGG-----------  261 (830)
T ss_pred             cccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCC-----------
Confidence            34577899999999999999999999999999976 679999999999999999999999999888754           


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                             .+.|+++|..+||+|-++.|++--..+|+++++
T Consensus       262 -------~KmlfLvPLVALANQKy~dF~~rYs~Lglkvai  294 (830)
T COG1202         262 -------KKMLFLVPLVALANQKYEDFKERYSKLGLKVAI  294 (830)
T ss_pred             -------CeEEEEehhHHhhcchHHHHHHHhhcccceEEE
Confidence                   469999999999999999998766888888754

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.36  E-value=4.4e-12  Score=101.58  Aligned_cols=80  Identities=20%  Similarity=0.112  Sum_probs=69.6

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|..+...+..|+  +++++||+|||+++.+|++......                   .++.|++||++||
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G-------------------~~V~VvTpt~~LA  110 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTG-------------------KGVHVVTVNDYLA  110 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhC-------------------CCEEEEcCCHHHH
Confidence            576 79999999998888887  8999999999999999996444432                   3499999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|.++++..+.+.+|+++.+++
T Consensus       111 ~qdae~~~~l~~~LGLsv~~i~  132 (745)
T TIGR00963       111 QRDAEWMGQVYRFLGLSVGLIL  132 (745)
T ss_pred             HHHHHHHHHHhccCCCeEEEEe
Confidence            9999999999999999998763

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.

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

Probab=99.35  E-value=5.7e-12  Score=102.99  Aligned_cols=82  Identities=29%  Similarity=0.319  Sum_probs=66.7

Q ss_pred             HHCCCCCCcHHHHHHHhHH----hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc
Q psy3307          27 ALARYDKPTPVQKYAIPVI----ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA  102 (130)
Q Consensus        27 ~~~~~~~~t~~Q~~~i~~~----~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~  102 (130)
                      ...|| +.++-|.+....+    .++..++++|+||+|||++|++|++....  .                  .++||++
T Consensus       240 ~~~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~~--~------------------~~vvI~t  298 (820)
T PRK07246        240 ALLGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQSD--Q------------------RQIIVSV  298 (820)
T ss_pred             ccCCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhcC--C------------------CcEEEEe
Confidence            33466 6899998855443    47789999999999999999999887431  1                  5799999


Q ss_pred             CcHHHHHHH-HHHHHHHHhcCCCceEEe
Q psy3307         103 PTRELATQI-YDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       103 Pt~~La~q~-~~~~~~l~~~~~~~~~~~  129 (130)
                      ||++|++|+ .+.+..+.+.++++++++
T Consensus       299 ~T~~Lq~Ql~~~~i~~l~~~~~~~~~~~  326 (820)
T PRK07246        299 PTKILQDQIMAEEVKAIQEVFHIDCHSL  326 (820)
T ss_pred             CcHHHHHHHHHHHHHHHHHhcCCcEEEE
Confidence            999999999 578899999898887654

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.32  E-value=1.5e-11  Score=99.03  Aligned_cols=79  Identities=20%  Similarity=0.148  Sum_probs=65.0

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|......+..|  .+++++||+|||++|++|++......                   ..++|++|+++||
T Consensus        67 lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g-------------------~~V~VVTpn~yLA  124 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTG-------------------KGAMLVTTNDYLA  124 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcC-------------------CceEEeCCCHHHH
Confidence            455 6677777666655555  69999999999999999987655432                   3599999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|..+++..+.+.+|+++.++
T Consensus       125 ~Rdae~m~~l~~~LGLsv~~~  145 (762)
T TIGR03714       125 KRDAEEMGPVYEWLGLTVSLG  145 (762)
T ss_pred             HHHHHHHHHHHhhcCCcEEEE
Confidence            999999999999999998765

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.

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

Probab=99.30  E-value=1.7e-11  Score=97.39  Aligned_cols=69  Identities=25%  Similarity=0.267  Sum_probs=56.2

Q ss_pred             hHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH-hc
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA-YR  121 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~-~~  121 (130)
                      ..+.+++.+++.|+||+|||++|++|++..+.....                 .++||++||++|+.|+.+.+..+. +.
T Consensus        11 ~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~~-----------------~rvlIstpT~~Lq~Ql~~~l~~l~~~~   73 (636)
T TIGR03117        11 TSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERPD-----------------QKIAIAVPTLALMGQLWSELERLTAEG   73 (636)
T ss_pred             HHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhccC-----------------ceEEEECCcHHHHHHHHHHHHHHHHhh
Confidence            344578899999999999999999999988764321                 579999999999999999999998 54


Q ss_pred             C--CCceEE
Q psy3307         122 S--QLRPCV  128 (130)
Q Consensus       122 ~--~~~~~~  128 (130)
                      +  ++++++
T Consensus        74 l~~~i~~~~   82 (636)
T TIGR03117        74 LAGPVQAGF   82 (636)
T ss_pred             cCCCeeEEE
Confidence            4  444444

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.30  E-value=5.2e-11  Score=95.82  Aligned_cols=67  Identities=27%  Similarity=0.329  Sum_probs=58.1

Q ss_pred             CCcHHHHHHHhHHhcC---CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          33 KPTPVQKYAIPVIISG---RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g---~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      .+|+.|.+++..+.++   +++++.++||||||.+|+.++...+...                   .++||++|+++|+.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g-------------------~~vLvLvPt~~L~~  204 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQG-------------------KQALVLVPEIALTP  204 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcC-------------------CeEEEEeCcHHHHH
Confidence            5899999999999874   7999999999999999988776665432                   46999999999999


Q ss_pred             HHHHHHHHH
Q psy3307         110 QIYDEAKKF  118 (130)
Q Consensus       110 q~~~~~~~l  118 (130)
                      |+.+.+++.
T Consensus       205 Q~~~~l~~~  213 (679)
T PRK05580        205 QMLARFRAR  213 (679)
T ss_pred             HHHHHHHHH
Confidence            999998764

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.28  E-value=4.2e-11  Score=80.97  Aligned_cols=78  Identities=44%  Similarity=0.517  Sum_probs=67.0

Q ss_pred             HCCCCCCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRE  106 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  106 (130)
                      ..++..+++.|.+++..+.++ +++++.+++|+|||.++..+++..+.....                 .++++++|+++
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~-----------------~~~l~~~p~~~   65 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG-----------------KRVLVLVPTRE   65 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCC-----------------CcEEEEeCCHH
Confidence            346678999999999999999 999999999999999998888887765421                 46999999999


Q ss_pred             HHHHHHHHHHHHHhcC
Q psy3307         107 LATQIYDEAKKFAYRS  122 (130)
Q Consensus       107 La~q~~~~~~~l~~~~  122 (130)
                      ++.|+.+.+..+....
T Consensus        66 ~~~~~~~~~~~~~~~~   81 (201)
T smart00487       66 LAEQWAEELKKLGPSL   81 (201)
T ss_pred             HHHHHHHHHHHHhccC
Confidence            9999999998877553

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.27  E-value=4.7e-11  Score=87.28  Aligned_cols=77  Identities=22%  Similarity=0.188  Sum_probs=60.9

Q ss_pred             CCCCCCcHHHHHHHh----HHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          29 ARYDKPTPVQKYAIP----VIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~----~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      +.| .|+|.|.+.+.    .+.+|.++++.||||+|||++|++|++.++......             ....+++|.++|
T Consensus         5 FPy-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~-------------~~~~kvi~~t~T   70 (289)
T smart00489        5 FPY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER-------------IQKIKLIYLSRT   70 (289)
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc-------------ccccceeEEecc
Confidence            455 46999999554    445889999999999999999999999887654321             011479999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy3307         105 RELATQIYDEAKKFA  119 (130)
Q Consensus       105 ~~La~q~~~~~~~l~  119 (130)
                      ..+..|....++++.
T Consensus        71 ~~~~~q~i~~l~~~~   85 (289)
T smart00489       71 VSEIEKRLEELRKLM   85 (289)
T ss_pred             HHHHHHHHHHHHhcc
Confidence            999999988888764

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.27  E-value=4.7e-11  Score=87.28  Aligned_cols=77  Identities=22%  Similarity=0.188  Sum_probs=60.9

Q ss_pred             CCCCCCcHHHHHHHh----HHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          29 ARYDKPTPVQKYAIP----VIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~----~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      +.| .|+|.|.+.+.    .+.+|.++++.||||+|||++|++|++.++......             ....+++|.++|
T Consensus         5 FPy-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~-------------~~~~kvi~~t~T   70 (289)
T smart00488        5 FPY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER-------------IQKIKLIYLSRT   70 (289)
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc-------------ccccceeEEecc
Confidence            455 46999999554    445889999999999999999999999887654321             011479999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy3307         105 RELATQIYDEAKKFA  119 (130)
Q Consensus       105 ~~La~q~~~~~~~l~  119 (130)
                      ..+..|....++++.
T Consensus        71 ~~~~~q~i~~l~~~~   85 (289)
T smart00488       71 VSEIEKRLEELRKLM   85 (289)
T ss_pred             HHHHHHHHHHHHhcc
Confidence            999999988888764

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.24  E-value=4.3e-11  Score=89.82  Aligned_cols=64  Identities=28%  Similarity=0.344  Sum_probs=54.8

Q ss_pred             HHHHHHhHHhcCCc--EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy3307          37 VQKYAIPVIISGRD--VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE  114 (130)
Q Consensus        37 ~Q~~~i~~~~~g~~--~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~  114 (130)
                      .|.++++.+.++.+  ++++||||||||++|++|++.    ..                  .++++++|+++|+.|.++.
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~----~~------------------~~~~~~~P~~aL~~~~~~~   58 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH----GE------------------NDTIALYPTNALIEDQTEA   58 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH----cC------------------CCEEEEeChHHHHHHHHHH
Confidence            48999999998875  788999999999999999884    11                  3589999999999999999


Q ss_pred             HHHHHhcC
Q psy3307         115 AKKFAYRS  122 (130)
Q Consensus       115 ~~~l~~~~  122 (130)
                      ++.+...+
T Consensus        59 ~~~~~~~~   66 (357)
T TIGR03158        59 IKEFVDVF   66 (357)
T ss_pred             HHHHHHhc
Confidence            98887543

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.22  E-value=5.2e-11  Score=95.41  Aligned_cols=74  Identities=20%  Similarity=0.105  Sum_probs=56.6

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHH---------HHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAA---------FLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~---------~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      ..+|.++++.+.+|+|++++|+||||||.+         |++|.+..+..-..             .....++++++|+|
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~-------------~~~~~~ilvt~Prr  232 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDP-------------NFIERPIVLSLPRV  232 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhccc-------------ccCCcEEEEECcHH
Confidence            348999999999999999999999999987         55566665532110             00125799999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q psy3307         106 ELATQIYDEAKKFAYR  121 (130)
Q Consensus       106 ~La~q~~~~~~~l~~~  121 (130)
                      +||.|+...+.+....
T Consensus       233 eLa~qi~~~i~~~vg~  248 (675)
T PHA02653        233 ALVRLHSITLLKSLGF  248 (675)
T ss_pred             HHHHHHHHHHHHHhCc
Confidence            9999999988765543

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.16  E-value=2e-10  Score=93.60  Aligned_cols=80  Identities=20%  Similarity=0.069  Sum_probs=65.6

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .++++|...--.+..|+  ++.++||+|||++|.+|++......                   ..++|++||++||
T Consensus        79 lg~-~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G-------------------~~V~VvTpn~yLA  136 (896)
T PRK13104         79 LGL-RHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISG-------------------RGVHIVTVNDYLA  136 (896)
T ss_pred             cCC-CcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcC-------------------CCEEEEcCCHHHH
Confidence            454 67778776554444554  7799999999999999999776542                   2489999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|.++++..+.+.+|+++.+++
T Consensus       137 ~qd~e~m~~l~~~lGLtv~~i~  158 (896)
T PRK13104        137 KRDSQWMKPIYEFLGLTVGVIY  158 (896)
T ss_pred             HHHHHHHHHHhcccCceEEEEe
Confidence            9999999999999999998763

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.13  E-value=1.8e-10  Score=86.10  Aligned_cols=52  Identities=29%  Similarity=0.345  Sum_probs=45.4

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      |+++.||||||||.+|+++++..+.....                 .++++++|+++|+.|+++.++.+
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~~-----------------~~ii~v~P~~~L~~q~~~~l~~~   52 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQKA-----------------DRVIIALPTRATINAMYRRAKEL   52 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCCC-----------------CeEEEEeehHHHHHHHHHHHHHH
Confidence            68999999999999999999987654321                 57999999999999999999886

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.12  E-value=5.9e-10  Score=90.88  Aligned_cols=71  Identities=27%  Similarity=0.310  Sum_probs=60.7

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      -+++++|..++..++.+ |.++++|||+|||+++++++...+....                  .++||++||++|+.|.
T Consensus        14 ~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~~~------------------~~vLvl~Pt~~L~~Q~   74 (773)
T PRK13766         14 IEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHKKG------------------GKVLILAPTKPLVEQH   74 (773)
T ss_pred             CCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHhCC------------------CeEEEEeCcHHHHHHH
Confidence            37899999999888887 9999999999999999988887763221                  5799999999999999


Q ss_pred             HHHHHHHHhc
Q psy3307         112 YDEAKKFAYR  121 (130)
Q Consensus       112 ~~~~~~l~~~  121 (130)
                      .+.++++...
T Consensus        75 ~~~~~~~~~~   84 (773)
T PRK13766         75 AEFFRKFLNI   84 (773)
T ss_pred             HHHHHHHhCC
Confidence            9999887644

>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=99.09  E-value=6.5e-10  Score=74.98  Aligned_cols=66  Identities=42%  Similarity=0.484  Sum_probs=53.1

Q ss_pred             CCcHHHHHHHhHHhc-------CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          33 KPTPVQKYAIPVIIS-------GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~-------g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      .+++.|.+++..+.+       .+.+++.+|||||||..++..+.... .                     ++++++|+.
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-~---------------------~~l~~~p~~   60 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA-R---------------------KVLIVAPNI   60 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH-C---------------------EEEEEESSH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc-c---------------------ceeEecCHH
Confidence            578999999998873       68999999999999998864443333 1                     499999999


Q ss_pred             HHHHHHHHHHHHHHh
Q psy3307         106 ELATQIYDEAKKFAY  120 (130)
Q Consensus       106 ~La~q~~~~~~~l~~  120 (130)
                      +|+.|..+.+..+..
T Consensus        61 ~l~~Q~~~~~~~~~~   75 (184)
T PF04851_consen   61 SLLEQWYDEFDDFGS   75 (184)
T ss_dssp             HHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHhhh
Confidence            999999999966554

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 ....

>KOG0349|consensus

Probab=99.08  E-value=3.1e-11  Score=91.37  Aligned_cols=66  Identities=38%  Similarity=0.596  Sum_probs=62.9

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +..|++++.-+++-.+..++.|.-||.+|.++||.++.|-|++..|.||||||-+|++|+++.+.+
T Consensus         1 m~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen    1 MTAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             CcchHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHH
Confidence            457999999999999999999999999999999999999999999999999999999999999875

>KOG0353|consensus

Probab=99.04  E-value=6.5e-10  Score=83.22  Aligned_cols=85  Identities=24%  Similarity=0.352  Sum_probs=74.0

Q ss_pred             cCCCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q psy3307          14 DDIQMTEIITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK   92 (130)
Q Consensus        14 ~~l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~   92 (130)
                      ++++++.+..+.|++ +..+.++|.|..+|...+.|+|+++..|||.||++||-+|.|-.   .                
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a---d----------------  134 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA---D----------------  134 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc---C----------------
Confidence            477888888888865 57788999999999999999999999999999999999998741   1                


Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          93 KVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        93 ~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                         ..+|+++|..+|.++..-.++.++-
T Consensus       135 ---g~alvi~plislmedqil~lkqlgi  159 (695)
T KOG0353|consen  135 ---GFALVICPLISLMEDQILQLKQLGI  159 (695)
T ss_pred             ---CceEeechhHHHHHHHHHHHHHhCc
Confidence               3599999999999999888888754

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

Probab=99.03  E-value=2.2e-09  Score=89.10  Aligned_cols=80  Identities=16%  Similarity=0.223  Sum_probs=61.1

Q ss_pred             CCCCCcHHHHHHHhHH----hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          30 RYDKPTPVQKYAIPVI----ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~----~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      +| ++++-|.+.+..+    .+++.+++.||||+|||++|++|.+.......                  .+++|.++|+
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~------------------~~vvIsT~T~  315 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKE------------------EPVVISTYTI  315 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccC------------------CeEEEEcCCH
Confidence            55 7899999866554    47789999999999999999999987665433                  4699999999


Q ss_pred             HHHHHHHH-HHHHHHhcCC--CceEE
Q psy3307         106 ELATQIYD-EAKKFAYRSQ--LRPCV  128 (130)
Q Consensus       106 ~La~q~~~-~~~~l~~~~~--~~~~~  128 (130)
                      .|.+|+.. .+..+.+-++  +++++
T Consensus       316 ~LQ~Ql~~kDiP~L~~~~~~~~~~~~  341 (928)
T PRK08074        316 QLQQQLLEKDIPLLQKIFPFPVEAAL  341 (928)
T ss_pred             HHHHHHHHhhHHHHHHHcCCCceEEE
Confidence            99999855 4544544443  45544

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.02  E-value=3.8e-09  Score=85.38  Aligned_cols=77  Identities=22%  Similarity=0.232  Sum_probs=60.5

Q ss_pred             CCCCCcHHHHHHHhHHh---c------CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEE
Q psy3307          30 RYDKPTPVQKYAIPVII---S------GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLV  100 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~---~------g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~li  100 (130)
                      || +.++-|.+.+..+.   +      ++.+++.||||+|||++|++|.+.......                  -++||
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~------------------k~vVI   83 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEK------------------KKLVI   83 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcC------------------CeEEE
Confidence            56 78999998776553   3      367899999999999999999988766544                  46999


Q ss_pred             EcCcHHHHHHHH-HHHHHHHhcCCCc
Q psy3307         101 LAPTRELATQIY-DEAKKFAYRSQLR  125 (130)
Q Consensus       101 l~Pt~~La~q~~-~~~~~l~~~~~~~  125 (130)
                      -+.|+.|.+|+. +.+-.+.+.++..
T Consensus        84 ST~T~~LQeQL~~kDlP~l~~~l~~~  109 (697)
T PRK11747         84 STATVALQEQLVSKDLPLLLKISGLD  109 (697)
T ss_pred             EcCCHHHHHHHHhhhhhHHHHHcCCC
Confidence            999999999994 5566666655543

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

Probab=98.98  E-value=3.4e-09  Score=83.83  Aligned_cols=94  Identities=24%  Similarity=0.322  Sum_probs=80.7

Q ss_pred             CCCCHHHHHH-HHHCCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307          16 IQMTEIITNN-IALARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus        16 l~l~~~i~~~-l~~~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      +..+.++++. ++.+.| .+|..|.+++..|...      .+-++++.-|||||+..+++++..+...            
T Consensus       245 ~~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G------------  311 (677)
T COG1200         245 LPANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAG------------  311 (677)
T ss_pred             CCccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcC------------
Confidence            4455555554 577898 7999999999999855      4779999999999999999999888654            


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                             .++..++||--||+|.++.+.++...+|++++.+
T Consensus       312 -------~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lL  345 (677)
T COG1200         312 -------YQAALMAPTEILAEQHYESLRKWLEPLGIRVALL  345 (677)
T ss_pred             -------CeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEe
Confidence                   5799999999999999999999999999998765

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.98  E-value=1.3e-09  Score=93.12  Aligned_cols=59  Identities=27%  Similarity=0.366  Sum_probs=44.3

Q ss_pred             EEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          53 ACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        53 ~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      ++||||||||++|++|+|.++..........      .....+.++|||+|+++|+.|+.+.++.
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~------~~~~~~~raLYISPLKALa~Dv~~~L~~   59 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTRE------AHKRKTSRILYISPIKALGTDVQRNLQI   59 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccc------cccCCCCEEEEEeChHHHHHHHHHHHHH
Confidence            4799999999999999999998643110000      0011237899999999999999999875

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.95  E-value=5.6e-09  Score=84.56  Aligned_cols=75  Identities=23%  Similarity=0.263  Sum_probs=63.6

Q ss_pred             CCCCCCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          29 ARYDKPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      +.|..++|.|.+.+..+.    +|.++++.||||+|||++.+.|.|.+.......                +++++.+.|
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~----------------~kIiy~sRT   69 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEV----------------RKIIYASRT   69 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcccc----------------ccEEEEccc
Confidence            456667999998886654    789999999999999999999999987654321                679999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy3307         105 RELATQIYDEAKKFA  119 (130)
Q Consensus       105 ~~La~q~~~~~~~l~  119 (130)
                      +.-..|+.++++++.
T Consensus        70 hsQl~q~i~Elk~~~   84 (705)
T TIGR00604        70 HSQLEQATEELRKLM   84 (705)
T ss_pred             chHHHHHHHHHHhhh
Confidence            999999999999965

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).

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.94  E-value=3.7e-09  Score=86.57  Aligned_cols=69  Identities=16%  Similarity=0.153  Sum_probs=53.5

Q ss_pred             HHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH-H
Q psy3307          39 KYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK-K  117 (130)
Q Consensus        39 ~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~-~  117 (130)
                      .+.+..+.++++++++|+||||||.+|.+++++....                   ..+++++.|+|++|.|+.+.+. .
T Consensus        11 ~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~-------------------~~~ilvlqPrR~aA~qia~rva~~   71 (812)
T PRK11664         11 PELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI-------------------NGKIIMLEPRRLAARNVAQRLAEQ   71 (812)
T ss_pred             HHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc-------------------CCeEEEECChHHHHHHHHHHHHHH
Confidence            3445566688999999999999999999998864211                   1479999999999999999874 5


Q ss_pred             HHhcCCCce
Q psy3307         118 FAYRSQLRP  126 (130)
Q Consensus       118 l~~~~~~~~  126 (130)
                      +++..|..+
T Consensus        72 l~~~~g~~V   80 (812)
T PRK11664         72 LGEKPGETV   80 (812)
T ss_pred             hCcccCceE
Confidence            555555444

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

Probab=98.94  E-value=3.5e-09  Score=83.32  Aligned_cols=74  Identities=26%  Similarity=0.385  Sum_probs=65.1

Q ss_pred             HHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc
Q psy3307          24 NNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA  102 (130)
Q Consensus        24 ~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~  102 (130)
                      ..|++ +|+..+.+-|.++|..+++|+|+++..|||.||++||-+|.+-.    .                  .-+|||+
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~----~------------------G~TLVVS   64 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL----E------------------GLTLVVS   64 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc----C------------------CCEEEEC
Confidence            44544 69999999999999999999999999999999999999999764    1                  2489999


Q ss_pred             CcHHHHHHHHHHHHHHH
Q psy3307         103 PTRELATQIYDEAKKFA  119 (130)
Q Consensus       103 Pt~~La~q~~~~~~~l~  119 (130)
                      |..+|..+..+.+++.+
T Consensus        65 PLiSLM~DQV~~l~~~G   81 (590)
T COG0514          65 PLISLMKDQVDQLEAAG   81 (590)
T ss_pred             chHHHHHHHHHHHHHcC
Confidence            99999999998888765

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.94  E-value=5e-09  Score=85.22  Aligned_cols=80  Identities=21%  Similarity=0.091  Sum_probs=66.2

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|...--.+..|+  ++.++||+|||+++.+|++-.....                   ..+-|++||..||
T Consensus        78 lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G-------------------~~V~IvTpn~yLA  135 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTG-------------------KGVHVVTVNDYLA  135 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcC-------------------CCEEEEecCHHHH
Confidence            566 78999988776666665  8899999999999999996433322                   2377999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|.++++..+.+.+|+++.++.
T Consensus       136 ~rd~e~~~~l~~~LGlsv~~i~  157 (830)
T PRK12904        136 KRDAEWMGPLYEFLGLSVGVIL  157 (830)
T ss_pred             HHHHHHHHHHHhhcCCeEEEEc
Confidence            9999999999999999998763

>KOG0354|consensus

Probab=98.91  E-value=4.3e-09  Score=84.22  Aligned_cols=71  Identities=25%  Similarity=0.224  Sum_probs=62.1

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++.+|.+....++ |+|+++++|||+|||+....-+..++.....                 .++|+++|++-|+.|..
T Consensus        62 ~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-----------------~KiVF~aP~~pLv~QQ~  123 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-----------------GKVVFLAPTRPLVNQQI  123 (746)
T ss_pred             cccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-----------------ceEEEeeCCchHHHHHH
Confidence            67899999999999 9999999999999999988888888776543                 57999999999999999


Q ss_pred             HHHHHHHhc
Q psy3307         113 DEAKKFAYR  121 (130)
Q Consensus       113 ~~~~~l~~~  121 (130)
                      ..+..++..
T Consensus       124 a~~~~~~~~  132 (746)
T KOG0354|consen  124 ACFSIYLIP  132 (746)
T ss_pred             HHHhhccCc
Confidence            777777654

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

Probab=98.89  E-value=2.7e-08  Score=81.67  Aligned_cols=74  Identities=28%  Similarity=0.428  Sum_probs=61.2

Q ss_pred             CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          30 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      |+ .|+..|.-....+..|++.-+.||||.|||..-++..+- +...+                  -+++||+||..|+.
T Consensus        80 G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~-~a~kg------------------kr~yii~PT~~Lv~  139 (1187)
T COG1110          80 GF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLY-LAKKG------------------KRVYIIVPTTTLVR  139 (1187)
T ss_pred             CC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHH-HHhcC------------------CeEEEEecCHHHHH
Confidence            55 899999999999999999999999999999754433332 22111                  47999999999999


Q ss_pred             HHHHHHHHHHhcCC
Q psy3307         110 QIYDEAKKFAYRSQ  123 (130)
Q Consensus       110 q~~~~~~~l~~~~~  123 (130)
                      |+++.++++++..+
T Consensus       140 Q~~~kl~~~~e~~~  153 (1187)
T COG1110         140 QVYERLKKFAEDAG  153 (1187)
T ss_pred             HHHHHHHHHHhhcC
Confidence            99999999998877

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

Probab=98.89  E-value=8.3e-09  Score=79.52  Aligned_cols=65  Identities=34%  Similarity=0.393  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHhHHhc----CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVIIS----GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~----g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .++++|.+++..+.+    ++..++..|||+|||+.++..+-    ...                  ..+|||+|+++|+
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~----~~~------------------~~~Lvlv~~~~L~   93 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIA----ELK------------------RSTLVLVPTKELL   93 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHH----Hhc------------------CCEEEEECcHHHH
Confidence            689999999999988    89999999999999997744432    222                  2499999999999


Q ss_pred             HHHHHHHHHHH
Q psy3307         109 TQIYDEAKKFA  119 (130)
Q Consensus       109 ~q~~~~~~~l~  119 (130)
                      .|..+.+.+..
T Consensus        94 ~Qw~~~~~~~~  104 (442)
T COG1061          94 DQWAEALKKFL  104 (442)
T ss_pred             HHHHHHHHHhc
Confidence            99986665543

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.86  E-value=1.7e-08  Score=82.77  Aligned_cols=68  Identities=16%  Similarity=0.093  Sum_probs=53.5

Q ss_pred             HHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH-H
Q psy3307          39 KYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK-K  117 (130)
Q Consensus        39 ~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~-~  117 (130)
                      .+.+..+.++.+++++|+||||||.+|.+++++....                   +.+++++.|+|++|.|+.+.+. .
T Consensus         8 ~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~-------------------~~~ilvlqPrR~aA~qiA~rva~~   68 (819)
T TIGR01970         8 PALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI-------------------GGKIIMLEPRRLAARSAAQRLASQ   68 (819)
T ss_pred             HHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc-------------------CCeEEEEeCcHHHHHHHHHHHHHH
Confidence            3445566688999999999999999999999876521                   1579999999999999999874 5


Q ss_pred             HHhcCCCc
Q psy3307         118 FAYRSQLR  125 (130)
Q Consensus       118 l~~~~~~~  125 (130)
                      ++...|..
T Consensus        69 ~~~~~g~~   76 (819)
T TIGR01970        69 LGEAVGQT   76 (819)
T ss_pred             hCCCcCcE
Confidence            55555443

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

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

Probab=98.85  E-value=2.1e-08  Score=80.53  Aligned_cols=73  Identities=27%  Similarity=0.375  Sum_probs=60.5

Q ss_pred             HCCCCCCcHHHHHHHhHH----hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcC
Q psy3307          28 LARYDKPTPVQKYAIPVI----ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAP  103 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~----~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~P  103 (130)
                      .+....+++.|.+.+..+    .+|+.+++.||||+|||++|++|++.......                  .+++|.++
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~------------------~~viist~   71 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG------------------KKVIISTR   71 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC------------------CcEEEECC
Confidence            344458999999988654    35566999999999999999999999887654                  45999999


Q ss_pred             cHHHHHHHHHHHHHH
Q psy3307         104 TRELATQIYDEAKKF  118 (130)
Q Consensus       104 t~~La~q~~~~~~~l  118 (130)
                      |+.+..|+.+....+
T Consensus        72 t~~lq~q~~~~~~~~   86 (654)
T COG1199          72 TKALQEQLLEEDLPI   86 (654)
T ss_pred             CHHHHHHHHHhhcch
Confidence            999999998887654

>KOG0951|consensus

Probab=98.84  E-value=1.6e-08  Score=84.33  Aligned_cols=100  Identities=16%  Similarity=0.150  Sum_probs=79.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCc
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFP   96 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (130)
                      ++++-..++.  |...++++|....+..+.+ .++++|||||+|||...++.+|+.+..+....        .+.+....
T Consensus       296 lP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~d--------gs~nl~~f  365 (1674)
T KOG0951|consen  296 LPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLRED--------GSVNLAPF  365 (1674)
T ss_pred             Ccchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccc--------cceecccc
Confidence            4555555543  5556999999999988866 69999999999999999999999988765421        11223347


Q ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhcCCCceE
Q psy3307          97 LGLVLAPTRELATQIYDEAKKFAYRSQLRPC  127 (130)
Q Consensus        97 ~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~  127 (130)
                      ++++++|++.|++.+...+.+-...+|++|.
T Consensus       366 KIVYIAPmKaLvqE~VgsfSkRla~~GI~V~  396 (1674)
T KOG0951|consen  366 KIVYIAPMKALVQEMVGSFSKRLAPLGITVL  396 (1674)
T ss_pred             eEEEEeeHHHHHHHHHHHHHhhccccCcEEE
Confidence            8999999999999999998887788888875

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.83  E-value=1.5e-08  Score=82.88  Aligned_cols=80  Identities=19%  Similarity=0.063  Sum_probs=64.3

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|...--.+..|  -++.++||.|||+++.+|++......                   ..+.|++|++.||
T Consensus        79 lgm-~~ydVQliGgl~L~~G--~IaEm~TGEGKTL~a~lp~~l~al~g-------------------~~VhIvT~ndyLA  136 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVLDSN--RIAEMRTGEGKTLTATLPAYLNALTG-------------------KGVHVITVNDYLA  136 (908)
T ss_pred             hCC-CcCchHHhcchHhcCC--ccccccCCCCchHHHHHHHHHHHhcC-------------------CCEEEEeCCHHHH
Confidence            444 5677776544344444  47799999999999999998776543                   2399999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|..+++..+.+.+|++|.++.
T Consensus       137 ~RD~e~m~~l~~~lGlsv~~i~  158 (908)
T PRK13107        137 RRDAENNRPLFEFLGLTVGINV  158 (908)
T ss_pred             HHHHHHHHHHHHhcCCeEEEec
Confidence            9999999999999999998763

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.80  E-value=4.9e-08  Score=62.27  Aligned_cols=56  Identities=48%  Similarity=0.540  Sum_probs=45.5

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                      +++++.+|||+|||..++..+........                 ..+++|++|++.++.|..+.+......
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~-----------------~~~~lv~~p~~~l~~~~~~~~~~~~~~   56 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLK-----------------GGQVLVLAPTRELANQVAERLKELFGE   56 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhccc-----------------CCCEEEEcCcHHHHHHHHHHHHHHhhC
Confidence            46899999999999998777777655421                 157999999999999999998887763

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

>KOG0352|consensus

Probab=98.80  E-value=2.1e-08  Score=76.13  Aligned_cols=75  Identities=24%  Similarity=0.366  Sum_probs=60.5

Q ss_pred             HHHHHHH-CCCCCC-cHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceE
Q psy3307          22 ITNNIAL-ARYDKP-TPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLG   98 (130)
Q Consensus        22 i~~~l~~-~~~~~~-t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (130)
                      +-++|++ +|+..+ ++.|..++..+..+ .|+.++.|||+||++||-+|.|-.  .                    .-.
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~--~--------------------gIT   64 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH--G--------------------GIT   64 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh--C--------------------CeE
Confidence            4455655 466544 89999999887755 699999999999999999999742  1                    247


Q ss_pred             EEEcCcHHHHHHHHHHHHHH
Q psy3307          99 LVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        99 lil~Pt~~La~q~~~~~~~l  118 (130)
                      ||++|..+|..+..+++.++
T Consensus        65 IV~SPLiALIkDQiDHL~~L   84 (641)
T KOG0352|consen   65 IVISPLIALIKDQIDHLKRL   84 (641)
T ss_pred             EEehHHHHHHHHHHHHHHhc
Confidence            89999999999999998776

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

Probab=98.75  E-value=4.3e-08  Score=81.18  Aligned_cols=75  Identities=24%  Similarity=0.307  Sum_probs=62.6

Q ss_pred             HHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          25 NIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        25 ~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      .....+| .+.++|++++..+.+|.+++++||||+|||+..-.++-..+..+                   -++++.+|.
T Consensus       112 ~~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~-------------------qrviYTsPI  171 (1041)
T COG4581         112 PAREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDG-------------------QRVIYTSPI  171 (1041)
T ss_pred             HHHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcC-------------------CceEeccch
Confidence            4456788 78999999999999999999999999999998766665554433                   359999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy3307         105 RELATQIYDEAKKFA  119 (130)
Q Consensus       105 ~~La~q~~~~~~~l~  119 (130)
                      ++|..|.++.+...-
T Consensus       172 KALsNQKyrdl~~~f  186 (1041)
T COG4581         172 KALSNQKYRDLLAKF  186 (1041)
T ss_pred             hhhhhhHHHHHHHHh
Confidence            999999999986543

>PRK09694 helicase Cas3; Provisional

Probab=98.74  E-value=6.3e-08  Score=79.81  Aligned_cols=73  Identities=21%  Similarity=0.167  Sum_probs=55.8

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..|+|+|..+......+..+++.||||+|||.+.+..+.........                 .++++..||++.++|+
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~-----------------~gi~~aLPT~Atan~m  347 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLA-----------------DSIIFALPTQATANAM  347 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCC-----------------CeEEEECcHHHHHHHH
Confidence            48999999886444456678999999999999987765543332211                 4689999999999999


Q ss_pred             HHHHHHHHhc
Q psy3307         112 YDEAKKFAYR  121 (130)
Q Consensus       112 ~~~~~~l~~~  121 (130)
                      ++.++++.+.
T Consensus       348 ~~Rl~~~~~~  357 (878)
T PRK09694        348 LSRLEALASK  357 (878)
T ss_pred             HHHHHHHHHH
Confidence            9999875543

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

Probab=98.74  E-value=4.9e-08  Score=82.30  Aligned_cols=70  Identities=23%  Similarity=0.279  Sum_probs=55.2

Q ss_pred             CCcHHHHHHHhHHh----cC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVII----SG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .++++|.+++..+.    +| +..++.++||||||+.. +.++.++......                .++|+++++++|
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~~~----------------~rVLfLvDR~~L  475 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAKRF----------------RRILFLVDRSAL  475 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcCcc----------------CeEEEEecHHHH
Confidence            58999999998775    33 68999999999999874 4455555443221                579999999999


Q ss_pred             HHHHHHHHHHHH
Q psy3307         108 ATQIYDEAKKFA  119 (130)
Q Consensus       108 a~q~~~~~~~l~  119 (130)
                      +.|..+.|+.+.
T Consensus       476 ~~Qa~~~F~~~~  487 (1123)
T PRK11448        476 GEQAEDAFKDTK  487 (1123)
T ss_pred             HHHHHHHHHhcc
Confidence            999999998763

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.66  E-value=1.6e-07  Score=75.97  Aligned_cols=65  Identities=18%  Similarity=0.232  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHhHHh-cC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          33 KPTPVQKYAIPVII-SG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~-~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      .++|+|.+++..++ +|  +..+++.|||+|||+..+..+ ..+   .                  .++|||||+.+|+.
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa-~~l---~------------------k~tLILvps~~Lv~  312 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAA-CTV---K------------------KSCLVLCTSAVSVE  312 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHH-HHh---C------------------CCEEEEeCcHHHHH
Confidence            68999999998887 44  478999999999999875443 222   1                  24999999999999


Q ss_pred             HHHHHHHHHH
Q psy3307         110 QIYDEAKKFA  119 (130)
Q Consensus       110 q~~~~~~~l~  119 (130)
                      |+.+.+.++.
T Consensus       313 QW~~ef~~~~  322 (732)
T TIGR00603       313 QWKQQFKMWS  322 (732)
T ss_pred             HHHHHHHHhc
Confidence            9999999875

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).

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

Probab=98.56  E-value=5.1e-07  Score=69.60  Aligned_cols=75  Identities=24%  Similarity=0.163  Sum_probs=60.5

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      +++.+|......++.+ |.+++.|||-|||+..++-+..++....                  .++|+++||+-|+.|..
T Consensus        15 e~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~------------------~kvlfLAPTKPLV~Qh~   75 (542)
T COG1111          15 EPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFG------------------GKVLFLAPTKPLVLQHA   75 (542)
T ss_pred             cHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcC------------------CeEEEecCCchHHHHHH
Confidence            6788888877777766 8999999999999988777777776543                  36999999999999999


Q ss_pred             HHHHHHHhcCCCce
Q psy3307         113 DEAKKFAYRSQLRP  126 (130)
Q Consensus       113 ~~~~~l~~~~~~~~  126 (130)
                      ..|+++..-..-.+
T Consensus        76 ~~~~~v~~ip~~~i   89 (542)
T COG1111          76 EFCRKVTGIPEDEI   89 (542)
T ss_pred             HHHHHHhCCChhhe
Confidence            99998866543333

>TIGR00595 priA primosomal protein N'

Probab=98.53  E-value=2.8e-07  Score=72.25  Aligned_cols=48  Identities=33%  Similarity=0.389  Sum_probs=37.8

Q ss_pred             EEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          52 MACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        52 l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      ++.|+||||||.+|+..+...+ ...                  .+++|++|+++|+.|+.+.+++.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l-~~g------------------~~vLvlvP~i~L~~Q~~~~l~~~   48 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVL-ALG------------------KSVLVLVPEIALTPQMIQRFKYR   48 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHH-HcC------------------CeEEEEeCcHHHHHHHHHHHHHH
Confidence            4689999999999965544333 322                  46999999999999999998764

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).

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.48  E-value=9e-07  Score=72.12  Aligned_cols=79  Identities=20%  Similarity=0.133  Sum_probs=68.5

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|...--.+..|+  ++...||+|||++..+|+........                   .+.+++||.-||
T Consensus        77 ~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~-------------------~v~vvT~neyLA  134 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGK-------------------GVHVVTVNEYLS  134 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC-------------------CeEEEeccHHHH
Confidence            565 78999988776666776  88999999999999998887776543                   589999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|-+..+..+.+.+|++|.++
T Consensus       135 ~Rd~e~~~~~~~~LGl~vg~i  155 (796)
T PRK12906        135 SRDATEMGELYRWLGLTVGLN  155 (796)
T ss_pred             HhhHHHHHHHHHhcCCeEEEe
Confidence            999999999999999999876

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.46  E-value=2.1e-06  Score=69.25  Aligned_cols=79  Identities=18%  Similarity=0.073  Sum_probs=69.0

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|....-.++.|+  ++...||+|||++..+|+.......                   ..+.+++|+--||
T Consensus        75 lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G-------------------~~VhvvT~NdyLA  132 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQG-------------------RRVHVITVNDYLA  132 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcC-------------------CCeEEEcCCHHHH
Confidence            566 78999999998888875  5699999999999999888776554                   3589999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|-++++..+.+.+|+++.++
T Consensus       133 ~RDae~m~~ly~~LGLsvg~i  153 (764)
T PRK12326        133 RRDAEWMGPLYEALGLTVGWI  153 (764)
T ss_pred             HHHHHHHHHHHHhcCCEEEEE
Confidence            999999999999999999876

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

Probab=98.42  E-value=3.4e-06  Score=70.60  Aligned_cols=93  Identities=25%  Similarity=0.245  Sum_probs=76.8

Q ss_pred             CCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          17 QMTEIITNNIAL-ARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        17 ~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      +.+.+..+.+.+ ++| .-|+-|..||..+.+.      .|-++|+.-|=|||-..+=+++..+...             
T Consensus       578 ~~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~G-------------  643 (1139)
T COG1197         578 PPDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDG-------------  643 (1139)
T ss_pred             CCChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCC-------------
Confidence            345555656544 677 5699999999999744      5999999999999999988888776544             


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                            .++.++|||.-||+|.++.|+.-..++++++..+
T Consensus       644 ------KQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~L  677 (1139)
T COG1197         644 ------KQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVL  677 (1139)
T ss_pred             ------CeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEe
Confidence                  5799999999999999999999889999988764

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

Probab=98.41  E-value=2.2e-06  Score=59.68  Aligned_cols=73  Identities=23%  Similarity=0.281  Sum_probs=49.4

Q ss_pred             CcHHHHHHHhHHhcCCc-EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRD-VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~-~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      +++-|.+|+..+++..+ .++.||+|||||... ..++..+......          .....+.++|+++|+..-++++.
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l-~~~i~~~~~~~~~----------~~~~~~~~il~~~~sN~avd~~~   70 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTL-ASIIAQLLQRFKS----------RSADRGKKILVVSPSNAAVDNIL   70 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHH-HHHHHHH-----------------HCCCSS-EEEEESSHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHH-HHHHHHhccchhh----------hhhhccccceeecCCchhHHHHH
Confidence            57899999999999998 999999999999543 3444444211000          00111267999999999999999


Q ss_pred             HHHHH
Q psy3307         113 DEAKK  117 (130)
Q Consensus       113 ~~~~~  117 (130)
                      ..+.+
T Consensus        71 ~~l~~   75 (236)
T PF13086_consen   71 ERLKK   75 (236)
T ss_dssp             HHHHC
T ss_pred             HHHHh
Confidence            88877

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

Probab=98.40  E-value=1.1e-06  Score=71.11  Aligned_cols=71  Identities=24%  Similarity=0.236  Sum_probs=53.3

Q ss_pred             CCcHHHHHHHhHHh----c------CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc
Q psy3307          33 KPTPVQKYAIPVII----S------GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA  102 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~------g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~  102 (130)
                      .+...|.+++..+.    +      .+..++..+||||||+..+..+...+ ....                .+++|+|+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~----------------~~~vl~lv  300 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLK----------------NPKVFFVV  300 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcC----------------CCeEEEEE
Confidence            36778999987763    2      25789999999999987654443332 2111                16899999


Q ss_pred             CcHHHHHHHHHHHHHHHh
Q psy3307         103 PTRELATQIYDEAKKFAY  120 (130)
Q Consensus       103 Pt~~La~q~~~~~~~l~~  120 (130)
                      |.++|..|..+.+..+..
T Consensus       301 dR~~L~~Q~~~~f~~~~~  318 (667)
T TIGR00348       301 DRRELDYQLMKEFQSLQK  318 (667)
T ss_pred             CcHHHHHHHHHHHHhhCC
Confidence            999999999999998863

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

>KOG0351|consensus

Probab=98.40  E-value=2.6e-07  Score=76.46  Aligned_cols=68  Identities=24%  Similarity=0.293  Sum_probs=59.2

Q ss_pred             HHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          26 IALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        26 l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      ...+|...+.+-|.++|...+.|+|.++..|||.||++||-+|.+-.   .                   .-.|||+|..
T Consensus       257 ~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~---~-------------------gitvVISPL~  314 (941)
T KOG0351|consen  257 KEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL---G-------------------GVTVVISPLI  314 (941)
T ss_pred             HHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc---C-------------------CceEEeccHH
Confidence            35579999999999999999999999999999999999998887531   1                   3589999999


Q ss_pred             HHHHHHHHHH
Q psy3307         106 ELATQIYDEA  115 (130)
Q Consensus       106 ~La~q~~~~~  115 (130)
                      +|.++....+
T Consensus       315 SLm~DQv~~L  324 (941)
T KOG0351|consen  315 SLMQDQVTHL  324 (941)
T ss_pred             HHHHHHHHhh
Confidence            9999887776

>PF13245 AAA_19: Part of AAA domain

Probab=98.35  E-value=4.4e-06  Score=49.37  Aligned_cols=60  Identities=27%  Similarity=0.349  Sum_probs=39.2

Q ss_pred             HHhHHhcCCc-EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy3307          41 AIPVIISGRD-VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEA  115 (130)
Q Consensus        41 ~i~~~~~g~~-~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~  115 (130)
                      ++...+++.+ +++.+|+|||||...+--+...+.....              . +.++++++||+..++++.+.+
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~--------------~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARAD--------------P-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhcC--------------C-CCeEEEECCCHHHHHHHHHHH
Confidence            3443334444 5559999999997654444443322111              0 156999999999999998887

>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=98.28  E-value=6.1e-06  Score=60.05  Aligned_cols=71  Identities=27%  Similarity=0.265  Sum_probs=51.8

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      +|+-|.+++..  ...++++.|..|||||.+.+-=++..+.....               ...++|+++.|+..+.++..
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~---------------~~~~Il~lTft~~aa~e~~~   63 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGV---------------PPERILVLTFTNAAAQEMRE   63 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSS---------------TGGGEEEEESSHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccC---------------ChHHheecccCHHHHHHHHH
Confidence            47889998876  77899999999999999765555544443321               12579999999999999999


Q ss_pred             HHHHHHhc
Q psy3307         114 EAKKFAYR  121 (130)
Q Consensus       114 ~~~~l~~~  121 (130)
                      .+......
T Consensus        64 ri~~~l~~   71 (315)
T PF00580_consen   64 RIRELLEE   71 (315)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHhcCc
Confidence            98876543

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 ....

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.18  E-value=1.5e-05  Score=65.77  Aligned_cols=79  Identities=18%  Similarity=0.032  Sum_probs=64.5

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .++++|...--.+..|  -++...||+|||++..+|++-.....                   ..+.|++|+.-||
T Consensus        79 lGm-~~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al~G-------------------~~VhvvT~ndyLA  136 (913)
T PRK13103         79 MGM-RHFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNALSG-------------------KGVHVVTVNDYLA  136 (913)
T ss_pred             hCC-CcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHcC-------------------CCEEEEeCCHHHH
Confidence            464 6788887655444444  46699999999999999998766554                   3589999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|-+.++..+.+.+|++|.++
T Consensus       137 ~RD~e~m~~l~~~lGl~v~~i  157 (913)
T PRK13103        137 RRDANWMRPLYEFLGLSVGIV  157 (913)
T ss_pred             HHHHHHHHHHhcccCCEEEEE
Confidence            999999999999999999876

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

Probab=98.16  E-value=1.7e-05  Score=64.46  Aligned_cols=67  Identities=30%  Similarity=0.365  Sum_probs=54.0

Q ss_pred             CCcHHHHHHHhHHhcC----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVIISG----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      ..++-|..+...+...    ...++.+.||||||-.|+=.+ ......+                  .++|+++|-.+|.
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i-~~~L~~G------------------kqvLvLVPEI~Lt  258 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAI-AKVLAQG------------------KQVLVLVPEIALT  258 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHH-HHHHHcC------------------CEEEEEeccccch
Confidence            5678999999888755    788999999999999995444 4444333                  4699999999999


Q ss_pred             HHHHHHHHHH
Q psy3307         109 TQIYDEAKKF  118 (130)
Q Consensus       109 ~q~~~~~~~l  118 (130)
                      .|+.+.++..
T Consensus       259 pq~~~rf~~r  268 (730)
T COG1198         259 PQLLARFKAR  268 (730)
T ss_pred             HHHHHHHHHH
Confidence            9999998754

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.11  E-value=1.8e-05  Score=64.71  Aligned_cols=77  Identities=26%  Similarity=0.244  Sum_probs=61.4

Q ss_pred             CCcHHHHHHHhHHhcC---C-cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVIISG---R-DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g---~-~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      ...+.|..++..+..+   . .+++.||||.|||.+.+.+.........               ....+++++.|++.+.
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~---------------~~~~r~i~vlP~~t~i  259 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKI---------------KLKSRVIYVLPFRTII  259 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccc---------------cccceEEEEccHHHHH
Confidence            4488899998877643   3 7889999999999999998888776531               0127899999999999


Q ss_pred             HHHHHHHHHHHhcCCC
Q psy3307         109 TQIYDEAKKFAYRSQL  124 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~  124 (130)
                      +++++.++......++
T Consensus       260 e~~~~r~~~~~~~~~~  275 (733)
T COG1203         260 EDMYRRAKEIFGLFSV  275 (733)
T ss_pred             HHHHHHHHhhhccccc
Confidence            9999999987665443

>KOG1132|consensus

Probab=98.10  E-value=2.1e-05  Score=64.29  Aligned_cols=95  Identities=19%  Similarity=0.253  Sum_probs=66.7

Q ss_pred             CCCCCCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC-----C-C-------CC--C---
Q psy3307          29 ARYDKPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT-----P-P-------AG--R---   86 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~-----~-~-------~~--~---   86 (130)
                      +.| .|++.|...+..++    ++.+.++.+|||+|||++.+...|.+....+....     . .       ..  .   
T Consensus        18 fP~-qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~   96 (945)
T KOG1132|consen   18 FPF-QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEK   96 (945)
T ss_pred             ccC-CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCc
Confidence            344 78999999887776    45789999999999999999888888765431110     0 0       00  0   


Q ss_pred             ----CCC-CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCC
Q psy3307          87 ----GYP-SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL  124 (130)
Q Consensus        87 ----~~~-~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~  124 (130)
                          ..+ .....-|++.+-+.|+....|+.+++++.+.....
T Consensus        97 s~e~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~vkm  139 (945)
T KOG1132|consen   97 SEEAGEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYRVKM  139 (945)
T ss_pred             hhhhcCccccccCCceEEEecchHHHHHHHHHHHhhcCCCCce
Confidence                001 01123578888899999999999999998777433

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

Probab=98.10  E-value=5.5e-05  Score=54.84  Aligned_cols=80  Identities=23%  Similarity=0.198  Sum_probs=61.7

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      ..|+ .|++.|..++-.+..|+  +++..||-|||+...+|..-.....                   ..+-|++.+.-|
T Consensus        73 ~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G-------------------~~V~vvT~NdyL  130 (266)
T PF07517_consen   73 TLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQG-------------------KGVHVVTSNDYL  130 (266)
T ss_dssp             HTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTS-------------------S-EEEEESSHHH
T ss_pred             HcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhc-------------------CCcEEEeccHHH
Confidence            4565 79999999997776776  8899999999999877776555433                   358899999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEe
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      |..=++++..+-+.+|+++.++
T Consensus       131 A~RD~~~~~~~y~~LGlsv~~~  152 (266)
T PF07517_consen  131 AKRDAEEMRPFYEFLGLSVGII  152 (266)
T ss_dssp             HHHHHHHHHHHHHHTT--EEEE
T ss_pred             hhccHHHHHHHHHHhhhccccC
Confidence            9999999999999999998875

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 ....

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

Probab=98.08  E-value=8.7e-06  Score=63.56  Aligned_cols=70  Identities=33%  Similarity=0.445  Sum_probs=53.8

Q ss_pred             CCcHHHHHHHhHHhcC-----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g-----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|+.-|-.||..+..|     +.-.+.+.||||||++. .-++..+.                     .-+||++|.+.|
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~-AnVI~~~~---------------------rPtLV~AhNKTL   69 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTM-ANVIAKVQ---------------------RPTLVLAHNKTL   69 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHH-HHHHHHhC---------------------CCeEEEecchhH
Confidence            6788888888877644     57788899999999863 34444332                     238999999999


Q ss_pred             HHHHHHHHHHHHhcCCC
Q psy3307         108 ATQIYDEAKKFAYRSQL  124 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~  124 (130)
                      |.|++.+++.|.-+-.+
T Consensus        70 AaQLy~Efk~fFP~NaV   86 (663)
T COG0556          70 AAQLYSEFKEFFPENAV   86 (663)
T ss_pred             HHHHHHHHHHhCcCcce
Confidence            99999999998665433

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

Probab=98.05  E-value=5.2e-05  Score=52.54  Aligned_cols=63  Identities=22%  Similarity=0.298  Sum_probs=44.9

Q ss_pred             CCcHHHHHHHhHHhcCC--cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGR--DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~--~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      ++++-|.+++..++.+.  -.++.++.|+|||.. +-.+...+....                  .++++++||...+..
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~g------------------~~v~~~apT~~Aa~~   61 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEAAG------------------KRVIGLAPTNKAAKE   61 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHTT--------------------EEEEESSHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhCC------------------CeEEEECCcHHHHHH
Confidence            36889999999997543  577889999999974 333444444432                  569999999999988


Q ss_pred             HHHH
Q psy3307         111 IYDE  114 (130)
Q Consensus       111 ~~~~  114 (130)
                      +.+.
T Consensus        62 L~~~   65 (196)
T PF13604_consen   62 LREK   65 (196)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            7766

>TIGR00376 DNA helicase, putative

Probab=98.04  E-value=5e-05  Score=61.27  Aligned_cols=66  Identities=24%  Similarity=0.332  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      .+++.|..++..++.. ...+++||+|||||... ..++..+....                  .++++++||..-+.++
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~-~~ii~~~~~~g------------------~~VLv~a~sn~Avd~l  217 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL-VELIRQLVKRG------------------LRVLVTAPSNIAVDNL  217 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHHcC------------------CCEEEEcCcHHHHHHH
Confidence            5689999999988876 67889999999999764 34444443322                  4699999999999999


Q ss_pred             HHHHHH
Q psy3307         112 YDEAKK  117 (130)
Q Consensus       112 ~~~~~~  117 (130)
                      .+.+..
T Consensus       218 ~e~l~~  223 (637)
T TIGR00376       218 LERLAL  223 (637)
T ss_pred             HHHHHh
Confidence            888765

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.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.00  E-value=3.8e-05  Score=63.15  Aligned_cols=79  Identities=16%  Similarity=0.029  Sum_probs=63.5

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|....-.+.  ..-++...||.|||+++.+|+.-.....                   ..+.|++++..||
T Consensus        73 lG~-r~ydvQlig~l~L~--~G~IaEm~TGEGKTL~a~l~ayl~aL~G-------------------~~VhVvT~NdyLA  130 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNALTG-------------------KGVHIVTVNDYLA  130 (870)
T ss_pred             hCC-CCCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHhcC-------------------CceEEEeCCHHHH
Confidence            566 58888877653333  4567899999999999999985443332                   3489999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .+-..++..+-+.+|++|.++
T Consensus       131 ~RD~e~m~pvy~~LGLsvg~i  151 (870)
T CHL00122        131 KRDQEWMGQIYRFLGLTVGLI  151 (870)
T ss_pred             HHHHHHHHHHHHHcCCceeee
Confidence            999999999999999999875

>KOG0947|consensus

Probab=97.99  E-value=2.9e-05  Score=64.19  Aligned_cols=76  Identities=21%  Similarity=0.205  Sum_probs=61.6

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      ..+| ++...|++||-++.+|.++++.|+|.+|||+..-.++...-..                   ..|+++-+|-++|
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h-------------------~TR~iYTSPIKAL  352 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKH-------------------MTRTIYTSPIKAL  352 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhh-------------------ccceEecchhhhh
Confidence            4566 7899999999999999999999999999999865544322111                   1579999999999


Q ss_pred             HHHHHHHHHHHHhcCC
Q psy3307         108 ATQIYDEAKKFAYRSQ  123 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~  123 (130)
                      .+|-++.|+.-....|
T Consensus       353 SNQKfRDFk~tF~Dvg  368 (1248)
T KOG0947|consen  353 SNQKFRDFKETFGDVG  368 (1248)
T ss_pred             ccchHHHHHHhccccc
Confidence            9999999987665554

>KOG0948|consensus

Probab=97.91  E-value=3.6e-05  Score=62.33  Aligned_cols=77  Identities=26%  Similarity=0.275  Sum_probs=63.9

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      ...| .+.|.|..+|..+-++.++++.|-|.+|||.+.-.++-..+...                   -|+++-+|-++|
T Consensus       125 ~YPF-~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~k-------------------QRVIYTSPIKAL  184 (1041)
T KOG0948|consen  125 TYPF-TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREK-------------------QRVIYTSPIKAL  184 (1041)
T ss_pred             CCCc-ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhc-------------------CeEEeeChhhhh
Confidence            3444 68999999999999999999999999999999877776666544                   479999999999


Q ss_pred             HHHHHHHHHHHHhcCCC
Q psy3307         108 ATQIYDEAKKFAYRSQL  124 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~  124 (130)
                      .+|-++++..=..+.|+
T Consensus       185 SNQKYREl~~EF~DVGL  201 (1041)
T KOG0948|consen  185 SNQKYRELLEEFKDVGL  201 (1041)
T ss_pred             cchhHHHHHHHhcccce
Confidence            99999998754455443

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

Probab=97.82  E-value=6.6e-05  Score=61.23  Aligned_cols=72  Identities=28%  Similarity=0.361  Sum_probs=57.2

Q ss_pred             CCcHHHHHHHhHHh----cC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVII----SG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .++.+|..||..+.    +| +.+++.+.||+|||... +.++.++.+....                -++|+|+-.+.|
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~----------------KRVLFLaDR~~L  227 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWV----------------KRVLFLADRNAL  227 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchh----------------heeeEEechHHH
Confidence            67889999997664    44 46899999999999876 6677777655432                579999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy3307         108 ATQIYDEAKKFAYR  121 (130)
Q Consensus       108 a~q~~~~~~~l~~~  121 (130)
                      +.|.+..+..+.-.
T Consensus       228 v~QA~~af~~~~P~  241 (875)
T COG4096         228 VDQAYGAFEDFLPF  241 (875)
T ss_pred             HHHHHHHHHHhCCC
Confidence            99999888776443

>KOG1802|consensus

Probab=97.82  E-value=0.0001  Score=59.15  Aligned_cols=82  Identities=17%  Similarity=0.174  Sum_probs=62.4

Q ss_pred             HHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          25 NIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        25 ~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      .+...++..++.-|..|..+++...=.++++|+|+|||..-.--+.+.+....                  ..+|+.+|+
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~------------------~~VLvcApS  463 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHA------------------GPVLVCAPS  463 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhcC------------------CceEEEccc
Confidence            34456778889999999999999999999999999999876444444333322                  469999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCceEE
Q psy3307         105 RELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus       105 ~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                      .--++|+...+.+-    |++++-
T Consensus       464 NiAVDqLaeKIh~t----gLKVvR  483 (935)
T KOG1802|consen  464 NIAVDQLAEKIHKT----GLKVVR  483 (935)
T ss_pred             chhHHHHHHHHHhc----CceEee
Confidence            99999988776543    455543

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

Probab=97.79  E-value=5.7e-05  Score=52.78  Aligned_cols=59  Identities=22%  Similarity=0.257  Sum_probs=41.5

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      +..|+-|..++..+.+..-+++.||.|||||+..+...++.+....-                 -+.+|.-|..+.
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~-----------------~kiii~Rp~v~~   61 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEY-----------------DKIIITRPPVEA   61 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS------------------SEEEEEE-S--T
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCC-----------------cEEEEEecCCCC
Confidence            45688999999999999999999999999999998888888876321                 457777677654

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

>KOG0951|consensus

Probab=97.79  E-value=2.3e-05  Score=66.21  Aligned_cols=75  Identities=28%  Similarity=0.393  Sum_probs=59.8

Q ss_pred             CCcHHHHHHHhHHh-cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          33 KPTPVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+|+|.++++.+. ..+++++.+|+|||||.+.-++++.    ...                ..+++++.|..+.+..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~----------------~~~~vyi~p~~~i~~~~ 1202 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDT----------------IGRAVYIAPLEEIADEQ 1202 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----Ccc----------------ceEEEEecchHHHHHHH
Confidence            45899999998776 4568999999999999999888876    111                15799999999999988


Q ss_pred             HHHH-HHHHhcCCCceE
Q psy3307         112 YDEA-KKFAYRSQLRPC  127 (130)
Q Consensus       112 ~~~~-~~l~~~~~~~~~  127 (130)
                      ++.+ +++...+|..+.
T Consensus      1203 ~~~w~~~f~~~~G~~~~ 1219 (1674)
T KOG0951|consen 1203 YRDWEKKFSKLLGLRIV 1219 (1674)
T ss_pred             HHHHHHhhccccCceEE
Confidence            7776 567777777654

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

Probab=97.74  E-value=0.00023  Score=59.52  Aligned_cols=51  Identities=16%  Similarity=0.170  Sum_probs=40.4

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                      .++.+..+||||||++|+-.++......+.                 .+.||+||+.+.-+.+.+.++
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~~-----------------~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYGL-----------------FKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcCC-----------------cEEEEEeCCHHHHHHHHHHhh
Confidence            589999999999999997777665444332                 579999999998888876654

>KOG1803|consensus

Probab=97.69  E-value=0.00015  Score=57.37  Aligned_cols=64  Identities=23%  Similarity=0.319  Sum_probs=49.6

Q ss_pred             CCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      .+.+-|..|+....+. .-.+++||+|+|||..... +++++....                  -++|+..||.+-++-+
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvE-iI~qlvk~~------------------k~VLVcaPSn~AVdNi  245 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVE-IISQLVKQK------------------KRVLVCAPSNVAVDNI  245 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHH-HHHHHHHcC------------------CeEEEEcCchHHHHHH
Confidence            6688999999888877 5568899999999988644 444444433                  4699999999988888


Q ss_pred             HHHH
Q psy3307         112 YDEA  115 (130)
Q Consensus       112 ~~~~  115 (130)
                      .+.+
T Consensus       246 verl  249 (649)
T KOG1803|consen  246 VERL  249 (649)
T ss_pred             HHHh
Confidence            7753

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.63  E-value=0.00049  Score=57.06  Aligned_cols=79  Identities=19%  Similarity=0.056  Sum_probs=63.9

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|...--.+..|  -++...||-|||+++.+|+.-.....                   ..+.|++++.-||
T Consensus        82 lG~-r~ydVQliGgl~Lh~G--~IAEM~TGEGKTL~atlpaylnAL~G-------------------kgVhVVTvNdYLA  139 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVLHEG--QIAEMKTGEGKTLVATLPSYLNALTG-------------------KGVHVVTVNDYLA  139 (939)
T ss_pred             hCC-CcchhHHHhhhhhcCC--ceeeecCCCChhHHHHHHHHHHhhcC-------------------CCeEEEeCCHHHH
Confidence            465 6788887655444444  46799999999999999887655543                   3489999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ..-..++..+-+.+|++|.++
T Consensus       140 ~RDae~m~~vy~~LGLtvg~i  160 (939)
T PRK12902        140 RRDAEWMGQVHRFLGLSVGLI  160 (939)
T ss_pred             HhHHHHHHHHHHHhCCeEEEE
Confidence            999999999999999999876

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

Probab=97.55  E-value=0.00013  Score=48.25  Aligned_cols=54  Identities=33%  Similarity=0.451  Sum_probs=39.5

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      +|+--++-..+|+|||--.+--++......+                  .++|||.|||-++..+.+.++..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~------------------~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRR------------------LRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT--------------------EEEEESSHHHHHHHHHHTTTS
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHcc------------------CeEEEecccHHHHHHHHHHHhcC
Confidence            4555677889999999877666666665554                  57999999999999999988643

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

>KOG0949|consensus

Probab=97.55  E-value=0.00029  Score=58.67  Aligned_cols=69  Identities=17%  Similarity=0.193  Sum_probs=55.7

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|..+|.+.+..+=.++.+++.|||.+|||+.- ...++...+..+.                --+|+++||+.|+.|+.
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfis-fY~iEKVLResD~----------------~VVIyvaPtKaLVnQvs  573 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFIS-FYAIEKVLRESDS----------------DVVIYVAPTKALVNQVS  573 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceecc-HHHHHHHHhhcCC----------------CEEEEecchHHHhhhhh
Confidence            788999999999999999999999999999863 4455565554432                45889999999999997


Q ss_pred             HHHHHH
Q psy3307         113 DEAKKF  118 (130)
Q Consensus       113 ~~~~~l  118 (130)
                      ..++..
T Consensus       574 a~VyaR  579 (1330)
T KOG0949|consen  574 ANVYAR  579 (1330)
T ss_pred             HHHHHh
Confidence            776543

>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=97.52  E-value=0.00085  Score=48.50  Aligned_cols=66  Identities=21%  Similarity=0.282  Sum_probs=39.3

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCce
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRP  126 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~  126 (130)
                      ..+..++....|+|||+.. +.++..+......             .....+||++|. .+..|..+++.++.....+++
T Consensus        24 ~~~g~lL~de~GlGKT~~~-i~~~~~l~~~~~~-------------~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v   88 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITA-IALISYLKNEFPQ-------------RGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRV   88 (299)
T ss_dssp             TT-EEEE---TTSSHHHHH-HHHHHHHHHCCTT-------------SS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-E
T ss_pred             CCCCEEEEECCCCCchhhh-hhhhhhhhhcccc-------------ccccceeEeecc-chhhhhhhhhccccccccccc
Confidence            4468899999999999875 4444444433221             000249999999 888999999999886544444


Q ss_pred             E
Q psy3307         127 C  127 (130)
Q Consensus       127 ~  127 (130)
                      .
T Consensus        89 ~   89 (299)
T PF00176_consen   89 I   89 (299)
T ss_dssp             E
T ss_pred             c
Confidence            4

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.

>KOG0950|consensus

Probab=97.50  E-value=0.00033  Score=57.93  Aligned_cols=95  Identities=14%  Similarity=0.088  Sum_probs=76.2

Q ss_pred             CCCCCHHHHHHHHHCCCCCCcHHHHHHH--hHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCC
Q psy3307          15 DIQMTEIITNNIALARYDKPTPVQKYAI--PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK   92 (130)
Q Consensus        15 ~l~l~~~i~~~l~~~~~~~~t~~Q~~~i--~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~   92 (130)
                      ..+++....-..++.|...+..+|.+++  +.++.+++.+...||+.|||++.-+-++.......               
T Consensus       205 ~~~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~r---------------  269 (1008)
T KOG0950|consen  205 KRLPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRR---------------  269 (1008)
T ss_pred             hcCchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHh---------------
Confidence            3334444444557788889999999988  67889999999999999999999888888877655               


Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceE
Q psy3307          93 KVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPC  127 (130)
Q Consensus        93 ~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~  127 (130)
                         ..++.+.|..+.+..-...+..+...+|+.+.
T Consensus       270 ---r~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve  301 (1008)
T KOG0950|consen  270 ---RNVLLILPYVSIVQEKISALSPFSIDLGFPVE  301 (1008)
T ss_pred             ---hceeEecceeehhHHHHhhhhhhccccCCcch
Confidence               24888889988888888888888888887654

>KOG1133|consensus

Probab=97.46  E-value=0.00026  Score=56.97  Aligned_cols=44  Identities=18%  Similarity=0.295  Sum_probs=38.7

Q ss_pred             CCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          33 KPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      +|+.+|...+..+.    .|+=-|..+|||+|||++.+.+.+.++...
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Confidence            78999999887654    889889999999999999999999998754

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.44  E-value=0.00091  Score=54.27  Aligned_cols=67  Identities=33%  Similarity=0.461  Sum_probs=51.4

Q ss_pred             CCcHHHHHHHhHHhcC-----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g-----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|+.-|..+|..+.+|     ++.++.+.||||||+... .++...   .                  ..+|||+|+..+
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a-~~~~~~---~------------------~p~Lvi~~n~~~   66 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA-NVIAQV---N------------------RPTLVIAHNKTL   66 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHH-HHHHHh---C------------------CCEEEEECCHHH
Confidence            6899999999887543     366789999999998642 233221   1                  238999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy3307         108 ATQIYDEAKKFAYR  121 (130)
Q Consensus       108 a~q~~~~~~~l~~~  121 (130)
                      |.|+++.++.+...
T Consensus        67 A~ql~~el~~f~p~   80 (655)
T TIGR00631        67 AAQLYNEFKEFFPE   80 (655)
T ss_pred             HHHHHHHHHHhCCC
Confidence            99999999988643

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

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=97.43  E-value=0.00057  Score=58.78  Aligned_cols=69  Identities=25%  Similarity=0.276  Sum_probs=42.9

Q ss_pred             HHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcC----cHHHHHHHHHH
Q psy3307          39 KYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAP----TRELATQIYDE  114 (130)
Q Consensus        39 ~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~P----t~~La~q~~~~  114 (130)
                      .+.+..+.++..++++|+||||||.  .+|.+........               . ..+++.-|    ++++|.++.++
T Consensus        80 ~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g~---------------~-g~I~~TQPRRlAArsLA~RVA~E  141 (1294)
T PRK11131         80 QDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRGV---------------K-GLIGHTQPRRLAARTVANRIAEE  141 (1294)
T ss_pred             HHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCC---------------C-CceeeCCCcHHHHHHHHHHHHHH
Confidence            3445555666778899999999999  5775433221110               0 11222224    68999999999


Q ss_pred             HHH-HHhcCCCc
Q psy3307         115 AKK-FAYRSQLR  125 (130)
Q Consensus       115 ~~~-l~~~~~~~  125 (130)
                      +.. ++...|.+
T Consensus       142 l~~~lG~~VGY~  153 (1294)
T PRK11131        142 LETELGGCVGYK  153 (1294)
T ss_pred             Hhhhhcceecee
Confidence            874 66666554

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.42  E-value=0.0024  Score=52.17  Aligned_cols=80  Identities=20%  Similarity=0.208  Sum_probs=53.6

Q ss_pred             CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          30 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      .-..+++-|.+++-  ....++++.|..|||||.+.+ .-+.++.....              ..+.++++++.|+..|.
T Consensus       193 e~~~L~~~Q~~av~--~~~~~~lV~agaGSGKT~vl~-~r~ayLl~~~~--------------~~~~~IL~ltft~~AA~  255 (684)
T PRK11054        193 ESSPLNPSQARAVV--NGEDSLLVLAGAGSGKTSVLV-ARAGWLLARGQ--------------AQPEQILLLAFGRQAAE  255 (684)
T ss_pred             cCCCCCHHHHHHHh--CCCCCeEEEEeCCCCHHHHHH-HHHHHHHHhCC--------------CCHHHeEEEeccHHHHH
Confidence            33478999999874  334578999999999998753 33333332221              11147999999999999


Q ss_pred             HHHHHHHHHHhcCCCce
Q psy3307         110 QIYDEAKKFAYRSQLRP  126 (130)
Q Consensus       110 q~~~~~~~l~~~~~~~~  126 (130)
                      .+.+.+.......++.+
T Consensus       256 em~eRL~~~lg~~~v~v  272 (684)
T PRK11054        256 EMDERIRERLGTEDITA  272 (684)
T ss_pred             HHHHHHHHhcCCCCcEE
Confidence            99988865443333433

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.24  E-value=0.0019  Score=52.57  Aligned_cols=70  Identities=19%  Similarity=0.135  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+++-|.+++..  ....+++.|..|||||.+..-=+...+.....               ..-++|+++-|+..|.++.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v---------------~p~~IL~lTFT~kAA~em~   64 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY---------------QARHIAAVTFTNKAAREMK   64 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC---------------CHHHeeeEechHHHHHHHH
Confidence            378999998854  24578889999999998754444333332111               1146999999999999999


Q ss_pred             HHHHHHH
Q psy3307         113 DEAKKFA  119 (130)
Q Consensus       113 ~~~~~l~  119 (130)
                      +.+.++.
T Consensus        65 ~Rl~~~l   71 (672)
T PRK10919         65 ERVAQTL   71 (672)
T ss_pred             HHHHHHh
Confidence            8887654

>PRK10536 hypothetical protein; Provisional

Probab=97.21  E-value=0.0015  Score=47.17  Aligned_cols=47  Identities=17%  Similarity=0.109  Sum_probs=37.8

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .++..-+..|...+..+.++..+++.+|.|||||+..+...++.+..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            34455688999999989888899999999999999877666665543

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=97.15  E-value=0.0026  Score=47.39  Aligned_cols=48  Identities=29%  Similarity=0.400  Sum_probs=33.5

Q ss_pred             HHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          23 TNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        23 ~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ++.+.+.|.  +++.|...+.. +..++++++.++||||||. ++-.++..+
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTT-ll~aL~~~~  172 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTT-LVNAIINEM  172 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHhh
Confidence            445555555  56777777764 4577899999999999994 445555544

>COG4889 Predicted helicase [General function prediction only]

Probab=97.15  E-value=0.00096  Score=55.46  Aligned_cols=75  Identities=28%  Similarity=0.355  Sum_probs=53.1

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHhHHhcC-----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCC
Q psy3307          21 IITNNIALARYDKPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF   95 (130)
Q Consensus        21 ~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (130)
                      ++..++.-..-+.|+|.|+.|+...++|     |.-++ ...|+|||+.. +-+.+.+..                    
T Consensus       149 e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLI-MAcGTGKTfTs-LkisEala~--------------------  206 (1518)
T COG4889         149 ELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLI-MACGTGKTFTS-LKISEALAA--------------------  206 (1518)
T ss_pred             ccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEE-EecCCCccchH-HHHHHHHhh--------------------
Confidence            4444444444568999999999988754     33333 34699999886 444444443                    


Q ss_pred             ceEEEEcCcHHHHHHHHHHHHH
Q psy3307          96 PLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        96 ~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      .++|+++|+.+|..|..+++..
T Consensus       207 ~~iL~LvPSIsLLsQTlrew~~  228 (1518)
T COG4889         207 ARILFLVPSISLLSQTLREWTA  228 (1518)
T ss_pred             hheEeecchHHHHHHHHHHHhh
Confidence            3699999999999999888754

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.11  E-value=0.004  Score=51.78  Aligned_cols=79  Identities=22%  Similarity=0.127  Sum_probs=63.9

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|...--.+..|+  +....||-|||++..+|+.-.....                   ..+-|++.+--||
T Consensus        75 lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~G-------------------kgVhVVTvNdYLA  132 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTG-------------------KGVIVSTVNEYLA  132 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcC-------------------CceEEEecchhhh
Confidence            465 78999988775655664  6899999999999988886544433                   2378888999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ..=..++..+-+.+|++|.++
T Consensus       133 ~RDae~mg~vy~fLGLsvG~i  153 (925)
T PRK12903        133 ERDAEEMGKVFNFLGLSVGIN  153 (925)
T ss_pred             hhhHHHHHHHHHHhCCceeee
Confidence            999999999999999998765

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.10  E-value=0.0028  Score=54.85  Aligned_cols=66  Identities=26%  Similarity=0.295  Sum_probs=51.0

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      .|+-|.++|.  ..|+++++.|..|||||.+.+-=++..+......                -++++++=|+..|..+..
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~----------------~~il~~tFt~~aa~e~~~   63 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDI----------------DRLLVVTFTNAAAREMKE   63 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCH----------------hhEEEEeccHHHHHHHHH
Confidence            5889999996  4789999999999999998765566555432110                359999999999988877


Q ss_pred             HHHH
Q psy3307         114 EAKK  117 (130)
Q Consensus       114 ~~~~  117 (130)
                      .+.+
T Consensus        64 ri~~   67 (1232)
T TIGR02785        64 RIEE   67 (1232)
T ss_pred             HHHH
Confidence            7654

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

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.08  E-value=0.0051  Score=49.67  Aligned_cols=68  Identities=22%  Similarity=0.190  Sum_probs=48.6

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE  114 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~  114 (130)
                      .+.|..|+-..+..+-.++.+++|+|||... .-++..+......              ...++++.+||..-|..+.+.
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~~~--------------~~~~i~l~APTgkAA~rL~e~  218 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQLADG--------------ERCRIRLAAPTGKAAARLTES  218 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhcCC--------------CCcEEEEECCcHHHHHHHHHH
Confidence            5899999999999999999999999999763 2223222221100              014688889999888888776


Q ss_pred             HHH
Q psy3307         115 AKK  117 (130)
Q Consensus       115 ~~~  117 (130)
                      +..
T Consensus       219 ~~~  221 (615)
T PRK10875        219 LGK  221 (615)
T ss_pred             HHh
Confidence            643

>TIGR01075 uvrD DNA helicase II

Probab=97.07  E-value=0.0032  Score=51.61  Aligned_cols=72  Identities=15%  Similarity=0.101  Sum_probs=52.0

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++-|.+++..  ....+++.|..|||||.+.. .-+.++......              ...++|+++-|+..|..+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~-~Ria~Li~~~~v--------------~p~~IL~lTFTnkAA~em   65 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLT-HRIAWLLSVENA--------------SPHSIMAVTFTNKAAAEM   65 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHH-HHHHHHHHcCCC--------------CHHHeEeeeccHHHHHHH
Confidence            3589999998854  34589999999999998753 333333332211              115699999999999999


Q ss_pred             HHHHHHHHh
Q psy3307         112 YDEAKKFAY  120 (130)
Q Consensus       112 ~~~~~~l~~  120 (130)
                      .+.+.++..
T Consensus        66 ~~Rl~~~~~   74 (715)
T TIGR01075        66 RHRIGALLG   74 (715)
T ss_pred             HHHHHHHhc
Confidence            999887754

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.07  E-value=0.0077  Score=49.52  Aligned_cols=67  Identities=27%  Similarity=0.227  Sum_probs=49.0

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .++ .+++-|.+++..+..++-+++.+++|||||... -.++..+......                ..+++.+||..-|
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~----------------~~v~l~ApTg~AA  381 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGL----------------LPVGLAAPTGRAA  381 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCC----------------ceEEEEeCchHHH
Confidence            454 789999999999999999999999999999743 3344433332110                3477889998887


Q ss_pred             HHHHH
Q psy3307         109 TQIYD  113 (130)
Q Consensus       109 ~q~~~  113 (130)
                      ..+.+
T Consensus       382 ~~L~e  386 (720)
T TIGR01448       382 KRLGE  386 (720)
T ss_pred             HHHHH
Confidence            76654

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=97.05  E-value=0.0041  Score=50.46  Aligned_cols=70  Identities=20%  Similarity=0.099  Sum_probs=50.4

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      +++-|.+++..  .+.++++.|..|||||.+.+-=+...+.....               ...++++++-|+..+.++.+
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~---------------~p~~IL~vTFt~~Aa~em~~   64 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGY---------------KARNIAAVTFTNKAAREMKE   64 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC---------------CHHHeEEEeccHHHHHHHHH
Confidence            68889988754  35689999999999998754444444432111               11468999999999999999


Q ss_pred             HHHHHHh
Q psy3307         114 EAKKFAY  120 (130)
Q Consensus       114 ~~~~l~~  120 (130)
                      .+.+...
T Consensus        65 Rl~~~l~   71 (664)
T TIGR01074        65 RVAKTLG   71 (664)
T ss_pred             HHHHHhC
Confidence            8876543

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

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.97  E-value=0.01  Score=50.35  Aligned_cols=64  Identities=20%  Similarity=0.086  Sum_probs=47.0

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCc-EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRD-VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~-~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|+ .+++-|..++..++.+++ +++.++.|+|||.. +-.+...+....                  .+++.++||---
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~G------------------~~V~~~ApTGkA  402 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEAAG------------------YEVRGAALSGIA  402 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHcC------------------CeEEEecCcHHH
Confidence            454 689999999999998654 68999999999974 333333333222                  568899999877


Q ss_pred             HHHHH
Q psy3307         108 ATQIY  112 (130)
Q Consensus       108 a~q~~  112 (130)
                      +..+.
T Consensus       403 A~~L~  407 (988)
T PRK13889        403 AENLE  407 (988)
T ss_pred             HHHHh
Confidence            76664

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.94  E-value=0.012  Score=48.57  Aligned_cols=76  Identities=13%  Similarity=0.119  Sum_probs=50.8

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCc
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFP   96 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (130)
                      .++..++..-..++ .+++-|..++..++.+ +-+++.++.|+|||..  +-.+.......                 +.
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtl--l~~i~~~~~~~-----------------g~  397 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTM--LKAAREAWEAA-----------------GY  397 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHH--HHHHHHHHHhC-----------------CC
Confidence            34444333322344 6899999999998874 6779999999999864  33333333322                 15


Q ss_pred             eEEEEcCcHHHHHHHHH
Q psy3307          97 LGLVLAPTRELATQIYD  113 (130)
Q Consensus        97 ~~lil~Pt~~La~q~~~  113 (130)
                      +++.++||.-.+..+.+
T Consensus       398 ~V~~~ApTg~Aa~~L~~  414 (744)
T TIGR02768       398 RVIGAALSGKAAEGLQA  414 (744)
T ss_pred             eEEEEeCcHHHHHHHHh
Confidence            68899999877776653

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.94  E-value=0.0039  Score=46.52  Aligned_cols=46  Identities=22%  Similarity=0.259  Sum_probs=31.4

Q ss_pred             HHHHCCCCCCcHHHHHHHhHH-hcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          25 NIALARYDKPTPVQKYAIPVI-ISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        25 ~l~~~~~~~~t~~Q~~~i~~~-~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      .+.+.|.  +++.|...+..+ ..+.+++++++||||||.. +-.++..+
T Consensus       122 ~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl-l~aL~~~i  168 (323)
T PRK13833        122 DYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL-ANAVIAEI  168 (323)
T ss_pred             HHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHH
Confidence            3444444  567777776544 4667999999999999974 34455544

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=96.93  E-value=0.0078  Score=48.39  Aligned_cols=69  Identities=20%  Similarity=0.251  Sum_probs=48.3

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE  114 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~  114 (130)
                      .+.|..++..++..+-.++.+++|||||... ..++..+......             ....++++.+||.--|..+.+.
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~~~-------------~~~~~I~l~APTGkAA~rL~e~  212 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTV-ARLLLALVKQSPK-------------QGKLRIALAAPTGKAAARLAES  212 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhccc-------------cCCCcEEEECCcHHHHHHHHHH
Confidence            3789999999999999999999999999753 2333333222110             0014689999998888877665


Q ss_pred             HHH
Q psy3307         115 AKK  117 (130)
Q Consensus       115 ~~~  117 (130)
                      +..
T Consensus       213 ~~~  215 (586)
T TIGR01447       213 LRK  215 (586)
T ss_pred             HHh
Confidence            543

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.93  E-value=0.0049  Score=45.51  Aligned_cols=49  Identities=20%  Similarity=0.342  Sum_probs=32.1

Q ss_pred             HHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          22 ITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        22 i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      -++.+.+.|.  +++.|...+.. +..+.+++++++||||||.. +-.++..+
T Consensus       107 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~al~~~i  156 (299)
T TIGR02782       107 TLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTL-ANALLAEI  156 (299)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHh
Confidence            3445555554  55666666654 44667999999999999974 34454444

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.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.88  E-value=0.0059  Score=50.13  Aligned_cols=71  Identities=14%  Similarity=0.099  Sum_probs=50.9

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+++-|.+++..  ....+++.|..|||||.+..- -+.++......              ..-++|+++-|+..|.++.
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~-Ria~Li~~~~v--------------~p~~IL~lTFT~kAA~Em~   71 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVH-RIAWLMQVENA--------------SPYSIMAVTFTNKAAAEMR   71 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHH-HHHHHHHcCCC--------------ChhHeEeeeccHHHHHHHH
Confidence            589999998853  245889999999999987533 33333322111              1146999999999999999


Q ss_pred             HHHHHHHh
Q psy3307         113 DEAKKFAY  120 (130)
Q Consensus       113 ~~~~~l~~  120 (130)
                      +.+.++..
T Consensus        72 ~Rl~~~~~   79 (721)
T PRK11773         72 HRIEQLLG   79 (721)
T ss_pred             HHHHHHhc
Confidence            98887654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=96.88  E-value=0.0076  Score=50.90  Aligned_cols=66  Identities=24%  Similarity=0.208  Sum_probs=48.9

Q ss_pred             CCcHHHHHHHhHHhc--CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          33 KPTPVQKYAIPVIIS--GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~--g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      .+.|+|..+...++.  ...+++.-..|.|||.-..+-+-..+.....                 -++||+||. .|..|
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~-----------------~rvLIVvP~-sL~~Q  213 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRA-----------------ERVLILVPE-TLQHQ  213 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCC-----------------CcEEEEcCH-HHHHH
Confidence            589999998877653  3478999999999998774444333332221                 369999998 89999


Q ss_pred             HHHHHH
Q psy3307         111 IYDEAK  116 (130)
Q Consensus       111 ~~~~~~  116 (130)
                      ...++.
T Consensus       214 W~~El~  219 (956)
T PRK04914        214 WLVEML  219 (956)
T ss_pred             HHHHHH
Confidence            988884

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

Probab=96.84  E-value=0.0028  Score=46.83  Aligned_cols=55  Identities=18%  Similarity=0.368  Sum_probs=38.2

Q ss_pred             cccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307           4 CLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus         4 ~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      +.+|....+|++|++++-+.+.+..     +.             -=+++.+|||||||.. +.+++.++.++.
T Consensus        99 R~Ip~~i~~~e~LglP~i~~~~~~~-----~~-------------GLILVTGpTGSGKSTT-lAamId~iN~~~  153 (353)
T COG2805          99 RLIPSKIPTLEELGLPPIVRELAES-----PR-------------GLILVTGPTGSGKSTT-LAAMIDYINKHK  153 (353)
T ss_pred             eccCccCCCHHHcCCCHHHHHHHhC-----CC-------------ceEEEeCCCCCcHHHH-HHHHHHHHhccC
Confidence            3567777888888888777663321     11             1478999999999976 467777776654

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

Probab=96.80  E-value=0.0033  Score=47.10  Aligned_cols=34  Identities=21%  Similarity=0.256  Sum_probs=29.8

Q ss_pred             CCCCCcHHHHHHHhHHhcCC-cEEEEccCCchHHH
Q psy3307          30 RYDKPTPVQKYAIPVIISGR-DVMACAQTGSGKTA   63 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~~g~-~~l~~aptGsGKT~   63 (130)
                      .|..+++-|..++..+.+++ ++++++.||||||.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTT  188 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTT  188 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHH
Confidence            45678999999998888776 99999999999997

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

Probab=96.79  E-value=0.0089  Score=44.99  Aligned_cols=70  Identities=23%  Similarity=0.291  Sum_probs=55.8

Q ss_pred             CCcHHHHHHHhHH----hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVI----ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~----~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .+++.|..+-..+    .+.+|.++.|.||+|||-- +.+.++.....+                  .++.|.+|-.+.+
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~G------------------~~vciASPRvDVc  157 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQG------------------GRVCIASPRVDVC  157 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhcC------------------CeEEEecCcccch
Confidence            6889998766544    4778999999999999974 467777777654                  5789999999999


Q ss_pred             HHHHHHHHHHHhc
Q psy3307         109 TQIYDEAKKFAYR  121 (130)
Q Consensus       109 ~q~~~~~~~l~~~  121 (130)
                      .+++..+++-..+
T Consensus       158 lEl~~Rlk~aF~~  170 (441)
T COG4098         158 LELYPRLKQAFSN  170 (441)
T ss_pred             HHHHHHHHHhhcc
Confidence            9999988765444

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.79  E-value=0.0087  Score=48.70  Aligned_cols=66  Identities=35%  Similarity=0.436  Sum_probs=50.7

Q ss_pred             CCcHHHHHHHhHHhcC-----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g-----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|++.|..++..+.++     +..++.+.+||||++... .++..   ..                  ..+|||+|+...
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~---~~------------------r~vLIVt~~~~~   69 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIAR---LQ------------------RPTLVLAHNKTL   69 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHH---hC------------------CCEEEEECCHHH
Confidence            7999999999887533     256799999999998642 22221   11                  249999999999


Q ss_pred             HHHHHHHHHHHHh
Q psy3307         108 ATQIYDEAKKFAY  120 (130)
Q Consensus       108 a~q~~~~~~~l~~  120 (130)
                      |.|+++.++.+..
T Consensus        70 A~~l~~dL~~~~~   82 (652)
T PRK05298         70 AAQLYSEFKEFFP   82 (652)
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999988854

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

Probab=96.65  E-value=0.0073  Score=41.23  Aligned_cols=48  Identities=21%  Similarity=0.427  Sum_probs=29.4

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      -+++++++.|++|+|||... ..+...+...+                   ..+..++..+|...+..
T Consensus        45 ~~~~~l~l~G~~G~GKThLa-~ai~~~~~~~g-------------------~~v~f~~~~~L~~~l~~   92 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLA-VAIANEAIRKG-------------------YSVLFITASDLLDELKQ   92 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHH-HHHHHHHHHTT---------------------EEEEEHHHHHHHHHC
T ss_pred             ccCeEEEEEhhHhHHHHHHH-HHHHHHhccCC-------------------cceeEeecCceeccccc
Confidence            36789999999999999764 34444444422                   23444566777776643

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.60  E-value=0.01  Score=45.11  Aligned_cols=26  Identities=27%  Similarity=0.388  Sum_probs=19.1

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      +..+++++|||||||.. +-.++..+.
T Consensus       149 ~GlilI~G~TGSGKTT~-l~al~~~i~  174 (372)
T TIGR02525       149 AGLGLICGETGSGKSTL-AASIYQHCG  174 (372)
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHHH
Confidence            44689999999999975 345555554

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).

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.57  E-value=0.013  Score=48.17  Aligned_cols=72  Identities=21%  Similarity=0.190  Sum_probs=50.9

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++-|.+++..  ...++++.|..|||||.+..-=+...+....-               ..-++|.++-|+..|..+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i---------------~P~~IL~lTFT~kAA~em   65 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNV---------------APWNILAITFTNKAAREM   65 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCC---------------CHHHeeeeeccHHHHHHH
Confidence            3589999998864  34679999999999998754433333322211               114689999999999999


Q ss_pred             HHHHHHHHh
Q psy3307         112 YDEAKKFAY  120 (130)
Q Consensus       112 ~~~~~~l~~  120 (130)
                      .+.+.++..
T Consensus        66 ~~Rl~~~~~   74 (726)
T TIGR01073        66 KERVEKLLG   74 (726)
T ss_pred             HHHHHHHhc
Confidence            888876643

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

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

Probab=96.55  E-value=0.011  Score=44.78  Aligned_cols=59  Identities=20%  Similarity=0.215  Sum_probs=42.9

Q ss_pred             CcHHHHHHHhHH------hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          34 PTPVQKYAIPVI------ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        34 ~t~~Q~~~i~~~------~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      +++-|++++..+      ..+..+++.++-|+|||+.  +-.+........                 ..+++++||-.-
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l--~~~i~~~~~~~~-----------------~~~~~~a~tg~A   62 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFL--IKAIIDYLRSRG-----------------KKVLVTAPTGIA   62 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHH--HHHHHHHhcccc-----------------ceEEEecchHHH
Confidence            577899998888      6888999999999999874  444433332221                 457888888777


Q ss_pred             HHHH
Q psy3307         108 ATQI  111 (130)
Q Consensus       108 a~q~  111 (130)
                      |..+
T Consensus        63 A~~i   66 (364)
T PF05970_consen   63 AFNI   66 (364)
T ss_pred             HHhc
Confidence            7666

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

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=96.48  E-value=0.027  Score=48.06  Aligned_cols=72  Identities=21%  Similarity=0.251  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .+.++|.+.+..+.    +|.+.|+.-..|.|||+-. +.++..+......               ....|||||. ++.
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~~~---------------~gp~LIVvP~-SlL  231 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYRGI---------------TGPHMVVAPK-STL  231 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhcCC---------------CCCEEEEeCh-HHH
Confidence            57899999987654    6788999999999999864 4444444432211               0248999996 677


Q ss_pred             HHHHHHHHHHHhc
Q psy3307         109 TQIYDEAKKFAYR  121 (130)
Q Consensus       109 ~q~~~~~~~l~~~  121 (130)
                      .++.++++++...
T Consensus       232 ~nW~~Ei~kw~p~  244 (1033)
T PLN03142        232 GNWMNEIRRFCPV  244 (1033)
T ss_pred             HHHHHHHHHHCCC
Confidence            8888888887643

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=96.45  E-value=0.0056  Score=50.62  Aligned_cols=53  Identities=17%  Similarity=0.276  Sum_probs=36.2

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      -++=+.+.||+|||+||+--+...-..-+.                 .+-+|+|||.+.-+-+....+..
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~YG~-----------------~KFIivVPs~AIkeGv~~~s~~~  127 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKKYGL-----------------FKFIIVVPSLAIKEGVFLTSKET  127 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHHhCc-----------------eeEEEEeccHHHHhhhHHHHHHH
Confidence            477789999999999996555443222221                 57899999987766654444333

>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=96.39  E-value=0.1  Score=37.15  Aligned_cols=94  Identities=23%  Similarity=0.349  Sum_probs=67.2

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh---cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII---SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~---~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ..|+-...+++++=.+. .++ -.++.|.+....+.   +|.|.+.+.-.|.|||.+ ++|++......+.         
T Consensus         3 ~~w~p~~~P~wLl~E~e-~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~---------   70 (229)
T PF12340_consen    3 RNWDPMEYPDWLLFEIE-SNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGS---------   70 (229)
T ss_pred             CCCCchhChHHHHHHHH-cCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCC---------
Confidence            35777777788776653 345 67999999888877   468999999999999976 5888887775442         


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHH-HHHhcCCCc
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAK-KFAYRSQLR  125 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~-~l~~~~~~~  125 (130)
                              .-+.+++|. .|..|..+.+. +++.-++-+
T Consensus        71 --------~LvrviVpk-~Ll~q~~~~L~~~lg~l~~r~  100 (229)
T PF12340_consen   71 --------RLVRVIVPK-ALLEQMRQMLRSRLGGLLNRR  100 (229)
T ss_pred             --------cEEEEEcCH-HHHHHHHHHHHHHHHHHhCCe
Confidence                    235555654 68999988886 454434433

There are two conserved sequence motifs: LLE and NMG.

>KOG1131|consensus

Probab=96.38  E-value=0.043  Score=43.61  Aligned_cols=77  Identities=17%  Similarity=0.106  Sum_probs=53.1

Q ss_pred             CCCCCCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          29 ARYDKPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      +.|...+|-|-.-+..+.    .+-+.++..|+|+|||.+.+--++..-......               ..+.++-+.|
T Consensus        12 FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~---------------~~KliYCSRT   76 (755)
T KOG1131|consen   12 FPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDE---------------HRKLIYCSRT   76 (755)
T ss_pred             cCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcc---------------cceEEEecCc
Confidence            356677888887776654    345789999999999998755555544333211               1467777788


Q ss_pred             HHHHHHHHHHHHHHHh
Q psy3307         105 RELATQIYDEAKKFAY  120 (130)
Q Consensus       105 ~~La~q~~~~~~~l~~  120 (130)
                      ..-.+....+++++..
T Consensus        77 vpEieK~l~El~~l~~   92 (755)
T KOG1131|consen   77 VPEIEKALEELKRLMD   92 (755)
T ss_pred             chHHHHHHHHHHHHHH
Confidence            8777777777777654

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

Probab=96.32  E-value=0.015  Score=41.92  Aligned_cols=67  Identities=15%  Similarity=0.307  Sum_probs=44.2

Q ss_pred             CCCCCcHHHHHHHhHHh-------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc
Q psy3307          30 RYDKPTPVQKYAIPVII-------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA  102 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~-------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~  102 (130)
                      .|......+..++..+.       .+.++++.||+|+|||... .++-..+.. .                  ...++++
T Consensus        80 d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa-~Ai~~~l~~-~------------------g~sv~f~  139 (254)
T COG1484          80 DFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLA-IAIGNELLK-A------------------GISVLFI  139 (254)
T ss_pred             cccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH-HHHHHHHHH-c------------------CCeEEEE
Confidence            34444445555444332       6789999999999999754 344444442 2                  2367778


Q ss_pred             CcHHHHHHHHHHHH
Q psy3307         103 PTRELATQIYDEAK  116 (130)
Q Consensus       103 Pt~~La~q~~~~~~  116 (130)
                      ++.+++.++...+.
T Consensus       140 ~~~el~~~Lk~~~~  153 (254)
T COG1484         140 TAPDLLSKLKAAFD  153 (254)
T ss_pred             EHHHHHHHHHHHHh
Confidence            89999999887654

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=96.32  E-value=0.021  Score=49.56  Aligned_cols=41  Identities=32%  Similarity=0.453  Sum_probs=27.6

Q ss_pred             CCCCCcHHHH---HHHhHHhcCCcEEEEccCCchHHHHHHHHHHHH
Q psy3307          30 RYDKPTPVQK---YAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        30 ~~~~~t~~Q~---~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      .|...-|+..   +.+..+.++..++++|+||||||.  .+|.+..
T Consensus        61 ~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~ll  104 (1283)
T TIGR01967        61 RYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKICL  104 (1283)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHH
Confidence            4544455543   344555566788999999999998  4676543

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.

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

Probab=96.25  E-value=0.025  Score=45.51  Aligned_cols=93  Identities=18%  Similarity=0.118  Sum_probs=58.5

Q ss_pred             CCCCCHHH-HHHHHHCCCCCCcH-------HHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3307          15 DIQMTEII-TNNIALARYDKPTP-------VQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGR   86 (130)
Q Consensus        15 ~l~l~~~i-~~~l~~~~~~~~t~-------~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~   86 (130)
                      +.+..+++ ...|.+.--..+..       -|-++| ..-.++-+++++..|||||.+.+-=+--.++..+..       
T Consensus       186 d~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneII-R~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~-------  257 (747)
T COG3973         186 DTGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEII-RFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGP-------  257 (747)
T ss_pred             CCchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHH-hccCCCeEEEecCCCCCchhHHHHHHHHHHhccccc-------
Confidence            44455554 55576654333333       333333 333667889999999999987644333333333221       


Q ss_pred             CCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        87 ~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                           -. ...+||+.|.+-...-+.+++-.|++.
T Consensus       258 -----l~-~k~vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         258 -----LQ-AKPVLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             -----cc-cCceEEEcCcHHHHHHHHHhchhhccC
Confidence                 00 123999999999999999999988875

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

Probab=96.24  E-value=0.01  Score=40.62  Aligned_cols=32  Identities=25%  Similarity=0.354  Sum_probs=25.4

Q ss_pred             CCcHHHHHHHhHH-hcCCcEEEEccCCchHHHH
Q psy3307          33 KPTPVQKYAIPVI-ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        33 ~~t~~Q~~~i~~~-~~g~~~l~~aptGsGKT~~   64 (130)
                      ..++-|...+... ..|..+++.+|||||||..
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            3567777777554 4788999999999999974

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

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

Probab=96.06  E-value=0.0063  Score=47.30  Aligned_cols=51  Identities=33%  Similarity=0.409  Sum_probs=37.9

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                      .++++.||||||||..+++|.+-.   ..                  .-++|.=|-.||........++.+.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~~------------------~s~iV~D~KgEl~~~t~~~r~~~G~   95 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---YP------------------GSMIVTDPKGELYEKTAGYRKKRGY   95 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---cc------------------CCEEEEECCCcHHHHHHHHHHHCCC
Confidence            369999999999999999998732   11                  1267777888888877776665543

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

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.04  E-value=0.0088  Score=45.28  Aligned_cols=26  Identities=27%  Similarity=0.445  Sum_probs=19.4

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      .+.-+++++|||||||... -.++..+
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            5678999999999999753 4444444

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.

>KOG2340|consensus

Probab=96.00  E-value=0.053  Score=43.07  Aligned_cols=91  Identities=18%  Similarity=0.240  Sum_probs=63.0

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccC-CchH--HHHHHHHHHHHHHhcCCCCC------------CCCCCCCCCCCCCCc
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQT-GSGK--TAAFLVPILNQMYERGPLPT------------PPAGRGYPSRKKVFP   96 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~apt-GsGK--T~~~~l~~l~~~~~~~~~~~------------~~~~~~~~~~~~~~~   96 (130)
                      ..+|+.|.+.+....+=+|++.--.+ +.|+  +-.|++-+|+++.+.+..-.            .+....+...+-..|
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            46799999999888888998643222 2344  45688999998876432111            112222233455579


Q ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhcC
Q psy3307          97 LGLVLAPTRELATQIYDEAKKFAYRS  122 (130)
Q Consensus        97 ~~lil~Pt~~La~q~~~~~~~l~~~~  122 (130)
                      ++||+||+|+-|..+.+.+..+..+.
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~  320 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGD  320 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCc
Confidence            99999999999999999999886554

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

Probab=95.98  E-value=0.018  Score=43.08  Aligned_cols=26  Identities=31%  Similarity=0.502  Sum_probs=19.5

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      ..|+++.+|||||||+  +.-.|.++..
T Consensus        97 KSNILLiGPTGsGKTl--LAqTLAk~Ln  122 (408)
T COG1219          97 KSNILLIGPTGSGKTL--LAQTLAKILN  122 (408)
T ss_pred             eccEEEECCCCCcHHH--HHHHHHHHhC
Confidence            3589999999999997  4455555543

>PRK08181 transposase; Validated

Probab=95.97  E-value=0.049  Score=39.70  Aligned_cols=30  Identities=23%  Similarity=0.396  Sum_probs=21.2

Q ss_pred             cHHHHHHHh----HHhcCCcEEEEccCCchHHHH
Q psy3307          35 TPVQKYAIP----VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        35 t~~Q~~~i~----~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...|..++.    .+-.++++++.||+|+|||..
T Consensus        89 ~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHL  122 (269)
T PRK08181         89 SKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHL  122 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHH
Confidence            345544442    233778999999999999964

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.96  E-value=0.016  Score=43.66  Aligned_cols=28  Identities=25%  Similarity=0.531  Sum_probs=20.7

Q ss_pred             HHhcCCcEEEEccCCchHHHHHHHHHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      .+..+.+++++++||||||.. +-.++..
T Consensus       158 ~v~~~~nilI~G~tGSGKTTl-l~aLl~~  185 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTM-SKTLISA  185 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHH-HHHHHcc
Confidence            445788999999999999964 3344443

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=95.94  E-value=0.029  Score=47.39  Aligned_cols=76  Identities=22%  Similarity=0.118  Sum_probs=60.2

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++++|...=-.+..|+  +....||-|||++..+|+.-......                   -+-|++-+--||..=.
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~G~-------------------gVHvVTvNDYLA~RDa  196 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALTGR-------------------GVHVVTVNDYLAQRDK  196 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHcCC-------------------CcEEEeechHhhhhhH
Confidence            46777765544444444  56999999999999999876665543                   2778888889999999


Q ss_pred             HHHHHHHhcCCCceEEe
Q psy3307         113 DEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~~~  129 (130)
                      .++..+-+.+|++|.|+
T Consensus       197 ewm~p~y~flGLtVg~i  213 (1025)
T PRK12900        197 EWMNPVFEFHGLSVGVI  213 (1025)
T ss_pred             HHHHHHHHHhCCeeeee
Confidence            99999999999999876

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

Probab=95.88  E-value=0.02  Score=47.29  Aligned_cols=52  Identities=23%  Similarity=0.287  Sum_probs=37.5

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      .-.++.||.|||||.+..- -+........                 .++++++..++|+.++...++.-
T Consensus        50 ~V~vVRSpMGTGKTtaLi~-wLk~~l~~~~-----------------~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIR-WLKDALKNPD-----------------KSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             CeEEEECCCCCCcHHHHHH-HHHHhccCCC-----------------CeEEEEEhHHHHHHHHHHHHhhc
Confidence            4558899999999987533 3332211111                 56999999999999999998754

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

>PRK05973 replicative DNA helicase; Provisional

Probab=95.85  E-value=0.035  Score=39.70  Aligned_cols=51  Identities=25%  Similarity=0.341  Sum_probs=32.0

Q ss_pred             CCCCCHHHHHHHHHCCCC----------CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHH
Q psy3307          15 DIQMTEIITNNIALARYD----------KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        15 ~l~l~~~i~~~l~~~~~~----------~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~   66 (130)
                      +.++++.+-+.-.+.||.          .+||... ...-+..|.-+++.|++|+|||...+
T Consensus        22 ~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT~lal   82 (237)
T PRK05973         22 NIPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEE-LFSQLKPGDLVLLGARPGHGKTLLGL   82 (237)
T ss_pred             CCcHHHHHHHHHHHhccchHHHHHHhccCCCCHHH-hcCCCCCCCEEEEEeCCCCCHHHHHH
Confidence            344555555555555664          4455322 33445577889999999999997543

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=95.84  E-value=0.14  Score=44.14  Aligned_cols=77  Identities=17%  Similarity=0.083  Sum_probs=53.1

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHhHHhc-CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCC
Q psy3307          17 QMTEIITNNIALARYDKPTPVQKYAIPVIIS-GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF   95 (130)
Q Consensus        17 ~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~-g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (130)
                      ++++..+++....++ .+++-|..++..+.. ++-.++.++.|+|||... -++...+....                  
T Consensus       366 ~v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~~G------------------  425 (1102)
T PRK13826        366 GVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEAAG------------------  425 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHHcC------------------
Confidence            445555555444444 789999999998864 567899999999999742 23333332222                  


Q ss_pred             ceEEEEcCcHHHHHHHHH
Q psy3307          96 PLGLVLAPTRELATQIYD  113 (130)
Q Consensus        96 ~~~lil~Pt~~La~q~~~  113 (130)
                      .+++.++||-.-+..+.+
T Consensus       426 ~~V~g~ApTgkAA~~L~e  443 (1102)
T PRK13826        426 YRVVGGALAGKAAEGLEK  443 (1102)
T ss_pred             CeEEEEcCcHHHHHHHHH
Confidence            568899999887777654

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

Probab=95.84  E-value=0.024  Score=44.51  Aligned_cols=41  Identities=24%  Similarity=0.376  Sum_probs=29.4

Q ss_pred             cHHHHHHHhHHhcCC--cEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          35 TPVQKYAIPVIISGR--DVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~--~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      ++.|...+..+++..  =+++.+|||||||.. +..+++.+...
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            666777776666543  467899999999976 46777766644

>PRK13764 ATPase; Provisional

Probab=95.84  E-value=0.03  Score=45.14  Aligned_cols=27  Identities=11%  Similarity=0.239  Sum_probs=20.4

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .++++++++|||||||.. +-.++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            467899999999999974 345555554

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

Probab=95.83  E-value=0.028  Score=42.31  Aligned_cols=52  Identities=15%  Similarity=0.176  Sum_probs=36.0

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      -+++.|.+|||||+.. +-++..+....                .+..+++++.+..|...+...+..-
T Consensus         3 v~~I~G~aGTGKTvla-~~l~~~l~~~~----------------~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    3 VILITGGAGTGKTVLA-LNLAKELQNSE----------------EGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEEecCCcCHHHHH-HHHHHHhhccc----------------cCCceEEEEecchHHHHHHHHHhhh
Confidence            4789999999999864 33343331111                1156899999999999888777543

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

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=95.83  E-value=0.0037  Score=47.51  Aligned_cols=48  Identities=27%  Similarity=0.319  Sum_probs=35.9

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      ++++.|+||||||.++++|-+...   .                  ..++|.=|--|+........++.
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~---~------------------~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW---P------------------GSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC---C------------------CCEEEEccchhHHHHHHHHHHHc
Confidence            478999999999999988876532   1                  23777778888887776666544

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.79  E-value=0.017  Score=47.18  Aligned_cols=48  Identities=13%  Similarity=0.124  Sum_probs=35.6

Q ss_pred             EEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          53 ACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        53 ~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      ..+.+|||||-.|+-.+-..+.. .                  .++||++|...|..|+.+.++...
T Consensus       165 ~~~~~GSGKTevyl~~i~~~l~~-G------------------k~vLvLvPEi~lt~q~~~rl~~~f  212 (665)
T PRK14873        165 WQALPGEDWARRLAAAAAATLRA-G------------------RGALVVVPDQRDVDRLEAALRALL  212 (665)
T ss_pred             hhcCCCCcHHHHHHHHHHHHHHc-C------------------CeEEEEecchhhHHHHHHHHHHHc
Confidence            33446999999995544444433 2                  359999999999999999998544

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

Probab=95.72  E-value=0.014  Score=43.36  Aligned_cols=41  Identities=27%  Similarity=0.383  Sum_probs=28.7

Q ss_pred             CCCcHHHHHH-HhHHhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          32 DKPTPVQKYA-IPVIISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        32 ~~~t~~Q~~~-i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ..+++.|..- |-.+..+++++++++||||||.. +.+++..+
T Consensus       126 gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~I  167 (312)
T COG0630         126 GTISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFI  167 (312)
T ss_pred             CCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhC
Confidence            3466666554 45566889999999999999963 44444443

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.72  E-value=0.041  Score=41.96  Aligned_cols=19  Identities=32%  Similarity=0.344  Sum_probs=16.5

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      +|..+++.+|||+|||...
T Consensus       136 ~g~ii~lvGptGvGKTTti  154 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTT  154 (374)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4678999999999999865

>PRK06921 hypothetical protein; Provisional

Probab=95.71  E-value=0.2  Score=36.42  Aligned_cols=28  Identities=25%  Similarity=0.363  Sum_probs=19.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .+.++++.|++|+|||... .++...+..
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~  143 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMR  143 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhh
Confidence            3678999999999999643 344444443

>PRK06526 transposase; Provisional

Probab=95.64  E-value=0.095  Score=37.85  Aligned_cols=21  Identities=24%  Similarity=0.352  Sum_probs=17.6

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +-.+.++++.||+|+|||...
T Consensus        95 i~~~~nlll~Gp~GtGKThLa  115 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLA  115 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHH
Confidence            346789999999999999654

>KOG0952|consensus

Probab=95.62  E-value=0.0095  Score=50.31  Aligned_cols=77  Identities=19%  Similarity=0.200  Sum_probs=57.4

Q ss_pred             CCcHHHHHHHhHHh-cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          33 KPTPVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ...|+|...+-... -..++++.+|||+|||++|.+++....+....                 .++++++|.+.|+...
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~-----------------~kvvyIap~kalvker  989 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPG-----------------SKVVYIAPDKALVKER  989 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCC-----------------ccEEEEcCCchhhccc
Confidence            55667766664433 33688999999999999999998877765432                 5799999999999998


Q ss_pred             HHHHHHHHhcCCCce
Q psy3307         112 YDEAKKFAYRSQLRP  126 (130)
Q Consensus       112 ~~~~~~l~~~~~~~~  126 (130)
                      .+.+.+....-|+++
T Consensus       990 ~~Dw~~r~~~~g~k~ 1004 (1230)
T KOG0952|consen  990 SDDWSKRDELPGIKV 1004 (1230)
T ss_pred             ccchhhhcccCCcee
Confidence            887765544446554

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=95.53  E-value=0.042  Score=46.72  Aligned_cols=76  Identities=18%  Similarity=0.030  Sum_probs=59.4

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++++|...=-.+..  .-+....||-|||++..+|+.-......                   -+-|++.+--||..=.
T Consensus       169 ~~yDVQliGgivLh~--G~IAEM~TGEGKTLvAtlp~yLnAL~Gk-------------------gVHvVTVNDYLA~RDa  227 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQ--GKIAEMATGEGKTLVATLPVYLNALTGN-------------------GVHVVTVNDYLAKRDS  227 (1112)
T ss_pred             cccchHHhhhhhhcC--CceeeecCCCCchhHHHHHHHHHHHcCC-------------------CcEEEEechhhhhccH
Confidence            456676654433334  4467999999999999999877666543                   2778888889999999


Q ss_pred             HHHHHHHhcCCCceEEe
Q psy3307         113 DEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~~~  129 (130)
                      .++..+-+.+|++|.++
T Consensus       228 ewmgply~fLGLsvg~i  244 (1112)
T PRK12901        228 EWMGPLYEFHGLSVDCI  244 (1112)
T ss_pred             HHHHHHHHHhCCceeec
Confidence            99999999999998875

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=95.53  E-value=0.0096  Score=48.02  Aligned_cols=50  Identities=24%  Similarity=0.154  Sum_probs=39.3

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      .++++.||||||||..+++|-+-..   .                  .-+||+=|--|+........++.+
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~---~------------------~S~VV~DpKGEl~~~Ta~~R~~~G  208 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW---E------------------DSVVVHDIKLENYELTSGWREKQG  208 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC---C------------------CCEEEEeCcHHHHHHHHHHHHHCC
Confidence            5889999999999999999988643   1                  127777788898888877776643

>PF12846 AAA_10: AAA-like domain

Probab=95.51  E-value=0.029  Score=40.37  Aligned_cols=27  Identities=33%  Similarity=0.514  Sum_probs=20.3

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      +++++.|+||||||.... .++......
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~~   28 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIRR   28 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHc
Confidence            578999999999997765 555555543

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.45  E-value=0.13  Score=38.52  Aligned_cols=27  Identities=22%  Similarity=0.326  Sum_probs=19.5

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .+.++++.|++|+|||... ..+...+.
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~  208 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELL  208 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHH
Confidence            4589999999999999732 34444444

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.43  E-value=0.079  Score=39.78  Aligned_cols=29  Identities=24%  Similarity=0.428  Sum_probs=21.4

Q ss_pred             HHhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      .+..+.+++++++||||||.. +-.++..+
T Consensus       156 ~v~~~~nili~G~tgSGKTTl-l~aL~~~i  184 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTF-TNAALREI  184 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHH-HHHHHhhC
Confidence            345788999999999999964 34445444

>PHA02533 17 large terminase protein; Provisional

Probab=95.41  E-value=0.19  Score=40.18  Aligned_cols=72  Identities=17%  Similarity=0.079  Sum_probs=54.3

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+.|.|...+..+..++-.++..+-..|||.....-.+.......                 +..+++++|+++.|..+.
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~-----------------~~~v~i~A~~~~QA~~vF  121 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNK-----------------DKNVGILAHKASMAAEVL  121 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCC-----------------CCEEEEEeCCHHHHHHHH
Confidence            578899999887766777788889999999876544443333221                 147999999999999999


Q ss_pred             HHHHHHHhc
Q psy3307         113 DEAKKFAYR  121 (130)
Q Consensus       113 ~~~~~l~~~  121 (130)
                      +.++.+.+.
T Consensus       122 ~~ik~~ie~  130 (534)
T PHA02533        122 DRTKQAIEL  130 (534)
T ss_pred             HHHHHHHHh
Confidence            888866554

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

Probab=95.41  E-value=0.077  Score=38.49  Aligned_cols=46  Identities=17%  Similarity=0.282  Sum_probs=29.2

Q ss_pred             HHHHCCCCCCcHHHHHHHhHHhc--CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          25 NIALARYDKPTPVQKYAIPVIIS--GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        25 ~l~~~~~~~~t~~Q~~~i~~~~~--g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .+.++|+   .+.|.+.+..+..  +..+++.++||||||... -.++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            3455554   4556666655543  346899999999999753 44555543

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

>KOG0744|consensus

Probab=95.37  E-value=0.079  Score=39.89  Aligned_cols=66  Identities=14%  Similarity=0.248  Sum_probs=41.0

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEE------------cCcHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVL------------APTRELATQIYDEAK  116 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil------------~Pt~~La~q~~~~~~  116 (130)
                      |-+++++|+|+|||- .+=++.+++.-+...              .+.+..++            .-+--|+.++++.+.
T Consensus       178 RliLlhGPPGTGKTS-LCKaLaQkLSIR~~~--------------~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~  242 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTS-LCKALAQKLSIRTND--------------RYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQ  242 (423)
T ss_pred             eEEEEeCCCCCChhH-HHHHHHHhheeeecC--------------ccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHH
Confidence            678999999999994 345666665543211              01222222            234457788888888


Q ss_pred             HHHhcCCCceEEe
Q psy3307         117 KFAYRSQLRPCVV  129 (130)
Q Consensus       117 ~l~~~~~~~~~~~  129 (130)
                      .+.+.-|.=++++
T Consensus       243 ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  243 ELVEDRGNLVFVL  255 (423)
T ss_pred             HHHhCCCcEEEEE
Confidence            8888766555544

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.35  E-value=0.12  Score=46.03  Aligned_cols=63  Identities=27%  Similarity=0.316  Sum_probs=45.6

Q ss_pred             CCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHH--HHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAF--LVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~--~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .+++-|..++..++.+  +-+++.+..|+|||...  ++.++..+.+..                 +..++.++||..-+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~-----------------g~~V~glAPTgkAa  897 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESE-----------------RPRVVGLGPTHRAV  897 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhcc-----------------CceEEEEechHHHH
Confidence            6899999999999854  78999999999999753  233333222211                 14688899998877


Q ss_pred             HHHH
Q psy3307         109 TQIY  112 (130)
Q Consensus       109 ~q~~  112 (130)
                      ..+.
T Consensus       898 ~~L~  901 (1623)
T PRK14712        898 GEMR  901 (1623)
T ss_pred             HHHH
Confidence            7654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.28  E-value=0.015  Score=36.45  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +..+++.+|+|+|||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            567899999999999753

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.

>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=95.25  E-value=0.043  Score=36.99  Aligned_cols=48  Identities=25%  Similarity=0.388  Sum_probs=28.6

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      +++.||+|+|||...+ -++.......                  .++++++ +.+-..++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~-~~~~~~~~~g------------------~~v~~~s-~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFAL-QFLYAGLARG------------------EPGLYVT-LEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHH-HHHHHHHHCC------------------CcEEEEE-CCCCHHHHHHHHHHc
Confidence            6889999999997543 2222222222                  3466665 445566666666555

A related protein is found in archaea.

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

Probab=95.24  E-value=0.047  Score=41.58  Aligned_cols=49  Identities=24%  Similarity=0.258  Sum_probs=39.4

Q ss_pred             CCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307          29 ARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      .|+..-+-.|..|+..+++.  .-+.+.++-|||||+..+.+.+.+....+
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~  274 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERK  274 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHh
Confidence            46655677899999988866  45678899999999999888888877654

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

Probab=95.23  E-value=0.034  Score=40.07  Aligned_cols=31  Identities=23%  Similarity=0.416  Sum_probs=22.6

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      +..+.++++.|+||||||... -.++..+...
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~  154 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE  154 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc
Confidence            346789999999999999753 5555555443

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 ....

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.23  E-value=0.023  Score=41.02  Aligned_cols=26  Identities=31%  Similarity=0.328  Sum_probs=20.8

Q ss_pred             HHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          40 YAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        40 ~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +++..+..|+++++.+|+|+|||...
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHH
Confidence            33445568899999999999999754

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

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

Probab=95.18  E-value=0.019  Score=44.14  Aligned_cols=56  Identities=23%  Similarity=0.250  Sum_probs=36.6

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|..+|+|++--+...+.+++.   .+..+.-++..-   +...+.+++.||+|+|||+..
T Consensus       138 ~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G---l~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG---IDPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC---CCCCceEEEECCCCCCHHHHH
Confidence            46778899988777777766552   233332222211   224688999999999999753

>PRK12377 putative replication protein; Provisional

Probab=95.14  E-value=0.17  Score=36.42  Aligned_cols=47  Identities=13%  Similarity=0.339  Sum_probs=29.5

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDE  114 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~  114 (130)
                      ..++++.|++|+|||... .++...+....                   ..++.++..++..++...
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~~g-------------------~~v~~i~~~~l~~~l~~~  147 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLAKG-------------------RSVIVVTVPDVMSRLHES  147 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHcC-------------------CCeEEEEHHHHHHHHHHH
Confidence            368999999999999642 34444444322                   233445666777766543

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

Probab=95.13  E-value=0.1  Score=44.52  Aligned_cols=58  Identities=22%  Similarity=0.208  Sum_probs=43.0

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCC
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ  123 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~  123 (130)
                      +.-++-=-+|||||++-+..+-. +.....                .|.+++|+-.++|-.|..+.+..+.....
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~-l~~~~~----------------~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~  331 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARL-LLELPK----------------NPKVLFVVDRKDLDDQTSDEFQSFGKVAF  331 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHH-HHhccC----------------CCeEEEEechHHHHHHHHHHHHHHHHhhh
Confidence            45778888999999885443322 222221                27899999999999999999999887644

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.10  E-value=0.086  Score=38.57  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++.+++.+|||+|||...
T Consensus       194 ~~vi~~vGptGvGKTTt~  211 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTL  211 (282)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            457889999999999764

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.02  E-value=0.093  Score=39.31  Aligned_cols=32  Identities=19%  Similarity=0.140  Sum_probs=25.1

Q ss_pred             CcHHHHHHHhHHhcC----CcEEEEccCCchHHHHH
Q psy3307          34 PTPVQKYAIPVIISG----RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g----~~~l~~aptGsGKT~~~   65 (130)
                      .+|+|...|..+...    ...+++||.|+||+...
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A   39 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALA   39 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHH
Confidence            478888888887744    26789999999999653

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=95.00  E-value=0.017  Score=47.17  Aligned_cols=49  Identities=20%  Similarity=0.180  Sum_probs=35.4

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      .++++.||||||||.++++|-+-..   .                  ..+||+=|--|+........++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~---~------------------gS~VV~DpKGE~~~~Ta~~R~~~  188 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF---K------------------GSVIALDVKGELFELTSRARKAS  188 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC---C------------------CCEEEEeCCchHHHHHHHHHHhC
Confidence            4899999999999999999986542   1                  12666667777776666555543

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

Probab=94.94  E-value=0.051  Score=38.08  Aligned_cols=29  Identities=31%  Similarity=0.387  Sum_probs=20.2

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .|..+++.+++|+|||.-.+--+...+..
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~   46 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKN   46 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhh
Confidence            45789999999999997543333344333

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 ....

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.92  E-value=0.054  Score=38.46  Aligned_cols=53  Identities=21%  Similarity=0.266  Sum_probs=33.7

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      .|..+++.+++|+|||...+--+...+. ..                  -++++++ +.+-..|+.+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~-~g------------------e~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQ-MG------------------EPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHH-cC------------------CcEEEEE-eeCCHHHHHHHHHHhC
Confidence            4679999999999999754333333332 22                  3477766 4556666666666554

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.

>PRK10436 hypothetical protein; Provisional

Probab=94.90  E-value=0.11  Score=40.69  Aligned_cols=39  Identities=26%  Similarity=0.344  Sum_probs=25.3

Q ss_pred             cHHHHHHHhHHh--cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          35 TPVQKYAIPVII--SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        35 t~~Q~~~i~~~~--~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .+.|.+.|..+.  .+--+++.+|||||||... ..++..+.
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            444555554444  3346889999999999864 45565553

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.84  E-value=0.042  Score=41.64  Aligned_cols=58  Identities=17%  Similarity=0.209  Sum_probs=37.9

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHH---CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIAL---ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~---~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +...|..+|++.|=-++.++.+++   +..++|--++.-.|   ---+.+++.+|+|+|||+..
T Consensus       142 v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI---~PPKGVLLYGPPGTGKTLLA  202 (406)
T COG1222         142 VEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGI---DPPKGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             eccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCC---CCCCceEeeCCCCCcHHHHH
Confidence            345678899999855555555544   45555444433322   12378999999999999853

>KOG0745|consensus

Probab=94.82  E-value=0.065  Score=41.74  Aligned_cols=58  Identities=21%  Similarity=0.306  Sum_probs=35.4

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH----HHHHHHHHHHHHhcC
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL----ATQIYDEAKKFAYRS  122 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L----a~q~~~~~~~l~~~~  122 (130)
                      +..|+++.+|||||||+  +.-.|.++..-                   |.+|-=|.|-..    .+++...+.+|....
T Consensus       225 eKSNvLllGPtGsGKTl--laqTLAr~ldV-------------------PfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A  283 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTL--LAQTLARVLDV-------------------PFAICDCTTLTQAGYVGEDVESVIQKLLQEA  283 (564)
T ss_pred             ecccEEEECCCCCchhH--HHHHHHHHhCC-------------------CeEEecccchhhcccccccHHHHHHHHHHHc
Confidence            44589999999999997  44555555432                   333333333222    356677777777665


Q ss_pred             CCc
Q psy3307         123 QLR  125 (130)
Q Consensus       123 ~~~  125 (130)
                      +.+
T Consensus       284 ~~n  286 (564)
T KOG0745|consen  284 EYN  286 (564)
T ss_pred             cCC
Confidence            544

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=94.79  E-value=0.08  Score=42.48  Aligned_cols=45  Identities=31%  Similarity=0.333  Sum_probs=29.4

Q ss_pred             HHHCCCCCCcHHHHHHHhHHhc--CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          26 IALARYDKPTPVQKYAIPVIIS--GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        26 l~~~~~~~~t~~Q~~~i~~~~~--g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      +.++|+   .+-|.+.|..+..  .--+++++|||||||.+. ..++..+.
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            455554   4556666655543  346789999999999764 45666553

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

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

Probab=94.72  E-value=0.068  Score=40.84  Aligned_cols=52  Identities=29%  Similarity=0.519  Sum_probs=32.6

Q ss_pred             hHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      |.-...+++++.|.||||||. ++-.++..+....                  -+++|.=|.-+.....++
T Consensus        10 ~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~g------------------~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   10 PKDSENRHILIIGATGSGKTQ-AIRHLLDQIRARG------------------DRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             -GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHTT-------------------EEEEEEETTHHHHHH--
T ss_pred             ccchhhCcEEEECCCCCCHHH-HHHHHHHHHHHcC------------------CEEEEEECCchHHHHhcC
Confidence            334566899999999999997 4567777776553                  356666677666554443

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

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=94.70  E-value=0.06  Score=42.43  Aligned_cols=45  Identities=20%  Similarity=0.296  Sum_probs=28.3

Q ss_pred             HHHCCCCCCcHHHHHHHhHHhcC-C-cEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          26 IALARYDKPTPVQKYAIPVIISG-R-DVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        26 l~~~~~~~~t~~Q~~~i~~~~~g-~-~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      +.++|+   .+-|.+.+..+... . -+++.+|||||||... ..++..+.
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            445554   45566666655543 3 4689999999999753 33455543

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

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=94.69  E-value=0.2  Score=45.76  Aligned_cols=64  Identities=33%  Similarity=0.280  Sum_probs=44.8

Q ss_pred             CCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHH--HHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          32 DKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFL--VPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~--l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      ..+++.|..++..++.+  +-+++.+..|+|||...-  +-.+....+..                 +.+++.++||..-
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~-----------------g~~v~glApT~~A 1080 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFESE-----------------QLQVIGLAPTHEA 1080 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHhc-----------------CCeEEEEeChHHH
Confidence            36899999999998865  567889999999997541  12222222211                 1568889999888


Q ss_pred             HHHHH
Q psy3307         108 ATQIY  112 (130)
Q Consensus       108 a~q~~  112 (130)
                      +.++.
T Consensus      1081 a~~L~ 1085 (1960)
T TIGR02760      1081 VGELK 1085 (1960)
T ss_pred             HHHHH
Confidence            87764

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.

>PRK09183 transposase/IS protein; Provisional

Probab=94.67  E-value=0.13  Score=37.20  Aligned_cols=21  Identities=24%  Similarity=0.343  Sum_probs=17.9

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..|.++++.||+|+|||...
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa  119 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLA  119 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHH
Confidence            457889999999999999643

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.63  E-value=0.069  Score=38.36  Aligned_cols=55  Identities=25%  Similarity=0.370  Sum_probs=34.4

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                      .|+.+++.+++|||||...+ -.+.......                  -++++ +.+.+...++.+.+..++..
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~-qfl~~~~~~g------------------e~vly-vs~~e~~~~l~~~~~~~g~d   76 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFAL-QFLYEGAREG------------------EPVLY-VSTEESPEELLENARSFGWD   76 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHH-HHHHHHHhcC------------------CcEEE-EEecCCHHHHHHHHHHcCCC
Confidence            46899999999999997542 2222222221                  23454 45667777777777665444

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=94.57  E-value=0.078  Score=39.25  Aligned_cols=20  Identities=40%  Similarity=0.594  Sum_probs=17.5

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.++++.++||||||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            45789999999999999974

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=94.50  E-value=0.064  Score=33.82  Aligned_cols=17  Identities=24%  Similarity=0.518  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      ++.+++.||+|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            68999999999999963

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.

>KOG0953|consensus

Probab=94.50  E-value=0.076  Score=42.42  Aligned_cols=51  Identities=27%  Similarity=0.393  Sum_probs=40.1

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS  122 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~  122 (130)
                      +=++-++||-||||.-.    |+++.+.+                   .+++--|.|-||.++++.+++.+-..
T Consensus       192 kIi~H~GPTNSGKTy~A----Lqrl~~ak-------------------sGvycGPLrLLA~EV~~r~na~gipC  242 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYRA----LQRLKSAK-------------------SGVYCGPLRLLAHEVYDRLNALGIPC  242 (700)
T ss_pred             eEEEEeCCCCCchhHHH----HHHHhhhc-------------------cceecchHHHHHHHHHHHhhhcCCCc
Confidence            34566789999999755    77776654                   37888899999999999998875443

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=94.48  E-value=0.23  Score=37.87  Aligned_cols=59  Identities=12%  Similarity=0.186  Sum_probs=44.8

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHH-HHHHHHHHHHHHHhcCCC
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRE-LATQIYDEAKKFAYRSQL  124 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~-La~q~~~~~~~l~~~~~~  124 (130)
                      -.++.+..|||||.+..+-++..+.....                +.+++++-++.. +-.-+...++.....+++
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~----------------~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~   62 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKK----------------QQNILAARKVQNSIRDSVFKDIENLLSIEGI   62 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCC----------------CcEEEEEehhhhHHHHHHHHHHHHHHHHcCC
Confidence            35788999999999988888877776411                156888888855 777778888877776665

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.

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=94.47  E-value=0.2  Score=43.43  Aligned_cols=55  Identities=20%  Similarity=0.209  Sum_probs=40.2

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      .+++++.|+.|||||....--++..+.....                .-++++|+-|+.-|.++...+...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~----------------~~~i~~~t~t~~aa~em~~Ri~~~   64 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVP----------------PSKILCLTYTKAAAAEMQNRVFDR   64 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCC----------------CCeEEEEecCHHHHHHHHHHHHHH
Confidence            4689999999999998766555555543211                136999999999999987666543

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

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=94.46  E-value=0.056  Score=41.61  Aligned_cols=32  Identities=25%  Similarity=0.360  Sum_probs=22.8

Q ss_pred             hHHhcCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +.-...+++++.|+||||||.. +..++..+..
T Consensus        37 ~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~   68 (410)
T cd01127          37 PKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRA   68 (410)
T ss_pred             CcchhhccEEEEcCCCCCHHHH-HHHHHHHHHh
Confidence            4444568999999999999975 4445555444

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

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=94.44  E-value=0.16  Score=38.21  Aligned_cols=40  Identities=20%  Similarity=0.209  Sum_probs=28.6

Q ss_pred             HHHHHHCCCCCCcHHHHHHHhHH-hcCCcEEEEccCCchHHHH
Q psy3307          23 TNNIALARYDKPTPVQKYAIPVI-ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        23 ~~~l~~~~~~~~t~~Q~~~i~~~-~~g~~~l~~aptGsGKT~~   64 (130)
                      ++.+.+.|+  +++.+...+..+ ..+.++++.++||||||..
T Consensus       154 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl  194 (340)
T TIGR03819       154 LDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL  194 (340)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH
Confidence            455556665  456666666554 4667999999999999864

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

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=94.41  E-value=0.12  Score=44.75  Aligned_cols=57  Identities=28%  Similarity=0.398  Sum_probs=43.4

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                      -.+.++++.|..|||||.+..-=++..+......              .-.++|+++-|+.-+..+...+.
T Consensus        14 ~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~--------------~v~~ILvvTFT~aAa~Emk~RI~   70 (1139)
T COG1074          14 PPGQSVLVEASAGTGKTFVLAERVLRLLLEGGPL--------------DVDEILVVTFTKAAAAEMKERIR   70 (1139)
T ss_pred             CCCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCC--------------ChhHeeeeeccHHHHHHHHHHHH
Confidence            3567999999999999998777777777664300              01569999999988888877764

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.38  E-value=0.2  Score=38.46  Aligned_cols=18  Identities=33%  Similarity=0.464  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++.+++.+|||+|||.+.
T Consensus       174 ~~vi~lvGptGvGKTTT~  191 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTI  191 (388)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            357899999999999865

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=94.38  E-value=0.078  Score=29.96  Aligned_cols=26  Identities=23%  Similarity=0.457  Sum_probs=18.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|...++.+++|||||.  ++-.++.+.
T Consensus        22 ~g~~tli~G~nGsGKST--llDAi~~~L   47 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKST--LLDAIQTVL   47 (62)
T ss_pred             CCcEEEEECCCCCCHHH--HHHHHHHHH
Confidence            35579999999999997  344444444

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.32  E-value=0.11  Score=36.50  Aligned_cols=19  Identities=32%  Similarity=0.349  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|..+++.+++|+|||...
T Consensus        19 ~G~~~~i~G~~G~GKT~l~   37 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFC   37 (229)
T ss_pred             CCeEEEEECCCCCChHHHH
Confidence            4689999999999998754

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.

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

Probab=94.32  E-value=0.064  Score=38.58  Aligned_cols=46  Identities=26%  Similarity=0.249  Sum_probs=26.7

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +++.++|...++....+.--..+--+..|.-+++.|++|+|||...
T Consensus         2 ~~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~   47 (271)
T cd01122           2 EEIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFL   47 (271)
T ss_pred             chhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHH
Confidence            3455666544443222211111233456788999999999999644

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

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=94.30  E-value=0.029  Score=43.62  Aligned_cols=56  Identities=21%  Similarity=0.210  Sum_probs=31.5

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|..+|.|++=-+..++.+++.   .+..+.-+...   -+...+.+++.+|+|+|||+..
T Consensus       176 ~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~---gi~~p~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        176 KAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDI---GIKPPKGVILYGPPGTGKTLLA  234 (438)
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCcEEEEECCCCCCHHHHH
Confidence            44567788876545555554432   11111111110   1234578999999999999753

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.28  E-value=0.37  Score=34.63  Aligned_cols=26  Identities=19%  Similarity=0.321  Sum_probs=18.5

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      ..+++.+++|+|||... ..+...+..
T Consensus       100 ~~~~l~G~~GtGKThLa-~aia~~l~~  125 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLA-AAICNELLL  125 (244)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            47999999999999643 344444443

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=94.24  E-value=0.33  Score=37.42  Aligned_cols=18  Identities=33%  Similarity=0.479  Sum_probs=16.3

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++-+.+.||||.|||.+.
T Consensus       203 ~~vi~LVGPTGVGKTTTl  220 (407)
T COG1419         203 KRVIALVGPTGVGKTTTL  220 (407)
T ss_pred             CcEEEEECCCCCcHHHHH
Confidence            788999999999999864

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

Probab=94.22  E-value=0.034  Score=40.52  Aligned_cols=20  Identities=35%  Similarity=0.660  Sum_probs=17.6

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +.+++.++++||+|+|||..
T Consensus        30 ~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHH
T ss_pred             HHcCCcEEEECCCCCchhHH
Confidence            34889999999999999974

>PHA02535 P terminase ATPase subunit; Provisional

Probab=94.21  E-value=0.42  Score=38.53  Aligned_cols=90  Identities=17%  Similarity=0.084  Sum_probs=65.8

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCc
Q psy3307          17 QMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFP   96 (130)
Q Consensus        17 ~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (130)
                      .+++...+.|.+.-...+.++|...+..-.+.+.-++.-.--+|||++|..-.+......+                  -
T Consensus       122 ~~s~~~~~~l~~~~~~~l~~YQ~~W~~~~~~~r~r~ilKSRQiG~T~~fA~EA~~dal~~G------------------~  183 (581)
T PHA02535        122 DISDEQTEKLIEAFLDSLFDYQKHWYRAGLHHRTRNILKSRQIGATYYFAREALEDALLTG------------------R  183 (581)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHhCccccceeeEeeecccchHHHHHHHHHHHHHhcC------------------C
Confidence            3777777787776667889999987644223455555666789999999887777666533                  2


Q ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhc-CCC
Q psy3307          97 LGLVLAPTRELATQIYDEAKKFAYR-SQL  124 (130)
Q Consensus        97 ~~lil~Pt~~La~q~~~~~~~l~~~-~~~  124 (130)
                      ..++++++++.+.+....+..+++. .++
T Consensus       184 nqiflSas~~QA~~f~~yi~~~a~~~~~v  212 (581)
T PHA02535        184 NQIFLSASKAQAHVFKQYIIAFAREAADV  212 (581)
T ss_pred             ceEEECCCHHHHHHHHHHHHHHHHhhcCc
Confidence            3788999999999988888888664 443

>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=94.21  E-value=0.054  Score=37.56  Aligned_cols=15  Identities=33%  Similarity=0.536  Sum_probs=13.1

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.+|||+|||.+.
T Consensus         4 i~lvGptGvGKTTt~   18 (196)
T PF00448_consen    4 IALVGPTGVGKTTTI   18 (196)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCchHhHH
Confidence            678999999999864

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 ....

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=94.19  E-value=0.31  Score=43.98  Aligned_cols=66  Identities=21%  Similarity=0.235  Sum_probs=45.4

Q ss_pred             CCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      .+++-|..++..++.+  +-+++.+..|+|||... -.++..+.....              ..+.+++.++||..-+..
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~--------------~~~~~V~glAPTgrAAk~ 1031 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPE--------------SERPRVVGLGPTHRAVGE 1031 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhc--------------ccCceEEEECCcHHHHHH
Confidence            6899999999999875  68899999999999752 233333221100              011468888999877776


Q ss_pred             HHH
Q psy3307         111 IYD  113 (130)
Q Consensus       111 ~~~  113 (130)
                      +.+
T Consensus      1032 L~e 1034 (1747)
T PRK13709       1032 MRS 1034 (1747)
T ss_pred             HHh
Confidence            543

>KOG0925|consensus

Probab=94.12  E-value=0.11  Score=41.08  Aligned_cols=54  Identities=15%  Similarity=0.171  Sum_probs=41.1

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHH
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.+.+.++.-.+.+++..--.....+.+.+..+.+..-+++.+.||||||.
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKtt   77 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTT   77 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccc
Confidence            567899999999998887764323344555555666678899999999999994

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=94.12  E-value=0.038  Score=44.99  Aligned_cols=50  Identities=24%  Similarity=0.315  Sum_probs=37.0

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      ..++++.||||+|||..+++|.+-.   ..                  .-++++=|..|+........++.
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~---~~------------------gS~VV~DpKgEl~~~Ta~~R~~~  273 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALK---WG------------------GPLVVLDPSTEVAPMVSEHRRDA  273 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhc---CC------------------CCEEEEeCcHHHHHHHHHHHHHC
Confidence            3688999999999999999997642   11                  12667778888887766655444

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=94.11  E-value=0.35  Score=33.64  Aligned_cols=19  Identities=26%  Similarity=0.420  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .+..+++.||+|+|||...
T Consensus        37 ~~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4578999999999999653

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.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=94.09  E-value=0.039  Score=45.09  Aligned_cols=49  Identities=24%  Similarity=0.201  Sum_probs=35.8

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      .++++.||||||||..+++|-|-..   .                  ..+||.=|--|+........++.
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~---~------------------~S~VV~D~KGEl~~~Ta~~R~~~  193 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW---P------------------GSAIVHDIKGENWQLTAGFRARF  193 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC---C------------------CCEEEEeCcchHHHHHHHHHHhC
Confidence            6899999999999999999987643   1                  12666667777766665554443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.09  E-value=0.16  Score=36.65  Aligned_cols=19  Identities=11%  Similarity=0.094  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.+++|+|||...
T Consensus        35 ~gs~~lI~G~pGtGKT~l~   53 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMV   53 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4678899999999999754

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>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=94.05  E-value=0.1  Score=37.46  Aligned_cols=23  Identities=26%  Similarity=0.525  Sum_probs=17.3

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      .+++.|++|||||. +++.++..+
T Consensus        15 r~viIG~sGSGKT~-li~~lL~~~   37 (241)
T PF04665_consen   15 RMVIIGKSGSGKTT-LIKSLLYYL   37 (241)
T ss_pred             eEEEECCCCCCHHH-HHHHHHHhh
Confidence            78899999999996 445555443

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

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=94.04  E-value=0.2  Score=40.88  Aligned_cols=54  Identities=26%  Similarity=0.367  Sum_probs=36.2

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH--HHHHHHHHHHHHHHhc
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR--ELATQIYDEAKKFAYR  121 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~--~La~q~~~~~~~l~~~  121 (130)
                      .++++.|+||+|||..+.+-+.+.+. ..                  ..++++=|-.  ++...+...+++.+..
T Consensus       177 ~H~lv~G~TGsGKT~l~~~l~~q~i~-~g------------------~~viv~DpKgD~~l~~~~~~~~~~~G~~  232 (634)
T TIGR03743       177 GHTLVLGTTGVGKTRLAELLITQDIR-RG------------------DVVIVIDPKGDADLKRRMRAEAKRAGRP  232 (634)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHH-cC------------------CeEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence            68899999999999876444433333 22                  2355555664  4778888888777654

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.98  E-value=0.48  Score=37.97  Aligned_cols=19  Identities=32%  Similarity=0.504  Sum_probs=16.5

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|..+.+.+|+|+|||...
T Consensus       349 ~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5678899999999999764

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

Probab=93.96  E-value=0.042  Score=34.80  Aligned_cols=19  Identities=37%  Similarity=0.469  Sum_probs=12.5

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      +++.+++.|++|+|||...
T Consensus         3 ~~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ----EEEEE-TTSSHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHH
Confidence            4567899999999999753

>KOG1805|consensus

Probab=93.96  E-value=0.33  Score=41.23  Aligned_cols=79  Identities=18%  Similarity=0.197  Sum_probs=52.8

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCc-EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCC
Q psy3307          17 QMTEIITNNIALARYDKPTPVQKYAIPVIISGRD-VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF   95 (130)
Q Consensus        17 ~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~-~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (130)
                      .+.+.+.+.    -...++.-|++|+-.++..+| .++.|=+|||||..... ++..+...+                  
T Consensus       657 ~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~-LIkiL~~~g------------------  713 (1100)
T KOG1805|consen  657 VLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISL-LIKILVALG------------------  713 (1100)
T ss_pred             ccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHH-HHHHHHHcC------------------
Confidence            345555553    224678999999998887764 57889999999986433 233333322                  


Q ss_pred             ceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          96 PLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        96 ~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      .++|+.+-|..-+.-+.-.++.+
T Consensus       714 kkVLLtsyThsAVDNILiKL~~~  736 (1100)
T KOG1805|consen  714 KKVLLTSYTHSAVDNILIKLKGF  736 (1100)
T ss_pred             CeEEEEehhhHHHHHHHHHHhcc
Confidence            35888888888777776666554

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

Probab=93.85  E-value=0.41  Score=40.29  Aligned_cols=31  Identities=32%  Similarity=0.440  Sum_probs=24.3

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +....+.+..+.+..-+++.|+||||||...
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTql   82 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQL   82 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHH
Confidence            4445556667778889999999999999854

>KOG0390|consensus

Probab=93.83  E-value=0.51  Score=39.26  Aligned_cols=76  Identities=21%  Similarity=0.316  Sum_probs=50.8

Q ss_pred             CCcHHHHHHHhHHh---cC-------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc
Q psy3307          33 KPTPVQKYAIPVII---SG-------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA  102 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~---~g-------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~  102 (130)
                      .++|.|.+.+.-+.   .|       ...++.-..|+|||+- +++.+.-+........+           .-.+.||++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq-~IsflwtlLrq~P~~~~-----------~~~k~lVV~  305 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQ-CISFIWTLLRQFPQAKP-----------LINKPLVVA  305 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHH-HHHHHHHHHHhCcCccc-----------cccccEEEc
Confidence            68999999997654   22       2456666789999985 35666665554322111           114589999


Q ss_pred             CcHHHHHHHHHHHHHHHhc
Q psy3307         103 PTRELATQIYDEAKKFAYR  121 (130)
Q Consensus       103 Pt~~La~q~~~~~~~l~~~  121 (130)
                      |. .|+.-+.++|.+..-.
T Consensus       306 P~-sLv~nWkkEF~KWl~~  323 (776)
T KOG0390|consen  306 PS-SLVNNWKKEFGKWLGN  323 (776)
T ss_pred             cH-HHHHHHHHHHHHhccc
Confidence            97 7888888888776553

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

Probab=93.83  E-value=0.074  Score=37.28  Aligned_cols=21  Identities=24%  Similarity=0.403  Sum_probs=14.8

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..+.++++.+|+|+|||...
T Consensus        19 AaG~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   19 AAGGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHCC--EEEES-CCCTHHHHH
T ss_pred             HcCCCCeEEECCCCCCHHHHH
Confidence            346789999999999999753

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

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=93.79  E-value=0.05  Score=34.29  Aligned_cols=14  Identities=29%  Similarity=0.563  Sum_probs=12.4

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +++.||+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            58899999999974

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=93.70  E-value=0.058  Score=43.79  Aligned_cols=50  Identities=22%  Similarity=0.323  Sum_probs=37.2

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      .++++.||||||||.++++|.+-.   ..                  --++++=|..|+.......-++.+
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~---~~------------------gS~VV~DpKgE~~~~Ta~~R~~~G  261 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALK---YG------------------GPLVCLDPSTEVAPMVCEHRRQAG  261 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhc---CC------------------CCEEEEEChHHHHHHHHHHHHHcC
Confidence            689999999999999999997542   11                  127777788888777766555554

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.70  E-value=0.15  Score=38.33  Aligned_cols=26  Identities=19%  Similarity=0.447  Sum_probs=19.0

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      .+..+++++|||||||... -.++..+
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i  146 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYI  146 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhh
Confidence            4568999999999999753 3444444

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.67  E-value=0.34  Score=37.59  Aligned_cols=19  Identities=37%  Similarity=0.473  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCchHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~   66 (130)
                      |+.+++.+|||+|||....
T Consensus       221 ~~~i~~vGptGvGKTTt~~  239 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLA  239 (424)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5678999999999997643

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=93.65  E-value=0.04  Score=42.16  Aligned_cols=55  Identities=22%  Similarity=0.247  Sum_probs=30.4

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|..+|++++--+...+.+.+.   .+..+..++..   -+..-+.+++.||+|+|||+.
T Consensus       124 ~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~---g~~~p~gvLL~GppGtGKT~l  181 (389)
T PRK03992        124 ESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEV---GIEPPKGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCCceEEECCCCCChHHH
Confidence            34556677776555555555432   12221111111   011236899999999999975

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.65  E-value=0.29  Score=34.46  Aligned_cols=28  Identities=25%  Similarity=0.297  Sum_probs=19.7

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..|.-+++.|++|+|||... +-++....
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~-~~~~~~~~   38 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFA-LNIAENIA   38 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHH-HHHHHHHH
Confidence            45678899999999999643 44443333

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.

>KOG0989|consensus

Probab=93.64  E-value=1.2  Score=33.31  Aligned_cols=79  Identities=9%  Similarity=-0.083  Sum_probs=43.8

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC----CCCCC---------------------CCCCCCCCCceEEEEc
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT----PPAGR---------------------GYPSRKKVFPLGLVLA  102 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~----~~~~~---------------------~~~~~~~~~~~~lil~  102 (130)
                      +-+.+..+|+|+|||-+.++..-+..-.......    +....                     ..-......++++|+=
T Consensus        57 lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlD  136 (346)
T KOG0989|consen   57 LPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILD  136 (346)
T ss_pred             CceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEe
Confidence            3588999999999998765443332211100000    00000                     0001122234788887


Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCce
Q psy3307         103 PTRELATQIYDEAKKFAYRSQLRP  126 (130)
Q Consensus       103 Pt~~La~q~~~~~~~l~~~~~~~~  126 (130)
                      -.-.+.......+.+..+...-.+
T Consensus       137 Ecdsmtsdaq~aLrr~mE~~s~~t  160 (346)
T KOG0989|consen  137 ECDSMTSDAQAALRRTMEDFSRTT  160 (346)
T ss_pred             chhhhhHHHHHHHHHHHhccccce
Confidence            777788888888888777644433

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.52  E-value=0.054  Score=37.45  Aligned_cols=23  Identities=26%  Similarity=0.569  Sum_probs=16.6

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHH
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      +++.+|||||||... ..++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            688999999999763 34454444

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK04328 hypothetical protein; Provisional

Probab=93.45  E-value=0.16  Score=36.37  Aligned_cols=53  Identities=21%  Similarity=0.278  Sum_probs=31.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      .|..+++.+++|+|||...+--+...+.. .                  -++++++ +.+-..++.+.++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~-g------------------e~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM-G------------------EPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc-C------------------CcEEEEE-eeCCHHHHHHHHHHcC
Confidence            46789999999999986443223332222 1                  2366665 5455556666655554

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=93.43  E-value=0.46  Score=38.67  Aligned_cols=71  Identities=23%  Similarity=0.151  Sum_probs=50.7

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+++-|.+++...  ...+++.|..|||||-+..-=+...+....-.               ..+++.++=|+..|.++.
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~---------------p~~Il~vTFTnkAA~em~   64 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVD---------------PEQILAITFTNKAAAEMR   64 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcC---------------hHHeeeeechHHHHHHHH
Confidence            4788999888555  56778888999999987544444433332211               135888889999999998


Q ss_pred             HHHHHHHh
Q psy3307         113 DEAKKFAY  120 (130)
Q Consensus       113 ~~~~~l~~  120 (130)
                      ..+.++..
T Consensus        65 ~Rl~~~~~   72 (655)
T COG0210          65 ERLLKLLG   72 (655)
T ss_pred             HHHHHHhC
Confidence            88887765

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.37  E-value=0.45  Score=32.20  Aligned_cols=64  Identities=16%  Similarity=0.136  Sum_probs=32.7

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                      .|.-.++.|++|+|||... +.+...+........        .......+++++..--. ..++.+.+.++..
T Consensus        31 ~g~l~~i~g~~g~GKT~~~-~~l~~~~~~g~~~~g--------~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLA-LQLAAALATGRPFLG--------ELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHH-HHHHHHHHT---TT-----------------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHH-HHHHHHHHhCCccCC--------cccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            5677899999999999754 444444443211100        00001246777764433 5566666665544

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

Probab=93.36  E-value=0.13  Score=40.31  Aligned_cols=32  Identities=16%  Similarity=0.256  Sum_probs=24.8

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +-......+..+..++++++.+|+|+|||...
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            33444555667778999999999999999754

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=93.34  E-value=0.063  Score=34.53  Aligned_cols=14  Identities=36%  Similarity=0.852  Sum_probs=12.4

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      ++++|++|||||..
T Consensus         2 ii~~G~pgsGKSt~   15 (143)
T PF13671_consen    2 IILCGPPGSGKSTL   15 (143)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            68899999999975

...

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=93.30  E-value=0.41  Score=39.11  Aligned_cols=55  Identities=22%  Similarity=0.290  Sum_probs=39.7

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc--HHHHHHHHHHHHHHHhcC
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT--RELATQIYDEAKKFAYRS  122 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt--~~La~q~~~~~~~l~~~~  122 (130)
                      .+.++.++||+|||..+.+-+.+.+...                   ..++++=|-  .++...+...+++.++.-
T Consensus       181 gHtlV~GtTGsGKT~l~~~li~q~i~~g-------------------~~vi~fDpkgD~el~~~~~~~~~~~GR~~  237 (643)
T TIGR03754       181 GHTLVLGTTRVGKTRLAELLITQDIRRG-------------------DVVIVFDPKGDADLLKRMYAEAKRAGRLD  237 (643)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHHcC-------------------CeEEEEeCCCCHHHHHHHHHHHHHhCCCC
Confidence            5789999999999988766555555322                   345666565  478888888888887753

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.28  E-value=0.23  Score=35.25  Aligned_cols=21  Identities=19%  Similarity=0.267  Sum_probs=17.4

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..|.-+++.+++|+|||...
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~   41 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILS   41 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            345789999999999999753

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=93.19  E-value=0.056  Score=40.84  Aligned_cols=56  Identities=21%  Similarity=0.252  Sum_probs=30.6

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|...|++++--+...+.+.+.   .+..+.-...  + -+...+.+++.||+|+|||...
T Consensus       115 ~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~--~-g~~~p~gvLL~GppGtGKT~la  173 (364)
T TIGR01242       115 ERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEE--V-GIEPPKGVLLYGPPGTGKTLLA  173 (364)
T ss_pred             cCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHh--c-CCCCCceEEEECCCCCCHHHHH
Confidence            34555667776655555555442   1212111111  1 1123467999999999999653

Many proteins may score above the trusted cutoff because an internal

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=93.17  E-value=0.062  Score=38.21  Aligned_cols=30  Identities=30%  Similarity=0.453  Sum_probs=23.8

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      +..|.-+.+.+|+|||||.  ++.++..+.+.
T Consensus        28 i~~Ge~vaI~GpSGSGKST--LLniig~ld~p   57 (226)
T COG1136          28 IEAGEFVAIVGPSGSGKST--LLNLLGGLDKP   57 (226)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHhcccCC
Confidence            4578899999999999997  66777666543

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=93.16  E-value=0.48  Score=35.48  Aligned_cols=31  Identities=26%  Similarity=0.191  Sum_probs=23.6

Q ss_pred             cHHHHHHHhHHh--cCC---cEEEEccCCchHHHHH
Q psy3307          35 TPVQKYAIPVII--SGR---DVMACAQTGSGKTAAF   65 (130)
Q Consensus        35 t~~Q~~~i~~~~--~g~---~~l~~aptGsGKT~~~   65 (130)
                      +|+|...|..+.  .|+   ..++.||.|.|||...
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la   38 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFA   38 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHH
Confidence            577777777766  333   6889999999999754

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=93.13  E-value=0.63  Score=42.70  Aligned_cols=63  Identities=14%  Similarity=0.162  Sum_probs=46.6

Q ss_pred             CCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      .+++-|.+++..++..  +-.++.++.|+|||..  +-.+..+.+..                 +.+++.++||..-+.+
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~--l~~l~~~~~~~-----------------G~~V~~lAPTgrAA~~  489 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI--AQLLLHLASEQ-----------------GYEIQIITAGSLSAQE  489 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH--HHHHHHHHHhc-----------------CCeEEEEeCCHHHHHH
Confidence            5789999999988865  6789999999999964  33333333322                 1569999999887777


Q ss_pred             HHHH
Q psy3307         111 IYDE  114 (130)
Q Consensus       111 ~~~~  114 (130)
                      +.+.
T Consensus       490 L~e~  493 (1960)
T TIGR02760       490 LRQK  493 (1960)
T ss_pred             HHHH
Confidence            6654

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.11  E-value=0.24  Score=39.01  Aligned_cols=54  Identities=22%  Similarity=0.348  Sum_probs=32.7

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      .|+.+++.+++|+|||...+--+.+.+....                  -++++++- .|-..++.+.+..++
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~~g------------------e~~lyvs~-eE~~~~l~~~~~~~G   73 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIHFD------------------EPGVFVTF-EESPQDIIKNARSFG   73 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCC------------------CCEEEEEE-ecCHHHHHHHHHHcC
Confidence            4689999999999999765433333333311                  23666663 355555555555544

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.

>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=93.10  E-value=0.068  Score=34.42  Aligned_cols=15  Identities=33%  Similarity=0.545  Sum_probs=13.3

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      ++++.+|+|+|||..
T Consensus         1 ~vlL~G~~G~GKt~l   15 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTL   15 (139)
T ss_dssp             EEEEEESSSSSHHHH
T ss_pred             CEEEECCCCCCHHHH
Confidence            579999999999974

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.08  E-value=0.21  Score=34.97  Aligned_cols=18  Identities=28%  Similarity=0.505  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+++.+++|+|||..
T Consensus        15 ~g~~~li~G~~G~GKt~~   32 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTF   32 (224)
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            357889999999999864

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.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=93.02  E-value=0.059  Score=43.85  Aligned_cols=46  Identities=26%  Similarity=0.263  Sum_probs=33.9

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEA  115 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~  115 (130)
                      .++++.||||||||..+++|.|-..   .                  ..+||+=|-.|+........
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~~---~------------------~S~VV~D~KGE~~~~Tag~R  221 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLSW---G------------------HSSVITDLKGELWALTAGWR  221 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhhC---C------------------CCEEEEeCcHHHHHHHHHHH
Confidence            5799999999999999999987531   1                  23677778888765554443

>KOG0733|consensus

Probab=93.01  E-value=0.14  Score=41.63  Aligned_cols=58  Identities=17%  Similarity=0.215  Sum_probs=36.3

Q ss_pred             cccccccCCCcCCCCCHHHHHHHHHC--CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           4 CLVSLKKQGFDDIQMTEIITNNIALA--RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         4 ~~~~~~~~~f~~l~l~~~i~~~l~~~--~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...+..-.+|+++|=-+..+..|-++  .+..|-.++...+   .--+.+++++|+|.|||..
T Consensus       180 ~~~~~snv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv---~PprGvLlHGPPGCGKT~l  239 (802)
T KOG0733|consen  180 LEFPESNVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGV---RPPRGVLLHGPPGCGKTSL  239 (802)
T ss_pred             cCCCCCCcchhhccChHHHHHHHHHHHHHhcCchhHhhcCC---CCCCceeeeCCCCccHHHH
Confidence            34455566899998555555554332  2445554444321   2237899999999999964

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.00  E-value=0.59  Score=36.32  Aligned_cols=19  Identities=32%  Similarity=0.326  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+.+.+|||+|||...
T Consensus       190 ~g~vi~lvGpnG~GKTTtl  208 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTT  208 (420)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4567899999999999864

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.99  E-value=0.092  Score=43.37  Aligned_cols=56  Identities=23%  Similarity=0.299  Sum_probs=32.4

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...+...|++++..+.+.+.|++.   .+..+.-++..   -+...+.+++.+|+|+|||+.
T Consensus       445 ~~~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~---g~~~~~giLL~GppGtGKT~l  503 (733)
T TIGR01243       445 VEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKM---GIRPPKGVLLFGPPGTGKTLL  503 (733)
T ss_pred             ccccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEECCCCCCHHHH
Confidence            334556777777777776666542   11111111111   011235799999999999974

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.

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

Probab=92.96  E-value=0.082  Score=38.86  Aligned_cols=21  Identities=29%  Similarity=0.523  Sum_probs=15.2

Q ss_pred             cEEEEccCCchHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILN   71 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~   71 (130)
                      -+++.++|||||+.+. .+++.
T Consensus       129 LviiVGaTGSGKSTtm-AaMi~  149 (375)
T COG5008         129 LVIIVGATGSGKSTTM-AAMIG  149 (375)
T ss_pred             eEEEECCCCCCchhhH-HHHhc
Confidence            4678999999998753 34444

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=92.96  E-value=0.92  Score=33.96  Aligned_cols=34  Identities=29%  Similarity=0.486  Sum_probs=26.5

Q ss_pred             CCCcHHHHHHHhHHh----cCC---cEEEEccCCchHHHHH
Q psy3307          32 DKPTPVQKYAIPVII----SGR---DVMACAQTGSGKTAAF   65 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~----~g~---~~l~~aptGsGKT~~~   65 (130)
                      ..++|+|..+|..+.    .|+   -+++.||.|+||+...
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA   43 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVA   43 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH
Confidence            457889999987765    444   5899999999998653

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=92.95  E-value=0.08  Score=33.11  Aligned_cols=14  Identities=29%  Similarity=0.591  Sum_probs=12.3

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +++.|++|||||..
T Consensus         2 I~I~G~~gsGKST~   15 (121)
T PF13207_consen    2 IIISGPPGSGKSTL   15 (121)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999974

...

>KOG0738|consensus

Probab=92.95  E-value=0.081  Score=40.70  Aligned_cols=56  Identities=18%  Similarity=0.419  Sum_probs=34.6

Q ss_pred             ccCCCcCCCCCHHHHHHHHHC--------CCCCCcH-------HHHHH-----HhHHhcC-----CcEEEEccCCchHHH
Q psy3307           9 KKQGFDDIQMTEIITNNIALA--------RYDKPTP-------VQKYA-----IPVIISG-----RDVMACAQTGSGKTA   63 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~--------~~~~~t~-------~Q~~~-----i~~~~~g-----~~~l~~aptGsGKT~   63 (130)
                      ....|+.++....+.+.+..-        .|...-.       ++..+     +|.++.|     +.+++.+|+|+|||+
T Consensus       181 ~~~~f~~~~~d~~Lve~lerdIl~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTl  260 (491)
T KOG0738|consen  181 EDKKFDSLGYDADLVEALERDILQRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTL  260 (491)
T ss_pred             ccCCCCcccchHHHHHHHHHHHhccCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHH
Confidence            445677778777777777431        1111111       22222     2455666     799999999999997


Q ss_pred             H
Q psy3307          64 A   64 (130)
Q Consensus        64 ~   64 (130)
                      .
T Consensus       261 L  261 (491)
T KOG0738|consen  261 L  261 (491)
T ss_pred             H
Confidence            4

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=92.95  E-value=1.4  Score=36.71  Aligned_cols=86  Identities=16%  Similarity=0.122  Sum_probs=57.8

Q ss_pred             HHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEE
Q psy3307          23 TNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLV  100 (130)
Q Consensus        23 ~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~li  100 (130)
                      -..+.+...+.+..-|.+.+..++++  +-+++.|.-|-|||.+.=+.+........                 ..+++|
T Consensus       204 ~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~-----------------~~~iiV  266 (758)
T COG1444         204 PRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAG-----------------SVRIIV  266 (758)
T ss_pred             CHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcC-----------------CceEEE
Confidence            33455544445555555555666644  36899999999999887666632222221                 146999


Q ss_pred             EcCcHHHHHHHHHHHHHHHhcCCCc
Q psy3307         101 LAPTRELATQIYDEAKKFAYRSQLR  125 (130)
Q Consensus       101 l~Pt~~La~q~~~~~~~l~~~~~~~  125 (130)
                      .+|+.+-++.+...+.+-.+.+|.+
T Consensus       267 TAP~~~nv~~Lf~fa~~~l~~lg~~  291 (758)
T COG1444         267 TAPTPANVQTLFEFAGKGLEFLGYK  291 (758)
T ss_pred             eCCCHHHHHHHHHHHHHhHHHhCCc
Confidence            9999999999988887777776654

>KOG0920|consensus

Probab=92.92  E-value=1.1  Score=38.14  Aligned_cols=66  Identities=21%  Similarity=0.229  Sum_probs=47.2

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      .+..+...+..+.+...+++.+.||+|||.=.---++....+.+.                ..++++--|-|--|..+++
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~----------------~~~IicTQPRRIsAIsvAe  237 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGA----------------ACNIICTQPRRISAISVAE  237 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCC----------------CCeEEecCCchHHHHHHHH
Confidence            366778888889999999999999999998654445554444331                1455555688888887766


Q ss_pred             HH
Q psy3307         114 EA  115 (130)
Q Consensus       114 ~~  115 (130)
                      +.
T Consensus       238 RV  239 (924)
T KOG0920|consen  238 RV  239 (924)
T ss_pred             HH
Confidence            65

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.89  E-value=0.36  Score=40.16  Aligned_cols=18  Identities=33%  Similarity=0.414  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |+-+.+.+|||+|||.+.
T Consensus       185 g~Vi~lVGpnGvGKTTTi  202 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTT  202 (767)
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            456789999999999865

>TIGR03689 pup_AAA proteasome ATPase

Probab=92.88  E-value=0.089  Score=41.75  Aligned_cols=53  Identities=19%  Similarity=0.269  Sum_probs=28.7

Q ss_pred             ccCCCcCCCCCHHHHHHHHH---CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           9 KKQGFDDIQMTEIITNNIAL---ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~---~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      |..+|++++=-+..++.+++   ..+..+..+...-   +...+.+++.+|+|+|||+.
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~g---l~~p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYD---LKPPKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhcc---CCCCcceEEECCCCCcHHHH
Confidence            55678887733333333332   1222222222111   11346899999999999974

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=92.79  E-value=0.19  Score=40.45  Aligned_cols=30  Identities=27%  Similarity=0.449  Sum_probs=22.0

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      ...+++++.|+||||||.. +-.++..+..+
T Consensus       174 ~e~~h~li~G~tGsGKs~~-i~~ll~~~~~~  203 (566)
T TIGR02759       174 SETQHILIHGTTGSGKSVA-IRKLLRWIRQR  203 (566)
T ss_pred             ccccceEEEcCCCCCHHHH-HHHHHHHHHhc
Confidence            3457999999999999964 45566665543

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>KOG1533|consensus

Probab=92.76  E-value=0.12  Score=37.12  Aligned_cols=25  Identities=16%  Similarity=0.228  Sum_probs=18.2

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      -++.+|+||||| +|+....+.+...
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~~   29 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSAI   29 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHHh
Confidence            467899999998 4666666655543

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=92.66  E-value=0.18  Score=41.56  Aligned_cols=55  Identities=15%  Similarity=0.187  Sum_probs=34.9

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHh--HHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIP--VIISGRDVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~--~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      +++.+.+++.+-.  .++-..-+|  .-...+++++.+-||||||.+. .-+|..+..+.
T Consensus       157 ~~l~k~lk~~~~~--s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~RG  213 (732)
T PRK13700        157 KDVARMLKKDGKD--SDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQRG  213 (732)
T ss_pred             HHHHHHHHhcCCC--CCeeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHHcC
Confidence            4566667665532  333222333  2346689999999999999854 66666666544

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=92.59  E-value=0.1  Score=35.87  Aligned_cols=20  Identities=40%  Similarity=0.511  Sum_probs=14.4

Q ss_pred             CCcEEEEccCCchHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLV   67 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l   67 (130)
                      .+.+++.||.|||||.-|..
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~   22 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQ   22 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            46799999999999986643

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>PRK08116 hypothetical protein; Validated

Probab=92.59  E-value=0.56  Score=34.11  Aligned_cols=27  Identities=26%  Similarity=0.367  Sum_probs=19.2

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      ..+++.|++|+|||... .++.+.+...
T Consensus       115 ~gl~l~G~~GtGKThLa-~aia~~l~~~  141 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLA-ACIANELIEK  141 (268)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHHc
Confidence            45999999999999643 3555555443

>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=92.54  E-value=0.36  Score=33.24  Aligned_cols=27  Identities=22%  Similarity=0.366  Sum_probs=16.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ...++++.+.||||||.+...-+.+.+
T Consensus        37 ~~~h~li~G~tgsGKS~~l~~ll~~l~   63 (205)
T PF01580_consen   37 KNPHLLIAGATGSGKSTLLRTLLLSLA   63 (205)
T ss_dssp             GS-SEEEE--TTSSHHHHHHHHHHHHH
T ss_pred             CCceEEEEcCCCCCccHHHHHHHHHHH
Confidence            345899999999999987544333333

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.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.53  E-value=0.46  Score=37.54  Aligned_cols=18  Identities=33%  Similarity=0.366  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |.-+.+.||||+|||.+.
T Consensus       256 g~Vi~LvGpnGvGKTTTi  273 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTT  273 (484)
T ss_pred             CcEEEEECCCCccHHHHH
Confidence            456889999999999865

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.42  E-value=0.94  Score=35.22  Aligned_cols=18  Identities=28%  Similarity=0.451  Sum_probs=15.2

Q ss_pred             CcEEEEccCCchHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~   66 (130)
                      +.+.+.+|+|+|||....
T Consensus       242 ~vI~LVGptGvGKTTTia  259 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLA  259 (436)
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            578999999999998643

>PRK13531 regulatory ATPase RavA; Provisional

Probab=92.37  E-value=0.28  Score=38.79  Aligned_cols=27  Identities=19%  Similarity=0.297  Sum_probs=21.7

Q ss_pred             HHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          39 KYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        39 ~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..++-.++.|.++++.+|+|+|||...
T Consensus        30 ~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         30 RLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHHHccCCCEEEECCCChhHHHHH
Confidence            334446679999999999999999754

>KOG0730|consensus

Probab=92.34  E-value=0.19  Score=40.87  Aligned_cols=61  Identities=25%  Similarity=0.391  Sum_probs=41.9

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      -|..++.|..+|+|.|=-+++.+.|++.   ..+.|-.+....   +.--+.+++.+|+|.|||+.+
T Consensus       422 Re~~ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~G---i~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  422 REILVEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFG---ISPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             hheeccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhc---CCCCceEEEECCCCcchHHHH
Confidence            3667889999999999777777777642   222322222221   123479999999999999865

>KOG0733|consensus

Probab=92.29  E-value=0.18  Score=40.92  Aligned_cols=60  Identities=23%  Similarity=0.391  Sum_probs=38.7

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHH---CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIAL---ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~---~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      |.+.--|..+|.|.|--+++-..|..   ..+++|--++...+.   .-..+++++|+|.|||+..
T Consensus       500 EGF~tVPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~---~PsGvLL~GPPGCGKTLlA  562 (802)
T KOG0733|consen  500 EGFATVPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGID---APSGVLLCGPPGCGKTLLA  562 (802)
T ss_pred             ccceecCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCC---CCCceEEeCCCCccHHHHH
Confidence            55666688899999966666655543   233443333333221   1357999999999999843

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=92.24  E-value=1.2  Score=33.52  Aligned_cols=31  Identities=19%  Similarity=0.225  Sum_probs=22.1

Q ss_pred             cHHHHHHHhHHh----cCC---cEEEEccCCchHHHHH
Q psy3307          35 TPVQKYAIPVII----SGR---DVMACAQTGSGKTAAF   65 (130)
Q Consensus        35 t~~Q~~~i~~~~----~g~---~~l~~aptGsGKT~~~   65 (130)
                      +|+|...|..+.    +|+   -.++.||.|.||+...
T Consensus         4 yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA   41 (325)
T PRK06871          4 YPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLI   41 (325)
T ss_pred             CcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHH
Confidence            566666665543    444   6789999999998654

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.21  E-value=0.97  Score=35.24  Aligned_cols=18  Identities=39%  Similarity=0.517  Sum_probs=14.5

Q ss_pred             CcEEEEccCCchHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~   66 (130)
                      .-+++.+|+|+|||....
T Consensus       224 ~vi~lvGptGvGKTTtaa  241 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIA  241 (432)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347899999999998643

>PRK08939 primosomal protein DnaI; Reviewed

Probab=92.20  E-value=0.53  Score=34.96  Aligned_cols=27  Identities=19%  Similarity=0.292  Sum_probs=18.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .++.+++.|++|+|||... .++...+.
T Consensus       155 ~~~gl~L~G~~G~GKThLa-~Aia~~l~  181 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLL-AAIANELA  181 (306)
T ss_pred             CCCeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            3568999999999999643 23444443

>KOG4150|consensus

Probab=92.15  E-value=0.12  Score=41.62  Aligned_cols=70  Identities=9%  Similarity=-0.102  Sum_probs=51.7

Q ss_pred             HHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          26 IALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        26 l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      +..+.-+....+|.+++..+-.|++.++.-.+.+||.++|-+..+.....-..                 ...+++.|++
T Consensus       279 ~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~-----------------s~~~~~~~~~  341 (1034)
T KOG4150|consen  279 LNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHA-----------------TNSLLPSEMV  341 (1034)
T ss_pred             HhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcc-----------------cceecchhHH
Confidence            34455567789999999999999999999999999999998877765543221                 2256666777


Q ss_pred             HHHHHHH
Q psy3307         106 ELATQIY  112 (130)
Q Consensus       106 ~La~q~~  112 (130)
                      ++++.-.
T Consensus       342 ~~~~~~~  348 (1034)
T KOG4150|consen  342 EHLRNGS  348 (1034)
T ss_pred             HHhhccC
Confidence            7665543

>KOG0387|consensus

Probab=92.14  E-value=0.36  Score=40.16  Aligned_cols=71  Identities=17%  Similarity=0.164  Sum_probs=46.9

Q ss_pred             CCcHHHHHHHhHHh----cCCcEEEEccCCchHHHH--HHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHH
Q psy3307          33 KPTPVQKYAIPVII----SGRDVMACAQTGSGKTAA--FLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRE  106 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~--~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  106 (130)
                      .+.++|+....-+.    ++..-|+.-.-|-|||.-  .+|..|+......                  -.+|||||. .
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~------------------~paLIVCP~-T  265 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLT------------------KPALIVCPA-T  265 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhccccc------------------CceEEEccH-H
Confidence            45778888776543    667788899999999943  2233333221111                  349999998 5


Q ss_pred             HHHHHHHHHHHHHhcC
Q psy3307         107 LATQIYDEAKKFAYRS  122 (130)
Q Consensus       107 La~q~~~~~~~l~~~~  122 (130)
                      +..|+.+++....-.+
T Consensus       266 ii~qW~~E~~~w~p~~  281 (923)
T KOG0387|consen  266 IIHQWMKEFQTWWPPF  281 (923)
T ss_pred             HHHHHHHHHHHhCcce
Confidence            7778888887765543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=92.10  E-value=0.12  Score=37.95  Aligned_cols=18  Identities=22%  Similarity=0.272  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +.++++.+|+|||||...
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999764

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.

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=92.09  E-value=0.39  Score=33.47  Aligned_cols=63  Identities=14%  Similarity=0.220  Sum_probs=39.2

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEE-cCcHHHHHHHHHHHHHHHhcCC
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVL-APTRELATQIYDEAKKFAYRSQ  123 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil-~Pt~~La~q~~~~~~~l~~~~~  123 (130)
                      +..|.-+.+.+|+|+|||.  ++=++.-+.....                 ..+.+= .|...-.++....+.-+++..+
T Consensus        25 l~~Ge~~~i~G~NG~GKTt--LLRilaGLl~p~~-----------------G~v~~~~~~i~~~~~~~~~~l~yLGH~~g   85 (209)
T COG4133          25 LNAGEALQITGPNGAGKTT--LLRILAGLLRPDA-----------------GEVYWQGEPIQNVRESYHQALLYLGHQPG   85 (209)
T ss_pred             EcCCCEEEEECCCCCcHHH--HHHHHHcccCCCC-----------------CeEEecCCCCccchhhHHHHHHHhhcccc
Confidence            4578889999999999997  4444444443221                 123332 3444555556677777777777


Q ss_pred             Cce
Q psy3307         124 LRP  126 (130)
Q Consensus       124 ~~~  126 (130)
                      +|.
T Consensus        86 iK~   88 (209)
T COG4133          86 IKT   88 (209)
T ss_pred             ccc
Confidence            764

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=92.05  E-value=0.12  Score=32.31  Aligned_cols=14  Identities=36%  Similarity=0.441  Sum_probs=12.3

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      |++.|++|||||..
T Consensus         1 I~i~G~~GsGKtTi   14 (129)
T PF13238_consen    1 IGISGIPGSGKTTI   14 (129)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             CEEECCCCCCHHHH
Confidence            57899999999975

...

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=92.05  E-value=0.28  Score=34.33  Aligned_cols=18  Identities=22%  Similarity=0.362  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .++.+++.|++|+|||..
T Consensus        41 ~~~~~~l~G~~G~GKT~L   58 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHL   58 (227)
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            356899999999999953

>KOG1123|consensus

Probab=92.02  E-value=0.064  Score=42.53  Aligned_cols=66  Identities=20%  Similarity=0.247  Sum_probs=51.1

Q ss_pred             CCcHHHHHHHhHHh-cC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          33 KPTPVQKYAIPVII-SG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~-~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      .++|+|..++...+ +|  |+-++.-|-|+|||+.-+-++.. +   +                  .++|++|.+---++
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t-i---k------------------K~clvLcts~VSVe  359 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT-I---K------------------KSCLVLCTSAVSVE  359 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee-e---c------------------ccEEEEecCccCHH
Confidence            67899999999887 33  68899999999999865333211 1   1                  35999999998999


Q ss_pred             HHHHHHHHHHh
Q psy3307         110 QIYDEAKKFAY  120 (130)
Q Consensus       110 q~~~~~~~l~~  120 (130)
                      |+...++.++-
T Consensus       360 QWkqQfk~wst  370 (776)
T KOG1123|consen  360 QWKQQFKQWST  370 (776)
T ss_pred             HHHHHHHhhcc
Confidence            99998887654

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.93  E-value=0.43  Score=33.64  Aligned_cols=19  Identities=16%  Similarity=0.179  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.+++|+|||...
T Consensus        24 ~g~~~~i~G~~GsGKt~l~   42 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLS   42 (234)
T ss_pred             CCcEEEEECCCCCChHHHH
Confidence            3578899999999999754

>PRK08727 hypothetical protein; Validated

Probab=91.92  E-value=0.61  Score=33.05  Aligned_cols=16  Identities=25%  Similarity=0.300  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ..+++.|++|+|||-.
T Consensus        42 ~~l~l~G~~G~GKThL   57 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL   57 (233)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4599999999999953

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=91.90  E-value=0.17  Score=39.65  Aligned_cols=20  Identities=25%  Similarity=0.484  Sum_probs=17.5

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|+++++.+|+|||||+..
T Consensus       196 AGgHnLl~~GpPGtGKTmla  215 (490)
T COG0606         196 AGGHNLLLVGPPGTGKTMLA  215 (490)
T ss_pred             hcCCcEEEecCCCCchHHhh
Confidence            47799999999999999753

>KOG0729|consensus

Probab=91.89  E-value=0.36  Score=35.66  Aligned_cols=58  Identities=14%  Similarity=0.135  Sum_probs=38.3

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHC-CCCCCcHHHHHHHhHHh-cCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALA-RYDKPTPVQKYAIPVII-SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~-~~~~~t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~   65 (130)
                      -.+|..+++|.+=..+.++.+++- ...-+.|-  +....-. --+.+++-+|+|+|||+|.
T Consensus       169 eekpdvty~dvggckeqieklrevve~pll~pe--rfv~lgidppkgvllygppgtgktl~a  228 (435)
T KOG0729|consen  169 EEKPDVTYSDVGGCKEQIEKLREVVELPLLHPE--RFVNLGIDPPKGVLLYGPPGTGKTLCA  228 (435)
T ss_pred             ecCCCcccccccchHHHHHHHHHHHhccccCHH--HHhhcCCCCCCceEEeCCCCCchhHHH
Confidence            356788999999888888777652 22223332  2111111 2378999999999999975

>KOG0926|consensus

Probab=91.87  E-value=0.24  Score=41.45  Aligned_cols=35  Identities=40%  Similarity=0.677  Sum_probs=24.8

Q ss_pred             HHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307          39 KYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus        39 ~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      ++.+.+|.+..-+++|+.||||||.-  +|  +.+++.+
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTTQ--vP--QFLYEAG  296 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTTQ--VP--QFLYEAG  296 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCcccc--ch--HHHHHcc
Confidence            34555667778889999999999973  34  4455544

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=91.87  E-value=0.29  Score=35.01  Aligned_cols=33  Identities=21%  Similarity=0.327  Sum_probs=23.6

Q ss_pred             CCcHHHHHHHhHHh----cCC-cEEEEccCCchHHHHH
Q psy3307          33 KPTPVQKYAIPVII----SGR-DVMACAQTGSGKTAAF   65 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~-~~l~~aptGsGKT~~~   65 (130)
                      .+++.+.+++..+.    .+. .+++.||+|+|||...
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            46667777776553    233 6889999999999753

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=91.81  E-value=0.13  Score=37.04  Aligned_cols=18  Identities=22%  Similarity=0.261  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ..++++.||+|+|||...
T Consensus        42 ~~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             cceEEEEcCCCCCHHHHH
Confidence            358899999999999754

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.

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=91.77  E-value=0.35  Score=40.97  Aligned_cols=24  Identities=21%  Similarity=0.389  Sum_probs=17.8

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      .+.++.|+||||||+....-+.+.
T Consensus       476 ~n~~I~G~TGSGKS~l~~~li~q~  499 (893)
T TIGR03744       476 AHLLILGPTGAGKSATLTNLLMQV  499 (893)
T ss_pred             ccEEEECCCCCCHHHHHHHHHHHH
Confidence            488999999999998654333333

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>CHL00181 cbbX CbbX; Provisional

Probab=91.75  E-value=0.13  Score=37.73  Aligned_cols=19  Identities=26%  Similarity=0.391  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.++++.+|+|+|||...
T Consensus        58 ~~~~ill~G~pGtGKT~lA   76 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTVA   76 (287)
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3557999999999999764

>PHA02244 ATPase-like protein

Probab=91.73  E-value=0.28  Score=37.50  Aligned_cols=22  Identities=23%  Similarity=0.302  Sum_probs=18.3

Q ss_pred             hHHhcCCcEEEEccCCchHHHH
Q psy3307          43 PVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ..+..+.++++.+|+|+|||..
T Consensus       114 r~l~~~~PVLL~GppGtGKTtL  135 (383)
T PHA02244        114 KIVNANIPVFLKGGAGSGKNHI  135 (383)
T ss_pred             HHHhcCCCEEEECCCCCCHHHH
Confidence            3445789999999999999964

>PRK04296 thymidine kinase; Provisional

Probab=91.64  E-value=0.46  Score=32.61  Aligned_cols=26  Identities=12%  Similarity=0.107  Sum_probs=17.7

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      |.-.++.+|+|+|||... +-.+.+..
T Consensus         2 g~i~litG~~GsGKTT~~-l~~~~~~~   27 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTEL-LQRAYNYE   27 (190)
T ss_pred             cEEEEEECCCCCHHHHHH-HHHHHHHH
Confidence            345688999999999654 44444443

>KOG1807|consensus

Probab=91.54  E-value=0.58  Score=39.01  Aligned_cols=71  Identities=17%  Similarity=0.052  Sum_probs=48.9

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      ....-|..|..-.+.-+-.++++|+|+|||+.-+..+ ..+..+......            ....+++|-|..-++|..
T Consensus       378 ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav-~tLL~n~s~~~~------------~epIlvvC~Tnhavdq~l  444 (1025)
T KOG1807|consen  378 ILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAV-DTLLLNSSGYTE------------PEPILVVCLTNHAVDQYL  444 (1025)
T ss_pred             eecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHH-HHHHhccccccc------------ccceeeeehhhHHHHHHH
Confidence            3455788888888888888999999999998865444 444433321100            134889999988888876


Q ss_pred             HHHH
Q psy3307         113 DEAK  116 (130)
Q Consensus       113 ~~~~  116 (130)
                      ..+.
T Consensus       445 igiy  448 (1025)
T KOG1807|consen  445 IGIY  448 (1025)
T ss_pred             HHHH
Confidence            5544

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=91.51  E-value=0.29  Score=36.09  Aligned_cols=16  Identities=44%  Similarity=0.607  Sum_probs=14.2

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.||+|+|||...
T Consensus        38 ~lll~Gp~GtGKT~la   53 (337)
T PRK12402         38 HLLVQGPPGSGKTAAV   53 (337)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999753

>PRK05642 DNA replication initiation factor; Validated

Probab=91.43  E-value=1  Score=31.99  Aligned_cols=16  Identities=13%  Similarity=0.270  Sum_probs=13.9

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.|++|+|||--
T Consensus        46 ~~l~l~G~~G~GKTHL   61 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL   61 (234)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5789999999999964

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=91.40  E-value=0.12  Score=34.55  Aligned_cols=29  Identities=38%  Similarity=0.653  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      .++.+++.|+.|+|||.. +-.++..+...
T Consensus        23 ~~~~~ll~G~~G~GKT~l-l~~~~~~~~~~   51 (185)
T PF13191_consen   23 SPRNLLLTGESGSGKTSL-LRALLDRLAER   51 (185)
T ss_dssp             ----EEE-B-TTSSHHHH-HHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHH-HHHHHHHHHhc
Confidence            457899999999999964 33455555544

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=91.39  E-value=1.1  Score=29.08  Aligned_cols=16  Identities=25%  Similarity=0.175  Sum_probs=12.8

Q ss_pred             EEEccCCchHHHHHHH
Q psy3307          52 MACAQTGSGKTAAFLV   67 (130)
Q Consensus        52 l~~aptGsGKT~~~~l   67 (130)
                      .++++||+||++..-+
T Consensus        57 SfHG~tGtGKn~v~~l   72 (127)
T PF06309_consen   57 SFHGWTGTGKNFVSRL   72 (127)
T ss_pred             EeecCCCCcHHHHHHH
Confidence            4899999999986533

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=91.35  E-value=0.14  Score=40.40  Aligned_cols=55  Identities=18%  Similarity=0.245  Sum_probs=32.8

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCC--CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALAR--YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~--~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      +.+..+|+|+.-.+...+.+.+.-  +..+..++...   ....+.+++.+|+|+|||..
T Consensus        48 ~~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~l  104 (495)
T TIGR01241        48 EKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLL  104 (495)
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHH
Confidence            356778888877776666554321  12222222111   11235799999999999975

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=91.23  E-value=0.5  Score=33.09  Aligned_cols=26  Identities=27%  Similarity=0.494  Sum_probs=19.6

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ++++.+.|.||||||... --+++.+.
T Consensus        23 ~~H~~I~G~TGsGKS~~~-~~ll~~l~   48 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTV-KVLLEELL   48 (229)
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            578999999999999754 44455554

It contains several conserved aspartates and histidines that could be metal ligands.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=91.23  E-value=0.47  Score=37.40  Aligned_cols=25  Identities=24%  Similarity=0.347  Sum_probs=19.0

Q ss_pred             HHhHHh-----cCCcEEEEccCCchHHHHH
Q psy3307          41 AIPVII-----SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~-----~g~~~l~~aptGsGKT~~~   65 (130)
                      .++.++     .|.-+++.+|+|+|||...
T Consensus       251 ~lD~~lgGG~~~gs~~li~G~~G~GKt~l~  280 (484)
T TIGR02655       251 RLDEMCGGGFFKDSIILATGATGTGKTLLV  280 (484)
T ss_pred             hHHHHhcCCccCCcEEEEECCCCCCHHHHH
Confidence            345555     4478999999999999743

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.

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=91.21  E-value=0.71  Score=34.86  Aligned_cols=40  Identities=18%  Similarity=0.165  Sum_probs=27.7

Q ss_pred             cHHHHHHHhHHh-cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          35 TPVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        35 t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ...|-+.|+.++ .|..+++-++.|.|||+..+.-.+....
T Consensus        75 rs~~P~lId~~fr~g~~~~~~gdsg~GKttllL~l~Ialaa  115 (402)
T COG3598          75 RSNSPQLIDEFFRKGYVSILYGDSGVGKTTLLLYLCIALAA  115 (402)
T ss_pred             cccChhhhhHHhhcCeeEEEecCCcccHhHHHHHHHHHHHh
Confidence            445666676655 5667788899999999886655554443

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=91.18  E-value=0.35  Score=31.26  Aligned_cols=21  Identities=24%  Similarity=0.395  Sum_probs=16.7

Q ss_pred             HHhcCCcEEEEccCCchHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ....+..+++.+++||||+.+
T Consensus        17 ~a~~~~pvli~GE~GtGK~~~   37 (138)
T PF14532_consen   17 LAKSSSPVLITGEPGTGKSLL   37 (138)
T ss_dssp             HHCSSS-EEEECCTTSSHHHH
T ss_pred             HhCCCCcEEEEcCCCCCHHHH
Confidence            345678999999999999974

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.16  E-value=0.076  Score=35.98  Aligned_cols=17  Identities=24%  Similarity=0.485  Sum_probs=13.9

Q ss_pred             EEEEccCCchHHHHHHH
Q psy3307          51 VMACAQTGSGKTAAFLV   67 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l   67 (130)
                      .++.+|+|||||..|..
T Consensus         5 ~IvaG~NGsGKstv~~~   21 (187)
T COG4185           5 DIVAGPNGSGKSTVYAS   21 (187)
T ss_pred             EEEecCCCCCceeeeec
Confidence            46789999999987744

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=91.14  E-value=2.7  Score=31.46  Aligned_cols=32  Identities=16%  Similarity=0.130  Sum_probs=23.4

Q ss_pred             CcHHHHHHHhHHh----cCC---cEEEEccCCchHHHHH
Q psy3307          34 PTPVQKYAIPVII----SGR---DVMACAQTGSGKTAAF   65 (130)
Q Consensus        34 ~t~~Q~~~i~~~~----~g~---~~l~~aptGsGKT~~~   65 (130)
                      .+|+|...|..+.    +|+   -.++.||.|.||+...
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA   42 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLV   42 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH
Confidence            4677777776554    454   7899999999998543

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=91.09  E-value=0.3  Score=36.68  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=18.9

Q ss_pred             HhHHhcCCcEEEEccCCchHHHH
Q psy3307          42 IPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        42 i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      +-.+..++++++.+++|+|||..
T Consensus        58 l~~l~~~~~ilL~G~pGtGKTtl   80 (327)
T TIGR01650        58 CAGFAYDRRVMVQGYHGTGKSTH   80 (327)
T ss_pred             HHHHhcCCcEEEEeCCCChHHHH
Confidence            33455789999999999999974

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=91.05  E-value=0.18  Score=34.30  Aligned_cols=18  Identities=28%  Similarity=0.512  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |..+++.+|+|+|||...
T Consensus         2 g~~i~l~G~sGsGKsTl~   19 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLL   19 (186)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            567899999999999743

>PRK11823 DNA repair protein RadA; Provisional

Probab=90.93  E-value=0.63  Score=36.37  Aligned_cols=24  Identities=21%  Similarity=0.450  Sum_probs=18.2

Q ss_pred             HhHHhc-----CCcEEEEccCCchHHHHH
Q psy3307          42 IPVIIS-----GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~-----g~~~l~~aptGsGKT~~~   65 (130)
                      ++.++.     |.-+++.+++|+|||...
T Consensus        69 LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~   97 (446)
T PRK11823         69 LDRVLGGGLVPGSVVLIGGDPGIGKSTLL   97 (446)
T ss_pred             HHHHhcCCccCCEEEEEECCCCCCHHHHH
Confidence            455554     467899999999999743

>PRK14974 cell division protein FtsY; Provisional

Probab=90.85  E-value=1.2  Score=33.63  Aligned_cols=17  Identities=24%  Similarity=0.386  Sum_probs=14.3

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .-+++.+++|+|||...
T Consensus       141 ~vi~~~G~~GvGKTTti  157 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTI  157 (336)
T ss_pred             eEEEEEcCCCCCHHHHH
Confidence            45789999999999853

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=90.78  E-value=0.41  Score=32.29  Aligned_cols=44  Identities=18%  Similarity=0.261  Sum_probs=32.2

Q ss_pred             HHHHHHHHHCCCC-----CCcHHHHHHHhHHhcCCcEEEEccCCchHHH
Q psy3307          20 EIITNNIALARYD-----KPTPVQKYAIPVIISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        20 ~~i~~~l~~~~~~-----~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~   63 (130)
                      ++.++..++.|+.     .-+......+...+.++-+++.+++|.||+.
T Consensus         2 ~~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k~~vl~G~SGvGKSS   50 (161)
T PF03193_consen    2 EELLEQYEKLGYPVFFISAKTGEGIEELKELLKGKTSVLLGQSGVGKSS   50 (161)
T ss_dssp             HHHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTSEEEEECSTTSSHHH
T ss_pred             HHHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCCEEEEECCCCCCHHH
Confidence            4556667777775     1234445666677888999999999999985

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=90.76  E-value=0.32  Score=37.87  Aligned_cols=24  Identities=17%  Similarity=0.455  Sum_probs=19.8

Q ss_pred             hHHhcCCcEEEEccCCchHHHHHH
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~~   66 (130)
                      +-+-++.|++..+|+|+|||..|.
T Consensus       204 ~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       204 PLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHH
Confidence            445588999999999999996654

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=90.74  E-value=0.21  Score=33.64  Aligned_cols=18  Identities=22%  Similarity=0.407  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |+-++++|++|||||...
T Consensus         2 ~~~i~l~G~~gsGKst~a   19 (175)
T cd00227           2 GRIIILNGGSSAGKSSIA   19 (175)
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            677899999999999754

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>KOG1806|consensus

Probab=90.69  E-value=0.62  Score=39.97  Aligned_cols=68  Identities=26%  Similarity=0.346  Sum_probs=48.4

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      ..|+-|-++|..-..-.+.++.+|+|+|||-.. .-++.-++.+..                .++++|++.+..-.+|..
T Consensus       738 ~ft~~qveai~sg~qpgltmvvgppgtgktd~a-vqil~~lyhn~p----------------~qrTlivthsnqaln~lf  800 (1320)
T KOG1806|consen  738 KFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVA-VQILSVLYHNSP----------------NQRTLIVTHSNQALNQLF  800 (1320)
T ss_pred             ccCHHHHHHHHhcCCCCceeeecCCCCCCcchh-hhhhhhhhhcCC----------------CcceEEEEecccchhHHH
Confidence            458888888876666679999999999999764 334444443332                278999998877777766


Q ss_pred             HHHHH
Q psy3307         113 DEAKK  117 (130)
Q Consensus       113 ~~~~~  117 (130)
                      ..+.+
T Consensus       801 eKi~~  805 (1320)
T KOG1806|consen  801 EKIMA  805 (1320)
T ss_pred             HHHHh
Confidence            55543

>PRK10867 signal recognition particle protein; Provisional

Probab=90.68  E-value=1.5  Score=34.29  Aligned_cols=16  Identities=31%  Similarity=0.451  Sum_probs=13.7

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+++|+|||.+.
T Consensus       102 vI~~vG~~GsGKTTta  117 (433)
T PRK10867        102 VIMMVGLQGAGKTTTA  117 (433)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            4789999999999764

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.60  E-value=0.91  Score=35.03  Aligned_cols=19  Identities=37%  Similarity=0.468  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .++-+++.+|+|+|||...
T Consensus       205 ~~~ii~lvGptGvGKTTt~  223 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTL  223 (407)
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4578899999999999754

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=90.58  E-value=0.33  Score=38.38  Aligned_cols=31  Identities=19%  Similarity=0.347  Sum_probs=24.8

Q ss_pred             CcHHHHHHHhHH-------hcCCcEEEEccCCchHHHH
Q psy3307          34 PTPVQKYAIPVI-------ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        34 ~t~~Q~~~i~~~-------~~g~~~l~~aptGsGKT~~   64 (130)
                      -+++|......+       ..|.-+.++||.|||||..
T Consensus        11 ~r~Ie~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKSTL   48 (504)
T TIGR03238        11 KRKIQTDLERILVKFNKELPSSSLLFLCGSSGDGKSEI   48 (504)
T ss_pred             chHHHHHHHHHHhCCceeecCCCEEEEECCCCCCHHHH
Confidence            478888776554       3678999999999999973

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=90.51  E-value=0.35  Score=36.02  Aligned_cols=24  Identities=29%  Similarity=0.468  Sum_probs=20.1

Q ss_pred             HHhHHhcCCcEEEEccCCchHHHH
Q psy3307          41 AIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        41 ~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ++-.++.|+.+++.+++|+|||..
T Consensus        36 ~l~a~~~~~~vll~G~PG~gKT~l   59 (329)
T COG0714          36 ALLALLAGGHVLLEGPPGVGKTLL   59 (329)
T ss_pred             HHHHHHcCCCEEEECCCCccHHHH
Confidence            334567999999999999999974

>PRK14530 adenylate kinase; Provisional

Probab=90.46  E-value=0.18  Score=35.13  Aligned_cols=18  Identities=22%  Similarity=0.379  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.+++|||||..
T Consensus         2 ~~~~I~i~G~pGsGKsT~   19 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQ   19 (215)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            466899999999999964

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=90.44  E-value=0.35  Score=35.09  Aligned_cols=29  Identities=28%  Similarity=0.360  Sum_probs=21.5

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +..|+-+.+.+|+|+|||.  ++=.+..+..
T Consensus        25 i~~G~i~~iiGpNG~GKST--LLk~l~g~l~   53 (258)
T COG1120          25 IPKGEITGILGPNGSGKST--LLKCLAGLLK   53 (258)
T ss_pred             ecCCcEEEEECCCCCCHHH--HHHHHhccCC
Confidence            3467888999999999997  4555555443

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=90.37  E-value=3.6  Score=34.19  Aligned_cols=73  Identities=15%  Similarity=0.100  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHhH---HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          33 KPTPVQKYAIPV---IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        33 ~~t~~Q~~~i~~---~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      .|+|.=.+=|..   .+..+-.++.+|-|.|||++..+.+...+....                  .+++|.+|...-+.
T Consensus       169 ~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f~G------------------i~IlvTAH~~~ts~  230 (752)
T PHA03333        169 APSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISFLE------------------IDIVVQAQRKTMCL  230 (752)
T ss_pred             CCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHhcC------------------CeEEEECCChhhHH
Confidence            344433333443   346678888999999999876554443332121                  57999999999999


Q ss_pred             HHHHHHHHHHhcCC
Q psy3307         110 QIYDEAKKFAYRSQ  123 (130)
Q Consensus       110 q~~~~~~~l~~~~~  123 (130)
                      ++.+.+++..+.++
T Consensus       231 evF~rv~~~le~lg  244 (752)
T PHA03333        231 TLYNRVETVVHAYQ  244 (752)
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999888877443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=90.34  E-value=0.34  Score=36.32  Aligned_cols=24  Identities=29%  Similarity=0.519  Sum_probs=17.7

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      .++++.||+|+|||... -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            58999999999999653 3444433

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=90.33  E-value=0.22  Score=38.01  Aligned_cols=19  Identities=37%  Similarity=0.739  Sum_probs=16.6

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      +.|+-+++.+|+|||||..
T Consensus        63 ~aGrgiLi~GppgTGKTAl   81 (450)
T COG1224          63 MAGRGILIVGPPGTGKTAL   81 (450)
T ss_pred             ccccEEEEECCCCCcHHHH
Confidence            3778999999999999953

>TIGR00609 recB exodeoxyribonuclease V, beta subunit

Probab=90.33  E-value=0.97  Score=39.22  Aligned_cols=56  Identities=25%  Similarity=0.323  Sum_probs=38.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      +| ..++.|..|||||++...-.+..+.+....              ...++|+|+=|+.-+.++...+++
T Consensus         9 ~G-~~lieAsAGtGKT~ti~~~~lrll~~~~~~--------------~~~~iLvvTFT~aAt~el~~RIr~   64 (1087)
T TIGR00609         9 NG-TFLIEASAGTGKTFTIAQLYLRLLLEGGPL--------------TVEEILVVTFTNAATEELKTRIRG   64 (1087)
T ss_pred             CC-CEEEEECCCCCHHHHHHHHHHHHHhcCCCC--------------ChhhEEEEehhHHHHHHHHHHHHH
Confidence            45 566789999999998766666666543210              114699999888877777777654

All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=90.19  E-value=0.57  Score=32.27  Aligned_cols=20  Identities=30%  Similarity=0.376  Sum_probs=16.4

Q ss_pred             cCCcEEEEccCCchHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~   66 (130)
                      .|.-+.+.+++|+|||...+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~   30 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICM   30 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            45678999999999997654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>KOG0060|consensus

Probab=90.13  E-value=0.15  Score=41.04  Aligned_cols=20  Identities=30%  Similarity=0.617  Sum_probs=17.6

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +.+|.++++++|+|+|||--
T Consensus       458 V~~g~~LLItG~sG~GKtSL  477 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSL  477 (659)
T ss_pred             ecCCCeEEEECCCCCchhHH
Confidence            45899999999999999963

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=90.11  E-value=1.1  Score=28.80  Aligned_cols=15  Identities=40%  Similarity=0.583  Sum_probs=12.7

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.|++|+|||...
T Consensus         2 ~~i~G~~G~GKT~l~   16 (165)
T cd01120           2 ILVFGPTGSGKTTLA   16 (165)
T ss_pred             eeEeCCCCCCHHHHH
Confidence            578999999999754

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=90.09  E-value=1.6  Score=30.97  Aligned_cols=18  Identities=11%  Similarity=0.300  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.||+|+|||..
T Consensus        44 ~~~~l~l~Gp~G~GKThL   61 (235)
T PRK08084         44 HSGYIYLWSREGAGRSHL   61 (235)
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            346899999999999963

>PRK13909 putative recombination protein RecB; Provisional

Probab=90.06  E-value=0.92  Score=38.61  Aligned_cols=50  Identities=26%  Similarity=0.265  Sum_probs=35.2

Q ss_pred             EEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          52 MACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        52 l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      ++.|+-|||||.+...-.+..+......                -.+|.++=|+.-+.++...+..
T Consensus         2 ~~~AsAGsGKT~~L~~~yl~ll~~~~~~----------------~~IlavTFT~kAa~Emk~Ri~~   51 (910)
T PRK13909          2 ALKASAGSGKTFALSVRFLALLFKGANP----------------SEILALTFTKKAANEMKERIID   51 (910)
T ss_pred             ceecCCCCchhHHHHHHHHHHHhcCCCc----------------ceEEEEeehHHHHHHHHHHHHH
Confidence            5789999999998766666665543211                3588888888888887666543

>PLN02796 D-glycerate 3-kinase

Probab=89.99  E-value=1.1  Score=34.02  Aligned_cols=14  Identities=36%  Similarity=0.465  Sum_probs=12.5

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +.+.|++|||||..
T Consensus       103 IGI~G~sGSGKSTL  116 (347)
T PLN02796        103 IGISAPQGCGKTTL  116 (347)
T ss_pred             EEEECCCCCcHHHH
Confidence            78899999999974

>KOG0924|consensus

Probab=89.96  E-value=1.6  Score=36.32  Aligned_cols=61  Identities=26%  Similarity=0.377  Sum_probs=38.2

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc--CcHHHHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA--PTRELATQIY  112 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~--Pt~~La~q~~  112 (130)
                      ...+.+.+..+-..+-+++.+.||||||.-.    -+.++..+-.                -..+|-|  |-|--|..+.
T Consensus       358 f~~R~~ll~~ir~n~vvvivgETGSGKTTQl----~QyL~edGY~----------------~~GmIGcTQPRRvAAiSVA  417 (1042)
T KOG0924|consen  358 FACRDQLLSVIRENQVVVIVGETGSGKTTQL----AQYLYEDGYA----------------DNGMIGCTQPRRVAAISVA  417 (1042)
T ss_pred             HHHHHHHHHHHhhCcEEEEEecCCCCchhhh----HHHHHhcccc----------------cCCeeeecCchHHHHHHHH
Confidence            3455556666667888999999999999742    3444443211                1123333  8888877776


Q ss_pred             HHH
Q psy3307         113 DEA  115 (130)
Q Consensus       113 ~~~  115 (130)
                      +..
T Consensus       418 krV  420 (1042)
T KOG0924|consen  418 KRV  420 (1042)
T ss_pred             HHH
Confidence            554

>PRK00131 aroK shikimate kinase; Reviewed

Probab=89.96  E-value=0.23  Score=32.84  Aligned_cols=19  Identities=21%  Similarity=0.375  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .+..+++.+++|||||...
T Consensus         3 ~~~~i~l~G~~GsGKstla   21 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIG   21 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHH
Confidence            5678999999999999753

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=89.93  E-value=0.24  Score=38.30  Aligned_cols=18  Identities=33%  Similarity=0.440  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ..++++.+|||+|||...
T Consensus       108 ~~~iLl~Gp~GtGKT~lA  125 (412)
T PRK05342        108 KSNILLIGPTGSGKTLLA  125 (412)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            367999999999999754

>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=89.93  E-value=0.25  Score=37.81  Aligned_cols=18  Identities=39%  Similarity=0.735  Sum_probs=14.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+.+++.+|+|||||..
T Consensus        49 aGr~iLiaGppGtGKTAl   66 (398)
T PF06068_consen   49 AGRAILIAGPPGTGKTAL   66 (398)
T ss_dssp             TT-EEEEEE-TTSSHHHH
T ss_pred             cCcEEEEeCCCCCCchHH
Confidence            689999999999999953

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.

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=89.85  E-value=0.25  Score=36.66  Aligned_cols=17  Identities=24%  Similarity=0.331  Sum_probs=13.9

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.||||||||-..
T Consensus         5 ~ii~I~GpTasGKS~LA   21 (300)
T PRK14729          5 KIVFIFGPTAVGKSNIL   21 (300)
T ss_pred             cEEEEECCCccCHHHHH
Confidence            45889999999999643

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=89.84  E-value=1.8  Score=33.74  Aligned_cols=16  Identities=38%  Similarity=0.472  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+++|+|||...
T Consensus       102 vi~lvG~~GvGKTTta  117 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTC  117 (429)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999754

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.

>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=89.83  E-value=0.85  Score=32.09  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=19.0

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      .+++.||+|+|||- .+-++.+.+.+.
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~   61 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQ   61 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhc
Confidence            58999999999997 345555555543

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.

>PRK08118 topology modulation protein; Reviewed

Probab=89.82  E-value=0.26  Score=33.21  Aligned_cols=15  Identities=27%  Similarity=0.510  Sum_probs=13.1

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.|++|||||..
T Consensus         3 rI~I~G~~GsGKSTl   17 (167)
T PRK08118          3 KIILIGSGGSGKSTL   17 (167)
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999963

>PLN02165 adenylate isopentenyltransferase

Probab=89.79  E-value=0.29  Score=36.87  Aligned_cols=19  Identities=32%  Similarity=0.380  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|+-+++.||||||||...
T Consensus        42 ~g~iivIiGPTGSGKStLA   60 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLS   60 (334)
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5567999999999999754

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=89.75  E-value=0.25  Score=33.48  Aligned_cols=24  Identities=21%  Similarity=0.361  Sum_probs=16.6

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      ++++.+|+|+|||..  .-.+..+..
T Consensus         5 ~~ll~GpsGvGKT~l--a~~la~~l~   28 (171)
T PF07724_consen    5 NFLLAGPSGVGKTEL--AKALAELLF   28 (171)
T ss_dssp             EEEEESSTTSSHHHH--HHHHHHHHT
T ss_pred             EEEEECCCCCCHHHH--HHHHHHHhc
Confidence            678999999999963  333444443

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>KOG0731|consensus

Probab=89.63  E-value=0.56  Score=38.98  Aligned_cols=56  Identities=16%  Similarity=0.214  Sum_probs=33.6

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHC-C-CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALA-R-YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~-~-~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +++...|.|.---++..+.|.+. . .++|-.+|..-.   .=-+-+++++|+|+|||+..
T Consensus       304 ~~t~V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGA---KiPkGvLL~GPPGTGKTLLA  361 (774)
T KOG0731|consen  304 GNTGVKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGA---KIPKGVLLVGPPGTGKTLLA  361 (774)
T ss_pred             CCCCCccccccCcHHHHHHHHHHHHHhcCHHHHHHcCC---cCcCceEEECCCCCcHHHHH
Confidence            44556788876666655555442 1 233333333211   11268999999999999854

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=89.51  E-value=0.27  Score=38.00  Aligned_cols=29  Identities=24%  Similarity=0.523  Sum_probs=22.0

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      .|+.+++.+.+|||||+. .+-++..+...
T Consensus         9 ~G~TLLIKG~PGTGKTtf-aLelL~~l~~~   37 (484)
T PF07088_consen    9 PGQTLLIKGEPGTGKTTF-ALELLNSLKDH   37 (484)
T ss_pred             CCcEEEEecCCCCCceee-ehhhHHHHhcc
Confidence            578999999999999964 45666655543

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>PRK00300 gmk guanylate kinase; Provisional

Probab=89.46  E-value=0.26  Score=33.83  Aligned_cols=17  Identities=24%  Similarity=0.495  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHH
Q psy3307          47 SGRDVMACAQTGSGKTA   63 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~   63 (130)
                      .|+-+++.||+|||||.
T Consensus         4 ~g~~i~i~G~sGsGKst   20 (205)
T PRK00300          4 RGLLIVLSGPSGAGKST   20 (205)
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57789999999999996

>PF13654 AAA_32: AAA domain; PDB: 3K1J_B

Probab=89.45  E-value=0.11  Score=41.32  Aligned_cols=81  Identities=14%  Similarity=0.245  Sum_probs=0.0

Q ss_pred             HHHHHHhHHh-------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc--HHH
Q psy3307          37 VQKYAIPVII-------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT--REL  107 (130)
Q Consensus        37 ~Q~~~i~~~~-------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt--~~L  107 (130)
                      -|.+|..++-       .|-|+.+.+++|+||+. ++.-.+.........+.....--.+. +-..|++|.+-|-  +.+
T Consensus        12 GQ~RA~~Al~~gl~i~~~GYNIfv~G~~GtGr~t-~v~~~l~~~a~~~~~P~D~cYV~NF~-~p~~P~~l~LpaG~G~~f   89 (509)
T PF13654_consen   12 GQERAVEALEFGLGIRKPGYNIFVMGPPGTGRRT-YVRRFLEERAKKKPTPPDWCYVNNFD-DPRKPKALSLPAGQGKKF   89 (509)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccc-cccccccccccccccccccccccccc-cccccccccccccccccc
Confidence            4667766653       56799999999999985 44555555554332222111111111 1123667776654  444


Q ss_pred             HHHHHHHHHHHH
Q psy3307         108 ATQIYDEAKKFA  119 (130)
Q Consensus       108 a~q~~~~~~~l~  119 (130)
                      ...+.+.++.+.
T Consensus        90 ~~~m~~lie~l~  101 (509)
T PF13654_consen   90 KKDMEELIEELK  101 (509)
T ss_dssp             ------------
T ss_pred             cccccccccccc
Confidence            444444444443

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=89.39  E-value=0.23  Score=35.31  Aligned_cols=19  Identities=32%  Similarity=0.531  Sum_probs=16.5

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+++|.|||||.
T Consensus        25 v~~Gevv~iiGpSGSGKST   43 (240)
T COG1126          25 VEKGEVVVIIGPSGSGKST   43 (240)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3477889999999999997

>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=89.36  E-value=1.3  Score=29.62  Aligned_cols=15  Identities=27%  Similarity=0.454  Sum_probs=12.8

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.+++|+|||...
T Consensus         3 ~~~~G~~G~GKTt~~   17 (173)
T cd03115           3 ILLVGLQGVGKTTTA   17 (173)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999764

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.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=89.35  E-value=0.28  Score=37.96  Aligned_cols=17  Identities=35%  Similarity=0.487  Sum_probs=14.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.+|||+|||...
T Consensus       117 ~~iLL~GP~GsGKT~lA  133 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLA  133 (413)
T ss_pred             ceEEEECCCCcCHHHHH
Confidence            47999999999999754

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=89.33  E-value=0.24  Score=32.78  Aligned_cols=14  Identities=29%  Similarity=0.456  Sum_probs=11.7

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +++.+|+|||||..
T Consensus         1 i~l~G~~GsGKSTl   14 (163)
T TIGR01313         1 FVLMGVAGSGKSTI   14 (163)
T ss_pred             CEEECCCCCCHHHH
Confidence            46889999999964

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK07261 topology modulation protein; Provisional

Probab=89.31  E-value=0.29  Score=33.01  Aligned_cols=16  Identities=25%  Similarity=0.387  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.|++|||||...
T Consensus         2 ri~i~G~~GsGKSTla   17 (171)
T PRK07261          2 KIAIIGYSGSGKSTLA   17 (171)
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            4789999999999754

>PRK06620 hypothetical protein; Validated

Probab=89.27  E-value=0.24  Score=34.78  Aligned_cols=16  Identities=25%  Similarity=0.233  Sum_probs=13.9

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.||+|+|||..
T Consensus        45 ~~l~l~Gp~G~GKThL   60 (214)
T PRK06620         45 FTLLIKGPSSSGKTYL   60 (214)
T ss_pred             ceEEEECCCCCCHHHH
Confidence            4589999999999963

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=89.26  E-value=0.45  Score=36.28  Aligned_cols=26  Identities=27%  Similarity=0.505  Sum_probs=18.4

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .++++-|+||||||... --++..+..
T Consensus        43 ~n~~iyG~~GTGKT~~~-~~v~~~l~~   68 (366)
T COG1474          43 SNIIIYGPTGTGKTATV-KFVMEELEE   68 (366)
T ss_pred             ccEEEECCCCCCHhHHH-HHHHHHHHh
Confidence            47999999999999763 334444443

>TIGR03263 guanyl_kin guanylate kinase

Probab=89.22  E-value=0.28  Score=32.94  Aligned_cols=16  Identities=25%  Similarity=0.495  Sum_probs=13.9

Q ss_pred             CCcEEEEccCCchHHH
Q psy3307          48 GRDVMACAQTGSGKTA   63 (130)
Q Consensus        48 g~~~l~~aptGsGKT~   63 (130)
                      |+-+++.+|+|||||.
T Consensus         1 g~ii~l~G~~GsGKsT   16 (180)
T TIGR03263         1 GLLIVISGPSGVGKST   16 (180)
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4568899999999997

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>TIGR00959 ffh signal recognition particle protein

Probab=89.22  E-value=2.6  Score=32.89  Aligned_cols=16  Identities=31%  Similarity=0.474  Sum_probs=14.0

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+++|+|||...
T Consensus       101 vi~~vG~~GsGKTTta  116 (428)
T TIGR00959       101 VILMVGLQGSGKTTTC  116 (428)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            5789999999999864

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>KOG0652|consensus

Probab=89.20  E-value=0.64  Score=34.27  Aligned_cols=59  Identities=17%  Similarity=0.059  Sum_probs=30.7

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHh-HHhcCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIP-VIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~-~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+|...++|.|=-+..++.|.+.=.-.+|-- .+.-. -+.--+.++.-+|+|+|||+-.
T Consensus       163 DekPtE~YsDiGGldkQIqELvEAiVLpmth~-ekF~~lgi~pPKGvLmYGPPGTGKTlmA  222 (424)
T KOG0652|consen  163 DEKPTEQYSDIGGLDKQIQELVEAIVLPMTHK-EKFENLGIRPPKGVLMYGPPGTGKTLMA  222 (424)
T ss_pred             ccCCcccccccccHHHHHHHHHHHhccccccH-HHHHhcCCCCCCceEeeCCCCCcHHHHH
Confidence            45677788888743333333322111111110 00000 1122368999999999999743

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=89.18  E-value=0.23  Score=41.05  Aligned_cols=53  Identities=21%  Similarity=0.255  Sum_probs=31.9

Q ss_pred             ccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           9 KKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..+|++++-.+..++.+.+.   .+..+.-.+..   .+..++.+++.+|+|+|||..
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---gi~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHL---GIEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCceEEEECCCCCChHHH
Confidence            456788887666666665442   12222211111   123567899999999999964

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.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=89.13  E-value=0.31  Score=32.73  Aligned_cols=18  Identities=28%  Similarity=0.575  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |+-+++.+|+|||||...
T Consensus         1 ~~~~~i~G~sGsGKttl~   18 (179)
T TIGR02322         1 GRLIYVVGPSGAGKDTLL   18 (179)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            345789999999999754

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=89.03  E-value=2.1  Score=32.21  Aligned_cols=95  Identities=14%  Similarity=0.114  Sum_probs=47.6

Q ss_pred             CcHHHHHHHhHHh----cCC---cEEEEccCCchHHHHHHHHHHHHHHhc--CCCCCCCCCCCCC-CCCCCCceEEEEcC
Q psy3307          34 PTPVQKYAIPVII----SGR---DVMACAQTGSGKTAAFLVPILNQMYER--GPLPTPPAGRGYP-SRKKVFPLGLVLAP  103 (130)
Q Consensus        34 ~t~~Q~~~i~~~~----~g~---~~l~~aptGsGKT~~~~l~~l~~~~~~--~~~~~~~~~~~~~-~~~~~~~~~lil~P  103 (130)
                      .+|+|...|..+.    +|+   -.++.||.|+||+... ...-..+.-.  .....|+.+.+.. -....+|-..++.|
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA-~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALI-YALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTP   81 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHH-HHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEec
Confidence            4567777776654    444   7789999999998654 3333333322  2222344332110 01122355666666


Q ss_pred             cH----HHHHHHHHHHHHHHh---cCCCceEEe
Q psy3307         104 TR----ELATQIYDEAKKFAY---RSQLRPCVV  129 (130)
Q Consensus       104 t~----~La~q~~~~~~~l~~---~~~~~~~~~  129 (130)
                      ..    --++|+.+..+.+..   .-+.+|++|
T Consensus        82 ~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI  114 (334)
T PRK07993         82 EKGKSSLGVDAVREVTEKLYEHARLGGAKVVWL  114 (334)
T ss_pred             ccccccCCHHHHHHHHHHHhhccccCCceEEEE
Confidence            42    234455444444432   234455544

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=89.01  E-value=0.35  Score=30.82  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=16.0

Q ss_pred             hcCCcEEEEccCCchHHH
Q psy3307          46 ISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~   63 (130)
                      ..|.-+.+.+++|+|||.
T Consensus         9 ~~g~~~~i~G~nGsGKSt   26 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKST   26 (137)
T ss_dssp             ETTSEEEEEESTTSSHHH
T ss_pred             cCCCEEEEEccCCCcccc
Confidence            467889999999999997

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

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

Probab=88.91  E-value=7.5  Score=29.00  Aligned_cols=83  Identities=13%  Similarity=0.118  Sum_probs=58.4

Q ss_pred             CCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh----------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCC
Q psy3307          15 DIQMTEIITNNIALARYDKPTPVQKYAIPVII----------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA   84 (130)
Q Consensus        15 ~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~----------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~   84 (130)
                      ++.|++.+++.    |  .++..|.+++-...          ...-.++--.||.||--...--++.......       
T Consensus        25 ~~~lp~~~~~~----g--~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr-------   91 (303)
T PF13872_consen   25 RLHLPEEVIDS----G--LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR-------   91 (303)
T ss_pred             ccCCCHHHHhc----c--cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC-------
Confidence            44666665533    2  47889988886554          2357788888999887543334444444433       


Q ss_pred             CCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          85 GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        85 ~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                                 .++|+++.+.+|-.+..+.++.++..
T Consensus        92 -----------~r~vwvS~s~dL~~Da~RDl~DIG~~  117 (303)
T PF13872_consen   92 -----------KRAVWVSVSNDLKYDAERDLRDIGAD  117 (303)
T ss_pred             -----------CceEEEECChhhhhHHHHHHHHhCCC
Confidence                       46999999999999999999988765

>KOG0736|consensus

Probab=88.90  E-value=0.13  Score=42.68  Aligned_cols=55  Identities=16%  Similarity=0.237  Sum_probs=31.1

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHH-HHHhHHhc-CCcEEEEccCCchHHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQK-YAIPVIIS-GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~-~~i~~~~~-g~~~l~~aptGsGKT~~~   65 (130)
                      -|..+|+|.|=-+++...+.+-   --.|.|+ +.+..-+. ...+++-+|+|+|||+..
T Consensus       666 IPnV~WdDVGGLeevK~eIldT---IqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlA  722 (953)
T KOG0736|consen  666 IPNVSWDDVGGLEEVKTEILDT---IQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLA  722 (953)
T ss_pred             CCccchhcccCHHHHHHHHHHH---hcCcccChhhhhccccccceeEEECCCCCchHHHH
Confidence            4677899998555554444321   1122222 11111122 347899999999999753

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=88.89  E-value=2  Score=33.72  Aligned_cols=26  Identities=23%  Similarity=0.293  Sum_probs=17.8

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +.+++.|++|+|||.. +-.+.+.+..
T Consensus       142 npl~i~G~~G~GKTHL-l~Ai~~~l~~  167 (450)
T PRK14087        142 NPLFIYGESGMGKTHL-LKAAKNYIES  167 (450)
T ss_pred             CceEEECCCCCcHHHH-HHHHHHHHHH
Confidence            4689999999999942 2444444443

>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=88.76  E-value=3  Score=30.65  Aligned_cols=26  Identities=27%  Similarity=0.244  Sum_probs=18.1

Q ss_pred             EEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307          52 MACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus        52 l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      ++.++.|+|||.....-++..+....
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~   26 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRP   26 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSS
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCC
Confidence            46789999999998877777766544

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.

>PLN03025 replication factor C subunit; Provisional

Probab=88.72  E-value=0.73  Score=34.17  Aligned_cols=17  Identities=24%  Similarity=0.550  Sum_probs=14.4

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        35 ~~lll~Gp~G~GKTtla   51 (319)
T PLN03025         35 PNLILSGPPGTGKTTSI   51 (319)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46899999999999653

>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=88.62  E-value=0.95  Score=32.04  Aligned_cols=53  Identities=21%  Similarity=0.380  Sum_probs=34.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|.=.-+.+|+|.||+.  +++++.++.......-...           .+-+--.|+.+||..+.
T Consensus        26 ~g~iTs~IGPNGAGKST--LLS~~sRL~~~d~G~i~i~-----------g~~~~~~~s~~LAk~lS   78 (252)
T COG4604          26 KGGITSIIGPNGAGKST--LLSMMSRLLKKDSGEITID-----------GLELTSTPSKELAKKLS   78 (252)
T ss_pred             CCceeEEECCCCccHHH--HHHHHHHhccccCceEEEe-----------eeecccCChHHHHHHHH
Confidence            56666778999999987  7788888876543211000           12344468899987663

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=88.61  E-value=2.1  Score=33.45  Aligned_cols=17  Identities=35%  Similarity=0.522  Sum_probs=14.4

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.+++|+|||.+.
T Consensus        96 ~vI~lvG~~GsGKTTta  112 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTA  112 (437)
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            36789999999999764

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=88.61  E-value=3.6  Score=30.01  Aligned_cols=23  Identities=30%  Similarity=0.372  Sum_probs=18.0

Q ss_pred             HHhcCC-cEEEEccCCchHHHHHH
Q psy3307          44 VIISGR-DVMACAQTGSGKTAAFL   66 (130)
Q Consensus        44 ~~~~g~-~~l~~aptGsGKT~~~~   66 (130)
                      .+-+|+ -+.++++-|||||+.--
T Consensus        46 ~i~d~qg~~~vtGevGsGKTv~~R   69 (269)
T COG3267          46 AIADGQGILAVTGEVGSGKTVLRR   69 (269)
T ss_pred             HHhcCCceEEEEecCCCchhHHHH
Confidence            344665 78899999999998754

>PF05729 NACHT: NACHT domain

Probab=88.58  E-value=0.35  Score=31.51  Aligned_cols=26  Identities=23%  Similarity=0.360  Sum_probs=17.8

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      -+++.|++|+|||... --+...+...
T Consensus         2 ~l~I~G~~G~GKStll-~~~~~~~~~~   27 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLL-RKLAQQLAEE   27 (166)
T ss_pred             EEEEECCCCCChHHHH-HHHHHHHHhc
Confidence            4789999999999743 4444444443

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=88.47  E-value=3.2  Score=32.64  Aligned_cols=72  Identities=29%  Similarity=0.337  Sum_probs=48.0

Q ss_pred             HHHHHHHhHHh-----cC----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHH
Q psy3307          36 PVQKYAIPVII-----SG----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRE  106 (130)
Q Consensus        36 ~~Q~~~i~~~~-----~g----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  106 (130)
                      |.|.-.+..++     .|    +.+++.-|-+.|||.....-.+-.+.-..               ..+..+++.+++++
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g---------------~~~~~i~~~A~~~~   65 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDG---------------EPGAEIYCAANTRD   65 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCC---------------ccCceEEEEeCCHH
Confidence            45666555554     22    47888889999999754322222222111               11267999999999


Q ss_pred             HHHHHHHHHHHHHhcC
Q psy3307         107 LATQIYDEAKKFAYRS  122 (130)
Q Consensus       107 La~q~~~~~~~l~~~~  122 (130)
                      .|..+++.++++.+..
T Consensus        66 QA~~~f~~~~~~i~~~   81 (477)
T PF03354_consen   66 QAKIVFDEAKKMIEAS   81 (477)
T ss_pred             HHHHHHHHHHHHHHhC
Confidence            9999999998887653

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=88.47  E-value=0.95  Score=37.71  Aligned_cols=18  Identities=17%  Similarity=0.340  Sum_probs=15.4

Q ss_pred             CcEEEEccCCchHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~   66 (130)
                      .++++.|+||||||+..-
T Consensus       431 ~n~~I~G~tGsGKS~~~~  448 (797)
T TIGR02746       431 YNIAVVGGSGAGKSFFMQ  448 (797)
T ss_pred             cceEEEcCCCCCHHHHHH
Confidence            479999999999998654

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=88.45  E-value=0.38  Score=36.48  Aligned_cols=17  Identities=29%  Similarity=0.530  Sum_probs=15.0

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        56 ~~~lI~G~~GtGKT~l~   72 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV   72 (394)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            57999999999999753

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.39  E-value=3.7  Score=32.73  Aligned_cols=16  Identities=25%  Similarity=0.337  Sum_probs=13.8

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+|+|+|||...
T Consensus        38 a~Lf~GppGtGKTTlA   53 (504)
T PRK14963         38 AYLFSGPRGVGKTTTA   53 (504)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3599999999999875

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=88.35  E-value=1.1  Score=35.53  Aligned_cols=19  Identities=32%  Similarity=0.517  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.+++|+|||...
T Consensus        30 ~Gs~~li~G~pGsGKT~l~   48 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFA   48 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHH
Confidence            4678999999999999754

>cd01394 radB RadB

Probab=88.32  E-value=0.95  Score=31.42  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=18.2

Q ss_pred             HhHHhc-----CCcEEEEccCCchHHHHH
Q psy3307          42 IPVIIS-----GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~-----g~~~l~~aptGsGKT~~~   65 (130)
                      ++.++.     |.-+.+.+++|+|||...
T Consensus         8 LD~~l~GGi~~g~i~~i~G~~GsGKT~l~   36 (218)
T cd01394           8 LDELLGGGVERGTVTQVYGPPGTGKTNIA   36 (218)
T ss_pred             HHHHhcCCccCCeEEEEECCCCCCHHHHH
Confidence            455554     466889999999999754

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=88.27  E-value=0.4  Score=31.16  Aligned_cols=13  Identities=23%  Similarity=0.588  Sum_probs=11.6

Q ss_pred             EEEEccCCchHHH
Q psy3307          51 VMACAQTGSGKTA   63 (130)
Q Consensus        51 ~l~~aptGsGKT~   63 (130)
                      +++.+|+|||||.
T Consensus         2 i~i~GpsGsGKst   14 (137)
T cd00071           2 IVLSGPSGVGKST   14 (137)
T ss_pred             EEEECCCCCCHHH
Confidence            5789999999996

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=88.25  E-value=0.68  Score=33.09  Aligned_cols=21  Identities=29%  Similarity=0.363  Sum_probs=13.9

Q ss_pred             EEccCCchHHHHHHHHHHHHHH
Q psy3307          53 ACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        53 ~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      +.||.|||||. |+-.+-+++.
T Consensus         1 ViGpaGSGKTT-~~~~~~~~~~   21 (238)
T PF03029_consen    1 VIGPAGSGKTT-FCKGLSEWLE   21 (238)
T ss_dssp             -EESTTSSHHH-HHHHHHHHHT
T ss_pred             CCCCCCCCHHH-HHHHHHHHHH
Confidence            46899999995 5455555443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>KOG0991|consensus

Probab=88.23  E-value=0.58  Score=33.94  Aligned_cols=18  Identities=28%  Similarity=0.601  Sum_probs=15.9

Q ss_pred             CcEEEEccCCchHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~   66 (130)
                      .++++.+|+|+|||.+..
T Consensus        49 P~liisGpPG~GKTTsi~   66 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSIL   66 (333)
T ss_pred             CceEeeCCCCCchhhHHH
Confidence            499999999999998754

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=88.22  E-value=0.58  Score=34.27  Aligned_cols=31  Identities=29%  Similarity=0.461  Sum_probs=24.4

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      +..|.-+++.+|+|||||.  .+=+++++.+..
T Consensus        24 I~~gef~vliGpSGsGKTT--tLkMINrLiept   54 (309)
T COG1125          24 IEEGEFLVLIGPSGSGKTT--TLKMINRLIEPT   54 (309)
T ss_pred             ecCCeEEEEECCCCCcHHH--HHHHHhcccCCC
Confidence            3478889999999999998  467777776543

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=88.09  E-value=0.95  Score=35.82  Aligned_cols=19  Identities=32%  Similarity=0.475  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|..+++.+++|+|||...
T Consensus       272 ~g~~~li~G~~G~GKT~l~  290 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLA  290 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3578889999999999754

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=88.08  E-value=0.78  Score=30.85  Aligned_cols=25  Identities=16%  Similarity=0.191  Sum_probs=17.0

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      -.++.|++|+|||..  +-++..+...
T Consensus        21 ~~vi~G~Ng~GKSti--l~ai~~~L~~   45 (202)
T PF13476_consen   21 LNVIYGPNGSGKSTI--LEAIRYALGG   45 (202)
T ss_dssp             EEEEEESTTSSHHHH--HHHHHHHHHS
T ss_pred             cEEEECCCCCCHHHH--HHHHHHHHcC
Confidence            456789999999974  3455555533

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=88.04  E-value=1  Score=37.85  Aligned_cols=16  Identities=31%  Similarity=0.459  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      .+.+++||||+|||..
T Consensus       437 ghT~I~G~tGaGKTvL  452 (796)
T COG3451         437 GHTLIIGPTGAGKTVL  452 (796)
T ss_pred             CCeEEECCCCCCHHHH
Confidence            4789999999999964

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=88.04  E-value=1.5  Score=28.73  Aligned_cols=24  Identities=25%  Similarity=0.412  Sum_probs=17.1

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +.++++.+||||.. +--++..+.+
T Consensus         3 v~VvG~~~sGKTTl-~~~Li~~l~~   26 (140)
T PF03205_consen    3 VQVVGPKNSGKTTL-IRKLINELKR   26 (140)
T ss_dssp             EEEEESTTSSHHHH-HHHHHHHHHH
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHhH
Confidence            67899999999964 3455555554

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=87.92  E-value=2.1  Score=33.42  Aligned_cols=26  Identities=23%  Similarity=0.268  Sum_probs=18.2

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      ..+++.||+|+|||... -.+.+.+..
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~  156 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQ  156 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHH
Confidence            46999999999999632 344444443

>KOG0726|consensus

Probab=87.91  E-value=1  Score=33.77  Aligned_cols=56  Identities=20%  Similarity=0.245  Sum_probs=35.2

Q ss_pred             cccccCCCcCCCCCHHHHHHHHH---CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIAL---ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~---~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...|..+|.|.|=-+..++.+++   +..++|--++.-.   +.--+.+++.+++|+|||+.
T Consensus       177 eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemG---ikpPKGVIlyG~PGTGKTLL  235 (440)
T KOG0726|consen  177 EKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMG---IKPPKGVILYGEPGTGKTLL  235 (440)
T ss_pred             ccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcC---CCCCCeeEEeCCCCCchhHH
Confidence            34577889998855554445544   3444443333322   22347899999999999974

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=87.90  E-value=0.49  Score=29.70  Aligned_cols=20  Identities=30%  Similarity=0.381  Sum_probs=16.5

Q ss_pred             cCCcEEEEccCCchHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~   66 (130)
                      .|+-+.+.+|+|+|||....
T Consensus        14 ~ge~v~I~GpSGsGKSTLl~   33 (107)
T cd00820          14 GKVGVLITGDSGIGKTELAL   33 (107)
T ss_pred             CCEEEEEEcCCCCCHHHHHH
Confidence            56778999999999998543

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=87.78  E-value=1.3  Score=29.99  Aligned_cols=15  Identities=20%  Similarity=0.288  Sum_probs=12.5

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.+++|||||...
T Consensus         2 ~li~G~~~sGKS~~a   16 (169)
T cd00544           2 ILVTGGARSGKSRFA   16 (169)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999654

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>KOG0741|consensus

Probab=87.78  E-value=0.62  Score=37.49  Aligned_cols=101  Identities=15%  Similarity=0.178  Sum_probs=52.8

Q ss_pred             ccccCCCcCCC---CCHHHHHHHHHCCCCCCcHHHHHHHh-HH------hcCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307           7 SLKKQGFDDIQ---MTEIITNNIALARYDKPTPVQKYAIP-VI------ISGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus         7 ~~~~~~f~~l~---l~~~i~~~l~~~~~~~~t~~Q~~~i~-~~------~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      ..|.-.|+++|   |+.+.-+.+++.       .-.+++| .+      .+-+.+++-+|+|+|||+-.  =-+-.+...
T Consensus       212 i~Pdf~Fe~mGIGGLd~EFs~IFRRA-------FAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiA--RqIGkMLNA  282 (744)
T KOG0741|consen  212 INPDFNFESMGIGGLDKEFSDIFRRA-------FASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIA--RQIGKMLNA  282 (744)
T ss_pred             cCCCCChhhcccccchHHHHHHHHHH-------HHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHH--HHHHHHhcC
Confidence            45666788886   556655554331       1122222 12      24478999999999999843  223333333


Q ss_pred             CCCCCCCCCCCCCCCCCCCceEE--EEcC----cHHHHHHHHHHHHHHHhcCCCceE
Q psy3307          77 GPLPTPPAGRGYPSRKKVFPLGL--VLAP----TRELATQIYDEAKKFAYRSQLRPC  127 (130)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~l--il~P----t~~La~q~~~~~~~l~~~~~~~~~  127 (130)
                      +..           +-.+||.+|  ++--    -|.|=.+..++.++++.+.++.+.
T Consensus       283 reP-----------KIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHII  328 (744)
T KOG0741|consen  283 REP-----------KIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHII  328 (744)
T ss_pred             CCC-----------cccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEE
Confidence            221           011122222  2222    355555666667777777666543

>PRK14531 adenylate kinase; Provisional

Probab=87.72  E-value=0.36  Score=32.77  Aligned_cols=16  Identities=19%  Similarity=0.401  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.+++|||||..
T Consensus         3 ~~i~i~G~pGsGKsT~   18 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQ   18 (183)
T ss_pred             cEEEEECCCCCCHHHH
Confidence            4689999999999965

>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=87.64  E-value=1.6  Score=32.36  Aligned_cols=25  Identities=20%  Similarity=0.108  Sum_probs=19.0

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      -+++.++-|.|||.+...-.+....
T Consensus         3 ~~~~~GKGGVGKTT~aaA~A~~~A~   27 (305)
T PF02374_consen    3 ILFFGGKGGVGKTTVAAALALALAR   27 (305)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEecCCCCCcHHHHHHHHHHHhh
Confidence            4688999999999987666665443

...

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=87.63  E-value=1.6  Score=29.03  Aligned_cols=14  Identities=29%  Similarity=0.351  Sum_probs=11.6

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +.+.+++|||||..
T Consensus         2 i~i~G~~gsGKTtl   15 (155)
T TIGR00176         2 LQIVGPKNSGKTTL   15 (155)
T ss_pred             EEEECCCCCCHHHH
Confidence            46789999999963

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=87.52  E-value=2.1  Score=33.41  Aligned_cols=26  Identities=27%  Similarity=0.310  Sum_probs=18.0

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +.+++.||+|+|||... -.+...+..
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~  174 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILE  174 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            46899999999999642 344444443

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=87.48  E-value=0.45  Score=35.38  Aligned_cols=17  Identities=35%  Similarity=0.401  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.||||||||...
T Consensus         5 ~~i~i~GptgsGKt~la   21 (307)
T PRK00091          5 KVIVIVGPTASGKTALA   21 (307)
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            45789999999999754

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=87.41  E-value=1.6  Score=34.49  Aligned_cols=48  Identities=13%  Similarity=0.341  Sum_probs=33.0

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      ..+.+|.+|++.+.+.|.+                  +.+.+++.+|+|+|||. |.-++-..+...
T Consensus       243 k~~ledY~L~dkl~eRL~e------------------raeGILIAG~PGaGKsT-FaqAlAefy~~~  290 (604)
T COG1855         243 KLSLEDYGLSDKLKERLEE------------------RAEGILIAGAPGAGKST-FAQALAEFYASQ  290 (604)
T ss_pred             EechhhcCCCHHHHHHHHh------------------hhcceEEecCCCCChhH-HHHHHHHHHHhc
Confidence            3456677777777776653                  24678999999999995 445555555543

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=87.38  E-value=0.72  Score=31.16  Aligned_cols=19  Identities=32%  Similarity=0.398  Sum_probs=15.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      .....+++.+++||||++.
T Consensus        20 ~~~~pVlI~GE~GtGK~~l   38 (168)
T PF00158_consen   20 SSDLPVLITGETGTGKELL   38 (168)
T ss_dssp             TSTS-EEEECSTTSSHHHH
T ss_pred             CCCCCEEEEcCCCCcHHHH
Confidence            4557999999999999974

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=87.25  E-value=1.2  Score=31.03  Aligned_cols=19  Identities=37%  Similarity=0.420  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCchHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~   66 (130)
                      |.-+.+.+++|+|||...+
T Consensus        23 g~i~~i~G~~GsGKT~l~~   41 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICL   41 (225)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            5688999999999997543

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=87.18  E-value=0.46  Score=34.96  Aligned_cols=16  Identities=31%  Similarity=0.578  Sum_probs=14.8

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ++++..+|+|+|||..
T Consensus       152 knVLFyGppGTGKTm~  167 (368)
T COG1223         152 KNVLFYGPPGTGKTMM  167 (368)
T ss_pred             ceeEEECCCCccHHHH
Confidence            7999999999999973

>PRK10876 recB exonuclease V subunit beta; Provisional

Probab=87.17  E-value=2.9  Score=36.80  Aligned_cols=64  Identities=19%  Similarity=0.191  Sum_probs=39.9

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      ++|. .++.|.-|||||++...-.+..+........       +.+.....++|+++=|+.-+.++...++.
T Consensus        16 L~G~-~LIEASAGTGKTyTIa~lyLrLlL~~g~~~~-------~~~~L~~~~ILvvTFT~aAt~Elr~RIr~   79 (1181)
T PRK10876         16 LQGE-RLIEASAGTGKTFTIAALYLRLLLGLGGSAA-------FPRPLTVEEILVVTFTEAATEELRGRIRS   79 (1181)
T ss_pred             CCCC-EEEEeCCCCcHHHHHHHHHHHHHccCCcccc-------ccCCCChhhEEEEechHHHHHHHHHHHHH
Confidence            4564 4569999999999876666666654321100       00011114699999888888877776653

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=87.14  E-value=1.3  Score=33.48  Aligned_cols=45  Identities=20%  Similarity=0.138  Sum_probs=36.0

Q ss_pred             CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        31 ~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +.--|+.|..-+..+.+..=++..+|-|+|||+.......+.+..
T Consensus       126 I~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~  170 (348)
T COG1702         126 IIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGA  170 (348)
T ss_pred             eEecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhh
Confidence            445688999988888888888999999999998776666666554

>PRK06893 DNA replication initiation factor; Validated

Probab=87.08  E-value=0.39  Score=33.97  Aligned_cols=15  Identities=20%  Similarity=0.122  Sum_probs=13.1

Q ss_pred             CcEEEEccCCchHHH
Q psy3307          49 RDVMACAQTGSGKTA   63 (130)
Q Consensus        49 ~~~l~~aptGsGKT~   63 (130)
                      ..+++.||+|+|||.
T Consensus        40 ~~l~l~G~~G~GKTh   54 (229)
T PRK06893         40 PFFYIWGGKSSGKSH   54 (229)
T ss_pred             CeEEEECCCCCCHHH
Confidence            457999999999995

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=86.98  E-value=3  Score=36.18  Aligned_cols=69  Identities=22%  Similarity=0.055  Sum_probs=46.6

Q ss_pred             CCcHHHHHHHhHHh--------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          33 KPTPVQKYAIPVII--------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~--------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      .-...|-.|+..+.        .|--++=-|.||+|||++=. =++..+..                ...+.|..|-.-.
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA-RImyaLsd----------------~~~g~RfsiALGL  470 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA-RAMYALRD----------------DKQGARFAIALGL  470 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH-HHHHHhCC----------------CCCCceEEEEccc
Confidence            34568888887765        33466777999999998631 11212221                1223678888889


Q ss_pred             HHHHHHHHHHHHHH
Q psy3307         105 RELATQIYDEAKKF  118 (130)
Q Consensus       105 ~~La~q~~~~~~~l  118 (130)
                      |.|..|..+.+++-
T Consensus       471 RTLTLQTGda~r~r  484 (1110)
T TIGR02562       471 RSLTLQTGHALKTR  484 (1110)
T ss_pred             cceeccchHHHHHh
Confidence            99999999888763

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=86.95  E-value=0.47  Score=37.55  Aligned_cols=18  Identities=22%  Similarity=0.403  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      .+.+++.||+|+|||+..
T Consensus       259 pkGILL~GPpGTGKTllA  276 (489)
T CHL00195        259 PRGLLLVGIQGTGKSLTA  276 (489)
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            367999999999999753

>PF14516 AAA_35: AAA-like domain

Probab=86.95  E-value=3  Score=31.24  Aligned_cols=39  Identities=23%  Similarity=0.371  Sum_probs=31.2

Q ss_pred             HHHHHHHhHHhc-CCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          36 PVQKYAIPVIIS-GRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        36 ~~Q~~~i~~~~~-g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      |+..+++..+.+ |..+.+.||-.+|||.. +.-+++++..
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKTSl-l~~l~~~l~~   57 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKTSL-LLRLLERLQQ   57 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHHHH-HHHHHHHHHH
Confidence            488888988887 99999999999999964 4555555554

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=86.93  E-value=3.3  Score=31.28  Aligned_cols=26  Identities=19%  Similarity=0.351  Sum_probs=18.2

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      -+++.+.+|+|||.+  +.=|.+.+...
T Consensus       141 Vil~vGVNG~GKTTT--IaKLA~~l~~~  166 (340)
T COG0552         141 VILFVGVNGVGKTTT--IAKLAKYLKQQ  166 (340)
T ss_pred             EEEEEecCCCchHhH--HHHHHHHHHHC
Confidence            568899999999986  34444445443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=86.86  E-value=11  Score=28.13  Aligned_cols=52  Identities=17%  Similarity=0.247  Sum_probs=28.9

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      ...++.||.|+||+... ......+....   .|..+....-....+|-..++.|+
T Consensus        27 ha~Lf~G~~G~Gk~~~A-~~~a~~llc~~---~c~~c~~~~~~~~~hPDl~~i~p~   78 (314)
T PRK07399         27 PAYLFAGPEGVGRKLAA-LCFIEGLLSQG---SPSKNIRRRLEEGNHPDLLWVEPT   78 (314)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHcCCC---CCCCcHhcccccCCCCCEEEEecc
Confidence            37899999999998643 34444444332   121111111223344777888875

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=86.83  E-value=0.45  Score=32.02  Aligned_cols=14  Identities=36%  Similarity=0.503  Sum_probs=12.3

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +++.|++|||||..
T Consensus         2 i~i~G~pGsGKst~   15 (183)
T TIGR01359         2 VFVLGGPGSGKGTQ   15 (183)
T ss_pred             EEEECCCCCCHHHH
Confidence            57899999999974

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=86.83  E-value=1.5  Score=33.48  Aligned_cols=16  Identities=19%  Similarity=0.316  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +-+++.||+|+|||..
T Consensus        79 ~il~L~GPPGsGKStl   94 (361)
T smart00763       79 QILYLLGPVGGGKSSL   94 (361)
T ss_pred             cEEEEECCCCCCHHHH
Confidence            5679999999999974

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=86.71  E-value=0.48  Score=33.28  Aligned_cols=27  Identities=22%  Similarity=0.434  Sum_probs=20.2

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      +..|.-+.+.+|+|||||.  ++-++..+
T Consensus        28 i~~Ge~~~l~G~nGsGKST--Ll~~l~G~   54 (233)
T cd03258          28 VPKGEIFGIIGRSGAGKST--LIRCINGL   54 (233)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHhCC
Confidence            4478899999999999997  34444433

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=86.68  E-value=2.5  Score=32.37  Aligned_cols=26  Identities=27%  Similarity=0.354  Sum_probs=18.1

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      ..+++.|++|+|||... -.+...+..
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~  162 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILE  162 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHH
Confidence            46899999999999643 344444443

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).

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=86.68  E-value=1.1  Score=33.38  Aligned_cols=46  Identities=9%  Similarity=0.107  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC---CcEEEEccCCchHHHH
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISG---RDVMACAQTGSGKTAA   64 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g---~~~l~~aptGsGKT~~   64 (130)
                      +.+.+.+.|.+.++..+.+- -..|..+...   --+++.|++|||||..
T Consensus        60 l~~~V~~~L~~~~~~~~~~~-y~~~~~i~~~~~p~iIlI~G~sgsGKStl  108 (301)
T PRK04220         60 LRRRVYYKLIEKDYEEVAEK-YLLWRRIRKSKEPIIILIGGASGVGTSTI  108 (301)
T ss_pred             HHHHHHHHHHHhCcHhHHHH-HHHHHHHhcCCCCEEEEEECCCCCCHHHH
Confidence            34456666777666554432 3334344432   2689999999999973

>PRK08233 hypothetical protein; Provisional

Probab=86.66  E-value=0.47  Score=31.73  Aligned_cols=16  Identities=31%  Similarity=0.464  Sum_probs=12.6

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      .=+.+.|++|||||..
T Consensus         4 ~iI~I~G~~GsGKtTl   19 (182)
T PRK08233          4 KIITIAAVSGGGKTTL   19 (182)
T ss_pred             eEEEEECCCCCCHHHH
Confidence            3467789999999963

>PRK06762 hypothetical protein; Provisional

Probab=86.64  E-value=0.55  Score=31.13  Aligned_cols=16  Identities=31%  Similarity=0.416  Sum_probs=13.2

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -++++|++|||||...
T Consensus         4 li~i~G~~GsGKST~A   19 (166)
T PRK06762          4 LIIIRGNSGSGKTTIA   19 (166)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4688999999999743

>TIGR02012 tigrfam_recA protein RecA

Probab=86.64  E-value=2.4  Score=31.81  Aligned_cols=19  Identities=37%  Similarity=0.414  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCchHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~   66 (130)
                      |+-+.+.+|+|||||...+
T Consensus        55 G~iteI~G~~GsGKTtLaL   73 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLAL   73 (321)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4678899999999997543

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.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=86.58  E-value=0.54  Score=26.69  Aligned_cols=14  Identities=29%  Similarity=0.546  Sum_probs=11.8

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +.+.++.|||||..
T Consensus         2 i~i~G~~gsGKst~   15 (69)
T cd02019           2 IAITGGSGSGKSTV   15 (69)
T ss_pred             EEEECCCCCCHHHH
Confidence            56789999999964

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>cd01918 HprK_C HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria

Probab=86.52  E-value=0.56  Score=31.23  Aligned_cols=19  Identities=26%  Similarity=0.422  Sum_probs=16.5

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|+-+++.++.|+|||...
T Consensus        13 ~g~gvLi~G~sG~GKStla   31 (149)
T cd01918          13 GGIGVLITGPSGIGKSELA   31 (149)
T ss_pred             CCEEEEEEcCCCCCHHHHH
Confidence            5789999999999999654

It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=86.46  E-value=0.57  Score=31.80  Aligned_cols=18  Identities=28%  Similarity=0.492  Sum_probs=15.5

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+-+.+.+++|+|||..
T Consensus         2 ~ge~i~l~G~sGsGKSTl   19 (176)
T PRK09825          2 AGESYILMGVSGSGKSLI   19 (176)
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            477789999999999974

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=86.46  E-value=1.6  Score=32.66  Aligned_cols=18  Identities=22%  Similarity=0.333  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +.-+.+.+|+|+|||...
T Consensus       114 ~~vi~lvGpnGsGKTTt~  131 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTI  131 (318)
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            456788999999999754

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=86.45  E-value=2.6  Score=30.74  Aligned_cols=17  Identities=24%  Similarity=0.405  Sum_probs=14.2

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.+|+|+|||...
T Consensus        73 ~vi~l~G~~G~GKTTt~   89 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTI   89 (272)
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            46778899999999764

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.

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=86.43  E-value=0.56  Score=32.14  Aligned_cols=23  Identities=30%  Similarity=0.379  Sum_probs=15.5

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      +.+.|++|||||...  -.|.....
T Consensus         2 IgI~G~sgSGKTTla--~~L~~~L~   24 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLA--KRLAQILN   24 (194)
T ss_dssp             EEEEESTTSSHHHHH--HHHHHHHT
T ss_pred             EEEECCCCCCHHHHH--HHHHHHhC
Confidence            468999999999743  34444443

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=86.42  E-value=0.87  Score=34.01  Aligned_cols=25  Identities=16%  Similarity=0.210  Sum_probs=19.4

Q ss_pred             HHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +-.....+..+++.|++||||+...
T Consensus        22 i~~~a~~~~pVlI~GE~GtGK~~lA   46 (326)
T PRK11608         22 VSRLAPLDKPVLIIGERGTGKELIA   46 (326)
T ss_pred             HHHHhCCCCCEEEECCCCCcHHHHH
Confidence            3334457789999999999999753

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=86.40  E-value=0.53  Score=32.07  Aligned_cols=20  Identities=25%  Similarity=0.242  Sum_probs=17.0

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|.-+.+.+|+|+|||..+
T Consensus        19 ~~G~~~~l~G~nG~GKSTLl   38 (176)
T cd03238          19 PLNVLVVVTGVSGSGKSTLV   38 (176)
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            46788899999999999754

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=86.37  E-value=0.9  Score=34.05  Aligned_cols=26  Identities=19%  Similarity=0.206  Sum_probs=19.6

Q ss_pred             HHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          40 YAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        40 ~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ++-.....+..+++.|++||||+...
T Consensus        14 ~~~~~a~~~~pVLI~GE~GtGK~~lA   39 (329)
T TIGR02974        14 QVSRLAPLDRPVLIIGERGTGKELIA   39 (329)
T ss_pred             HHHHHhCCCCCEEEECCCCChHHHHH
Confidence            33334456789999999999999743

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=86.37  E-value=0.52  Score=32.04  Aligned_cols=19  Identities=21%  Similarity=0.338  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        15 i~~Ge~~~i~G~nGsGKST   33 (190)
T TIGR01166        15 AERGEVLALLGANGAGKST   33 (190)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3478889999999999997

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>KOG2373|consensus

Probab=86.32  E-value=0.24  Score=37.78  Aligned_cols=26  Identities=31%  Similarity=0.299  Sum_probs=18.0

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      .|.-.++.+|||||||....=..+..
T Consensus       272 ~GElTvlTGpTGsGKTTFlsEYsLDL  297 (514)
T KOG2373|consen  272 PGELTVLTGPTGSGKTTFLSEYSLDL  297 (514)
T ss_pred             CCceEEEecCCCCCceeEehHhhHHH
Confidence            34577899999999996543344433

>PRK05748 replicative DNA helicase; Provisional

Probab=86.31  E-value=1.4  Score=34.41  Aligned_cols=27  Identities=22%  Similarity=0.271  Sum_probs=19.1

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.|++|+|||.. .+-++....
T Consensus       202 ~G~livIaarpg~GKT~~-al~ia~~~a  228 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAF-ALNIAQNVA  228 (448)
T ss_pred             CCceEEEEeCCCCCchHH-HHHHHHHHH
Confidence            446789999999999964 445544443

>KOG0737|consensus

Probab=86.24  E-value=0.84  Score=34.83  Aligned_cols=56  Identities=20%  Similarity=0.285  Sum_probs=36.3

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHH----hHHhcCCcEEEEccCCchHHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAI----PVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i----~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .....+|.|.+=-+.+.+++++.-.   -|.|..-+    .....-+.+++.+|+|+|||.+.
T Consensus        85 ~~I~v~f~DIggLe~v~~~L~e~Vi---lPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlA  144 (386)
T KOG0737|consen   85 SEIGVSFDDIGGLEEVKDALQELVI---LPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLA  144 (386)
T ss_pred             hhceeehhhccchHHHHHHHHHHHh---hcccchhhhcccccccCCccceecCCCCchHHHHH
Confidence            4456789999888888888876422   23322111    01113379999999999999854

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=86.16  E-value=0.54  Score=32.49  Aligned_cols=19  Identities=32%  Similarity=0.545  Sum_probs=16.5

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|||||.
T Consensus        24 i~~G~~~~i~G~nGsGKST   42 (214)
T cd03292          24 ISAGEFVFLVGPSGAGKST   42 (214)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3478889999999999997

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport

Probab=86.15  E-value=0.91  Score=33.79  Aligned_cols=23  Identities=39%  Similarity=0.622  Sum_probs=16.9

Q ss_pred             hHHhcCC--cEEEEccCCchHHHHH
Q psy3307          43 PVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ..+++|.  .++.-|+||||||.+.
T Consensus        68 ~~~l~G~n~~i~ayG~tgSGKT~Tm   92 (335)
T PF00225_consen   68 DSVLDGYNATIFAYGQTGSGKTYTM   92 (335)
T ss_dssp             HHHHTT-EEEEEEEESTTSSHHHHH
T ss_pred             HHhhcCCceEEEeeccccccccccc
Confidence            4456886  4677889999999764

The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=86.11  E-value=0.51  Score=31.71  Aligned_cols=17  Identities=24%  Similarity=0.384  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .-+++.|++|||||...
T Consensus         4 ~ii~i~G~~GsGKsTl~   20 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQC   20 (188)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35788999999999753

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=86.10  E-value=0.65  Score=31.47  Aligned_cols=17  Identities=29%  Similarity=0.546  Sum_probs=14.8

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      ++-+++.||+||||+..
T Consensus         2 ~r~ivl~Gpsg~GK~~l   18 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTL   18 (183)
T ss_dssp             SSEEEEESSTTSSHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            57789999999999963

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=86.09  E-value=0.54  Score=32.77  Aligned_cols=21  Identities=29%  Similarity=0.214  Sum_probs=17.2

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..|.-+.+.+|+|+|||..+
T Consensus        10 i~~Ge~~~l~G~NGsGKSTLl   30 (213)
T PRK15177         10 MGYHEHIGILAAPGSGKTTLT   30 (213)
T ss_pred             EcCCCEEEEECCCCCCHHHHH
Confidence            346788899999999999743

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=86.07  E-value=0.52  Score=32.35  Aligned_cols=26  Identities=31%  Similarity=0.500  Sum_probs=19.4

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      +..|.-+.+.+|+|+|||.  ++-++.-
T Consensus        21 i~~Ge~~~i~G~nGsGKST--Ll~~l~G   46 (206)
T TIGR03608        21 IEKGKMYAIIGESGSGKST--LLNIIGL   46 (206)
T ss_pred             EeCCcEEEEECCCCCCHHH--HHHHHhc
Confidence            3478889999999999997  3444443

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=86.06  E-value=1  Score=35.45  Aligned_cols=59  Identities=22%  Similarity=0.254  Sum_probs=32.6

Q ss_pred             cccccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           4 CLVSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         4 ~~~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .....+..+|.+.+--+...+.+++.   ....+.-.+..   -+-..+.+++.+|+|+|||+..
T Consensus       232 ~~~~~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~---~~~~~~giLl~GpPGtGKT~lA  293 (494)
T COG0464         232 VLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKL---GLRPPKGVLLYGPPGTGKTLLA  293 (494)
T ss_pred             cccCCCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhc---CCCCCCeeEEECCCCCCHHHHH
Confidence            34556677788876444444444331   22222221110   1223358999999999999854

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=86.02  E-value=0.59  Score=34.78  Aligned_cols=17  Identities=29%  Similarity=0.372  Sum_probs=14.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.||+|+|||...
T Consensus        52 ~~~ll~GppG~GKT~la   68 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLA   68 (328)
T ss_pred             CcEEEECCCCccHHHHH
Confidence            57999999999999754

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=86.02  E-value=0.62  Score=31.50  Aligned_cols=15  Identities=27%  Similarity=0.472  Sum_probs=12.8

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.|++|||||..
T Consensus         1 ~I~i~G~pGsGKst~   15 (194)
T cd01428           1 RILLLGPPGSGKGTQ   15 (194)
T ss_pred             CEEEECCCCCCHHHH
Confidence            378999999999954

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK13891 conjugal transfer protein TrbE; Provisional

Probab=85.98  E-value=1.5  Score=37.15  Aligned_cols=17  Identities=24%  Similarity=0.388  Sum_probs=14.4

Q ss_pred             cEEEEccCCchHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFL   66 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~   66 (130)
                      +.++.||||+|||+..-
T Consensus       490 h~~I~G~tGsGKS~l~~  506 (852)
T PRK13891        490 HTFMFGPTGAGKSTHLG  506 (852)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            57999999999997643

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=85.98  E-value=0.55  Score=32.51  Aligned_cols=19  Identities=26%  Similarity=0.406  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        23 i~~Ge~~~i~G~nGsGKST   41 (213)
T cd03259          23 VEPGEFLALLGPSGCGKTT   41 (213)
T ss_pred             EcCCcEEEEECCCCCCHHH
Confidence            3478889999999999997

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=85.96  E-value=0.56  Score=32.42  Aligned_cols=20  Identities=30%  Similarity=0.453  Sum_probs=17.1

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+.+.+|+|+|||..
T Consensus        25 i~~G~~~~l~G~nGsGKSTL   44 (214)
T TIGR02673        25 IRKGEFLFLTGPSGAGKTTL   44 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            45788899999999999973

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=85.95  E-value=0.63  Score=30.26  Aligned_cols=15  Identities=27%  Similarity=0.445  Sum_probs=12.5

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.+++|||||...
T Consensus         2 i~l~G~~GsGKST~a   16 (150)
T cd02021           2 IVVMGVSGSGKSTVG   16 (150)
T ss_pred             EEEEcCCCCCHHHHH
Confidence            578999999999753

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>KOG0349|consensus

Probab=85.91  E-value=1.8  Score=34.10  Aligned_cols=28  Identities=29%  Similarity=0.564  Sum_probs=24.1

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHHHhcC
Q psy3307          95 FPLGLVLAPTRELATQIYDEAKKFAYRS  122 (130)
Q Consensus        95 ~~~~lil~Pt~~La~q~~~~~~~l~~~~  122 (130)
                      -|+++|+-|+|+|++|.++.+++|-.++
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~  313 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHT  313 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhc
Confidence            4899999999999999999887776554

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=85.86  E-value=0.58  Score=31.53  Aligned_cols=19  Identities=26%  Similarity=0.567  Sum_probs=16.7

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+++|+|||.
T Consensus        25 i~~Ge~~~i~G~nGsGKSt   43 (178)
T cd03247          25 LKQGEKIALLGRSGSGKST   43 (178)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3478899999999999997

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>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=85.82  E-value=1.7  Score=32.64  Aligned_cols=13  Identities=38%  Similarity=0.529  Sum_probs=11.1

Q ss_pred             EEEEccCCchHHH
Q psy3307          51 VMACAQTGSGKTA   63 (130)
Q Consensus        51 ~l~~aptGsGKT~   63 (130)
                      .++-||||+||+-
T Consensus        90 ~~VYGPTG~GKSq  102 (369)
T PF02456_consen   90 GVVYGPTGSGKSQ  102 (369)
T ss_pred             EEEECCCCCCHHH
Confidence            4778999999985

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

>PRK05541 adenylylsulfate kinase; Provisional

Probab=85.80  E-value=0.6  Score=31.33  Aligned_cols=19  Identities=32%  Similarity=0.382  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.|++|||||...
T Consensus         6 ~~~~I~i~G~~GsGKst~a   24 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIA   24 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            5678999999999999743

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=85.78  E-value=0.67  Score=30.03  Aligned_cols=16  Identities=25%  Similarity=0.397  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      ++++.+++|+|||...
T Consensus         1 ~i~l~G~~GsGKstla   16 (154)
T cd00464           1 NIVLIGMMGAGKTTVG   16 (154)
T ss_pred             CEEEEcCCCCCHHHHH
Confidence            4789999999999753

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=85.75  E-value=1.5  Score=36.89  Aligned_cols=18  Identities=22%  Similarity=0.494  Sum_probs=15.1

Q ss_pred             cEEEEccCCchHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLV   67 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l   67 (130)
                      +.++.|+||||||+..-.
T Consensus       443 n~~I~G~tGsGKS~l~~~  460 (811)
T PRK13873        443 HTLVVGPTGAGKSVLLAL  460 (811)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            789999999999976433

>PRK14532 adenylate kinase; Provisional

Probab=85.72  E-value=0.52  Score=31.93  Aligned_cols=15  Identities=13%  Similarity=0.348  Sum_probs=13.1

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      ++++.+++|||||..
T Consensus         2 ~i~~~G~pGsGKsT~   16 (188)
T PRK14532          2 NLILFGPPAAGKGTQ   16 (188)
T ss_pred             EEEEECCCCCCHHHH
Confidence            588999999999964

>PHA00729 NTP-binding motif containing protein

Probab=85.69  E-value=0.65  Score=33.07  Aligned_cols=15  Identities=33%  Similarity=0.492  Sum_probs=13.6

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      ++++.|++|+|||..
T Consensus        19 nIlItG~pGvGKT~L   33 (226)
T PHA00729         19 SAVIFGKQGSGKTTY   33 (226)
T ss_pred             EEEEECCCCCCHHHH
Confidence            899999999999964

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=85.66  E-value=4  Score=29.19  Aligned_cols=28  Identities=29%  Similarity=0.249  Sum_probs=19.0

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .|.=+++.|.+|.|||... +-+...+..
T Consensus        18 ~g~L~vi~a~pg~GKT~~~-l~ia~~~a~   45 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFA-LQIALNAAL   45 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHH-HHHHHHHHH
T ss_pred             cCcEEEEEecccCCchHHH-HHHHHHHHH
Confidence            4467889999999999654 444444444

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 ....

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=85.64  E-value=0.58  Score=32.46  Aligned_cols=19  Identities=37%  Similarity=0.497  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        27 i~~G~~~~l~G~nGsGKST   45 (218)
T cd03255          27 IEKGEFVAIVGPSGSGKST   45 (218)
T ss_pred             EcCCCEEEEEcCCCCCHHH
Confidence            3478899999999999997

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=85.59  E-value=0.59  Score=32.75  Aligned_cols=19  Identities=21%  Similarity=0.426  Sum_probs=16.7

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        30 i~~Ge~~~i~G~nGsGKST   48 (225)
T PRK10247         30 LRAGEFKLITGPSGCGKST   48 (225)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3478899999999999997

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=85.57  E-value=0.59  Score=32.32  Aligned_cols=27  Identities=26%  Similarity=0.449  Sum_probs=19.9

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      +..|.-+.+.+|+|+|||.  ++-++..+
T Consensus        23 i~~Ge~~~l~G~nGsGKST--Ll~~l~G~   49 (213)
T cd03301          23 IADGEFVVLLGPSGCGKTT--TLRMIAGL   49 (213)
T ss_pred             EcCCcEEEEECCCCCCHHH--HHHHHhCC
Confidence            3478889999999999997  34444433

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=85.56  E-value=0.52  Score=32.55  Aligned_cols=26  Identities=19%  Similarity=0.273  Sum_probs=19.3

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      +..|.-+.+.+|+|+|||.  ++-++..
T Consensus        23 i~~G~~~~i~G~nGsGKST--Ll~~l~G   48 (210)
T cd03269          23 VEKGEIFGLLGPNGAGKTT--TIRMILG   48 (210)
T ss_pred             EcCCcEEEEECCCCCCHHH--HHHHHhC
Confidence            3477888999999999997  3444443

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []

Probab=85.53  E-value=3.2  Score=24.69  Aligned_cols=56  Identities=14%  Similarity=0.137  Sum_probs=35.3

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      +++-.|+|+|--.   +.+++.+..                    ..+++++.-.+++.+..+..-.+.+.+++.+..+
T Consensus         4 LiiD~PPGTgD~~---l~~~~~~~~--------------------~g~ivVTTPq~la~~dv~r~~~~~~~~~vpilGv   59 (81)
T PF10609_consen    4 LIIDLPPGTGDEH---LTLMQYLPI--------------------DGAIVVTTPQELALADVRRAIDMFRKLNVPILGV   59 (81)
T ss_dssp             EEEE--SCSSSHH---HHHHHHH----------------------SEEEEEE-CCC--HHHHHHHHHHHHCTT-EEEEE
T ss_pred             EEEeCCCCCCcHH---HHHHHhCCC--------------------CeEEEEeCCHHHHHHHHHHHHHHHHhcCCCcEEE
Confidence            5678899999975   344444431                    2366666667889999999889999999887654

It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=85.52  E-value=0.43  Score=32.60  Aligned_cols=26  Identities=35%  Similarity=0.447  Sum_probs=20.0

Q ss_pred             HHHhHHhcCC--cEEEEccCCchHHHHH
Q psy3307          40 YAIPVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        40 ~~i~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      .++..+++|.  .++.-++||||||.+.
T Consensus        14 ~~v~~~~~G~n~~i~~yG~tGsGKT~Tm   41 (186)
T cd01363          14 PLLQSALDGYNVCIFAYGQTGSGKTYTM   41 (186)
T ss_pred             HHHHHHhCCcceeEEEECCCCCcceEec
Confidence            5566777885  5688899999999653

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

>KOG0732|consensus

Probab=85.40  E-value=0.7  Score=39.72  Aligned_cols=55  Identities=24%  Similarity=0.180  Sum_probs=35.7

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCC-CCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYD-KPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~-~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ....|.+.|..+..+..|++.-.. -.+|-+..-+ .+.--+.++.++|+|||||+-
T Consensus       260 ~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~-~itpPrgvL~~GppGTGkTl~  315 (1080)
T KOG0732|consen  260 SSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNF-NITPPRGVLFHGPPGTGKTLM  315 (1080)
T ss_pred             cccCccccccHHHHHHHHHHHHHhHhhhhhHhhhc-ccCCCcceeecCCCCCchhHH
Confidence            356788999888888888876432 1122111100 223357899999999999974

>PRK14737 gmk guanylate kinase; Provisional

Probab=85.38  E-value=0.64  Score=31.91  Aligned_cols=17  Identities=18%  Similarity=0.341  Sum_probs=14.5

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      ++-++++||+|+||+..
T Consensus         4 ~~~ivl~GpsG~GK~tl   20 (186)
T PRK14737          4 PKLFIISSVAGGGKSTI   20 (186)
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            56689999999999964

>KOG1942|consensus

Probab=85.38  E-value=0.67  Score=34.72  Aligned_cols=24  Identities=38%  Similarity=0.609  Sum_probs=18.9

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPIL   70 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l   70 (130)
                      +.|+-+++.+|+|+|||... +.+-
T Consensus        62 maGravLlaGppgtGKTAlA-lais   85 (456)
T KOG1942|consen   62 MAGRAVLLAGPPGTGKTALA-LAIS   85 (456)
T ss_pred             ccCcEEEEecCCCCchhHHH-HHHH
Confidence            48899999999999999543 4443

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=85.34  E-value=0.63  Score=31.39  Aligned_cols=19  Identities=32%  Similarity=0.403  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        24 ~~G~~~~i~G~nGsGKSTL   42 (178)
T cd03229          24 EAGEIVALLGPSGSGKSTL   42 (178)
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4778889999999999973

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=85.34  E-value=0.61  Score=32.91  Aligned_cols=20  Identities=30%  Similarity=0.419  Sum_probs=17.1

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+.+.+|+|+|||..
T Consensus        25 i~~Ge~~~l~G~nGsGKSTL   44 (243)
T TIGR02315        25 INPGEFVAIIGPSGAGKSTL   44 (243)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34788999999999999973

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=85.31  E-value=0.68  Score=33.84  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=14.4

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.+|+|+|||...
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999643

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK08356 hypothetical protein; Provisional

Probab=85.21  E-value=0.69  Score=31.73  Aligned_cols=17  Identities=24%  Similarity=0.163  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .-+++++|+|||||...
T Consensus         6 ~~i~~~G~~gsGK~t~a   22 (195)
T PRK08356          6 MIVGVVGKIAAGKTTVA   22 (195)
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            35788999999999753

>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=85.17  E-value=8.9  Score=25.53  Aligned_cols=25  Identities=16%  Similarity=0.270  Sum_probs=16.8

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .+++.||.|+||+... ......+..
T Consensus        21 a~L~~G~~g~gk~~~a-~~~a~~ll~   45 (162)
T PF13177_consen   21 ALLFHGPSGSGKKTLA-LAFARALLC   45 (162)
T ss_dssp             EEEEECSTTSSHHHHH-HHHHHHHC-
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHcC
Confidence            5799999999998654 344444443

...

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=85.15  E-value=0.59  Score=32.54  Aligned_cols=19  Identities=26%  Similarity=0.440  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        27 i~~G~~~~i~G~nGsGKST   45 (220)
T cd03293          27 VEEGEFVALVGPSGCGKST   45 (220)
T ss_pred             EeCCcEEEEECCCCCCHHH
Confidence            3478889999999999997

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=85.14  E-value=0.64  Score=32.09  Aligned_cols=19  Identities=32%  Similarity=0.541  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        23 i~~G~~~~l~G~nGsGKST   41 (213)
T cd03262          23 VKKGEVVVIIGPSGSGKST   41 (213)
T ss_pred             ECCCCEEEEECCCCCCHHH
Confidence            3478889999999999996

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>PRK01184 hypothetical protein; Provisional

Probab=85.14  E-value=0.66  Score=31.31  Aligned_cols=16  Identities=25%  Similarity=0.167  Sum_probs=13.3

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.|++|||||...
T Consensus         3 ~i~l~G~~GsGKsT~a   18 (184)
T PRK01184          3 IIGVVGMPGSGKGEFS   18 (184)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999853

>PRK06547 hypothetical protein; Provisional

Probab=85.10  E-value=0.72  Score=31.29  Aligned_cols=16  Identities=38%  Similarity=0.499  Sum_probs=12.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+++|||||...
T Consensus        17 ~i~i~G~~GsGKTt~a   32 (172)
T PRK06547         17 TVLIDGRSGSGKTTLA   32 (172)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5566699999999743

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=85.09  E-value=0.66  Score=31.11  Aligned_cols=20  Identities=25%  Similarity=0.278  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+.+.+++|+|||..
T Consensus        23 i~~Ge~~~i~G~nGsGKStL   42 (173)
T cd03230          23 VEKGEIYGLLGPNGAGKTTL   42 (173)
T ss_pred             EcCCcEEEEECCCCCCHHHH
Confidence            34788899999999999973

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=85.08  E-value=3.1  Score=31.28  Aligned_cols=27  Identities=26%  Similarity=0.399  Sum_probs=19.7

Q ss_pred             HHHhHHhc------CCcEEEEccCCchHHHHHH
Q psy3307          40 YAIPVIIS------GRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        40 ~~i~~~~~------g~~~l~~aptGsGKT~~~~   66 (130)
                      ..++.++.      |+-+.+.+|+|||||...+
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal   73 (325)
T cd00983          41 LSLDIALGIGGYPKGRIIEIYGPESSGKTTLAL   73 (325)
T ss_pred             HHHHHHhcCCCccCCeEEEEECCCCCCHHHHHH
Confidence            34556665      4678899999999996543

RecA couples ATP hydrolysis to DNA strand exchange.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=85.08  E-value=0.67  Score=31.72  Aligned_cols=14  Identities=36%  Similarity=0.527  Sum_probs=11.9

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +.+.|++|||||..
T Consensus         2 igi~G~~GsGKSTl   15 (198)
T cd02023           2 IGIAGGSGSGKTTV   15 (198)
T ss_pred             EEEECCCCCCHHHH
Confidence            46889999999974

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=85.04  E-value=0.66  Score=31.92  Aligned_cols=19  Identities=26%  Similarity=0.531  Sum_probs=16.7

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        23 i~~Ge~~~i~G~nGsGKST   41 (205)
T cd03226          23 LYAGEIIALTGKNGAGKTT   41 (205)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            4478889999999999997

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=85.04  E-value=0.67  Score=31.03  Aligned_cols=27  Identities=33%  Similarity=0.587  Sum_probs=20.0

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      +..|.-+.+.+|+|+|||.  ++-++.-+
T Consensus        25 i~~G~~~~l~G~nGsGKst--Ll~~i~G~   51 (171)
T cd03228          25 IKPGEKVAIVGPSGSGKST--LLKLLLRL   51 (171)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHHcC
Confidence            4478899999999999996  34444333

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PTZ00301 uridine kinase; Provisional

Probab=85.01  E-value=0.7  Score=32.43  Aligned_cols=15  Identities=27%  Similarity=0.399  Sum_probs=12.4

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +.+.|++|||||...
T Consensus         6 IgIaG~SgSGKTTla   20 (210)
T PTZ00301          6 IGISGASGSGKSSLS   20 (210)
T ss_pred             EEEECCCcCCHHHHH
Confidence            568899999999743

>cd03114 ArgK-like The function of this protein family is unkown

Probab=85.00  E-value=2.8  Score=27.62  Aligned_cols=14  Identities=21%  Similarity=0.378  Sum_probs=11.8

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +.+.++.|+|||..
T Consensus         2 i~~~G~~GsGKTt~   15 (148)
T cd03114           2 IGITGVPGAGKSTL   15 (148)
T ss_pred             EEEECCCCCcHHHH
Confidence            56789999999974

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=84.96  E-value=0.75  Score=29.48  Aligned_cols=14  Identities=29%  Similarity=0.480  Sum_probs=12.1

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +++.+++|||||..
T Consensus         2 I~i~G~~GsGKst~   15 (147)
T cd02020           2 IAIDGPAGSGKSTV   15 (147)
T ss_pred             EEEECCCCCCHHHH
Confidence            57899999999974

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=84.95  E-value=0.82  Score=32.66  Aligned_cols=15  Identities=27%  Similarity=0.414  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      ++++.+|+|.|||..
T Consensus        52 h~lf~GPPG~GKTTL   66 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTL   66 (233)
T ss_dssp             EEEEESSTTSSHHHH
T ss_pred             eEEEECCCccchhHH
Confidence            789999999999973

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=84.95  E-value=0.66  Score=32.16  Aligned_cols=19  Identities=32%  Similarity=0.599  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|+|||.
T Consensus        26 i~~Ge~~~i~G~nGsGKST   44 (216)
T TIGR00960        26 ITKGEMVFLVGHSGAGKST   44 (216)
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3478889999999999997

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	130
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-39
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-27
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-23
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		8e-15
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		1e-13
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-13
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		3e-11
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-11
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		6e-11
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		7e-11
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		1e-10
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		2e-10
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-10
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-10
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		3e-10
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		8e-10
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		1e-09
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		1e-09
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-09
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-09
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-09
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-09
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-09
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-09
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-09
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-09
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-09
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		2e-09
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		3e-09
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-08
3ly5_A	262	Ddx18 Dead-Domain Length = 262		4e-08
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		5e-08
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		7e-08
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		9e-08
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		3e-07
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		3e-07
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		8e-07
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		1e-06
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		1e-06
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-06
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-06
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		3e-06
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		3e-06
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		3e-06
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		3e-06
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-06
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-06
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		4e-06
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-05

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 75/121 (61%), Positives = 94/121 (77%), Gaps = 2/121 (1%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL
Sbjct: 15  ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 74
Query: 71  NQMYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +Q+Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCV
Sbjct: 75  SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 134
Query: 129 V 129
           V
Sbjct: 135 V 135

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score =  117 bits (293), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/119 (50%), Positives = 80/119 (67%), Gaps = 7/119 (5%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           + FD++++   I NNI LA Y +PTP+QK AIP I+  RD+MACAQTGSGKTAAFL+PI+
Sbjct: 23  ENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII 82
Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           N +     +      + Y   K  +P  L+LAPTRELA QI  E++KF+  + LR CVV
Sbjct: 83  NHL-----VCQDLNQQRYS--KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVV 134

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  104 bits (259), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/120 (46%), Positives = 80/120 (66%), Gaps = 13/120 (10%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
           Q F    + +II +N+  + Y  PTP+QK +IPVI SGRD+MACAQTGSGKTAAFL+PIL
Sbjct: 56  QHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPIL 115
Query: 71  NQMYERGPLPTPPAGRGYPSRKKV-FPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +++ E             P   ++  P  ++++PTRELA QI++EA+KFA+ S L+  +V
Sbjct: 116 SKLLED------------PHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIV 163

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 75.5 bits (184), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 42/104 (40%), Positives = 63/104 (60%), Gaps = 15/104 (14%)
Query: 22  ITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT 81
           +  NI  A +  PTP+Q  AIPV++ GR+++A A TGSGKT AF +PIL Q+ +      
Sbjct: 40  LLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQ------ 93
Query: 82  PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
            PA +G+ +        L+++PTRELA+QI+ E  K +  +  R
Sbjct: 94  -PANKGFRA--------LIISPTRELASQIHRELIKISEGTGFR 128

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 42/118 (35%), Positives = 66/118 (55%), Gaps = 16/118 (13%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F D+ +T+++        + KPT +Q  AIP+ + GRD++  A+TGSGKT AF +PILN 
Sbjct: 45  FKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNA 104
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL 130
           + E     TP         +++F   LVL PTRELA QI ++ +       ++  V++
Sbjct: 105 LLE-----TP---------QRLF--ALVLTPTRELAFQISEQFEALGSSIGVQSAVIV 146

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 61/106 (57%), Gaps = 16/106 (15%)
Query: 5   LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA 64
           +++ K   F+D  +   +   I  A ++KP+P+Q+ AIPV I+GRD++A A+ G+GKTAA
Sbjct: 15  VLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAA 74
Query: 65  FLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           F++P L ++               P   K+    L++ PTRELA Q
Sbjct: 75  FVIPTLEKV--------------KPKLNKI--QALIMVPTRELALQ 104

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 58/118 (49%), Gaps = 12/118 (10%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F D  +++     +  A+Y   T +QK  I + + G+DV+  A+TGSGKT AFLVP+L  
Sbjct: 27  FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEA 86
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL 130
           +Y      T   G             L+++PTRELA Q ++  +K          +++
Sbjct: 87  LYRLQWTSTDGLGV------------LIISPTRELAYQTFEVLRKVGKNHDFSAGLII 132

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 53/96 (55%), Gaps = 10/96 (10%)
Query: 33  KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK 92
           KPTP+Q  A P+I+ G D++  AQTG+GKT ++L+P          L + P  R     +
Sbjct: 42  KPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIH------LDSQPISR----EQ 91
Query: 93  KVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +  P  LVL PTRELA  +  E  K++Y+     C+
Sbjct: 92  RNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICI 127

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/99 (40%), Positives = 54/99 (54%), Gaps = 16/99 (16%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+ ++E +   I    ++KP+ +Q+ AI   I G DV+A AQ+G+GKTA F + IL Q
Sbjct: 42  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 101
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
           +     L    A              LVLAPTRELA QI
Sbjct: 102 I--ELDLKATQA--------------LVLAPTRELAQQI 124

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 40/100 (40%), Positives = 54/100 (54%), Gaps = 16/100 (16%)
Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
            FDD+ ++E +   I    ++KP+ +Q+ AI   I G DV+A AQ+G+GKTA F + IL 
Sbjct: 15  SFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 74
Query: 72  QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
           Q+     L    A              LVLAPTRELA QI
Sbjct: 75  QI--ELDLKATQA--------------LVLAPTRELAQQI 98

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 16/81 (19%)
Query: 31  YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS 90
           ++KP+P+Q+ +IP+ +SGRD++A A+ G+GK+ A+L+P+L ++                 
Sbjct: 23  WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERL----------------D 66
Query: 91  RKKVFPLGLVLAPTRELATQI 111
            KK     +V+ PTRELA Q+
Sbjct: 67  LKKDNIQAMVIVPTRELALQV 87

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 37/108 (34%), Positives = 58/108 (53%), Gaps = 11/108 (10%)
Query: 22  ITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT 81
           + + IA   + +PT +Q    PV +SG D++  AQTGSGKT ++L+P +  +  +   P 
Sbjct: 40  VMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQ---PF 96
Query: 82  PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
              G G        P+ LVLAPTRELA Q+   A ++    +L+   +
Sbjct: 97  LERGDG--------PICLVLAPTRELAQQVQQVAAEYCRACRLKSTCI 136

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/115 (28%), Positives = 60/115 (52%), Gaps = 18/115 (15%)
Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGR-DVMACAQTGSGKTAAFLVPIL 70
            F+++ +++ I N I    ++KPT +Q   IP+ ++   +++A A+TGSGKTA+F +P++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
             + E   +                   ++L PTRELA Q+ DE +       L+
Sbjct: 67  ELVNENNGIE-----------------AIILTPTRELAIQVADEIESLKGNKNLK 104

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/108 (34%), Positives = 58/108 (53%), Gaps = 11/108 (10%)
Query: 22  ITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT 81
           + + IA   + +PT +Q    PV +SG D++  AQTGSGKT ++L+P +  +  +   P 
Sbjct: 54  VMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQ---PF 110
Query: 82  PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
              G G        P+ LVLAPTRELA Q+   A ++    +L+   +
Sbjct: 111 LERGDG--------PICLVLAPTRELAQQVQQVAAEYCRACRLKSTCI 150

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 52/100 (52%), Gaps = 16/100 (16%)
Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
            FDD+ + E +   I    ++KP+ +Q+ AI   I G DV+A AQ+G+GKTA F + IL 
Sbjct: 31  NFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ 90
Query: 72  QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
           Q+          A              LVLAPTRELA QI
Sbjct: 91  QL--EIEFKETQA--------------LVLAPTRELAQQI 114

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 58.9 bits (141), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 48/81 (59%), Gaps = 13/81 (16%)
Query: 34  PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKK 93
           PTP+Q  A+P+ + G+D++  A+TG+GKT AF +PI  ++        P   RG   RK 
Sbjct: 24  PTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL-------APSQERG---RK- 72
Query: 94  VFPLGLVLAPTRELATQIYDE 114
             P  LVL PTRELA Q+  E
Sbjct: 73  --PRALVLTPTRELALQVASE 91

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 57/113 (50%), Gaps = 16/113 (14%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L  
Sbjct: 23  FDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ- 81
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
                        R   S K   P  L+LAPTRELA QI       A+   ++
Sbjct: 82  -------------RIDTSVKA--PQALMLAPTRELALQIQKVVMALAFHMDIK 119

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 57/113 (50%), Gaps = 16/113 (14%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L  
Sbjct: 16  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ- 74
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
                        R   S K   P  L+LAPTRELA QI       A+   ++
Sbjct: 75  -------------RIDTSVKA--PQALMLAPTRELALQIQKVVMALAFHMDIK 112

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/113 (30%), Positives = 54/113 (47%), Gaps = 16/113 (14%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD ++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L +
Sbjct: 23  FDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
           +                      P  L LAPTRELA QI       A+   ++
Sbjct: 83  I----------------DTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIK 119

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 53/103 (51%), Gaps = 24/103 (23%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN- 71
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F + +L  
Sbjct: 39  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 98
Query: 72  ---QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
              Q+ E                       L+LAPTRELA QI
Sbjct: 99  LDIQVRE--------------------TQALILAPTRELAVQI 121

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 53/103 (51%), Gaps = 24/103 (23%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN- 71
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F + +L  
Sbjct: 40  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 99
Query: 72  ---QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
              Q+ E                       L+LAPTRELA QI
Sbjct: 100 LDIQVRE--------------------TQALILAPTRELAVQI 122

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 53/103 (51%), Gaps = 24/103 (23%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN- 71
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F + +L  
Sbjct: 40  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 99
Query: 72  ---QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
              Q+ E                       L+LAPTRELA QI
Sbjct: 100 LDIQVRE--------------------TQALILAPTRELAVQI 122

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/99 (37%), Positives = 53/99 (53%), Gaps = 16/99 (16%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F V +L Q
Sbjct: 3   FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVL-Q 61
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
             +     T                 L+LAPTRELA Q+
Sbjct: 62  CLDIQVRETQ---------------ALILAPTRELAVQV 85

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/99 (37%), Positives = 53/99 (53%), Gaps = 16/99 (16%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F + +L Q
Sbjct: 18  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVL-Q 76
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
             +     T                 L+LAPTRELA QI
Sbjct: 77  CLDIQVRETQ---------------ALILAPTRELAVQI 100

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 57/113 (50%), Gaps = 16/113 (14%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L +
Sbjct: 24  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 83
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLR 125
                 + T              P  L+LAPTRELA QI       A+   ++
Sbjct: 84  ------IDTSVKA----------PQALMLAPTRELALQIQKVVMALAFHMDIK 120

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 48/81 (59%), Gaps = 13/81 (16%)
Query: 34  PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKK 93
           PTP++  A+P+ + G+D++  A+TG+GKT AF +PI  ++        P   RG   RK 
Sbjct: 24  PTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERL-------APSQERG---RK- 72
Query: 94  VFPLGLVLAPTRELATQIYDE 114
             P  LVL PTRELA Q+  E
Sbjct: 73  --PRALVLTPTRELALQVASE 91

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 53/103 (51%), Gaps = 24/103 (23%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN- 71
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F V +L  
Sbjct: 3   FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQC 62
Query: 72  ---QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
              Q+ E                       L+LAPTRELA Q+
Sbjct: 63  LDIQVRE--------------------TQALILAPTRELAVQV 85

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 50/96 (52%), Gaps = 16/96 (16%)
Query: 22  ITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT 81
           I   I   R+ KPT +Q+  IP  + G   +  +QTG+GKT A+L+PI  ++        
Sbjct: 15  IIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKI-------- 66
Query: 82  PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
                  P R +V    ++ APTRELATQIY E  K
Sbjct: 67  ------KPERAEV--QAVITAPTRELATQIYHETLK 94

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 38/99 (38%), Positives = 52/99 (52%), Gaps = 16/99 (16%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+ ++E +   I    ++ P+ +Q+ AI   I G DV+A AQ+G+G TA F + IL Q
Sbjct: 17  FDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQ 76
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
           + E     T                 LVLAPTRELA QI
Sbjct: 77  I-ELDLXATQ---------------ALVLAPTRELAQQI 99

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 54/114 (47%), Gaps = 16/114 (14%)
Query: 6   VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF 65
           VS+   GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F
Sbjct: 9   VSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVF 68
Query: 66  LVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           ++  L Q+        P  G+            LV+  TRELA QI  E ++F+
Sbjct: 69  VLATLQQL-------EPVTGQVSV---------LVMCHTRELAFQISKEYERFS 106

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 12/88 (13%)
Query: 31  YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS 90
           +   T +Q  +I  ++ GRD++A A+TGSGKT AFL+P +  + +   +P    G     
Sbjct: 74  FTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGV---- 129
Query: 91  RKKVFPLGLVLAPTRELATQIYDEAKKF 118
                   L+L+PTRELA Q +   K+ 
Sbjct: 130 --------LILSPTRELAMQTFGVLKEL 149

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 43/117 (36%), Positives = 62/117 (52%), Gaps = 22/117 (18%)
Query: 5   LVSLKKQGFDDIQMTEIITNNIALARYDKP--TPVQKYAIPVIISGRD--VMACAQTGSG 60
           L SL ++G  D ++ + IT      R + P  TPVQ+  I  I+S  D  V+A A+TG+G
Sbjct: 19  LDSLLEEGVLDKEIHKAIT------RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTG 72
Query: 61  KTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
           KT AFL+PI   +              + S+  V    +++APTR+LA QI  E KK
Sbjct: 73  KTFAFLIPIFQHLIN----------TKFDSQYMV--KAVIVAPTRDLALQIEAEVKK 117

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 43/117 (36%), Positives = 62/117 (52%), Gaps = 22/117 (18%)
Query: 5   LVSLKKQGFDDIQMTEIITNNIALARYDKP--TPVQKYAIPVIISGRD--VMACAQTGSG 60
           L SL ++G  D ++ + IT      R + P  TPVQ+  I  I+S  D  V+A A+TG+G
Sbjct: 70  LDSLLEEGVLDKEIHKAIT------RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTG 123
Query: 61  KTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
           KT AFL+PI   +              + S+  V    +++APTR+LA QI  E KK
Sbjct: 124 KTFAFLIPIFQHLIN----------TKFDSQYMV--KAVIVAPTRDLALQIEAEVKK 168

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 43/117 (36%), Positives = 62/117 (52%), Gaps = 22/117 (18%)
Query: 5   LVSLKKQGFDDIQMTEIITNNIALARYDKP--TPVQKYAIPVIISGRD--VMACAQTGSG 60
           L SL ++G  D ++ + IT      R + P  TPVQ+  I  I+S  D  V+A A+TG+G
Sbjct: 19  LDSLLEEGVLDKEIHKAIT------RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTG 72
Query: 61  KTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 117
           KT AFL+PI   +              + S+  V    +++APTR+LA QI  E KK
Sbjct: 73  KTFAFLIPIFQHLIN----------TKFDSQYMV--KAVIVAPTRDLALQIEAEVKK 117

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 16/108 (14%)
Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
           GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F++  L 
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68
Query: 72  QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           Q+        P  G+            LV+  TRELA QI  E ++F+
Sbjct: 69  QL-------EPVTGQVSV---------LVMCHTRELAFQISKEYERFS 100

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 16/108 (14%)
Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
           GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F++  L 
Sbjct: 8   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 67
Query: 72  QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           Q+        P  G+            LV+  TRELA QI  E ++F+
Sbjct: 68  QL-------EPVTGQVSV---------LVMCHTRELAFQISKEYERFS 99

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 16/108 (14%)
Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
           GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F++  L 
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68
Query: 72  QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           Q+        P  G+            LV+  TRELA QI  E ++F+
Sbjct: 69  QL-------EPVTGQVSV---------LVMCHTRELAFQISKEYERFS 100

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 60/113 (53%), Gaps = 21/113 (18%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + FD++ +   +   I   ++ KP+ +Q+ A+P+++    R+++A +Q+G+GKTAAF + 
Sbjct: 22  KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 81
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ---IYDEAKKF 118
           +L ++                + +   P  + LAP+RELA Q   +  E  KF
Sbjct: 82  MLTRV----------------NPEDASPQAICLAPSRELARQTLEVVQEMGKF 118

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 45/94 (47%), Gaps = 22/94 (23%)
Query: 18  MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG 77
           M E I   I    +   T VQ   IP+++ G++V+  A+TGSGKTAA+ +PIL       
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 78  PLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI 111
                    G  S        LV+ PTREL  Q+
Sbjct: 56  ---------GMKS--------LVVTPTRELTRQV 72

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 60/113 (53%), Gaps = 21/113 (18%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + FD++ +   +   I   ++ KP+ +Q+ A+P+++    R+++A +Q+G+GKTAAF + 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ---IYDEAKKF 118
           +L ++      P   +           P  + LAP+RELA Q   +  E  KF
Sbjct: 65  MLTRVN-----PEDAS-----------PQAICLAPSRELARQTLEVVQEMGKF 101

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 60/113 (53%), Gaps = 21/113 (18%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + FD++ +   +   I   ++ KP+ +Q+ A+P+++    R+++A +Q+G+GKTAAF + 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ---IYDEAKKF 118
           +L ++      P   +           P  + LAP+RELA Q   +  E  KF
Sbjct: 65  MLTRVN-----PEDAS-----------PQAICLAPSRELARQTLEVVQEMGKF 101

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 61/102 (59%), Gaps = 18/102 (17%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ 
Sbjct: 25  KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA 84
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           +L+Q+         PA +        +P  L L+PT ELA Q
Sbjct: 85  MLSQV--------EPANK--------YPQCLCLSPTYELALQ 110

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 61/102 (59%), Gaps = 18/102 (17%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ 
Sbjct: 41  KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA 100
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           +L+Q+         PA +        +P  L L+PT ELA Q
Sbjct: 101 MLSQV--------EPANK--------YPQCLCLSPTYELALQ 126

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 61/102 (59%), Gaps = 18/102 (17%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ 
Sbjct: 25  KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA 84
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           +L+Q+         PA +        +P  L L+PT ELA Q
Sbjct: 85  MLSQV--------EPANK--------YPQCLCLSPTYELALQ 110

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 61/102 (59%), Gaps = 18/102 (17%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ 
Sbjct: 62  KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA 121
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           +L+Q+         PA +        +P  L L+PT ELA Q
Sbjct: 122 MLSQV--------EPANK--------YPQCLCLSPTYELALQ 147

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 61/102 (59%), Gaps = 18/102 (17%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ 
Sbjct: 92  KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA 151
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           +L+Q+         PA +        +P  L L+PT ELA Q
Sbjct: 152 MLSQV--------EPANK--------YPQCLCLSPTYELALQ 177

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 61/102 (59%), Gaps = 18/102 (17%)
Query: 11  QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVP 68
           + F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ 
Sbjct: 92  KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLA 151
Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 110
           +L+Q+         PA +        +P  L L+PT ELA Q
Sbjct: 152 MLSQV--------EPANK--------YPQCLCLSPTYELALQ 177

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/118 (25%), Positives = 55/118 (46%), Gaps = 16/118 (13%)
Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F+ + ++  +   +  A +++P+PVQ  AIP+   G D++  A++G+GKT  F    L+ 
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL 130
           +                  + +    L+LAPTRE+A QI+        + +   C V 
Sbjct: 86  LV----------------LENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVF 127

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	130
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	3e-62
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	4e-61
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	6e-58
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-49
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	8e-48
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	2e-42
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	3e-39
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	2e-35
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-33
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-33
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-30
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	1e-30
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-30
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	5e-29
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-27
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-27
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-27
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-27
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	8e-27
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	9e-27
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-26
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-26
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-26
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-26
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-26
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	6e-26
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	6e-23
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	7e-23
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-22
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-22
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	3e-21
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	3e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-06
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	2e-06
3b6e_A	216	Interferon-induced helicase C domain-containing P;	3e-06
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	1e-05
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-05
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-04
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	3e-04
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	4e-04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	9e-04

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  194 bits (496), Expect = 3e-62
 Identities = 75/119 (63%), Positives = 93/119 (78%), Gaps = 2/119 (1%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F D++M EII  NI L RY +PTPVQK+AIP+I   RD+MACAQTGSGKTAAFL+PIL+Q
Sbjct: 17  FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQ 76

Query: 73  MYERGPLPTPPAGR--GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +Y  GP     A +  G   R+K +P+ LVLAPTRELA QIY+EA+KF+YRS++RPCVV
Sbjct: 77  IYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVV 135

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score =  186 bits (476), Expect = 4e-61
 Identities = 59/117 (50%), Positives = 77/117 (65%), Gaps = 7/117 (5%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD++++   I NNI LA Y +PTP+QK AIP I+  RD+MACAQTGSGKTAAFL+PI+N 
Sbjct: 25  FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINH 84

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +  +               K  +P  L+LAPTRELA QI  E++KF+  + LR CVV
Sbjct: 85  LVCQDLNQQRY-------SKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVV 134

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  183 bits (468), Expect = 6e-58
 Identities = 54/117 (46%), Positives = 77/117 (65%), Gaps = 11/117 (9%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F    + +II +N+  + Y  PTP+QK +IPVI SGRD+MACAQTGSGKTAAFL+PIL++
Sbjct: 58  FTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSK 117

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           + E                +   P  ++++PTRELA QI++EA+KFA+ S L+  +V
Sbjct: 118 LLEDPHE-----------LELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIV 163

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  156 bits (398), Expect = 2e-49
 Identities = 36/117 (30%), Positives = 59/117 (50%), Gaps = 11/117 (9%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F +      + + IA   + +PT +Q    PV +SG D++  AQTGSGKT ++L+P +  
Sbjct: 31  FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVH 90

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +  +  L            +   P+ LVLAPTRELA Q+   A ++    +L+   +
Sbjct: 91  INHQPFL-----------ERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCI 136

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  152 bits (387), Expect = 8e-48
 Identities = 43/121 (35%), Positives = 65/121 (53%), Gaps = 19/121 (15%)

Query: 13  FDDIQMT----EIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
           F  +         +  NI  A +  PTP+Q  AIPV++ GR+++A A TGSGKT AF +P
Sbjct: 27  FQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIP 86

Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           IL Q+ +       PA +G           L+++PTRELA+QI+ E  K +  +  R  +
Sbjct: 87  ILMQLKQ-------PANKG--------FRALIISPTRELASQIHRELIKISEGTGFRIHM 131

Query: 129 V 129
           +
Sbjct: 132 I 132

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  138 bits (350), Expect = 2e-42
 Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 11/108 (10%)

Query: 22  ITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT 81
           +  +I      KPTP+Q  A P+I+ G D++  AQTG+GKT ++L+P    +  +     
Sbjct: 31  LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE 90

Query: 82  PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
              G          P  LVL PTRELA  +  E  K++Y+  L+   +
Sbjct: 91  QRNG----------PGMLVLTPTRELALHVEAECSKYSYKG-LKSICI 127

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  134 bits (340), Expect = 3e-39
 Identities = 20/110 (18%), Positives = 33/110 (30%), Gaps = 20/110 (18%)

Query: 20  EIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPL 79
           E   +          T  Q+     I+ G+     A TG GKT   ++  L     +G  
Sbjct: 8   EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-RKGK- 65

Query: 80  PTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
                        K      ++ PT  L  Q  +  +K A    ++    
Sbjct: 66  -------------KS----ALVFPTVTLVKQTLERLQKLADEK-VKIFGF 97

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  120 bits (304), Expect = 2e-35
 Identities = 36/121 (29%), Positives = 58/121 (47%), Gaps = 12/121 (9%)

Query: 9   KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
           +   F D  +++     +  A+Y   T +QK  I + + G+DV+  A+TGSGKT AFLVP
Sbjct: 23  EITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVP 82

Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV 128
           +L  +Y      T   G             L+++PTRELA Q ++  +K          +
Sbjct: 83  VLEALYRLQWTSTDGLG------------VLIISPTRELAYQTFEVLRKVGKNHDFSAGL 130

Query: 129 V 129
           +
Sbjct: 131 I 131

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score =  116 bits (292), Expect = 2e-33
 Identities = 40/117 (34%), Positives = 63/117 (53%), Gaps = 16/117 (13%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F D+ +T+++        + KPT +Q  AIP+ + GRD++  A+TGSGKT AF +PILN 
Sbjct: 45  FKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNA 104

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           + E                +++F   LVL PTRELA QI ++ +       ++  V+
Sbjct: 105 LLET--------------PQRLF--ALVLTPTRELAFQISEQFEALGSSIGVQSAVI 145

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score =  116 bits (292), Expect = 3e-33
 Identities = 33/125 (26%), Positives = 55/125 (44%), Gaps = 14/125 (11%)

Query: 7   SLKKQGFDD--IQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA 64
           + +   F      + E     I    +   T +Q  +I  ++ GRD++A A+TGSGKT A
Sbjct: 48  AFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLA 107

Query: 65  FLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL 124
           FL+P +  + +   +P    G             L+L+PTRELA Q +   K+       
Sbjct: 108 FLIPAVELIVKLRFMPRNGTG------------VLILSPTRELAMQTFGVLKELMTHHVH 155

Query: 125 RPCVV 129
              ++
Sbjct: 156 TYGLI 160

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score =  113 bits (284), Expect = 1e-30
 Identities = 34/113 (30%), Positives = 50/113 (44%), Gaps = 14/113 (12%)

Query: 9   KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFL 66
                ++  + + I   I    +   TPVQ+  I  I+S    DV+A A+TG+GKT AFL
Sbjct: 19  LDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL 78

Query: 67  VPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +PI   +                         +++APTR+LA QI  E KK  
Sbjct: 79  IPIFQHLINTKFDSQYMVK------------AVIVAPTRDLALQIEAEVKKIH 119

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  108 bits (271), Expect = 1e-30
 Identities = 36/111 (32%), Positives = 53/111 (47%), Gaps = 16/111 (14%)

Query: 9   KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
            +  F        I   I   R+ KPT +Q+  IP  + G  ++  +QTG+GKT A+L+P
Sbjct: 2   AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLP 61

Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           I+ ++               P R +     ++ APTRELATQIY E  K  
Sbjct: 62  IMEKI--------------KPERAE--VQAVITAPTRELATQIYHETLKIT 96

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score =  112 bits (281), Expect = 3e-30
 Identities = 34/115 (29%), Positives = 50/115 (43%), Gaps = 14/115 (12%)

Query: 7   SLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAA 64
                  ++  + + I   I    +   TPVQ+  I  I+S    DV+A A+TG+GKT A
Sbjct: 68  VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFA 127

Query: 65  FLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           FL+PI   +                         +++APTR+LA QI  E KK  
Sbjct: 128 FLIPIFQHLINTKFDSQYMVK------------AVIVAPTRDLALQIEAEVKKIH 170

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score =  103 bits (260), Expect = 5e-29
 Identities = 37/107 (34%), Positives = 53/107 (49%), Gaps = 13/107 (12%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           F D  +   I   +       PTP+Q  A+P+ + G+D++  A+TG+GKT AF +PI  +
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +      P+   GR         P  LVL PTRELA Q+  E    A
Sbjct: 63  L-----APSQERGRK--------PRALVLTPTRELALQVASELTAVA 96

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 99.1 bits (248), Expect = 2e-27
 Identities = 31/111 (27%), Positives = 58/111 (52%), Gaps = 16/111 (14%)

Query: 9   KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
           K   F+D  +   +   I    ++KP+P+Q+ +IP+ +SGRD++A A+ G+GK+ A+L+P
Sbjct: 1   KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIP 60

Query: 69  ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +L ++                 +       +V+ PTRELA Q+     + +
Sbjct: 61  LLERL--------------DLKKDN--IQAMVIVPTRELALQVSQICIQVS 95

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 99.6 bits (249), Expect = 2e-27
 Identities = 36/114 (31%), Positives = 53/114 (46%), Gaps = 16/114 (14%)

Query: 6   VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF 65
           VS+   GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F
Sbjct: 9   VSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVF 68

Query: 66  LVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           ++  L Q+               P   +     LV+  TRELA QI  E ++F+
Sbjct: 69  VLATLQQL--------------EPVTGQ--VSVLVMCHTRELAFQISKEYERFS 106

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score =  101 bits (254), Expect = 5e-27
 Identities = 30/99 (30%), Positives = 44/99 (44%), Gaps = 22/99 (22%)

Query: 31  YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS 90
           +   T VQ   IP+++ G++V+  A+TGSGKTAA+ +PIL    E G             
Sbjct: 14  FKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPIL----ELG------------- 56

Query: 91  RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
                   LV+ PTREL  Q+    +        +   V
Sbjct: 57  -----MKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEV 90

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score =  101 bits (255), Expect = 5e-27
 Identities = 37/114 (32%), Positives = 59/114 (51%), Gaps = 16/114 (14%)

Query: 6   VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF 65
           ++ K   F+D  +   +   I  A ++KP+P+Q+ AIPV I+GRD++A A+ G+GKTAAF
Sbjct: 16  LNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAF 75

Query: 66  LVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           ++P L ++                  K      L++ PTRELA Q     +   
Sbjct: 76  VIPTLEKV----------------KPKLNKIQALIMVPTRELALQTSQVVRTLG 113

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 98.5 bits (246), Expect = 8e-27
 Identities = 28/114 (24%), Positives = 51/114 (44%), Gaps = 16/114 (14%)

Query: 6   VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF 65
           +  +   F+ + ++  +   +  A +++P+PVQ  AIP+   G D++  A++G+GKT  F
Sbjct: 19  LLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVF 78

Query: 66  LVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
               L+ +                         L+LAPTRE+A QI+       
Sbjct: 79  STIALDSL--------------VLENLS--TQILILAPTREIAVQIHSVITAIG 116

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 98.4 bits (246), Expect = 9e-27
 Identities = 37/107 (34%), Positives = 55/107 (51%), Gaps = 16/107 (14%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L +
Sbjct: 16  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 75

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +                S K   P  L+LAPTRELA QI       A
Sbjct: 76  I--------------DTSVKA--PQALMLAPTRELALQIQKVVMALA 106

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 98.4 bits (246), Expect = 1e-26
 Identities = 39/107 (36%), Positives = 53/107 (49%), Gaps = 16/107 (14%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+ + E +   I    ++KP+ +Q+ AI   I G DV+A AQ+G+GKTA F + IL Q
Sbjct: 32  FDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQ 91

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +                  K+     LVLAPTRELA QI        
Sbjct: 92  L--------------EIEFKE--TQALVLAPTRELAQQIQKVILALG 122

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score =   99 bits (250), Expect = 2e-26
 Identities = 32/121 (26%), Positives = 62/121 (51%), Gaps = 18/121 (14%)

Query: 6   VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGR-DVMACAQTGSGKTAA 64
           + ++   F+++ +++ I N I    ++KPT +Q   IP+ ++   +++A A+TGSGKTA+
Sbjct: 1   MEVEYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTAS 60

Query: 65  FLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL 124
           F +P++  +                +        ++L PTRELA Q+ DE +       L
Sbjct: 61  FAIPLIELV--------------NENNG---IEAIILTPTRELAIQVADEIESLKGNKNL 103

Query: 125 R 125
           +
Sbjct: 104 K 104

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score =   99 bits (250), Expect = 3e-26
 Identities = 35/107 (32%), Positives = 53/107 (49%), Gaps = 16/107 (14%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L +
Sbjct: 23  FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 82

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +                      P  L+LAPTRELA QI       A
Sbjct: 83  I----------------DTSVKAPQALMLAPTRELALQIQKVVMALA 113

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 99.6 bits (249), Expect = 4e-26
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 16/108 (14%)

Query: 12  GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
           GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F++  L 
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

Query: 72  QMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           Q+               P   +V    LV+  TRELA QI  E ++F+
Sbjct: 69  QL--------------EPVTGQVS--VLVMCHTRELAFQISKEYERFS 100

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 99.2 bits (248), Expect = 6e-26
 Identities = 38/107 (35%), Positives = 52/107 (48%), Gaps = 16/107 (14%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+ ++E +   I    ++KP+ +Q+ AI   I G DV+A AQ+G+GKTA F + IL Q
Sbjct: 42  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 101

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +                         LVLAPTRELA QI        
Sbjct: 102 I----------------ELDLKATQALVLAPTRELAQQIQKVVMALG 132

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 99.2 bits (248), Expect = 6e-26
 Identities = 35/107 (32%), Positives = 52/107 (48%), Gaps = 16/107 (14%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F + +L  
Sbjct: 39  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 98

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +                  +      L+LAPTRELA QI        
Sbjct: 99  L----------------DIQVRETQALILAPTRELAVQIQKGLLALG 129

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score = 91.1 bits (227), Expect = 6e-23
 Identities = 28/109 (25%), Positives = 58/109 (53%), Gaps = 18/109 (16%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPIL 70
           FD++ +   +   I   ++ KP+ +Q+ A+P+++    R+++A +Q+G+GKTAAF + +L
Sbjct: 7   FDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTML 66

Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
            ++                + +   P  + LAP+RELA Q  +  ++  
Sbjct: 67  TRV----------------NPEDASPQAICLAPSRELARQTLEVVQEMG 99

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 91.1 bits (227), Expect = 7e-23
 Identities = 25/109 (22%), Positives = 59/109 (54%), Gaps = 18/109 (16%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPIL 70
           F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ +L
Sbjct: 27  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 86

Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +Q+                     +P  L L+PT ELA Q     ++  
Sbjct: 87  SQV----------------EPANKYPQCLCLSPTYELALQTGKVIEQMG 119

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 89.0 bits (221), Expect = 1e-22
 Identities = 27/109 (24%), Positives = 61/109 (55%), Gaps = 18/109 (16%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPIL 70
           F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ +L
Sbjct: 94  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 153

Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +Q+               P+ K   P  L L+PT ELA Q     ++  
Sbjct: 154 SQV--------------EPANKY--PQCLCLSPTYELALQTGKVIEQMG 186

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score = 89.7 bits (223), Expect = 3e-22
 Identities = 25/109 (22%), Positives = 59/109 (54%), Gaps = 18/109 (16%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPIL 70
           F+++++   +   +    +++P+ +Q+ A+P++++   ++++A +Q+G+GKTAAF++ +L
Sbjct: 94  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 153

Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 119
           +Q+                     +P  L L+PT ELA Q     ++  
Sbjct: 154 SQV----------------EPANKYPQCLCLSPTYELALQTGKVIEQMG 186

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 46.7 bits (110), Expect = 3e-07
 Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 19/86 (22%)

Query: 33  KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK 92
           +P   Q+          + +    TG GKT   ++    ++ + G               
Sbjct: 9   QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYG--------------G 53

Query: 93  KVFPLGLVLAPTRELATQIYDEAKKF 118
           KV    L+LAPT+ L  Q  +  ++ 
Sbjct: 54  KV----LMLAPTKPLVLQHAESFRRL 75

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 19/84 (22%)

Query: 36  PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF 95
           P Q  A+  + SG++++    T +GKT    + ++ +  + G              K ++
Sbjct: 28  PPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG--------------KSLY 73

Query: 96  PLGLVLAPTRELATQIYDEAKKFA 119
                + P R LA + Y+  KK+ 
Sbjct: 74  -----VVPLRALAGEKYESFKKWE 92

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 19/85 (22%)

Query: 36  PVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 94
           P Q  A+   +  G  ++  + TGSGKT    + I++ + + G               K 
Sbjct: 33  PPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNG--------------GKA 78

Query: 95  FPLGLVLAPTRELATQIYDEAKKFA 119
               + + P R L  + Y   K + 
Sbjct: 79  ----IYVTPLRALTNEKYLTFKDWE 99

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 15/81 (18%)

Query: 38  QKYAIPVIISGRDVMACAQTGSGKTA-AFLVPILNQMYERGPLPTPPAGRGYPSRKKVFP 96
           Q       + G++++ C  TGSGKT  A  +   +   ++    +           KV  
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYI-AKD-HLDKKKKASE--------PGKV-- 85

Query: 97  LGLVLAPTRELATQIYDEAKK 117
             +VL     L  Q++ +  +
Sbjct: 86  --IVLVNKVLLVEQLFRKEFQ 104

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 19/85 (22%)

Query: 36  PVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 94
           P Q  A+   I  G++ +    T SGKT    + +++++  +G              K V
Sbjct: 26  PPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQG-------------GKAV 72

Query: 95  FPLGLVLAPTRELATQIYDEAKKFA 119
           +     + P + LA + + E + + 
Sbjct: 73  Y-----IVPLKALAEEKFQEFQDWE 92

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 41.4 bits (96), Expect = 2e-05
 Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 14/81 (17%)

Query: 38  QKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 97
           Q         G++ + CA TG GKT   L+   +   ++ P            + KV   
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEH-HLKKFP---------CGQKGKV--- 55

Query: 98  GLVLAPTRELATQIYDEAKKF 118
            +  A    +  Q      ++
Sbjct: 56  -VFFANQIPVYEQQATVFSRY 75

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 38.4 bits (88), Expect = 2e-04
 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 14/86 (16%)

Query: 33  KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRK 92
           KP   Q       + G++ + CA TG GKT   L+   +   ++ P            + 
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEH-HLKKFP---------QGQKG 62

Query: 93  KVFPLGLVLAPTRELATQIYDEAKKF 118
           KV    +  A    +  Q      K+
Sbjct: 63  KV----VFFANQIPVYEQNKSVFSKY 84

>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} Length = 1108

 Score = 38.3 bits (88), Expect = 3e-04
 Identities = 12/27 (44%), Positives = 14/27 (51%)

Query: 36  PVQKYAIPVIISGRDVMACAQTGSGKT 62
           P Q  AI  I  G  V+  A T +GKT
Sbjct: 187 PFQDTAISCIDRGESVLVSAHTSAGKT 213

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 12/27 (44%), Positives = 14/27 (51%)

Query: 36  PVQKYAIPVIISGRDVMACAQTGSGKT 62
           P Q  AI  I  G  V+  A T +GKT
Sbjct: 89  PFQDTAISCIDRGESVLVSAHTSAGKT 115

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 36.8 bits (84), Expect = 9e-04
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 14/81 (17%)

Query: 38  QKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 97
           Q       I+G++ + CA TGSGKT   ++   +  ++  P             K VF  
Sbjct: 12  QIELAQPAINGKNALICAPTGSGKTFVSILICEH-HFQNMPAGRK--------AKVVF-- 60

Query: 98  GLVLAPTRELATQIYDEAKKF 118
              LA    +  Q  +  K  
Sbjct: 61  ---LATKVPVYEQQKNVFKHH 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	130
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.95
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.94
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.93
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.93
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.93
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.93
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.93
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.93
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.93
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.93
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.93
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.93
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.92
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.92
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.92
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.91
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.9
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.9
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.89
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.89
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.89
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.88
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.88
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.88
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.88
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.86
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.85
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.84
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.82
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.79
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.78
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.77
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.77
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.76
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.76
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.74
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.73
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.72
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.71
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.7
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.69
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.68
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.67
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.66
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.65
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.65
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.65
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.64
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.64
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.63
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.6
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.59
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.56
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.56
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.55
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.55
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.52
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.51
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.51
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.51
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.5
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.48
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.47
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.46
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.44
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.42
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.38
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.36
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.33
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.32
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.3
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.23
3h1t_A	590	Type I site-specific restriction-modification syst	99.15
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.08
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.04
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.04
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.95
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.81
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.77
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.69
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.41
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.36
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.19
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.08
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.07
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.92
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.92
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.78
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.76
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.67
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.62
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.48
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.46
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.21
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.13
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.91
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.32
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.29
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.25
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.09
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	95.46
3co5_A	143	Putative two-component system transcriptional RES	95.36
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	95.32
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.19
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.17
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.11
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	95.1
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	95.01
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	94.9
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.77
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	94.55
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	94.32
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.28
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	94.19
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.15
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	94.09
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	94.01
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.0
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.94
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.74
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	93.71
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	93.45
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	93.4
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.39
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	93.33
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	93.22
1tue_A	212	Replication protein E1; helicase, replication, E1E	93.17
2r44_A	331	Uncharacterized protein; putative ATPase, structur	93.17
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	93.14
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.12
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	93.01
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	92.98
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	92.87
3bos_A	242	Putative DNA replication factor; P-loop containing	92.81
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.79
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	92.74
2qgz_A	308	Helicase loader, putative primosome component; str	92.66
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.5
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	92.47
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	92.38
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.34
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	92.32
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	92.31
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	92.28
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	92.22
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	92.1
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	91.79
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	91.74
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	91.63
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	91.63
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	91.63
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.51
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	91.5
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	91.41
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	91.35
2ewv_A	372	Twitching motility protein PILT; pilus retraction	91.33
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	91.23
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	91.17
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	91.15
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	91.13
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	91.1
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	90.7
2chg_A	226	Replication factor C small subunit; DNA-binding pr	90.65
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	90.64
1p9r_A	418	General secretion pathway protein E; bacterial typ	90.63
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	90.58
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	90.55
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	90.55
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	90.55
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	90.45
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	90.43
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	90.4
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	90.4
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	90.4
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	90.39
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	90.34
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	90.16
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	90.08
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.08
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	90.02
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	90.01
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	89.95
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	89.87
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	89.85
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	89.79
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	89.67
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	89.65
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	89.57
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	89.53
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.51
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	89.49
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	89.42
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	89.32
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	89.31
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	89.31
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	89.21
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	89.16
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	89.15
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	88.99
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	88.85
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	88.84
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	88.75
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	88.71
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	88.68
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	88.55
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	88.54
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	88.48
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	88.45
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	88.33
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	88.32
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	88.2
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	88.16
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	88.06
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.05
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	87.96
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	87.8
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	87.71
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	87.58
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	87.48
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	87.46
2cvh_A	220	DNA repair and recombination protein RADB; filamen	87.38
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	87.33
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	87.29
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	87.28
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	87.24
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	87.2
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	87.14
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	87.1
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	87.04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	87.03
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	86.95
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	86.92
4a74_A	231	DNA repair and recombination protein RADA; hydrola	86.88
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	86.86
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	86.85
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	86.78
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	86.78
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	86.72
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	86.68
1u94_A	356	RECA protein, recombinase A; homologous recombinat	86.68
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	86.65
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	86.43
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	86.42
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	86.34
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	86.28
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	86.26
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	86.25
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	86.22
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	86.19
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	86.18
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	86.14
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	86.11
1sgw_A	214	Putative ABC transporter; structural genomics, P p	86.09
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	86.05
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	85.73
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	85.7
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	85.67
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	85.66
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	85.61
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	85.61
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	85.57
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	85.57
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	85.52
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	85.5
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	85.49
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	85.47
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	85.45
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	85.42
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	85.4
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	85.37
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	85.31
1xp8_A	366	RECA protein, recombinase A; recombination, radior	85.31
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	85.31
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	85.31
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	85.3
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	85.29
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	85.29
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	85.28
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	85.28
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	85.25
1g6h_A	257	High-affinity branched-chain amino acid transport	85.23
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	85.19
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	85.17
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	85.17
1via_A	175	Shikimate kinase; structural genomics, transferase	85.11
3pvs_A	447	Replication-associated recombination protein A; ma	85.11
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	85.09
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	85.08
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	85.05
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	85.05
1ji0_A	240	ABC transporter; ATP binding protein, structural g	85.03
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	84.98
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	84.98
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	84.96
3kta_A	182	Chromosome segregation protein SMC; structural mai	84.92
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	84.9
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	84.89
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	84.88
2z43_A	324	DNA repair and recombination protein RADA; archaea	84.87
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	84.86
3u06_A	412	Protein claret segregational; motor domain, stalk	84.86
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	84.85
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	84.83
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	84.81
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	84.8
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	84.78
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	84.77
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	84.69
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	84.67
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	84.66
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	84.66
2ghi_A	260	Transport protein; multidrug resistance protein, M	84.65
1b0u_A	262	Histidine permease; ABC transporter, transport pro	84.6
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	84.59
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	84.59
2og2_A	359	Putative signal recognition particle receptor; nuc	84.53
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	84.52
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	84.42
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	84.4
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	84.38
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	84.38
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	84.36
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	84.32
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	84.24
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	84.22
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	84.18
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	84.16
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	84.15
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	84.12
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	84.07
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	84.0
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	83.92
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	83.91
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	83.9
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	83.87
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	83.87
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	83.84
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	83.84
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	83.77
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	83.65
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	83.6
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	83.52
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	83.5
2r6a_A	454	DNAB helicase, replicative helicase; replication,	83.5
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	83.5
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	83.49
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	83.46
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	83.41
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	83.41
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	83.37
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	83.3
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	83.2
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	83.19
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	83.13
2vli_A	183	Antibiotic resistance protein; transferase, tunica	83.13
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	83.02
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	82.94
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	82.75
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	82.74
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	82.68
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	82.68
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	82.59
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	82.31
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	82.29
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	82.27
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	82.26
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	82.01
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	81.92
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	81.79
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	81.76
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	81.72
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	81.52
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	81.5
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	81.49
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	81.45
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	81.44
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	81.42
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	81.15
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	81.07
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	80.98
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	80.75
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	80.64
4h1g_A	715	Maltose binding protein-cakar3 motor domain fusio;	80.51
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	80.48
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	80.48
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	80.47
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	80.02

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.95  E-value=7.1e-27  Score=164.57  Aligned_cols=118  Identities=31%  Similarity=0.459  Sum_probs=104.6

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      ++...|.+..+|+++++++.+++++.+.||..|+++|.++|+.+++|+|+++++|||||||++|++|++..+......  
T Consensus        20 ~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~--   97 (242)
T 3fe2_A           20 RGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFL--   97 (242)
T ss_dssp             ESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCC--
T ss_pred             eCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhcccc--
Confidence            456788999999999999999999999999999999999999999999999999999999999999999998754321  


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                               ....++++||++||++|+.|+.+.++++....++++.+++
T Consensus        98 ---------~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~  137 (242)
T 3fe2_A           98 ---------ERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIY  137 (242)
T ss_dssp             ---------CTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             ---------ccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEE
Confidence                     1122378999999999999999999999999888877653

>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=99.94  E-value=1.9e-26  Score=174.64  Aligned_cols=117  Identities=48%  Similarity=0.718  Sum_probs=103.9

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      +...|.+..+|++++|++.+++++++.||..|||+|.++|+.+++|+|++++||||||||++|++|+++++......   
T Consensus        48 ~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~---  124 (434)
T 2db3_A           48 GSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE---  124 (434)
T ss_dssp             SSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC---
T ss_pred             CCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc---
Confidence            45567889999999999999999999999999999999999999999999999999999999999999998875421   


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                              ....++++||++|||+|+.|+++++++++...++++.+++
T Consensus       125 --------~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~  164 (434)
T 2db3_A          125 --------LELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVY  164 (434)
T ss_dssp             --------CCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEEC
T ss_pred             --------cccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEE
Confidence                    1122478999999999999999999999998888876653

>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=99.93  E-value=1.2e-25  Score=163.38  Aligned_cols=105  Identities=25%  Similarity=0.489  Sum_probs=93.0

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGR   86 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~   86 (130)
                      ...+|++++|++.+++++.++||..||++|.++|+.+++|  +|++++||||||||++|++|+++++.....        
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~--------  161 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK--------  161 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSC--------
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCC--------
Confidence            4578999999999999999999999999999999999988  999999999999999999999998754322        


Q ss_pred             CCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        87 ~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                              ++++||++|||+||.|+++.+++++... ++++..+
T Consensus       162 --------~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~  197 (300)
T 3fmo_B          162 --------YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYA  197 (300)
T ss_dssp             --------SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEE
T ss_pred             --------CceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEE
Confidence                    2789999999999999999999998864 5555543

>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=99.93  E-value=1.5e-25  Score=156.77  Aligned_cols=111  Identities=27%  Similarity=0.396  Sum_probs=92.7

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      ++..+.+..+|+++++++.+.+++++.||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.....    
T Consensus        16 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~----   91 (230)
T 2oxc_A           16 GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENL----   91 (230)
T ss_dssp             --------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSC----
T ss_pred             CCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCC----
Confidence            4567778899999999999999999999999999999999999999999999999999999999999988754321    


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                                  ++++||++||++|+.|+.+.+++++... ++++.++
T Consensus        92 ------------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  127 (230)
T 2oxc_A           92 ------------STQILILAPTREIAVQIHSVITAIGIKMEGLECHVF  127 (230)
T ss_dssp             ------------SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEE
T ss_pred             ------------CceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEE
Confidence                        2689999999999999999999998765 6666554

>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=99.93  E-value=1e-25  Score=158.62  Aligned_cols=113  Identities=36%  Similarity=0.512  Sum_probs=100.6

Q ss_pred             cccccccccCCCcCC----CCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcC
Q psy3307           2 QECLVSLKKQGFDDI----QMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG   77 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l----~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~   77 (130)
                      ++...|.|..+|+++    ++++.+++++.+.||..|+++|.++|+.+++|+|+++++|||||||++|++|++..+....
T Consensus        16 ~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~   95 (245)
T 3dkp_A           16 QGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA   95 (245)
T ss_dssp             ESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCC
T ss_pred             cCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcc
Confidence            356688999999988    8999999999999999999999999999999999999999999999999999999885422


Q ss_pred             CCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          78 PLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                     ..++++||++||++|+.|+.+.++++....++++..+
T Consensus        96 ---------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  132 (245)
T 3dkp_A           96 ---------------NKGFRALIISPTRELASQIHRELIKISEGTGFRIHMI  132 (245)
T ss_dssp             ---------------SSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECC
T ss_pred             ---------------cCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEE
Confidence                           1136899999999999999999999998888776543

>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=99.93  E-value=2.2e-25  Score=154.57  Aligned_cols=113  Identities=32%  Similarity=0.444  Sum_probs=92.3

Q ss_pred             CcccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCC
Q psy3307           1 MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLP   80 (130)
Q Consensus         1 ~~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~   80 (130)
                      |++.+.+.+..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+.....  
T Consensus         4 ~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~--   81 (220)
T 1t6n_A            4 VKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG--   81 (220)
T ss_dssp             ----------CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTT--
T ss_pred             CCCCcccccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCC--
Confidence            356677788889999999999999999999999999999999999999999999999999999999999987643221  


Q ss_pred             CCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          81 TPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                                    ++++||++||++|+.|+.+.++++.+.. ++++..+
T Consensus        82 --------------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~  117 (220)
T 1t6n_A           82 --------------QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVF  117 (220)
T ss_dssp             --------------CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEE
T ss_pred             --------------CEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEE
Confidence                          2579999999999999999999998776 6766654

>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=99.93  E-value=1.2e-25  Score=157.98  Aligned_cols=111  Identities=35%  Similarity=0.393  Sum_probs=95.8

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      +...+.+..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|+++.+.....    
T Consensus        22 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~----   97 (237)
T 3bor_A           22 ESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFK----   97 (237)
T ss_dssp             -----CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSC----
T ss_pred             cCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCC----
Confidence            4456778889999999999999999999999999999999999999999999999999999999999988653221    


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                  ++++||++||++|+.|+.+.+++++...++++..+
T Consensus        98 ------------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  132 (237)
T 3bor_A           98 ------------ETQALVLAPTRELAQQIQKVILALGDYMGATCHAC  132 (237)
T ss_dssp             ------------SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEE
T ss_pred             ------------CceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEE
Confidence                        26799999999999999999999998877776554

>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=99.93  E-value=2.7e-25  Score=157.48  Aligned_cols=107  Identities=36%  Similarity=0.582  Sum_probs=97.8

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGR   86 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~   86 (130)
                      +.+..+|+++++++.+.++++++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.....        
T Consensus        39 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~--------  110 (249)
T 3ber_A           39 EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQ--------  110 (249)
T ss_dssp             HHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCC--------
T ss_pred             ccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCC--------
Confidence            455778999999999999999999999999999999999999999999999999999999999998876542        


Q ss_pred             CCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        87 ~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                              ++++||++||++|+.|+.+.+++++...++++..+
T Consensus       111 --------~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~  145 (249)
T 3ber_A          111 --------RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVI  145 (249)
T ss_dssp             --------SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEE
T ss_pred             --------CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEE
Confidence                    26799999999999999999999999888887665

>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=99.93  E-value=1.3e-25  Score=156.47  Aligned_cols=116  Identities=32%  Similarity=0.446  Sum_probs=97.0

Q ss_pred             ccccccccCCCcC-CCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           3 ECLVSLKKQGFDD-IQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         3 ~~~~~~~~~~f~~-l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      +...|.|..+|++ +++++.+++++.+.||..|+++|.++|+.+++|+|+++++|||||||++|++|++..+....... 
T Consensus        11 ~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~-   89 (228)
T 3iuy_A           11 KRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR-   89 (228)
T ss_dssp             CCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-------
T ss_pred             cCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchh-
Confidence            5678999999999 89999999999999999999999999999999999999999999999999999999876432110 


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                               ....++++||++||++|+.|+.+.++++. ..++++..+
T Consensus        90 ---------~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~  127 (228)
T 3iuy_A           90 ---------EQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICI  127 (228)
T ss_dssp             ------------CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEE
T ss_pred             ---------hccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEE
Confidence                     01123789999999999999999999986 445665544

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.93  E-value=5.3e-25  Score=154.15  Aligned_cols=113  Identities=30%  Similarity=0.439  Sum_probs=99.5

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCC
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA   84 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~   84 (130)
                      ..+.+..+|+++++++.+++.+.+.|+..|+++|.++++.+++|+|+++++|||||||++|++|+++.+......     
T Consensus        19 ~~~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~-----   93 (236)
T 2pl3_A           19 INVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWT-----   93 (236)
T ss_dssp             CCGGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCC-----
T ss_pred             CCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhccc-----
Confidence            345677889999999999999999999999999999999999999999999999999999999999998764311     


Q ss_pred             CCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          85 GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        85 ~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                             ...++++||++||++|+.|+.+.++++....++++.++
T Consensus        94 -------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  131 (236)
T 2pl3_A           94 -------STDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLI  131 (236)
T ss_dssp             -------GGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEE
T ss_pred             -------ccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEE
Confidence                   11236899999999999999999999998888877654

>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=99.93  E-value=3.6e-25  Score=153.68  Aligned_cols=111  Identities=32%  Similarity=0.458  Sum_probs=99.5

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      +...+++..+|+++++++.+++.+.+.||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+.....    
T Consensus         6 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~----   81 (224)
T 1qde_A            6 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK----   81 (224)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC----
T ss_pred             ccccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCC----
Confidence            4556778889999999999999999999999999999999999999999999999999999999999988754321    


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                  ++++||++|+++|+.|+.+.++++....++++..+
T Consensus        82 ------------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  116 (224)
T 1qde_A           82 ------------APQALMLAPTRELALQIQKVVMALAFHMDIKVHAC  116 (224)
T ss_dssp             ------------SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEE
T ss_pred             ------------CceEEEEECCHHHHHHHHHHHHHHhcccCceEEEE
Confidence                        26899999999999999999999998888876654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.93  E-value=4.2e-25  Score=153.26  Aligned_cols=105  Identities=32%  Similarity=0.496  Sum_probs=92.1

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      +..+|+++++++.+++++++.|+..|+++|.++++.+++|+|+++++|||||||++|++|++..+.....          
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~----------   71 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERA----------   71 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSC----------
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcC----------
Confidence            4467999999999999999999999999999999999999999999999999999999999988754321          


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC----CCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS----QLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~----~~~~~~~  129 (130)
                            ++++||++||++|+.|+.+.++++....    ++++..+
T Consensus        72 ------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~  110 (219)
T 1q0u_A           72 ------EVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCL  110 (219)
T ss_dssp             ------SCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEE
T ss_pred             ------CceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEE
Confidence                  2689999999999999999999998876    5555543

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.92  E-value=6.9e-25  Score=163.73  Aligned_cols=128  Identities=58%  Similarity=0.931  Sum_probs=104.2

Q ss_pred             cccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           2 QECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         2 ~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      .+...|.++.+|+++++++.+.+++.+.||..|+|+|.++|+.+++|+|++++||||||||++|++|+++.+........
T Consensus         6 ~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~   85 (417)
T 2i4i_A            6 TGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEA   85 (417)
T ss_dssp             ESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHH
T ss_pred             CCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccch
Confidence            35678899999999999999999999999999999999999999999999999999999999999999999876432100


Q ss_pred             CC--CCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          82 PP--AGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        82 ~~--~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ..  ...........++++||++||++|+.|+++.++++....++++..+
T Consensus        86 ~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  135 (417)
T 2i4i_A           86 LRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVV  135 (417)
T ss_dssp             HHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEE
T ss_pred             hhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEE
Confidence            00  0000001122347899999999999999999999998888877654

>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=99.92  E-value=1e-24  Score=149.57  Aligned_cols=103  Identities=29%  Similarity=0.517  Sum_probs=92.0

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      .+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++.+|||||||++|++|++..+.....            
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~------------   70 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKD------------   70 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSC------------
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCC------------
Confidence            57999999999999999999999999999999999999999999999999999999999987643221            


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                          ++++||++||++|+.|+.+.++++.+.. ++++..+
T Consensus        71 ----~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  106 (206)
T 1vec_A           71 ----NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMAT  106 (206)
T ss_dssp             ----SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEE
T ss_pred             ----CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEE
Confidence                2689999999999999999999998876 6666543

>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=99.92  E-value=2.6e-25  Score=157.29  Aligned_cols=114  Identities=52%  Similarity=0.843  Sum_probs=97.7

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      +..+|+++++++.+++++.+.||..|+++|.++|+.+++|+|+++++|||||||++|++|++..+.........      
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~------   94 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQR------   94 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----------
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhcccccc------
Confidence            77889999999999999999999999999999999999999999999999999999999999998754321000      


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                       .....++++||++||++|+.|+.+.++++....++++..+
T Consensus        95 -~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (253)
T 1wrb_A           95 -YSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVV  134 (253)
T ss_dssp             ---CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEE
T ss_pred             -ccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEE
Confidence             0112237899999999999999999999998888877654

>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=99.91  E-value=7.5e-24  Score=151.04  Aligned_cols=108  Identities=29%  Similarity=0.396  Sum_probs=91.6

Q ss_pred             cCCCcCCC--CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307          10 KQGFDDIQ--MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus        10 ~~~f~~l~--l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ..+|++++  +++.+++++++.||..|+++|.++++.++.|+|++++||||||||++|++|+++.+......        
T Consensus        51 ~~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~--------  122 (262)
T 3ly5_A           51 DTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM--------  122 (262)
T ss_dssp             GGCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCC--------
T ss_pred             cCChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhcccc--------
Confidence            34577777  99999999999999999999999999999999999999999999999999999998864321        


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                          ...+.++||++||++|+.|+.+.++++....++++..+
T Consensus       123 ----~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~  160 (262)
T 3ly5_A          123 ----PRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLI  160 (262)
T ss_dssp             ----GGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEE
T ss_pred             ----ccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEE
Confidence                11236799999999999999999999999888877654

>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=99.90  E-value=3.9e-23  Score=141.60  Aligned_cols=97  Identities=35%  Similarity=0.537  Sum_probs=86.9

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSR   91 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~   91 (130)
                      +|+++++++.+.+.+++.|+..|+++|.++++.+++|+|+++.+|||||||++|++|++..+.....             
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~-------------   68 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQE-------------   68 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCC-------------
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccc-------------
Confidence            6999999999999999999999999999999999999999999999999999999999988754221             


Q ss_pred             CCCCceEEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          92 KKVFPLGLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        92 ~~~~~~~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                      ...+++++|++|+++|+.|+.+.++++...
T Consensus        69 ~~~~~~~lil~P~~~L~~q~~~~~~~~~~~   98 (207)
T 2gxq_A           69 RGRKPRALVLTPTRELALQVASELTAVAPH   98 (207)
T ss_dssp             TTCCCSEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             cCCCCcEEEEECCHHHHHHHHHHHHHHhhc
Confidence            112378999999999999999999998765

>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=99.90  E-value=3.5e-23  Score=154.47  Aligned_cols=106  Identities=33%  Similarity=0.429  Sum_probs=94.9

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      .+..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|+++.+.....         
T Consensus        34 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~---------  104 (410)
T 2j0s_A           34 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR---------  104 (410)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSC---------
T ss_pred             cCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccC---------
Confidence            45678999999999999999999999999999999999999999999999999999999999987643211         


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                             +.++||++||++|+.|+.+.+++++...++++..+
T Consensus       105 -------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  139 (410)
T 2j0s_A          105 -------ETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC  139 (410)
T ss_dssp             -------SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEE
T ss_pred             -------CceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEE
Confidence                   26799999999999999999999999888877654

>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=99.89  E-value=9.6e-23  Score=151.55  Aligned_cols=110  Identities=34%  Similarity=0.529  Sum_probs=93.4

Q ss_pred             cccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCC
Q psy3307           4 CLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPP   83 (130)
Q Consensus         4 ~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~   83 (130)
                      ...+....+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++.+|||+|||++|++|++..+.....     
T Consensus        14 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~-----   88 (400)
T 1s2m_A           14 DVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLN-----   88 (400)
T ss_dssp             -------CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSC-----
T ss_pred             cccccccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccC-----
Confidence            345556678999999999999999999999999999999999999999999999999999999999987643221     


Q ss_pred             CCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          84 AGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        84 ~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                 +.+++|++|+++|+.|+.+.++++....++++..+
T Consensus        89 -----------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  123 (400)
T 1s2m_A           89 -----------KIQALIMVPTRELALQTSQVVRTLGKHCGISCMVT  123 (400)
T ss_dssp             -----------SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEE
T ss_pred             -----------CccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEE
Confidence                       26799999999999999999999998888876654

>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=99.89  E-value=1.6e-22  Score=149.34  Aligned_cols=106  Identities=26%  Similarity=0.531  Sum_probs=93.4

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAG   85 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~   85 (130)
                      ....+|+++++++.+++++.+.|+..|+|+|.++++.+++|  +++++++|||+|||++|++|++..+.....       
T Consensus         2 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~-------   74 (395)
T 3pey_A            2 AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDA-------   74 (395)
T ss_dssp             --CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCC-------
T ss_pred             ccccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCC-------
Confidence            34689999999999999999999999999999999999988  999999999999999999999987653321       


Q ss_pred             CCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        86 ~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                               ++++||++|+++|+.|+.+.+++++...++.+..+
T Consensus        75 ---------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  109 (395)
T 3pey_A           75 ---------SPQAICLAPSRELARQTLEVVQEMGKFTKITSQLI  109 (395)
T ss_dssp             ---------SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEE
T ss_pred             ---------CccEEEECCCHHHHHHHHHHHHHHhcccCeeEEEE
Confidence                     26799999999999999999999998877766543

>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=99.89  E-value=1.1e-22  Score=150.43  Aligned_cols=109  Identities=32%  Similarity=0.463  Sum_probs=97.4

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCC
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA   84 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~   84 (130)
                      ....+..+|+++++++.+++++.+.|+..|+++|.++++.+++|+|+++.+|||+|||++|++|++..+.....      
T Consensus        15 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~------   88 (394)
T 1fuu_A           15 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK------   88 (394)
T ss_dssp             SSCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCC------
T ss_pred             hcccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCC------
Confidence            45566788999999999999999999999999999999999999999999999999999999999987654321      


Q ss_pred             CCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          85 GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        85 ~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                ++++||++|+++|+.|+.+.++++....++++..+
T Consensus        89 ----------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  123 (394)
T 1fuu_A           89 ----------APQALMLAPTRELALQIQKVVMALAFHMDIKVHAC  123 (394)
T ss_dssp             ----------SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEE
T ss_pred             ----------CCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEE
Confidence                      26899999999999999999999998888877654

>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=99.88  E-value=4.3e-22  Score=148.09  Aligned_cols=104  Identities=25%  Similarity=0.497  Sum_probs=91.5

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAG   85 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~   85 (130)
                      .+..+|+++++++.+++++.+.||..|+++|.++++.+++|  +|+++++|||+|||++|++|++..+.....       
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~-------   94 (412)
T 3fht_A           22 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK-------   94 (412)
T ss_dssp             CCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSC-------
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCC-------
Confidence            45678999999999999999999999999999999999987  999999999999999999999987754322       


Q ss_pred             CCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceE
Q psy3307          86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPC  127 (130)
Q Consensus        86 ~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~  127 (130)
                               ++++||++|+++|+.|+.+.++++.... ++++.
T Consensus        95 ---------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~  128 (412)
T 3fht_A           95 ---------YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLA  128 (412)
T ss_dssp             ---------SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEE
T ss_pred             ---------CCCEEEECCCHHHHHHHHHHHHHHHhhcccceEE
Confidence                     2689999999999999999999998764 44443

>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=99.88  E-value=4.8e-22  Score=148.06  Aligned_cols=109  Identities=35%  Similarity=0.403  Sum_probs=96.7

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCC
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA   84 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~   84 (130)
                      ..+....+|+++++++.+++.+.+.|+..|+++|.++|+.+++|+|+++.+|||||||++|++|+++.+.....      
T Consensus        34 ~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~------  107 (414)
T 3eiq_A           34 NWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLK------  107 (414)
T ss_dssp             CCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSC------
T ss_pred             CccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCC------
Confidence            34556678999999999999999999999999999999999999999999999999999999999987654321      


Q ss_pred             CCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          85 GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        85 ~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                +.+++|++|+++|+.|+.+.+++++...++.+..+
T Consensus       108 ----------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~  142 (414)
T 3eiq_A          108 ----------ATQALVLAPTRELAQQIQKVVMALGDYMGASCHAC  142 (414)
T ss_dssp             ----------SCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEEC
T ss_pred             ----------ceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEE
Confidence                      26799999999999999999999998888776654

>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=99.88  E-value=4.4e-22  Score=147.32  Aligned_cols=105  Identities=32%  Similarity=0.437  Sum_probs=91.0

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ...+|+++++++.++++|.+.||..|+|+|.++++.+++|+|+++.+|||+|||++|++|++..+.....          
T Consensus         6 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~----------   75 (391)
T 1xti_A            6 MSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG----------   75 (391)
T ss_dssp             ---CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTT----------
T ss_pred             CCCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCC----------
Confidence            3467999999999999999999999999999999999999999999999999999999999987643221          


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~~~  129 (130)
                            +.++||++|+++|+.|+.+.++++.... ++++..+
T Consensus        76 ------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~  111 (391)
T 1xti_A           76 ------QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVF  111 (391)
T ss_dssp             ------CCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEE
T ss_pred             ------CeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEE
Confidence                  2679999999999999999999998775 6666544

>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=99.88  E-value=4.4e-22  Score=151.81  Aligned_cols=103  Identities=25%  Similarity=0.502  Sum_probs=90.0

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGR   86 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~   86 (130)
                      +..+|++++|++.+++++.++||..|+++|.++|+.++.|  +|++++||||||||++|++|++..+.....        
T Consensus        90 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~--------  161 (479)
T 3fmp_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK--------  161 (479)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSC--------
T ss_pred             CcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCC--------
Confidence            3568999999999999999999999999999999999987  999999999999999999999986643321        


Q ss_pred             CCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcC-CCceE
Q psy3307          87 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS-QLRPC  127 (130)
Q Consensus        87 ~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~-~~~~~  127 (130)
                              ++++||++||++|+.|+.+.++++.+.. ++.+.
T Consensus       162 --------~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~  195 (479)
T 3fmp_B          162 --------YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLA  195 (479)
T ss_dssp             --------SCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEE
T ss_pred             --------CCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEE
Confidence                    2689999999999999999999998753 34433

>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=99.86  E-value=2.9e-21  Score=141.39  Aligned_cols=104  Identities=32%  Similarity=0.539  Sum_probs=92.1

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ...+|+++++++.+.+++++.|+..|+|+|.++++.+++| +++++.+|||+|||++|++|++..+....          
T Consensus         4 ~~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~----------   73 (367)
T 1hv8_A            4 EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENN----------   73 (367)
T ss_dssp             CCCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSS----------
T ss_pred             ccCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccC----------
Confidence            4567999999999999999999999999999999999988 79999999999999999999988764321          


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                             +.+++|++|+++|+.|+.+.++++....++++..+
T Consensus        74 -------~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~  108 (367)
T 1hv8_A           74 -------GIEAIILTPTRELAIQVADEIESLKGNKNLKIAKI  108 (367)
T ss_dssp             -------SCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEE
T ss_pred             -------CCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEE
Confidence                   26799999999999999999999988777776543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.85  E-value=6.9e-21  Score=148.48  Aligned_cols=101  Identities=35%  Similarity=0.479  Sum_probs=87.7

Q ss_pred             cccCCCcCCC----CCHHHHHHHHHCCCCCCcHHHHHHHhHHh--cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCC
Q psy3307           8 LKKQGFDDIQ----MTEIITNNIALARYDKPTPVQKYAIPVII--SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPT   81 (130)
Q Consensus         8 ~~~~~f~~l~----l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~--~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~   81 (130)
                      ....+|+++.    |++++++++.++||..|+|+|.++|+.++  .|+|++++||||||||++|++|+++.+......  
T Consensus        14 ~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~--   91 (579)
T 3sqw_A           14 SKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD--   91 (579)
T ss_dssp             CCCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS--
T ss_pred             CCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcccc--
Confidence            3445677665    99999999999999999999999999999  789999999999999999999999998875421  


Q ss_pred             CCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          82 PPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        82 ~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                                ...++++||++||++|+.|+.+.++++..
T Consensus        92 ----------~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~  120 (579)
T 3sqw_A           92 ----------SQYMVKAVIVAPTRDLALQIEAEVKKIHD  120 (579)
T ss_dssp             ----------STTSCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             ----------ccCCCeEEEEcchHHHHHHHHHHHHHHHh
Confidence                      11236899999999999999999999864

>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=99.84  E-value=1.2e-20  Score=146.27  Aligned_cols=99  Identities=34%  Similarity=0.485  Sum_probs=85.9

Q ss_pred             cCCCcCCC----CCHHHHHHHHHCCCCCCcHHHHHHHhHHh--cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCC
Q psy3307          10 KQGFDDIQ----MTEIITNNIALARYDKPTPVQKYAIPVII--SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPP   83 (130)
Q Consensus        10 ~~~f~~l~----l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~--~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~   83 (130)
                      ..+|+++.    |++++++++.+.||..|+|+|.++|+.++  .|+|++++||||||||++|++|+++.+......    
T Consensus        67 ~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~----  142 (563)
T 3i5x_A           67 EVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD----  142 (563)
T ss_dssp             CCCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS----
T ss_pred             CcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc----
Confidence            34566664    99999999999999999999999999999  678999999999999999999999999875421    


Q ss_pred             CCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          84 AGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        84 ~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                              ...++++||++||++|+.|+.+.++++..
T Consensus       143 --------~~~~~~~lil~Ptr~La~Q~~~~~~~~~~  171 (563)
T 3i5x_A          143 --------SQYMVKAVIVAPTRDLALQIEAEVKKIHD  171 (563)
T ss_dssp             --------STTSCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             --------ccCCeeEEEEcCcHHHHHHHHHHHHHHHh
Confidence                    11236899999999999999999998755

>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=99.82  E-value=1.6e-19  Score=130.88  Aligned_cols=90  Identities=37%  Similarity=0.546  Sum_probs=82.6

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCce
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL   97 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (130)
                      |++++.++++++|+..|+|+|.++++.+++|+++++.+|||+|||++|++|++..    .                  .+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~----~------------------~~   58 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----G------------------MK   58 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH----T------------------CC
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh----c------------------CC
Confidence            5789999999999999999999999999999999999999999999999998763    1                  56


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          98 GLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        98 ~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ++|++|+++|+.|+.+.++++....++++..+
T Consensus        59 ~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~   90 (337)
T 2z0m_A           59 SLVVTPTRELTRQVASHIRDIGRYMDTKVAEV   90 (337)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSCCCEEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEE
Confidence            99999999999999999999998888877654

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.79  E-value=1.1e-18  Score=138.84  Aligned_cols=101  Identities=20%  Similarity=0.315  Sum_probs=88.6

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           9 KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ...+|++++|++.+.+.+++.||..++++|.++++. +.+|++++++||||||||++|.+++++.+....          
T Consensus         6 ~~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~----------   75 (715)
T 2va8_A            6 EWMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNG----------   75 (715)
T ss_dssp             CCCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC----------
T ss_pred             ccCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCC----------
Confidence            345799999999999999999999999999999999 789999999999999999999999998876432          


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                              .+++|++|+++|+.|+.+.++++.. .|+++..
T Consensus        76 --------~~il~i~P~r~La~q~~~~~~~~~~-~g~~v~~  107 (715)
T 2va8_A           76 --------GKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAM  107 (715)
T ss_dssp             --------SEEEEECSCHHHHHHHHHHHGGGGG-GTCCEEE
T ss_pred             --------CeEEEEeCcHHHHHHHHHHHHHhhc-CCCEEEE
Confidence                    5799999999999999999965543 4666543

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.78  E-value=5.8e-19  Score=140.68  Aligned_cols=99  Identities=20%  Similarity=0.358  Sum_probs=88.4

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhH-HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~-~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      +|++++|++.+.+.+++.||..++++|.++++. +.+|+++++++|||||||++|.+++++.+....             
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~-------------   68 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQG-------------   68 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHC-------------
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCC-------------
Confidence            599999999999999999999999999999998 889999999999999999999999998887543             


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                           .+++|++|+++|+.|+.+.++++.+ .|+++..+
T Consensus        69 -----~~~l~i~P~raLa~q~~~~~~~l~~-~g~~v~~~  101 (720)
T 2zj8_A           69 -----GKAVYIVPLKALAEEKFQEFQDWEK-IGLRVAMA  101 (720)
T ss_dssp             -----SEEEEECSSGGGHHHHHHHTGGGGG-GTCCEEEE
T ss_pred             -----CEEEEEcCcHHHHHHHHHHHHHHHh-cCCEEEEe
Confidence                 5799999999999999999976654 36666543

>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=99.77  E-value=1e-18  Score=135.25  Aligned_cols=87  Identities=22%  Similarity=0.318  Sum_probs=80.0

Q ss_pred             cCCCcCCCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      +..|++++|++.+.+.+++ +||..++|+|.++|+.+++|+|+++.+|||+|||++|++|++..    .           
T Consensus         1 ~~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~----~-----------   65 (523)
T 1oyw_A            1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL----N-----------   65 (523)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS----S-----------
T ss_pred             CCChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh----C-----------
Confidence            4689999999999999998 89999999999999999999999999999999999999999742    1           


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                             .++||++|+++|+.|+.+.++++
T Consensus        66 -------g~~lvi~P~~aL~~q~~~~l~~~   88 (523)
T 1oyw_A           66 -------GLTVVVSPLISLMKDQVDQLQAN   88 (523)
T ss_dssp             -------SEEEEECSCHHHHHHHHHHHHHT
T ss_pred             -------CCEEEECChHHHHHHHHHHHHHc
Confidence                   46999999999999999998875

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.77  E-value=1.4e-18  Score=130.07  Aligned_cols=88  Identities=19%  Similarity=0.123  Sum_probs=75.0

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEE
Q psy3307          21 IITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGL   99 (130)
Q Consensus        21 ~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   99 (130)
                      ++.+.+++ .++ .|+|+|.++++.+++|+|+++++|||||||++|++|++.....                   ++++|
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~-------------------~~~~l   68 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK-------------------GKKSA   68 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTT-------------------TCCEE
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcC-------------------CCEEE
Confidence            44555555 466 7999999999999999999999999999999999998876621                   16799


Q ss_pred             EEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307         100 VLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       100 il~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      |++||++|+.|+.+.+++++. .++++..+
T Consensus        69 il~Pt~~L~~q~~~~~~~~~~-~~~~v~~~   97 (414)
T 3oiy_A           69 LVFPTVTLVKQTLERLQKLAD-EKVKIFGF   97 (414)
T ss_dssp             EEESSHHHHHHHHHHHHHHCC-SSCCEEEC
T ss_pred             EEECCHHHHHHHHHHHHHHcc-CCceEEEE
Confidence            999999999999999999988 77777654

>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=99.76  E-value=3.4e-18  Score=134.02  Aligned_cols=84  Identities=23%  Similarity=0.362  Sum_probs=76.9

Q ss_pred             CcCCCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q psy3307          13 FDDIQMTEIITNNIAL-ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSR   91 (130)
Q Consensus        13 f~~l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~   91 (130)
                      +.++++++.+.+.|++ +||..|+|+|.++|+.+++|+|+++.+|||+|||++|.+|++..    .              
T Consensus        23 ~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~----~--------------   84 (591)
T 2v1x_A           23 KEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS----D--------------   84 (591)
T ss_dssp             CSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS----S--------------
T ss_pred             cccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc----C--------------
Confidence            3468899999999998 69999999999999999999999999999999999999999751    1              


Q ss_pred             CCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          92 KKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        92 ~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                          .++||++|+++|+.|+.+.++++
T Consensus        85 ----g~~lVisP~~~L~~q~~~~l~~~  107 (591)
T 2v1x_A           85 ----GFTLVICPLISLMEDQLMVLKQL  107 (591)
T ss_dssp             ----SEEEEECSCHHHHHHHHHHHHHH
T ss_pred             ----CcEEEEeCHHHHHHHHHHHHHhc
Confidence                47999999999999999999887

>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=99.74  E-value=8.8e-19  Score=139.28  Aligned_cols=97  Identities=20%  Similarity=0.321  Sum_probs=83.4

Q ss_pred             CCcCCC--CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          12 GFDDIQ--MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        12 ~f~~l~--l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      +|++++  |++.+.+.+++.||+.++++|.++++.+.+|+++++++|||||||++|.++++..+...             
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------------   68 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG-------------   68 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT-------------
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-------------
Confidence            688999  99999999999999999999999999999999999999999999999999999887631             


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEE
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCV  128 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~  128 (130)
                            .+++|++|+++|+.|+.+.++++. ..|+++..
T Consensus        69 ------~~~l~i~P~r~La~q~~~~~~~~~-~~g~~v~~  100 (702)
T 2p6r_A           69 ------GKSLYVVPLRALAGEKYESFKKWE-KIGLRIGI  100 (702)
T ss_dssp             ------CCEEEEESSHHHHHHHHHHHTTTT-TTTCCEEE
T ss_pred             ------CcEEEEeCcHHHHHHHHHHHHHHH-hcCCEEEE
Confidence                  479999999999999999996554 34666654

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.73  E-value=3.2e-17  Score=129.69  Aligned_cols=93  Identities=19%  Similarity=0.108  Sum_probs=76.9

Q ss_pred             HHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEc
Q psy3307          23 TNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLA  102 (130)
Q Consensus        23 ~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~  102 (130)
                      .+++..+|+..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+......              .+.++||++
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~--------------~~~~~lvl~   68 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQG--------------QKGKVVFFA   68 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTT--------------CCCCEEEEC
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccC--------------CCCeEEEEE
Confidence            456788999999999999999999999999999999999999999999988764311              115799999


Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307         103 PTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       103 Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ||++|+.|+.+.+++++...++++..+
T Consensus        69 Pt~~L~~Q~~~~~~~~~~~~~~~v~~~   95 (696)
T 2ykg_A           69 NQIPVYEQNKSVFSKYFERHGYRVTGI   95 (696)
T ss_dssp             SSHHHHHHHHHHHHHHTTTTTCCEEEE
T ss_pred             CCHHHHHHHHHHHHHHhccCCceEEEE
Confidence            999999999999999998888887655

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.72  E-value=2.9e-17  Score=131.77  Aligned_cols=81  Identities=21%  Similarity=0.114  Sum_probs=73.1

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .+|+ .||++|..++|.++.|+  ++.++||+|||++|.+|++.....                   ++.++|++||++|
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~-------------------g~~vlVltptreL  136 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT-------------------GKGVHVVTVNEYL  136 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT-------------------SSCEEEEESSHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc-------------------CCCEEEEeCCHHH
Confidence            5799 99999999999999999  899999999999999999854322                   1469999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      |.|..+++..+.+.+|+++.+++
T Consensus       137 A~qd~e~~~~l~~~lgl~v~~i~  159 (844)
T 1tf5_A          137 ASRDAEQMGKIFEFLGLTVGLNL  159 (844)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEECC
T ss_pred             HHHHHHHHHHHHhhcCCeEEEEe
Confidence            99999999999999999998875

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.71  E-value=7.6e-17  Score=123.66  Aligned_cols=83  Identities=18%  Similarity=0.103  Sum_probs=73.9

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|+|+|.++++.+++|+|+++.+|||+|||++|++|+++.+.....              ..+.++||++||++|+.|+.
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~--------------~~~~~~lil~P~~~L~~q~~   69 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC--------------GQKGKVVFFANQIPVYEQQA   69 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS--------------SCCCCEEEECSSHHHHHHHH
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc--------------CCCCEEEEEeCCHHHHHHHH
Confidence            6999999999999999999999999999999999999998876431              11267999999999999999


Q ss_pred             HHHHHHHhcCCCceEEe
Q psy3307         113 DEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~~~  129 (130)
                      +.++++....++++..+
T Consensus        70 ~~~~~~~~~~~~~~~~~   86 (555)
T 3tbk_A           70 TVFSRYFERLGYNIASI   86 (555)
T ss_dssp             HHHHHHHHTTTCCEEEE
T ss_pred             HHHHHHhccCCcEEEEE
Confidence            99999999888887765

>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=99.70  E-value=8.3e-17  Score=123.72  Aligned_cols=85  Identities=20%  Similarity=0.128  Sum_probs=72.7

Q ss_pred             CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        31 ~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      ...|+|+|.++++.+++|+|+++.+|||+|||++|++|+++.+.....              ..++++||++||++|+.|
T Consensus         5 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~--------------~~~~~~lil~P~~~L~~q   70 (556)
T 4a2p_A            5 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA--------------GRKAKVVFLATKVPVYEQ   70 (556)
T ss_dssp             ---CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS--------------SCCCCEEEECSSHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc--------------cCCCeEEEEeCCHHHHHH
Confidence            347999999999999999999999999999999999999998876431              112679999999999999


Q ss_pred             HHHHHHHHHhcCCCceEEe
Q psy3307         111 IYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       111 ~~~~~~~l~~~~~~~~~~~  129 (130)
                      +.+.++++....++++..+
T Consensus        71 ~~~~~~~~~~~~~~~~~~~   89 (556)
T 4a2p_A           71 QKNVFKHHFERQGYSVQGI   89 (556)
T ss_dssp             HHHHHHHHHGGGTCCEEEC
T ss_pred             HHHHHHHHhcccCceEEEE
Confidence            9999999998888887664

>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=99.69  E-value=1.3e-16  Score=131.86  Aligned_cols=97  Identities=21%  Similarity=0.153  Sum_probs=79.8

Q ss_pred             CCcCCCCCHHH-----HHHH-HHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy3307          12 GFDDIQMTEII-----TNNI-ALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAG   85 (130)
Q Consensus        12 ~f~~l~l~~~i-----~~~l-~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~   85 (130)
                      .+...++++..     .+.+ +.+||. | ++|.++|+.+++|+|++++||||||||+ |.+|++..+....        
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~--------   99 (1054)
T 1gku_B           31 AASLCLFPEDFLLKEFVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALKG--------   99 (1054)
T ss_dssp             CCCCSCCTTHHHHHHHHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTTS--------
T ss_pred             cccccccccccchHHHHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcC--------
Confidence            34455554433     2333 348998 9 9999999999999999999999999998 9999998876532        


Q ss_pred             CCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCC----ceEEe
Q psy3307          86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL----RPCVV  129 (130)
Q Consensus        86 ~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~----~~~~~  129 (130)
                                +++||++||++|+.|+.+.+++++..+++    ++.++
T Consensus       100 ----------~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~  137 (1054)
T 1gku_B          100 ----------KRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYY  137 (1054)
T ss_dssp             ----------CCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEEC
T ss_pred             ----------CeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEE
Confidence                      67999999999999999999999998888    66554

>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=99.68  E-value=2.5e-16  Score=126.85  Aligned_cols=89  Identities=19%  Similarity=0.115  Sum_probs=74.3

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      ..|+..|+|+|.++++.+++|+|+++++|||+|||++|++|++..+.....              ..+.++||++||++|
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~--------------~~~~~~Lvl~Pt~~L  308 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA--------------GRKAKVVFLATKVPV  308 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS--------------SCCCCEEEECSSHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc--------------cCCCeEEEEeCCHHH
Confidence            356789999999999999999999999999999999999999998876431              112679999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      +.|+.+.++++....++++..++
T Consensus       309 ~~Q~~~~~~~~~~~~~~~v~~~~  331 (797)
T 4a2q_A          309 YEQQKNVFKHHFERQGYSVQGIS  331 (797)
T ss_dssp             HHHHHHHHHHHHGGGTCCEEEEC
T ss_pred             HHHHHHHHHHhcccCCceEEEEe
Confidence            99999999999988888877653

>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=99.67  E-value=5.2e-16  Score=124.77  Aligned_cols=90  Identities=22%  Similarity=0.204  Sum_probs=79.0

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcC------CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCC
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISG------RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKK   93 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g------~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~   93 (130)
                      +.+.+.++.++| .+|++|.++|+.++++      +|+++++|||||||++|++|++..+...                 
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g-----------------  417 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG-----------------  417 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT-----------------
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcC-----------------
Confidence            444555688999 8999999999999866      6999999999999999999999987643                 


Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          94 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        94 ~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                        .+++|++||++|+.|+++.++++...+++++..+
T Consensus       418 --~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l  451 (780)
T 1gm5_A          418 --FQTAFMVPTSILAIQHYRRTVESFSKFNIHVALL  451 (780)
T ss_dssp             --SCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEEC
T ss_pred             --CeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEE
Confidence              5799999999999999999999999888888765

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.66  E-value=4.5e-16  Score=128.99  Aligned_cols=82  Identities=21%  Similarity=0.160  Sum_probs=71.8

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      ..|| .||++|.++++.+++|+|++++||||||||++|+++++..+..                   ++++||++||++|
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~-------------------~~~~Lil~PtreL  133 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARK-------------------GKKSALVFPTVTL  133 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTT-------------------TCCEEEEESSHHH
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhc-------------------CCeEEEEechHHH
Confidence            3688 6999999999999999999999999999999988888876621                   1679999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      +.|+++.+++++ ..++++..++
T Consensus       134 a~Q~~~~l~~l~-~~~i~v~~l~  155 (1104)
T 4ddu_A          134 VKQTLERLQKLA-DEKVKIFGFY  155 (1104)
T ss_dssp             HHHHHHHHHTTS-CTTSCEEEEC
T ss_pred             HHHHHHHHHHhh-CCCCeEEEEe
Confidence            999999999987 7778877653

>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=99.65  E-value=1.1e-15  Score=130.86  Aligned_cols=95  Identities=21%  Similarity=0.300  Sum_probs=82.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCc
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFP   96 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (130)
                      |.+...+++...+|+.++|+|.++++.++++ +|++++||||||||++|.+|+++.+.+...                 .
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~-----------------~  973 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSE-----------------G  973 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTT-----------------C
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCC-----------------C
Confidence            5567788888889999999999999999754 689999999999999999999999876532                 4


Q ss_pred             eEEEEcCcHHHHHHHHHHHH-HHHhcCCCceEEe
Q psy3307          97 LGLVLAPTRELATQIYDEAK-KFAYRSQLRPCVV  129 (130)
Q Consensus        97 ~~lil~Pt~~La~q~~~~~~-~l~~~~~~~~~~~  129 (130)
                      ++||++|+|+||.|.++.++ ++++.+|+++..+
T Consensus       974 kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~l 1007 (1724)
T 4f92_B          974 RCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLL 1007 (1724)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEEC
T ss_pred             EEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEE
Confidence            79999999999999999986 5777788887654

>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=99.65  E-value=1.1e-15  Score=130.83  Aligned_cols=92  Identities=16%  Similarity=0.183  Sum_probs=77.7

Q ss_pred             CCCCCcHHHHHHHhHHh-cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          30 RYDKPTPVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      ||+.++++|.++++.++ .++|++++||||||||+++.+++++.+.+.......        ....+.++||++|+++|+
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~--------~~~~~~k~lyiaP~kALa  147 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGT--------INVDDFKIIYIAPMRSLV  147 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSS--------CCTTSCEEEEECSSHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhcccccc--------ccCCCCEEEEECCHHHHH
Confidence            79999999999999887 578999999999999999999999999875432111        122347899999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|+++.+.+....+|++|..+
T Consensus       148 ~e~~~~l~~~~~~~gi~V~~~  168 (1724)
T 4f92_B          148 QEMVGSFGKRLATYGITVAEL  168 (1724)
T ss_dssp             HHHHHHHHHHHTTTTCCEEEC
T ss_pred             HHHHHHHHHHHhhCCCEEEEE
Confidence            999999999888899888654

>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=99.65  E-value=9.5e-16  Score=104.97  Aligned_cols=85  Identities=20%  Similarity=0.194  Sum_probs=68.6

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .....|+++|.++++.+++|+++++.+|||+|||++|+++++..+......             ..+.++||++|+++|+
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~-------------~~~~~~lil~p~~~L~   95 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKA-------------SEPGKVIVLVNKVLLV   95 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHT-------------TCCCCEEEEESSHHHH
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccc-------------cCCCcEEEEECHHHHH
Confidence            344589999999999999999999999999999999999999877653210             0125799999999999


Q ss_pred             HH-HHHHHHHHHhcCCCceE
Q psy3307         109 TQ-IYDEAKKFAYRSQLRPC  127 (130)
Q Consensus       109 ~q-~~~~~~~l~~~~~~~~~  127 (130)
                      .| +.+.++++... ++++.
T Consensus        96 ~q~~~~~~~~~~~~-~~~v~  114 (216)
T 3b6e_A           96 EQLFRKEFQPFLKK-WYRVI  114 (216)
T ss_dssp             HHHHHHTHHHHHTT-TSCEE
T ss_pred             HHHHHHHHHHHhcc-CceEE
Confidence            99 78888888664 44443

>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=99.64  E-value=1.6e-16  Score=131.74  Aligned_cols=92  Identities=24%  Similarity=0.208  Sum_probs=81.0

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ...|..+++++.+...+...+...|+++|.++|+.+.+|+|++++||||||||++|.+|++..+...             
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g-------------  227 (1108)
T 3l9o_A          161 PPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNK-------------  227 (1108)
T ss_dssp             SSCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTT-------------
T ss_pred             CCCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcC-------------
Confidence            4478888888888777767667789999999999999999999999999999999999999887432             


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                            .+++|++||++|+.|+++.++++..
T Consensus       228 ------~rvlvl~PtraLa~Q~~~~l~~~~~  252 (1108)
T 3l9o_A          228 ------QRVIYTSPIKALSNQKYRELLAEFG  252 (1108)
T ss_dssp             ------CEEEEEESSHHHHHHHHHHHHHHTS
T ss_pred             ------CeEEEEcCcHHHHHHHHHHHHHHhC
Confidence                  5799999999999999999988765

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.64  E-value=6.7e-16  Score=123.87  Aligned_cols=80  Identities=19%  Similarity=0.052  Sum_probs=71.9

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .|+++|..+++.++.|+  ++.++||||||++|++|++......                   ++++|++||++||
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g-------------------~~vlVltPTreLA  128 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTG-------------------KGVHVVTVNDYLA  128 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTS-------------------SCCEEEESSHHHH
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcC-------------------CcEEEEcCCHHHH
Confidence            565 89999999999999998  8999999999999999998654321                   4699999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|+++++..+.+.+|+++.+++
T Consensus       129 ~Q~~e~~~~l~~~lgl~v~~i~  150 (853)
T 2fsf_A          129 QRDAENNRPLFEFLGLTVGINL  150 (853)
T ss_dssp             HHHHHHHHHHHHHTTCCEEECC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEe
Confidence            9999999999999999998875

>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=99.63  E-value=8.7e-16  Score=125.63  Aligned_cols=89  Identities=19%  Similarity=0.115  Sum_probs=73.2

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      -.++..|+++|.++++.+++|+|+++.+|||+|||++|++|++..+.....              ..+.++||++||++|
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~--------------~~~~~vLvl~Pt~~L  308 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA--------------GRKAKVVFLATKVPV  308 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCS--------------SCCCCEEEECSSHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccc--------------cCCCeEEEEeCCHHH
Confidence            345779999999999999999999999999999999999999887654321              112679999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      +.|+.+.++++....++++..++
T Consensus       309 ~~Q~~~~~~~~~~~~~~~v~~~~  331 (936)
T 4a2w_A          309 YEQQKNVFKHHFERQGYSVQGIS  331 (936)
T ss_dssp             HHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             HHHHHHHHHHHhcccCceEEEEE
Confidence            99999999999998888877653

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.60  E-value=3.1e-15  Score=120.48  Aligned_cols=81  Identities=20%  Similarity=0.166  Sum_probs=72.8

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .+|+ .|+++|..+++.++.|+  +++++||+|||++|.+|++......                   ..++|++||++|
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g-------------------~~v~VvTpTreL  164 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAG-------------------NGVHIVTVNDYL  164 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTT-------------------SCEEEEESSHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhC-------------------CCeEEEeCCHHH
Confidence            4788 89999999999999998  9999999999999999997554321                   359999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      |.|..+++..+.+.+|+++.+++
T Consensus       165 A~Qdae~m~~l~~~lGLsv~~i~  187 (922)
T 1nkt_A          165 AKRDSEWMGRVHRFLGLQVGVIL  187 (922)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEECC
T ss_pred             HHHHHHHHHHHHhhcCCeEEEEe
Confidence            99999999999999999998875

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.59  E-value=7.4e-15  Score=118.45  Aligned_cols=81  Identities=19%  Similarity=0.063  Sum_probs=72.5

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .+|+ .|+++|..+++.++.|+  +++++||+|||++|.+|++......                   .+++|++||++|
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G-------------------~qv~VvTPTreL  132 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTG-------------------KGVHVVTVNDYL  132 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTC-------------------SCCEEEESSHHH
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhC-------------------CCEEEEeCCHHH
Confidence            3798 89999999999999998  8999999999999999996544321                   359999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      |.|.++++..+.+.+|+++.+++
T Consensus       133 A~Qdae~m~~l~~~lGLsv~~i~  155 (997)
T 2ipc_A          133 ARRDAEWMGPVYRGLGLSVGVIQ  155 (997)
T ss_dssp             HHHHHHHHHHHHHTTTCCEEECC
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEe
Confidence            99999999999999999998764

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.56  E-value=1.1e-14  Score=111.66  Aligned_cols=78  Identities=19%  Similarity=0.108  Sum_probs=68.3

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|++.|.++++.+++++|+++++|||+|||++|+.++...+....                  .++||++|+++|+.|+.
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~------------------~~vlvl~P~~~L~~Q~~  174 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE------------------GKILIIVPTTALTTQMA  174 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCS------------------SEEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCC------------------CeEEEEECcHHHHHHHH
Confidence            799999999999999999999999999999999999888776432                  47999999999999999


Q ss_pred             HHHHHHHhcCCCceEE
Q psy3307         113 DEAKKFAYRSQLRPCV  128 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~~  128 (130)
                      +.++++....++++..
T Consensus       175 ~~~~~~~~~~~~~v~~  190 (510)
T 2oca_A          175 DDFVDYRLFSHAMIKK  190 (510)
T ss_dssp             HHHHHTTSSCGGGEEE
T ss_pred             HHHHHhhcCCccceEE
Confidence            9999986665555544

>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=99.56  E-value=1.4e-14  Score=103.70  Aligned_cols=78  Identities=19%  Similarity=0.108  Sum_probs=66.1

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++++|.++++.++++++.++++|||+|||++++.++...+....                  .++||++|+++|+.|+.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~------------------~~~lil~Pt~~L~~q~~  174 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE------------------GKILIIVPTTALTTQMA  174 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCS------------------SEEEEECSSHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCC------------------CeEEEEECCHHHHHHHH
Confidence            799999999999998888999999999999999888777665332                  47999999999999999


Q ss_pred             HHHHHHHhcCCCceEE
Q psy3307         113 DEAKKFAYRSQLRPCV  128 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~~  128 (130)
                      +.++++....+..+..
T Consensus       175 ~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          175 DDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             HHHHHHTSCCGGGEEE
T ss_pred             HHHHHhcccccceEEE
Confidence            9999987655444443

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.55  E-value=2.8e-16  Score=123.74  Aligned_cols=82  Identities=22%  Similarity=0.256  Sum_probs=65.9

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCC
Q psy3307          16 IQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF   95 (130)
Q Consensus        16 l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (130)
                      +++++..++++... ...++|+|..+++.+++|+|++++||||||||++|++|+++.+....                  
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~------------------  215 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRR------------------  215 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT------------------
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCC------------------
Confidence            56777776666554 36889998889999999999999999999999999999999987632                  


Q ss_pred             ceEEEEcCcHHHHHHHHHHHH
Q psy3307          96 PLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        96 ~~~lil~Pt~~La~q~~~~~~  116 (130)
                      +++||++|||+||.|+.+.++
T Consensus       216 ~~vLvl~PtreLa~Qi~~~l~  236 (618)
T 2whx_A          216 LRTLILAPTRVVAAEMEEALR  236 (618)
T ss_dssp             CCEEEEESSHHHHHHHHHHTT
T ss_pred             CeEEEEcChHHHHHHHHHHhc
Confidence            679999999999999998875

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.55  E-value=2.4e-14  Score=112.81  Aligned_cols=80  Identities=25%  Similarity=0.198  Sum_probs=69.1

Q ss_pred             CCcHHHHHHHhH----HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPV----IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~----~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .|++.|.+.+..    +.+|++++++||||+|||++|++|++..+....                  .+++|++||++++
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~------------------~kvli~t~T~~l~   64 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERK------------------LKVLYLVRTNSQE   64 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHT------------------CEEEEEESSHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcC------------------CeEEEECCCHHHH
Confidence            578999888854    458999999999999999999999999987543                  5799999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEeC
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      .|+.+.++++.+..++++++++
T Consensus        65 ~Qi~~el~~l~~~~~~~~~~l~   86 (620)
T 4a15_A           65 EQVIKELRSLSSTMKIRAIPMQ   86 (620)
T ss_dssp             HHHHHHHHHHHHHSCCCEEECC
T ss_pred             HHHHHHHHHHhhccCeEEEEEE
Confidence            9999999999998888887653

>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=99.52  E-value=1.3e-14  Score=114.77  Aligned_cols=82  Identities=20%  Similarity=0.217  Sum_probs=68.8

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH-
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI-  111 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~-  111 (130)
                      .|+++|.++++.+++|+|+++.+|||+|||++|++|++..+......             ..+.++||++|+++|+.|+ 
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~-------------~~~~~vlvl~P~~~L~~Q~~   73 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKA-------------SEPGKVIVLVNKVLLVEQLF   73 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHH-------------TCCCCBCCEESCSHHHHHHH
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc-------------CCCCeEEEEECCHHHHHHHH
Confidence            79999999999999999999999999999999999999987764210             0014699999999999999 


Q ss_pred             HHHHHHHHhcCCCceEE
Q psy3307         112 YDEAKKFAYRSQLRPCV  128 (130)
Q Consensus       112 ~~~~~~l~~~~~~~~~~  128 (130)
                      .+.++++... ++++..
T Consensus        74 ~~~l~~~~~~-~~~v~~   89 (699)
T 4gl2_A           74 RKEFQPFLKK-WYRVIG   89 (699)
T ss_dssp             HHTHHHHHTT-TSCEEE
T ss_pred             HHHHHHHcCc-CceEEE
Confidence            9999998875 345444

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.51  E-value=2.7e-14  Score=111.06  Aligned_cols=75  Identities=24%  Similarity=0.150  Sum_probs=66.0

Q ss_pred             CCcHHHHHHHhH----HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPV----IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~----~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .++|.|.+++..    +.+|+|++++||||+|||++|++|++.    ..                  ++++|++||++|+
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~----~~------------------~~v~i~~pt~~l~   60 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE----VK------------------PKVLFVVRTHNEF   60 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH----HC------------------SEEEEEESSGGGH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh----CC------------------CeEEEEcCCHHHH
Confidence            689999997764    458999999999999999999999997    11                  6899999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      .|+.+.++++.+..+++++++
T Consensus        61 ~q~~~~~~~l~~~~~~~~~~l   81 (551)
T 3crv_A           61 YPIYRDLTKIREKRNITFSFL   81 (551)
T ss_dssp             HHHHHHHTTCCCSSCCCEEEC
T ss_pred             HHHHHHHHHHhhhcCccEEEE
Confidence            999999999988888887765

>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=99.51  E-value=3.7e-15  Score=113.37  Aligned_cols=68  Identities=24%  Similarity=0.292  Sum_probs=60.3

Q ss_pred             CCCCCcHHHHHHHhHHhcCCcE-EEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          30 RYDKPTPVQKYAIPVIISGRDV-MACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~~g~~~-l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      |+..++|+|. +||.+++|+|+ ++++|||||||++|++|++.......                  ++++|++||++|+
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~------------------~~~lvl~Ptr~La   61 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRR------------------LRTLILAPTRVVA   61 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTT------------------CCEEEEESSHHHH
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcC------------------CcEEEECCCHHHH
Confidence            6778999985 79999999888 99999999999999999998876533                  5799999999999


Q ss_pred             HHHHHHHH
Q psy3307         109 TQIYDEAK  116 (130)
Q Consensus       109 ~q~~~~~~  116 (130)
                      .|+.+.+.
T Consensus        62 ~Q~~~~l~   69 (451)
T 2jlq_A           62 AEMEEALR   69 (451)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHhc
Confidence            99999885

>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=99.51  E-value=1.8e-13  Score=114.04  Aligned_cols=95  Identities=23%  Similarity=0.239  Sum_probs=78.2

Q ss_pred             CCCCCHHHHHHH-HHCCCCCCcHHHHHHHhHHhc----CC--cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307          15 DIQMTEIITNNI-ALARYDKPTPVQKYAIPVIIS----GR--DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus        15 ~l~l~~~i~~~l-~~~~~~~~t~~Q~~~i~~~~~----g~--~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      .++.+....+.+ ..++| .+||+|.++++.+++    |+  |+++++|||+|||++|+++++..+...           
T Consensus       585 ~~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g-----------  652 (1151)
T 2eyq_A          585 AFKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH-----------  652 (1151)
T ss_dssp             CCCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT-----------
T ss_pred             CCCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhC-----------
Confidence            455677777776 45687 579999999999986    66  999999999999999998888765321           


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                              .+++|++||++|+.|+++.+++.....++++..+
T Consensus       653 --------~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l  686 (1151)
T 2eyq_A          653 --------KQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMI  686 (1151)
T ss_dssp             --------CEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEE
T ss_pred             --------CeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEE
Confidence                    5799999999999999999998877777776654

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.50  E-value=1.2e-13  Score=113.74  Aligned_cols=75  Identities=24%  Similarity=0.259  Sum_probs=66.3

Q ss_pred             HHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          26 IALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        26 l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      ...++| .++++|.++++.+.+|+++++++|||||||++|.++++..+...                   .+++|++|++
T Consensus        80 ~~~~~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g-------------------~rvL~l~Ptk  139 (1010)
T 2xgj_A           80 ARTYPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNK-------------------QRVIYTSPIK  139 (1010)
T ss_dssp             SCCCSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTT-------------------CEEEEEESSH
T ss_pred             HHhCCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccC-------------------CeEEEECChH
Confidence            345677 59999999999999999999999999999999999998877432                   5799999999


Q ss_pred             HHHHHHHHHHHHHHh
Q psy3307         106 ELATQIYDEAKKFAY  120 (130)
Q Consensus       106 ~La~q~~~~~~~l~~  120 (130)
                      +|+.|+++.++++..
T Consensus       140 aLa~Q~~~~l~~~~~  154 (1010)
T 2xgj_A          140 ALSNQKYRELLAEFG  154 (1010)
T ss_dssp             HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999999999988765

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.48  E-value=6.4e-16  Score=122.68  Aligned_cols=76  Identities=18%  Similarity=0.222  Sum_probs=63.3

Q ss_pred             HHHHCCCC-----CCcHHHH-----HHHhHHh------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307          25 NIALARYD-----KPTPVQK-----YAIPVII------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus        25 ~l~~~~~~-----~~t~~Q~-----~~i~~~~------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      ++...||.     .||++|.     ++|+.++      +|+|+++++|||||||++|++|+++.+....           
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~-----------  270 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKR-----------  270 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTT-----------
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCC-----------
Confidence            44555666     8999999     9999888      8999999999999999999999999876533           


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                             ++++|++||++||.|+++.++.+
T Consensus       271 -------~~~lilaPTr~La~Q~~~~l~~~  293 (673)
T 2wv9_A          271 -------LRTAVLAPTRVVAAEMAEALRGL  293 (673)
T ss_dssp             -------CCEEEEESSHHHHHHHHHHTTTS
T ss_pred             -------CcEEEEccHHHHHHHHHHHHhcC
Confidence                   67999999999999999988754

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.47  E-value=9.8e-14  Score=114.18  Aligned_cols=73  Identities=21%  Similarity=0.190  Sum_probs=63.4

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .++| .++++|.++|+.+++|+|+++.+|||||||++|.+++.......                   .+++|++|+++|
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g-------------------~~vlvl~PtraL   94 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNM-------------------TKTIYTSPIKAL   94 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTT-------------------CEEEEEESCGGG
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcC-------------------CeEEEEeCCHHH
Confidence            3566 58999999999999999999999999999999999888765421                   579999999999


Q ss_pred             HHHHHHHHHHHHh
Q psy3307         108 ATQIYDEAKKFAY  120 (130)
Q Consensus       108 a~q~~~~~~~l~~  120 (130)
                      +.|+++.++++..
T Consensus        95 a~Q~~~~l~~~~~  107 (997)
T 4a4z_A           95 SNQKFRDFKETFD  107 (997)
T ss_dssp             HHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999987643

>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=99.46  E-value=4.4e-13  Score=100.46  Aligned_cols=76  Identities=20%  Similarity=0.186  Sum_probs=64.7

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|+|+|.++++.++++ ++++.+|||+|||++++++++..+....                  .++||++|+++|+.|+.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~------------------~~~liv~P~~~L~~q~~   69 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKYG------------------GKVLMLAPTKPLVLQHA   69 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHHSC------------------SCEEEECSSHHHHHHHH
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhcCC------------------CeEEEEECCHHHHHHHH
Confidence            6899999999999999 9999999999999999999988876322                  57999999999999999


Q ss_pred             HHHHHHHhcCCCceE
Q psy3307         113 DEAKKFAYRSQLRPC  127 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~  127 (130)
                      +.++++....+.++.
T Consensus        70 ~~~~~~~~~~~~~v~   84 (494)
T 1wp9_A           70 ESFRRLFNLPPEKIV   84 (494)
T ss_dssp             HHHHHHBCSCGGGEE
T ss_pred             HHHHHHhCcchhheE
Confidence            999988643333443

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.44  E-value=7.3e-13  Score=100.61  Aligned_cols=64  Identities=25%  Similarity=0.238  Sum_probs=58.0

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|+++|.++++.+++++++++++|||+|||++|+.++...    .                  .++||++|+++|+.|+.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~----~------------------~~~Lvl~P~~~L~~Q~~  150 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----S------------------TPTLIVVPTLALAEQWK  150 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH----C------------------SCEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc----C------------------CCEEEEECCHHHHHHHH
Confidence            6899999999999999999999999999999998888753    1                  46999999999999999


Q ss_pred             HHHHHH
Q psy3307         113 DEAKKF  118 (130)
Q Consensus       113 ~~~~~l  118 (130)
                      +.++++
T Consensus       151 ~~~~~~  156 (472)
T 2fwr_A          151 ERLGIF  156 (472)
T ss_dssp             HHGGGG
T ss_pred             HHHHhC
Confidence            998884

>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=99.42  E-value=8e-13  Score=92.38  Aligned_cols=72  Identities=18%  Similarity=0.112  Sum_probs=61.0

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++++|.++++.+.+|+++++.||||||||.++.++++........              ....+++++.|+++++.|+.
T Consensus        61 p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~--------------~~~~~~l~~~p~~~la~q~~  126 (235)
T 3llm_A           61 PVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR--------------AAECNIVVTQPRRISAVSVA  126 (235)
T ss_dssp             GGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC--------------GGGCEEEEEESSHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC--------------CCceEEEEeccchHHHHHHH
Confidence            5689999999999999999999999999999999999887765432              11258999999999999998


Q ss_pred             HHHHHH
Q psy3307         113 DEAKKF  118 (130)
Q Consensus       113 ~~~~~l  118 (130)
                      +.+...
T Consensus       127 ~~~~~~  132 (235)
T 3llm_A          127 ERVAFE  132 (235)
T ss_dssp             HHHHHT
T ss_pred             HHHHHH
Confidence            877543

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.38  E-value=8.7e-13  Score=102.38  Aligned_cols=67  Identities=21%  Similarity=0.216  Sum_probs=54.1

Q ss_pred             CCCCCCcHHHHHHHhH----HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          29 ARYDKPTPVQKYAIPV----IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~----~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      .|| .++|.|.+++..    +.+|++++++||||+|||++|++|++..    .                  .+++|++||
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~----~------------------~~~~~~~~t   60 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL----K------------------KKVLIFTRT   60 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH----T------------------CEEEEEESC
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC----C------------------CcEEEEcCC
Confidence            466 799999998754    4588999999999999999999998753    1                  579999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy3307         105 RELATQIYDEAKKF  118 (130)
Q Consensus       105 ~~La~q~~~~~~~l  118 (130)
                      ++|+.|+.+.++++
T Consensus        61 ~~l~~q~~~~~~~l   74 (540)
T 2vl7_A           61 HSQLDSIYKNAKLL   74 (540)
T ss_dssp             HHHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999888764

>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=99.36  E-value=5.9e-12  Score=88.36  Aligned_cols=64  Identities=25%  Similarity=0.238  Sum_probs=56.4

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++++|.+++..+++++++++++|||+|||++++.++...    .                  .+++|++|+++|+.|+.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~----~------------------~~~liv~P~~~L~~q~~  150 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----S------------------TPTLIVVPTLALAEQWK  150 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS----C------------------SCEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc----C------------------CCEEEEeCCHHHHHHHH
Confidence            7899999999999999999999999999999987776542    1                  46999999999999999


Q ss_pred             HHHHHH
Q psy3307         113 DEAKKF  118 (130)
Q Consensus       113 ~~~~~l  118 (130)
                      +.++++
T Consensus       151 ~~~~~~  156 (237)
T 2fz4_A          151 ERLGIF  156 (237)
T ss_dssp             HHHGGG
T ss_pred             HHHHhC
Confidence            998874

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.33  E-value=4.3e-12  Score=102.15  Aligned_cols=93  Identities=18%  Similarity=0.178  Sum_probs=73.4

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh-cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCC
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII-SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAG   85 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~-~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~   85 (130)
                      +.+...|+++++++.+.+.+++.+ ..|++.|..+|+.++ .|++++++||||||||+  ++|++........       
T Consensus        68 ~~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~-------  137 (773)
T 2xau_A           68 DGKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPH-------  137 (773)
T ss_dssp             HSSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGG-------
T ss_pred             cCCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhcccc-------
Confidence            345778999999999999999888 689999999998877 55789999999999999  5676633222110       


Q ss_pred             CCCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          86 RGYPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        86 ~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                             ..+.++++++|+++|+.|+.+.+.
T Consensus       138 -------~~g~~ilvl~P~r~La~q~~~~l~  161 (773)
T 2xau_A          138 -------LENTQVACTQPRRVAAMSVAQRVA  161 (773)
T ss_dssp             -------GGTCEEEEEESCHHHHHHHHHHHH
T ss_pred             -------CCCceEEecCchHHHHHHHHHHHH
Confidence                   012579999999999999987653

>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=99.32  E-value=6.9e-13  Score=100.64  Aligned_cols=57  Identities=30%  Similarity=0.404  Sum_probs=50.5

Q ss_pred             HHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      .+++|+|+++++|||||||++|++|+++.+....                  ++++|++||++||.|+++.++.+
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~------------------~~~lil~Ptr~La~Q~~~~l~~~   60 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRR------------------LRTLVLAPTRVVLSEMKEAFHGL   60 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT------------------CCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcC------------------CeEEEEcchHHHHHHHHHHHhcC
Confidence            4678999999999999999999999999877543                  67999999999999999988744

>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=99.30  E-value=1.1e-12  Score=100.03  Aligned_cols=57  Identities=25%  Similarity=0.310  Sum_probs=49.9

Q ss_pred             HhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          42 IPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        42 i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                      ...+.+|+++++++|||||||++|++|+++.+....                  +++||++|||+|+.|+.+.++
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~------------------~~~lvl~Ptr~La~Q~~~~l~   71 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQR------------------LRTAVLAPTRVVAAEMAEALR   71 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTT------------------CCEEEEECSHHHHHHHHHHTT
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCC------------------CcEEEECchHHHHHHHHHHhc
Confidence            345667899999999999999999999999887533                  579999999999999999886

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.23  E-value=7.7e-12  Score=94.61  Aligned_cols=52  Identities=23%  Similarity=0.398  Sum_probs=45.4

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                      +|+|+++++|||||||++|++|+++.+....                  .+++|++||++|+.|+++.++
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g------------------~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKR------------------LRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTT------------------CCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCC------------------CCEEEECcHHHHHHHHHHHhC
Confidence            4789999999999999999999997776543                  579999999999999998775

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.15  E-value=2.5e-11  Score=94.65  Aligned_cols=77  Identities=22%  Similarity=0.203  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHhHHhc----C-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVIIS----G-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~----g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .++++|.++++.++.    | ++++++++||||||+++ ++++..+.......         .....+.++||++|+++|
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~~~~~~~---------~~~~~~~~vlil~P~~~L  247 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLWSARWNR---------TGDYRKPRILFLADRNVL  247 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHHHTTCCS---------SCSSSCCCEEEEEC----
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHHhccccc---------ccccCCCeEEEEeCCHHH
Confidence            699999999998875    4 67899999999999996 44555554432100         001123689999999999


Q ss_pred             HHHHH-HHHHHHH
Q psy3307         108 ATQIY-DEAKKFA  119 (130)
Q Consensus       108 a~q~~-~~~~~l~  119 (130)
                      +.|+. +.++.++
T Consensus       248 ~~Q~~~~~~~~~~  260 (590)
T 3h1t_A          248 VDDPKDKTFTPFG  260 (590)
T ss_dssp             -------CCTTTC
T ss_pred             HHHHHHHHHHhcc
Confidence            99999 7777654

>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=99.08  E-value=1.7e-11  Score=97.13  Aligned_cols=63  Identities=24%  Similarity=0.067  Sum_probs=50.6

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYD  113 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~  113 (130)
                      +.+.|..+++.+.+++|++++||||||||++|.+++++.    .                  .+++|++|||+||.|+.+
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~----g------------------~~vLVl~PTReLA~Qia~  275 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ----G------------------YKVLVLNPSVAATLGFGA  275 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT----T------------------CCEEEEESCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC----C------------------CeEEEEcchHHHHHHHHH
Confidence            345555556666688999999999999999999988751    1                  479999999999999988


Q ss_pred             HHHHH
Q psy3307         114 EAKKF  118 (130)
Q Consensus       114 ~~~~l  118 (130)
                      .+.+.
T Consensus       276 ~l~~~  280 (666)
T 3o8b_A          276 YMSKA  280 (666)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=99.04  E-value=2e-10  Score=94.96  Aligned_cols=71  Identities=21%  Similarity=0.125  Sum_probs=57.8

Q ss_pred             CCcHHHHHHHhHHhc--------------CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceE
Q psy3307          33 KPTPVQKYAIPVIIS--------------GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLG   98 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~--------------g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (130)
                      .|+++|..+++.++.              +++.++.++||||||+++ ++++..+.....                ..++
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~----------------~~rv  333 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDF----------------IDKV  333 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTT----------------CCEE
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCC----------------CceE
Confidence            599999999998875              378999999999999997 666654432111                1589


Q ss_pred             EEEcCcHHHHHHHHHHHHHHHh
Q psy3307          99 LVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        99 lil~Pt~~La~q~~~~~~~l~~  120 (130)
                      |||+|+++|+.|+.+.++.+..
T Consensus       334 Lvlvpr~eL~~Q~~~~f~~f~~  355 (1038)
T 2w00_A          334 FFVVDRKDLDYQTMKEYQRFSP  355 (1038)
T ss_dssp             EEEECGGGCCHHHHHHHHTTST
T ss_pred             EEEeCcHHHHHHHHHHHHHhcc
Confidence            9999999999999999988764

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.04  E-value=5.5e-10  Score=88.84  Aligned_cols=53  Identities=19%  Similarity=0.344  Sum_probs=43.3

Q ss_pred             hHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHH
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF  118 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l  118 (130)
                      ...++|++++++||||||||+    +++..+....                   +++|++|||+||.|+++.+++.
T Consensus       150 ar~l~rk~vlv~apTGSGKT~----~al~~l~~~~-------------------~gl~l~PtR~LA~Qi~~~l~~~  202 (677)
T 3rc3_A          150 ARAMQRKIIFHSGPTNSGKTY----HAIQKYFSAK-------------------SGVYCGPLKLLAHEIFEKSNAA  202 (677)
T ss_dssp             HHTSCCEEEEEECCTTSSHHH----HHHHHHHHSS-------------------SEEEEESSHHHHHHHHHHHHHT
T ss_pred             HHhcCCCEEEEEcCCCCCHHH----HHHHHHHhcC-------------------CeEEEeCHHHHHHHHHHHHHhc
Confidence            455789999999999999998    4555555432                   3699999999999999998875

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.95  E-value=5.8e-09  Score=83.32  Aligned_cols=81  Identities=22%  Similarity=0.083  Sum_probs=70.6

Q ss_pred             HCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          28 LARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        28 ~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .+|. .|+++|....-.+..|+  ++...||+|||+++.+|++-.....                   ..+.|++|++.|
T Consensus        71 ~lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G-------------------~~vhVvT~ndyL  128 (822)
T 3jux_A           71 TLGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIG-------------------KGVHLVTVNDYL  128 (822)
T ss_dssp             HTSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTS-------------------SCEEEEESSHHH
T ss_pred             HhCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcC-------------------CceEEEeccHHH
Confidence            3676 78999999998888887  8899999999999999997655432                   359999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEeC
Q psy3307         108 ATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus       108 a~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                      |.|-..++..+.+.+|++|.+++
T Consensus       129 A~rdae~m~~l~~~Lglsvg~i~  151 (822)
T 3jux_A          129 ARRDALWMGPVYLFLGLRVGVIN  151 (822)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHhHHHHHHHHHHHhCCEEEEEc
Confidence            99999999999999999998863

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=98.81  E-value=1.1e-08  Score=77.98  Aligned_cols=71  Identities=21%  Similarity=0.280  Sum_probs=55.2

Q ss_pred             CCcHHHHHHHhHH----hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVI----ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~----~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .++|+|.+++..+    ..|++.++..+||+|||+..+ +++..+......                .++||++|+ +|+
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~~~~----------------~~~LIv~P~-~l~   98 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKENEL----------------TPSLVICPL-SVL   98 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTTCC----------------SSEEEEECS-TTH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH-HHHHHHHhcCCC----------------CCEEEEccH-HHH
Confidence            6899999999766    367899999999999999864 444444433211                469999995 699


Q ss_pred             HHHHHHHHHHHhc
Q psy3307         109 TQIYDEAKKFAYR  121 (130)
Q Consensus       109 ~q~~~~~~~l~~~  121 (130)
                      .|+.++++++...
T Consensus        99 ~qw~~e~~~~~~~  111 (500)
T 1z63_A           99 KNWEEELSKFAPH  111 (500)
T ss_dssp             HHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHCCC
Confidence            9999999988654

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.77  E-value=1.5e-08  Score=79.68  Aligned_cols=72  Identities=26%  Similarity=0.190  Sum_probs=58.3

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHH--HHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKT--AAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT--~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      ++.|..+++.++.++++++.|++|||||  ++++++.+.......                 +.++++++||..+|.++.
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~-----------------~~~vll~APTg~AA~~L~  213 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGE-----------------RCRIRLAAPTGKAAARLT  213 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSC-----------------CCCEEEEBSSHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcC-----------------CCeEEEEeCChhHHHHHH
Confidence            7899999999999999999999999999  566777766542111                 157999999999999999


Q ss_pred             HHHHHHHhcCC
Q psy3307         113 DEAKKFAYRSQ  123 (130)
Q Consensus       113 ~~~~~l~~~~~  123 (130)
                      +.+......++
T Consensus       214 e~~~~~~~~l~  224 (608)
T 1w36_D          214 ESLGKALRQLP  224 (608)
T ss_dssp             HHHTHHHHHSS
T ss_pred             HHHHHHHhcCC
Confidence            88877665544

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=98.69  E-value=5.4e-08  Score=80.13  Aligned_cols=68  Identities=19%  Similarity=0.147  Sum_probs=54.9

Q ss_pred             CCcHHHHHHHhHHhc--CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          33 KPTPVQKYAIPVIIS--GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~--g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      .++|+|.+++..++.  +.+++++++||+|||+.++..+...+.....                 .++|||||+ +|+.|
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~-----------------~rvLIVvP~-sLl~Q  214 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAA-----------------ERVLIIVPE-TLQHQ  214 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSC-----------------CCEEEECCT-TTHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCC-----------------CeEEEEeCH-HHHHH
Confidence            789999999988875  4589999999999999987766665543321                 369999999 99999


Q ss_pred             HHHHHHHH
Q psy3307         111 IYDEAKKF  118 (130)
Q Consensus       111 ~~~~~~~l  118 (130)
                      ..+.+.+.
T Consensus       215 w~~E~~~~  222 (968)
T 3dmq_A          215 WLVEMLRR  222 (968)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99888543

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.41  E-value=2.2e-06  Score=67.76  Aligned_cols=76  Identities=18%  Similarity=0.250  Sum_probs=55.2

Q ss_pred             CCcHHHHHHHhHHh---------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcC
Q psy3307          33 KPTPVQKYAIPVII---------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAP  103 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~---------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~P  103 (130)
                      .+.|+|.+++..+.         .+...++..++|+|||+..+..+...+......            .....++||++|
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~------------~p~~~~~LiV~P  122 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDC------------KPEIDKVIVVSP  122 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTS------------SCSCSCEEEEEC
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccc------------cCCCCcEEEEec
Confidence            68999999998763         456889999999999998755554443322110            001135899999


Q ss_pred             cHHHHHHHHHHHHHHHhc
Q psy3307         104 TRELATQIYDEAKKFAYR  121 (130)
Q Consensus       104 t~~La~q~~~~~~~l~~~  121 (130)
                      + +|+.|..++++++...
T Consensus       123 ~-sll~qW~~E~~~~~~~  139 (644)
T 1z3i_X          123 S-SLVRNWYNEVGKWLGG  139 (644)
T ss_dssp             H-HHHHHHHHHHHHHHGG
T ss_pred             H-HHHHHHHHHHHHHcCC
Confidence            7 8999999999988654

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.36  E-value=8.1e-07  Score=71.81  Aligned_cols=72  Identities=18%  Similarity=0.179  Sum_probs=55.3

Q ss_pred             CCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .++|+|.+++..+.    .+++.++..++|.|||+..+..+...+......                ..+||||| .+++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~----------------~~~LIV~P-~sll  298 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQN----------------GPHIIVVP-LSTM  298 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCC----------------SCEEEECC-TTTH
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCC----------------CCEEEEEC-chHH
Confidence            68899999997655    889999999999999998655544433332211                35899999 6889


Q ss_pred             HHHHHHHHHHHhc
Q psy3307         109 TQIYDEAKKFAYR  121 (130)
Q Consensus       109 ~q~~~~~~~l~~~  121 (130)
                      .|..++++++...
T Consensus       299 ~qW~~E~~~~~p~  311 (800)
T 3mwy_W          299 PAWLDTFEKWAPD  311 (800)
T ss_dssp             HHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHCCC
Confidence            9999999888644

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.19  E-value=7.7e-06  Score=64.66  Aligned_cols=67  Identities=21%  Similarity=0.254  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhHHhcCCc-EEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRD-VMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~-~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      .+++-|.+|+..++..++ .+++||+|||||.+.. .++..+....                  .++|+.+||..-++++
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~-~~I~~l~~~~------------------~~ILv~a~TN~AvD~i  249 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVV-EIILQAVKQG------------------LKVLCCAPSNIAVDNL  249 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHH-HHHHHHHHTT------------------CCEEEEESSHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHH-HHHHHHHhCC------------------CeEEEEcCchHHHHHH
Confidence            578999999999887764 6899999999998754 3444444332                  4699999999999998


Q ss_pred             HHHHHHH
Q psy3307         112 YDEAKKF  118 (130)
Q Consensus       112 ~~~~~~l  118 (130)
                      ...+...
T Consensus       250 ~erL~~~  256 (646)
T 4b3f_X          250 VERLALC  256 (646)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhc
Confidence            8777543

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.08  E-value=1.5e-05  Score=62.87  Aligned_cols=69  Identities=20%  Similarity=0.254  Sum_probs=54.0

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++.|..++..++.+.-.++.||+|||||... ..++..+....                 +.++++++||...+.++
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~-~~~i~~l~~~~-----------------~~~ilv~a~tn~A~~~l  240 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQG-----------------NGPVLVCAPSNIAVDQL  240 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHH-HHHHHHHHTSS-----------------SCCEEEEESSHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHH-HHHHHHHHHcC-----------------CCeEEEEeCcHHHHHHH
Confidence            4679999999999888888999999999999864 34444444321                 14699999999999999


Q ss_pred             HHHHHHH
Q psy3307         112 YDEAKKF  118 (130)
Q Consensus       112 ~~~~~~l  118 (130)
                      ...+.+.
T Consensus       241 ~~~l~~~  247 (624)
T 2gk6_A          241 TEKIHQT  247 (624)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHhc
Confidence            8877654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.07  E-value=2.1e-05  Score=63.76  Aligned_cols=69  Identities=16%  Similarity=0.191  Sum_probs=54.1

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++.|.+|+..++.+.-.++.||+|||||... ..++..+.....                 .++++++||...+.++
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i-~~~i~~l~~~~~-----------------~~ILv~a~tn~A~d~l  420 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTS-ATIVYHLSKIHK-----------------DRILVCAPSNVAVDHL  420 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHH-HHHHHHHHHHHC-----------------CCEEEEESSHHHHHHH
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHH-HHHHHHHHhCCC-----------------CeEEEEcCcHHHHHHH
Confidence            4578999999999988888899999999999764 334444433111                 4699999999999999


Q ss_pred             HHHHHHH
Q psy3307         112 YDEAKKF  118 (130)
Q Consensus       112 ~~~~~~l  118 (130)
                      .+.+.+.
T Consensus       421 ~~rL~~~  427 (802)
T 2xzl_A          421 AAKLRDL  427 (802)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhh
Confidence            9888764

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.92  E-value=7.6e-05  Score=58.51  Aligned_cols=71  Identities=18%  Similarity=0.143  Sum_probs=52.7

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++-|.+++..  .+..+++.|+.|||||.+.+-=+...+.....               ..-+++++++|+..+.++
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~---------------~~~~iL~ltft~~aa~e~   70 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENC---------------SPYSIMAVTFTNKAAAEM   70 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCC---------------CGGGEEEEESSHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCC---------------ChhhEEEEeccHHHHHHH
Confidence            4689999999963  35689999999999998754444333332211               114699999999999999


Q ss_pred             HHHHHHHH
Q psy3307         112 YDEAKKFA  119 (130)
Q Consensus       112 ~~~~~~l~  119 (130)
                      .+.+.++.
T Consensus        71 ~~rl~~~~   78 (647)
T 3lfu_A           71 RHRIGQLM   78 (647)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99988764

>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=97.92  E-value=4.4e-05  Score=61.88  Aligned_cols=69  Identities=20%  Similarity=0.254  Sum_probs=53.9

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++.|.+++..++.+.-.++.||+|||||... ..++..+....                 +.++++++||...+.++
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~~-----------------~~~ilv~a~tn~A~~~l  416 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQG-----------------NGPVLVCAPSNIAVDQL  416 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTTC-----------------SSCEEEEESSHHHHHHH
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHcC-----------------CCcEEEEcCcHHHHHHH
Confidence            3578999999999988888999999999999864 34444444321                 14699999999999999


Q ss_pred             HHHHHHH
Q psy3307         112 YDEAKKF  118 (130)
Q Consensus       112 ~~~~~~l  118 (130)
                      .+.+.+.
T Consensus       417 ~~~l~~~  423 (800)
T 2wjy_A          417 TEKIHQT  423 (800)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHHh
Confidence            8877653

>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=97.78  E-value=0.00012  Score=55.55  Aligned_cols=71  Identities=20%  Similarity=0.244  Sum_probs=51.4

Q ss_pred             HHCCCCCCcHHHHHHHhHHhcC-----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEE
Q psy3307          27 ALARYDKPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVL  101 (130)
Q Consensus        27 ~~~~~~~~t~~Q~~~i~~~~~g-----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil  101 (130)
                      .-..|..+++-|.+++..++..     ..+++.|+.|||||... ..++..+.....                 ..++++
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-----------------~~il~~   80 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-----------------TGIILA   80 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-----------------CCEEEE
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-----------------ceEEEe
Confidence            4467788999999999877532     39999999999999643 455555544331                 258999


Q ss_pred             cCcHHHHHHHHHHH
Q psy3307         102 APTRELATQIYDEA  115 (130)
Q Consensus       102 ~Pt~~La~q~~~~~  115 (130)
                      +||...+..+...+
T Consensus        81 a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           81 APTHAAKKILSKLS   94 (459)
T ss_dssp             ESSHHHHHHHHHHH
T ss_pred             cCcHHHHHHHHhhh
Confidence            99998888776543

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.76  E-value=0.00014  Score=56.98  Aligned_cols=63  Identities=17%  Similarity=0.131  Sum_probs=49.8

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+++.|..++..++.++.+++.|++|||||... ..++..+....                  .++++++||...+..+.
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~~g------------------~~Vl~~ApT~~Aa~~L~  249 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAESLG------------------LEVGLCAPTGKAARRLG  249 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHHTT------------------CCEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHhcC------------------CeEEEecCcHHHHHHhH
Confidence            579999999999999999999999999999753 34444443322                  46899999999998876


Q ss_pred             HH
Q psy3307         113 DE  114 (130)
Q Consensus       113 ~~  114 (130)
                      +.
T Consensus       250 e~  251 (574)
T 3e1s_A          250 EV  251 (574)
T ss_dssp             HH
T ss_pred             hh
Confidence            53

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=97.67  E-value=9.8e-05  Score=58.68  Aligned_cols=68  Identities=31%  Similarity=0.405  Sum_probs=51.7

Q ss_pred             CCCCCcHHHHHHHhHHh----cCC-cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCc
Q psy3307          30 RYDKPTPVQKYAIPVII----SGR-DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPT  104 (130)
Q Consensus        30 ~~~~~t~~Q~~~i~~~~----~g~-~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt  104 (130)
                      +| .|++.|..++..+.    .|. ..++.+.||||||+.+. .++...   .                  ..+|||+|+
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a-~~~~~~---~------------------~~~lvv~~~   62 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEAL---G------------------RPALVLAPN   62 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH---T------------------CCEEEEESS
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHH-HHHHHh---C------------------CCEEEEecC
Confidence            55 89999999987665    333 56788999999998653 233332   1                  238999999


Q ss_pred             HHHHHHHHHHHHHHHh
Q psy3307         105 RELATQIYDEAKKFAY  120 (130)
Q Consensus       105 ~~La~q~~~~~~~l~~  120 (130)
                      ..+|.|+++.++.+..
T Consensus        63 ~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A           63 KILAAQLAAEFRELFP   78 (664)
T ss_dssp             HHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHCC
Confidence            9999999999999853

>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=97.62  E-value=0.00025  Score=56.20  Aligned_cols=71  Identities=18%  Similarity=0.111  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+++-|.+++..  .+..+++.|+.|||||.+..-=+...+......               ..++++++.|+..+.++.
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~---------------~~~IL~lTfT~~Aa~em~   64 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQ---------------ARHIAAVTFTNKAAREMK   64 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCC---------------GGGEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCC---------------HHHeEEEeccHHHHHHHH
Confidence            478999998864  367899999999999987644444444432211               146999999999999999


Q ss_pred             HHHHHHHh
Q psy3307         113 DEAKKFAY  120 (130)
Q Consensus       113 ~~~~~l~~  120 (130)
                      +.+.+...
T Consensus        65 ~Rl~~~l~   72 (673)
T 1uaa_A           65 ERVGQTLG   72 (673)
T ss_dssp             HHHHHHSC
T ss_pred             HHHHHHcC
Confidence            99877643

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.48  E-value=0.00071  Score=54.19  Aligned_cols=71  Identities=20%  Similarity=0.142  Sum_probs=52.4

Q ss_pred             CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHH
Q psy3307          32 DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQI  111 (130)
Q Consensus        32 ~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~  111 (130)
                      ..+++-|.+++..  .+..+++.|+.|||||.+..-=+...+.....               ...++|+++.|+..|.++
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~---------------~p~~IL~vTFTnkAA~Em   72 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV---------------APWNILAITFTNKAAREM   72 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC---------------CGGGEEEEESSHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCC---------------CHHHeEEEeccHHHHHHH
Confidence            4689999998865  35689999999999998754444443432211               114699999999999999


Q ss_pred             HHHHHHHH
Q psy3307         112 YDEAKKFA  119 (130)
Q Consensus       112 ~~~~~~l~  119 (130)
                      .+.+.++.
T Consensus        73 ~~Rl~~~l   80 (724)
T 1pjr_A           73 RERVQSLL   80 (724)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            98887764

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=97.46  E-value=0.00035  Score=59.01  Aligned_cols=70  Identities=24%  Similarity=0.229  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+|+-|.++|..-  +.++++.|..|||||.+.+-=++..+.....             ....-++++++.|+..+..+.
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~-------------~~~~~~il~~Tft~~aa~e~~   74 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEEN-------------PIDVDRLLVVTFTNASAAEMK   74 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSS-------------CCCGGGEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCC-------------CCCccceEEEeccHHHHHHHH
Confidence            5799999998643  8899999999999998765445554443211             011146999999999999998


Q ss_pred             HHHHH
Q psy3307         113 DEAKK  117 (130)
Q Consensus       113 ~~~~~  117 (130)
                      +.+..
T Consensus        75 ~ri~~   79 (1232)
T 3u4q_A           75 HRIAE   79 (1232)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88765

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=97.21  E-value=0.003  Score=49.45  Aligned_cols=74  Identities=14%  Similarity=0.069  Sum_probs=57.9

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++|.|...+..+...+.+++..+.++|||.....-++-.+....                 +..++++.++++.|..+.
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~-----------------~~~i~~va~t~~qA~~~~  225 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-----------------DKAVGILAHKGSMSAEVL  225 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS-----------------SCEEEEEESSHHHHHHHH
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC-----------------CCeEEEEECCHHHHHHHH
Confidence            579999999987766788999999999999876544444443221                 146999999999999999


Q ss_pred             HHHHHHHhcCC
Q psy3307         113 DEAKKFAYRSQ  123 (130)
Q Consensus       113 ~~~~~l~~~~~  123 (130)
                      +.++.+.+..+
T Consensus       226 ~~i~~~i~~~p  236 (592)
T 3cpe_A          226 DRTKQAIELLP  236 (592)
T ss_dssp             HHHHHHHTTSC
T ss_pred             HHHHHHHHhCh
Confidence            98988877654

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.13  E-value=0.0041  Score=46.45  Aligned_cols=74  Identities=14%  Similarity=0.069  Sum_probs=57.0

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++|.|...+..+...+.+++..+-+.|||.....-++..+....                 +..+++++|+++.|..+.
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~-----------------g~~v~~vA~t~~qA~~vf  225 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-----------------DKAVGILAHKGSMSAEVL  225 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSS-----------------SCEEEEEESSHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCC-----------------CCeEEEEeCCHHHHHHHH
Confidence            689999999987666677899999999999876555544333211                 146999999999999999


Q ss_pred             HHHHHHHhcCC
Q psy3307         113 DEAKKFAYRSQ  123 (130)
Q Consensus       113 ~~~~~l~~~~~  123 (130)
                      +.++.+.+..+
T Consensus       226 ~~i~~mi~~~P  236 (385)
T 2o0j_A          226 DRTKQAIELLP  236 (385)
T ss_dssp             HHHHHHHHHSC
T ss_pred             HHHHHHHHhCh
Confidence            88888776543

>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=96.91  E-value=0.0025  Score=50.63  Aligned_cols=66  Identities=30%  Similarity=0.433  Sum_probs=49.6

Q ss_pred             CCcHHHHHHHhHHh----cCC-cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVII----SGR-DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~-~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|+..|..++..+.    .|. ...+.+.||||||+... .++...   .                  ..+|||+|+..+
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a-~~~~~~---~------------------~~~lvv~~~~~~   69 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVS-NLIKEV---N------------------KPTLVIAHNKTL   69 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH---C------------------CCEEEECSSHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHH-HHHHHh---C------------------CCEEEEECCHHH
Confidence            78999998887654    343 46788999999997542 233322   1                  138999999999


Q ss_pred             HHHHHHHHHHHHh
Q psy3307         108 ATQIYDEAKKFAY  120 (130)
Q Consensus       108 a~q~~~~~~~l~~  120 (130)
                      |.|+++.++.+..
T Consensus        70 A~~l~~el~~~~~   82 (661)
T 2d7d_A           70 AGQLYSEFKEFFP   82 (661)
T ss_dssp             HHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999999853

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.32  E-value=0.0018  Score=49.06  Aligned_cols=56  Identities=13%  Similarity=0.201  Sum_probs=38.4

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...|..+|+|.+--+...+.|.+.   .+..|.-++...+   .-.+.+++.||+|+|||+.
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHH
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHH
Confidence            456888999999888888888652   1223333322211   1247899999999999975

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=96.29  E-value=0.0013  Score=47.13  Aligned_cols=62  Identities=19%  Similarity=0.262  Sum_probs=40.6

Q ss_pred             CcccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHH-HHHh--HHhcCCcEEEEccCCchHHHHH
Q psy3307           1 MQECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQK-YAIP--VIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         1 ~~~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~-~~i~--~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +.|.+...|..+|+++.-.+...+.+.+.-.   .+... +.+.  .+..++.+++.||+|+|||...
T Consensus         2 ~~~~~~~~~~~~~~di~G~~~~~~~l~~~v~---~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A            2 LRETVVEVPQVTWEDIGGLEDVKRELQELVQ---YPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCCCEECCCCCGGGSCSCHHHHHHHHHHHH---HHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CccccccCCCCCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            3567778888999999888888777765310   11110 0011  1234678999999999999753

>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=96.25  E-value=0.016  Score=37.86  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+.+++.+|+|+|||..
T Consensus        37 ~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             GCCEEEECCSSSSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            578999999999999974

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.09  E-value=0.0029  Score=47.54  Aligned_cols=58  Identities=16%  Similarity=0.191  Sum_probs=37.9

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHHCC---CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIALAR---YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~~~---~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ....|..+|+|.+=-+...+.|++.=   +..|.-++...   +.-.+.+++.||+|+|||+..
T Consensus       139 ~~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          139 VEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             EECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHHH
T ss_pred             ccCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHHH
Confidence            44567899999997788877776531   11222222211   112478999999999999753

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=95.46  E-value=0.0055  Score=43.01  Aligned_cols=57  Identities=18%  Similarity=0.161  Sum_probs=36.5

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHCCCCCCcHHH-HHHHhH--HhcCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQ-KYAIPV--IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q-~~~i~~--~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ...+..+|+++.-.+...+.+.+.=.   .+.+ ...+..  +..++.+++.||+|+|||...
T Consensus         9 ~~~~~~~~~~i~G~~~~~~~l~~~~~---~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A            9 DERPNVRYEDIGGLEKQMQEIREVVE---LPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             ESSCCCCGGGSCSCHHHHHHHHHHTH---HHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             cCCCCCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            34566789999888888888765311   1111 111111  235678999999999999743

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.36  E-value=0.017  Score=36.61  Aligned_cols=20  Identities=15%  Similarity=0.094  Sum_probs=17.1

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...+.++++.+|+|+|||..
T Consensus        24 ~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHH
T ss_pred             hCCCCcEEEECCCCccHHHH
Confidence            34678999999999999974

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.32  E-value=0.0064  Score=46.47  Aligned_cols=56  Identities=13%  Similarity=0.150  Sum_probs=37.3

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCC---CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALAR---YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~---~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|..+|+|.+--+++.+.|++.=   +..|--++..-   +.--+.+++.||+|+|||+..
T Consensus       202 e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          202 EKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHHH
Confidence            467899999998888888887631   11221111111   123479999999999999743

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.19  E-value=0.0054  Score=46.54  Aligned_cols=58  Identities=19%  Similarity=0.194  Sum_probs=37.2

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ....|..+|+|.+--++..+.+.+.   .+..|.-++...   +.--+.+++.||+|+|||+..
T Consensus       172 ~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          172 SFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             EEESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             eccCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHHH
Confidence            4457888999999777777777652   111222111111   112379999999999999753

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.17  E-value=0.0095  Score=45.14  Aligned_cols=57  Identities=19%  Similarity=0.229  Sum_probs=37.4

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ...|..+|+|.+=-++..+.|++.   .+..|.-++..-+   --.+.+++.+|+|+|||+..
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi---~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI---KPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTC---CCCSEEEEESSTTTTHHHHH
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCCCceECCCCchHHHHH
Confidence            456788999999777777777652   2223333322211   12478999999999999753

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.11  E-value=0.023  Score=36.04  Aligned_cols=20  Identities=15%  Similarity=0.217  Sum_probs=17.1

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+.++++.+|+|+|||...
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            46789999999999999753

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=95.10  E-value=0.039  Score=39.83  Aligned_cols=54  Identities=17%  Similarity=0.238  Sum_probs=35.8

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh-----cCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII-----SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~-----~g~~~l~~aptGsGKT~~~   65 (130)
                      ...|..+|+|++-.+...+.+.+.=   -.|...   +.++     ..+.+++.||+|+|||...
T Consensus         4 ~~~~~~~~~di~G~~~~k~~l~~~v---~~p~~~---~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            4 IERPNVKWSDVAGLEGAKEALKEAV---ILPIKF---PHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHH---HHHHHC---GGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             ecCCCCCHHHhcCHHHHHHHHHHHH---HHHHhC---HHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            4567789999998888887776521   011111   2222     2368999999999999743

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=95.01  E-value=0.024  Score=43.06  Aligned_cols=45  Identities=29%  Similarity=0.397  Sum_probs=32.8

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      +-.++.|+.|+|||...    .+.+ ..                   .+.+|++||++++.++.+.+.+
T Consensus       162 ~v~~I~G~aGsGKTt~I----~~~~-~~-------------------~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEI----LSRV-NF-------------------EEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEEECTTSCHHHHH----HHHC-CT-------------------TTCEEEESCHHHHHHHHHHHTT
T ss_pred             cEEEEEcCCCCCHHHHH----HHHh-cc-------------------CCeEEEeCCHHHHHHHHHHhhh
Confidence            35688999999999854    1111 11                   1369999999999998887754

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.90  E-value=0.0078  Score=45.51  Aligned_cols=57  Identities=18%  Similarity=0.194  Sum_probs=36.0

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ...|..+|+|.+--+...+.+.+.   .+..|--++...   +.-.+.+++.||+|+|||+..
T Consensus       164 ~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          164 NEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            346778999999777777777552   111222121111   123468999999999999753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.77  E-value=0.039  Score=38.76  Aligned_cols=20  Identities=25%  Similarity=0.278  Sum_probs=17.2

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+.+.+|||||||..
T Consensus        22 i~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHH
T ss_pred             hCCCCEEEEECCCCccHHHH
Confidence            45678899999999999974

>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=94.55  E-value=0.009  Score=43.03  Aligned_cols=57  Identities=18%  Similarity=0.260  Sum_probs=38.1

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh-----cCCcEEEEccCCchHHHHH
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII-----SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~-----~g~~~l~~aptGsGKT~~~   65 (130)
                      +.....|..+|+++.-.+...+.+.+.=.   .|..   .+...     ..+.+++.||+|+|||...
T Consensus         7 ~~~~~~~~~~~~di~G~~~~~~~l~~~i~---~~~~---~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A            7 AILSEKPNVKWEDVAGLEGAKEALKEAVI---LPVK---FPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CSEEECCCCCGGGSCSCHHHHHHHHHHTH---HHHH---CGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             ceeecCCCCCHHHhcChHHHHHHHHHHHH---HHHh---CHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            34556777889999988888888865311   1211   12221     2357999999999999753

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=94.32  E-value=0.008  Score=42.56  Aligned_cols=55  Identities=22%  Similarity=0.355  Sum_probs=27.5

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHH-HHHhHH--hcCCcEEEEccCCchHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALARYDKPTPVQK-YAIPVI--ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~-~~i~~~--~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|..+|+|++-.+++.+.+.+.=   ..|+.. .++..+  .-.+.+++.+|+|+|||..
T Consensus         3 ~~~~~~~~di~g~~~~~~~l~~~i---~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtL   60 (274)
T 2x8a_A            3 TVPNVTWADIGALEDIREELTMAI---LAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLL   60 (274)
T ss_dssp             ---------CCHHHHHHHHHHHHH---THHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHH
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHH---HHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHH
Confidence            346788999998888888776521   122211 122211  1123499999999999974

>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=94.28  E-value=0.061  Score=36.95  Aligned_cols=53  Identities=13%  Similarity=0.098  Sum_probs=31.3

Q ss_pred             cCCCcCCCCCHHHHHHHHHCC--CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          10 KQGFDDIQMTEIITNNIALAR--YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~--~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+|+++.-.+...+.+.+.-  +..+..+...   .+...+.+++.||+|+|||...
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---g~~~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVDYLKSPERFLQL---GAKVPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHc---CCCCCceEEEECCCCCCHHHHH
Confidence            467888887777777775421  1111111110   1123468999999999999743

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=94.19  E-value=0.014  Score=41.18  Aligned_cols=58  Identities=14%  Similarity=0.181  Sum_probs=35.7

Q ss_pred             ccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHH-HHHhHH-hcCCcEEEEccCCchHHHHH
Q psy3307           5 LVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQK-YAIPVI-ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         5 ~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~-~~i~~~-~~g~~~l~~aptGsGKT~~~   65 (130)
                      ....+..+|+++.-.+...+.+.+.=.   .+... +.+..+ ..++.+++.||+|+|||...
T Consensus        12 ~~~~~~~~~~~i~G~~~~~~~l~~~i~---~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           12 VEGGAKVEWTDIAGQDVAKQALQEMVI---LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             BCCSSCCCGGGSCCCHHHHHHHHHHTH---HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHH
T ss_pred             ccCCCCCCHHHhCChHHHHHHHHHHHH---hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHH
Confidence            344567789998878888777765310   11110 000011 13579999999999999753

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.15  E-value=0.051  Score=34.81  Aligned_cols=18  Identities=22%  Similarity=0.455  Sum_probs=16.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+.+++.+|+|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            688999999999999964

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=94.09  E-value=0.064  Score=40.07  Aligned_cols=45  Identities=18%  Similarity=0.331  Sum_probs=30.3

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      ....++++.|+||||||... -.++..+....                  ..++|+=|..++..
T Consensus        51 ~~~~h~~i~G~tGsGKs~~~-~~li~~~~~~g------------------~~viv~Dpkge~~~   95 (437)
T 1e9r_A           51 AEPRHLLVNGATGTGKSVLL-RELAYTGLLRG------------------DRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHTT------------------CEEEEEEETTHHHH
T ss_pred             cCcceEEEECCCCCCHHHHH-HHHHHHHHHCC------------------CcEEEEeCCCchhH
Confidence            34579999999999999874 44555544432                  34666667666653

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=94.01  E-value=0.072  Score=36.73  Aligned_cols=54  Identities=22%  Similarity=0.235  Sum_probs=31.6

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCC--CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALAR--YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~--~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+|+++.-.+...+.+.+.-  +..+..++..   .....+.+++.+|+|+|||..
T Consensus         6 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~vll~G~~GtGKT~l   61 (257)
T 1lv7_A            6 QIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLL   61 (257)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHH
T ss_pred             CCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHc---CCCCCCeEEEECcCCCCHHHH
Confidence            35578999988888777765420  0011000000   011235799999999999974

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.00  E-value=0.098  Score=40.36  Aligned_cols=40  Identities=15%  Similarity=0.016  Sum_probs=26.2

Q ss_pred             HHHHHHCCCCCCcHHHHHHHh-HHhcCCcEEEEccCCchHHHH
Q psy3307          23 TNNIALARYDKPTPVQKYAIP-VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        23 ~~~l~~~~~~~~t~~Q~~~i~-~~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..+.+.|.  +++.+...+. .+..|..+++.||||||||..
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHH
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            344555553  3443333333 355888999999999999974

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=93.94  E-value=0.1  Score=37.05  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=31.9

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHH-HhHHhcCC-----cEEEEccCCchHHHHHH
Q psy3307          19 TEIITNNIALARYDKPTPVQKYA-IPVIISGR-----DVMACAQTGSGKTAAFL   66 (130)
Q Consensus        19 ~~~i~~~l~~~~~~~~t~~Q~~~-i~~~~~g~-----~~l~~aptGsGKT~~~~   66 (130)
                      ...+.+-|+..|+.   +++-.. +..+++|+     .+++.||+|+|||+.+.
T Consensus        72 ~n~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           72 SNRIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             GCHHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             hHHHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            34788888888873   555333 45556553     59999999999998653

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.74  E-value=0.25  Score=32.57  Aligned_cols=16  Identities=25%  Similarity=0.312  Sum_probs=14.7

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.+|+|+|||..
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999974

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=93.71  E-value=0.022  Score=39.30  Aligned_cols=56  Identities=16%  Similarity=0.093  Sum_probs=33.9

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh--cCCcEEEEccCCchHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII--SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~--~g~~~l~~aptGsGKT~~   64 (130)
                      ...|..+|+++.-.+.....+++.-..  .. ....+..+-  -.+.+++.+|+|+|||..
T Consensus         8 ~~~~~~~~~~i~g~~~~~~~l~~l~~~--~~-~~~~~~~~~~~~~~g~ll~G~~G~GKTtl   65 (254)
T 1ixz_A            8 TEAPKVTFKDVAGAEEAKEELKEIVEF--LK-NPSRFHEMGARIPKGVLLVGPPGVGKTHL   65 (254)
T ss_dssp             CCCCSCCGGGCCSCHHHHHHHHHHHHH--HH-CHHHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             cCCCCCCHHHhCCcHHHHHHHHHHHHH--HH-CHHHHHHcCCCCCCeEEEECCCCCCHHHH
Confidence            445678899998877777776553211  00 011222211  123499999999999964

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=93.45  E-value=0.15  Score=37.07  Aligned_cols=19  Identities=32%  Similarity=0.424  Sum_probs=16.1

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .+..+++.+|+|+|||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4578999999999999753

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=93.40  E-value=0.14  Score=37.61  Aligned_cols=18  Identities=33%  Similarity=0.451  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+++.+|||||||..
T Consensus       122 ~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             SSEEEEEECSTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            455889999999999974

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.39  E-value=0.088  Score=35.70  Aligned_cols=31  Identities=32%  Similarity=0.209  Sum_probs=25.8

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +--|..++..+..|.-+.+.+|+|+|||...
T Consensus         9 ~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            9 TLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             SHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             CHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            4456778888889999999999999999753

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=93.33  E-value=0.046  Score=44.49  Aligned_cols=60  Identities=22%  Similarity=0.356  Sum_probs=38.5

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCC-C--CCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALAR-Y--DKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~-~--~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..+..|..+|++.+.-++..+.|.+.= +  ..|..++..   -+...+.+++.+|+|+|||+..
T Consensus       466 ~~~~~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~---g~~~~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          466 ETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF---GMTPSKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CCCCBCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSS---CCCCCSCCEEESSTTSSHHHHH
T ss_pred             cccccCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEecCCCCCchHHH
Confidence            3445667789999998888888887642 1  111111000   0112368999999999999743

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=93.22  E-value=0.17  Score=38.92  Aligned_cols=30  Identities=17%  Similarity=0.277  Sum_probs=23.2

Q ss_pred             cHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307          35 TPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        35 t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...=..+.-.+..|.++++.||+|+|||..
T Consensus        28 ~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           28 SHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            334345555667889999999999999974

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=93.17  E-value=0.14  Score=35.01  Aligned_cols=51  Identities=12%  Similarity=0.186  Sum_probs=31.9

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcC----CcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISG----RDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g----~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ..|.+-|+-.++ .+... ...+..++++    +.+++.+|+|+|||... ..+...+
T Consensus        28 ~~I~~~l~yq~~-~~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~l   82 (212)
T 1tue_A           28 RPIVQFLRYQQI-EFITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHFI   82 (212)
T ss_dssp             HHHHHHHHHTTC-CHHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHcCc-CHHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHHh
Confidence            456666665554 34444 4445555555    35999999999999754 4555544

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=93.17  E-value=0.066  Score=38.35  Aligned_cols=25  Identities=20%  Similarity=0.211  Sum_probs=19.9

Q ss_pred             HHHhHHhcCCcEEEEccCCchHHHH
Q psy3307          40 YAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        40 ~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+...+..|.++++.||+|+|||..
T Consensus        38 ~l~~~l~~~~~vll~G~pGtGKT~l   62 (331)
T 2r44_A           38 RLLIGICTGGHILLEGVPGLAKTLS   62 (331)
T ss_dssp             HHHHHHHHTCCEEEESCCCHHHHHH
T ss_pred             HHHHHHHcCCeEEEECCCCCcHHHH
Confidence            3334556789999999999999964

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=93.14  E-value=0.079  Score=38.47  Aligned_cols=28  Identities=7%  Similarity=0.088  Sum_probs=20.2

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .+.++++.||+|+|||... -.++..+..
T Consensus        44 ~~~~lli~GpPGTGKT~~v-~~v~~~L~~   71 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLV-NDVMDELIT   71 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHH-HHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH-HHHHHHHHH
Confidence            4468999999999999764 444455543

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=93.12  E-value=0.036  Score=38.89  Aligned_cols=55  Identities=16%  Similarity=0.088  Sum_probs=33.5

Q ss_pred             ccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh--cCCcEEEEccCCchHHHH
Q psy3307           7 SLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII--SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         7 ~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~--~g~~~l~~aptGsGKT~~   64 (130)
                      ..+..+|+++.-.+...+.+++.-...-.   ...+..+-  -.+.+++.+|+|+|||..
T Consensus        33 ~~~~~~~~~i~g~~~~~~~l~~l~~~~~~---~~~l~~~~~~~~~gvll~Gp~GtGKTtl   89 (278)
T 1iy2_A           33 EAPKVTFKDVAGAEEAKEELKEIVEFLKN---PSRFHEMGARIPKGVLLVGPPGVGKTHL   89 (278)
T ss_dssp             CCCCCCGGGSSSCHHHHHHHHHHHHHHHC---HHHHHHTTCCCCCEEEEECCTTSSHHHH
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHHHHC---HHHHHHcCCCCCCeEEEECCCcChHHHH
Confidence            34678899998888887777653211000   11222111  123499999999999974

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=93.01  E-value=0.051  Score=34.97  Aligned_cols=17  Identities=29%  Similarity=0.407  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.||+|+|||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46899999999999975

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=92.98  E-value=0.096  Score=37.89  Aligned_cols=18  Identities=50%  Similarity=0.739  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++.+++.||+|+|||...
T Consensus        70 ~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             TCEEEEEESTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            358999999999999753

>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=92.87  E-value=0.29  Score=37.47  Aligned_cols=52  Identities=17%  Similarity=0.256  Sum_probs=38.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                      .|....+.+-+||||++..  +.+..  ...                  ...|||+|+...|.|+++.++.+..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~--a~l~~--~~~------------------~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLV--AEIAE--RHA------------------GPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHH--HHHHH--HSS------------------SCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHH--HHHHH--HhC------------------CCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            4667889999999998742  32221  111                  2389999999999999999998753

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=92.81  E-value=0.056  Score=36.35  Aligned_cols=19  Identities=16%  Similarity=0.198  Sum_probs=16.3

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .++.+++.||+|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4689999999999999743

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.79  E-value=0.11  Score=35.17  Aligned_cols=19  Identities=26%  Similarity=0.279  Sum_probs=16.4

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.+|+|+|||...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFS   40 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5678899999999999754

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=92.74  E-value=0.16  Score=36.99  Aligned_cols=19  Identities=21%  Similarity=0.336  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+.+++.+|+|+|||...
T Consensus       116 ~~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          116 PPKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CCSEEEEESSTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999753

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=92.66  E-value=0.33  Score=34.76  Aligned_cols=18  Identities=17%  Similarity=0.320  Sum_probs=15.8

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++++++.||+|+|||...
T Consensus       152 ~~~lll~G~~GtGKT~La  169 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLL  169 (308)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            689999999999999743

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=92.50  E-value=0.42  Score=33.41  Aligned_cols=18  Identities=28%  Similarity=0.464  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +..+++.||+|+|||...
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            578999999999999743

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=92.47  E-value=0.063  Score=35.19  Aligned_cols=19  Identities=11%  Similarity=0.211  Sum_probs=16.1

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      +.|+-+++.+|+|+|||..
T Consensus         3 ~~g~~i~i~GpsGsGKSTL   21 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHI   21 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3577889999999999974

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=92.38  E-value=0.13  Score=34.33  Aligned_cols=26  Identities=27%  Similarity=0.327  Sum_probs=17.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|+-+.+.||+|+|||..  +-+|...+
T Consensus         3 ~g~~i~lvGpsGaGKSTL--l~~L~~~~   28 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTL--LKKLFQEH   28 (198)
T ss_dssp             --CCEEEECCTTSSHHHH--HHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHH--HHHHHhhC
Confidence            477899999999999974  34444443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.34  E-value=0.084  Score=38.78  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=18.0

Q ss_pred             HHhcCCcEEEEccCCchHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+..|..+++.+|||||||..
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHH
Confidence            345889999999999999973

>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=92.32  E-value=0.046  Score=41.24  Aligned_cols=57  Identities=14%  Similarity=0.135  Sum_probs=34.1

Q ss_pred             cccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHH-HHh-HHhcCCcEEEEccCCchHHHHH
Q psy3307           6 VSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKY-AIP-VIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         6 ~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~-~i~-~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ...+..+|+++.-.+...+.+.+.-.   .|.... .+. .....+.+++.||+|+|||...
T Consensus       126 ~~~~~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          126 IERPNVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CCCCCCCGGGSCSCHHHHHHHHHHHT---HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHH
T ss_pred             ccCCCCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHhhccCCCCceEEEECCCCCCHHHHH
Confidence            34566788888877777777754211   111110 000 1123478999999999999753

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=92.31  E-value=0.055  Score=34.80  Aligned_cols=17  Identities=29%  Similarity=0.401  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      ...+++.+|+|+|||..
T Consensus        43 ~~~vll~G~~G~GKT~l   59 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAI   59 (187)
T ss_dssp             SCEEEEESCGGGCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46899999999999964

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=92.28  E-value=0.13  Score=35.50  Aligned_cols=19  Identities=21%  Similarity=0.344  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..+..+++.|++|+|||..
T Consensus        27 ~~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHH
T ss_pred             CCCCCEEEECCCCCcHHHH
Confidence            3568999999999999974

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=92.22  E-value=0.07  Score=37.67  Aligned_cols=17  Identities=24%  Similarity=0.309  Sum_probs=14.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            47999999999999754

>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=92.10  E-value=0.085  Score=36.51  Aligned_cols=55  Identities=16%  Similarity=0.109  Sum_probs=30.3

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHH--hcCCcEEEEccCCchHHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVI--ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~--~~g~~~l~~aptGsGKT~~~   65 (130)
                      .+...|+++.-.+...+.+.+.--.-..+   ..+..+  ...+.+++.||+|+|||...
T Consensus         5 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~---~~~~~~~~~~~~~vll~G~~GtGKT~la   61 (268)
T 2r62_A            5 KPNVRFKDMAGNEEAKEEVVEIVDFLKYP---ERYANLGAKIPKGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             CCCCCSTTSSSCTTTHHHHHHHHHHHHCH---HHHHHHSCCCCSCCCCBCSSCSSHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHHHCh---HHHHHCCCCCCceEEEECCCCCcHHHHH
Confidence            44567888876666655554320000000   111111  12457999999999999753

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=91.79  E-value=0.099  Score=37.96  Aligned_cols=19  Identities=53%  Similarity=0.948  Sum_probs=17.2

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|..+.+.+|||||||.
T Consensus       168 i~~g~~v~i~G~~GsGKTT  186 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTT  186 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHH
T ss_pred             ccCCCEEEEECCCCCCHHH
Confidence            4588999999999999997

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=91.74  E-value=0.053  Score=40.00  Aligned_cols=18  Identities=28%  Similarity=0.444  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      .+.+++.||+|+|||...
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            579999999999999753

>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=91.63  E-value=0.43  Score=33.95  Aligned_cols=17  Identities=24%  Similarity=0.356  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.||+|+|||..
T Consensus        37 ~~~lll~G~~GtGKT~l   53 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHL   53 (324)
T ss_dssp             CSSEEEECSSSSSHHHH
T ss_pred             CCeEEEECCCCCcHHHH
Confidence            46899999999999974

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=91.63  E-value=0.076  Score=34.57  Aligned_cols=20  Identities=25%  Similarity=0.177  Sum_probs=16.6

Q ss_pred             cCCcEEEEccCCchHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~   66 (130)
                      .|.-+.+.+|+|||||..+-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            56778999999999997653

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=91.63  E-value=0.33  Score=32.06  Aligned_cols=26  Identities=19%  Similarity=0.259  Sum_probs=18.3

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      |+-.++.+|.|+|||... +-++.++.
T Consensus         3 g~i~vi~G~~gsGKTT~l-l~~~~~~~   28 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTEL-LSFVEIYK   28 (184)
T ss_dssp             CCEEEEEESTTSSHHHHH-HHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            566789999999999865 33444443

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.51  E-value=0.2  Score=33.86  Aligned_cols=19  Identities=37%  Similarity=0.518  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.|++|+|||...
T Consensus        29 ~G~l~~i~G~pG~GKT~l~   47 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFA   47 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH
Confidence            3578899999999999644

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=91.50  E-value=0.1  Score=35.03  Aligned_cols=18  Identities=22%  Similarity=0.383  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+-+++.||+|+|||..
T Consensus         7 ~g~~i~l~GpsGsGKsTl   24 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTV   24 (208)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECcCCCCHHHH
Confidence            577889999999999974

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=91.41  E-value=0.11  Score=34.57  Aligned_cols=20  Identities=20%  Similarity=0.134  Sum_probs=16.5

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..++.+++.|++|||||...
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHH
Confidence            36789999999999999753

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=91.35  E-value=0.088  Score=34.20  Aligned_cols=20  Identities=20%  Similarity=0.238  Sum_probs=16.8

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..++.+++.+++|||||...
T Consensus         9 ~~~~~i~i~G~~GsGKst~~   28 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLG   28 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHH
Confidence            45678999999999999753

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=91.33  E-value=0.14  Score=37.77  Aligned_cols=20  Identities=25%  Similarity=0.278  Sum_probs=16.8

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|..+++.+|||||||..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTl  152 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTT  152 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHH
Confidence            34677899999999999974

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=91.23  E-value=0.086  Score=34.46  Aligned_cols=20  Identities=25%  Similarity=0.463  Sum_probs=16.8

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+++.+|+|||||..
T Consensus         6 i~~g~~i~l~G~~GsGKSTl   25 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTI   25 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHH
Confidence            44677899999999999974

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=91.17  E-value=0.57  Score=39.61  Aligned_cols=64  Identities=19%  Similarity=0.190  Sum_probs=41.7

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      ++|.. ++.|.-|||||.+..-=++..+.......       .........++|+|+=|+.-|.++...+.+
T Consensus        15 l~g~~-lV~AsAGSGKT~~L~~r~lrLll~~g~~~-------~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~   78 (1180)
T 1w36_B           15 LQGER-LIEASAGTGKTFTIAALYLRLLLGLGGSA-------AFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (1180)
T ss_dssp             CSSCE-EEECCTTSCHHHHHHHHHHHHHTTCSSSS-------SCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCCE-EEEECCCCCHHHHHHHHHHHHHhcCCccc-------ccCCCCCHHHEEEEeccHHHHHHHHHHHHH
Confidence            35555 89999999999987666666665322000       000111225799999999888888777754

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=91.15  E-value=0.12  Score=34.17  Aligned_cols=18  Identities=28%  Similarity=0.416  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+.+.||+|||||..
T Consensus         6 ~g~ii~l~Gp~GsGKSTl   23 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSL   23 (205)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECcCCCCHHHH
Confidence            577889999999999974

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=91.13  E-value=0.31  Score=32.46  Aligned_cols=20  Identities=25%  Similarity=0.235  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|.-+++.+|+|+|||...
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           21 PQGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEEcCCCCCHHHHH
Confidence            35678899999999999643

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=91.10  E-value=0.11  Score=34.35  Aligned_cols=20  Identities=20%  Similarity=0.258  Sum_probs=16.3

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+.+.||+|||||..
T Consensus         3 i~~g~~i~l~G~~GsGKSTl   22 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTV   22 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHH
Confidence            34678899999999999974

>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=90.70  E-value=0.32  Score=33.39  Aligned_cols=27  Identities=22%  Similarity=0.208  Sum_probs=19.3

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.+++|+|||... +-.+.++.
T Consensus        11 ~G~i~litG~mGsGKTT~l-l~~~~r~~   37 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAEL-IRRLHRLE   37 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHH-HHHHHHHH
T ss_pred             CcEEEEEECCCCCcHHHHH-HHHHHHHH
Confidence            4667788999999999765 44444444

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=90.65  E-value=0.16  Score=33.42  Aligned_cols=16  Identities=31%  Similarity=0.536  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ..+++.||+|+|||..
T Consensus        39 ~~~ll~G~~G~GKT~l   54 (226)
T 2chg_A           39 PHLLFSGPPGTGKTAT   54 (226)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999964

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=90.64  E-value=0.13  Score=33.16  Aligned_cols=18  Identities=17%  Similarity=0.313  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++-+++.|++|||||...
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            466899999999999753

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=90.63  E-value=0.22  Score=37.47  Aligned_cols=27  Identities=22%  Similarity=0.334  Sum_probs=18.6

Q ss_pred             HHHHHhHHh--cCCcEEEEccCCchHHHH
Q psy3307          38 QKYAIPVII--SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        38 Q~~~i~~~~--~g~~~l~~aptGsGKT~~   64 (130)
                      +..++..++  .|.-+++.+|||||||..
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            334444333  455689999999999974

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=90.58  E-value=0.16  Score=32.61  Aligned_cols=17  Identities=24%  Similarity=0.546  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+.+.+++|||||..
T Consensus         4 ~~~i~l~G~~GsGKSTl   20 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTI   20 (173)
T ss_dssp             CCCEEEECCTTSCHHHH
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            56799999999999974

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=90.55  E-value=0.16  Score=34.43  Aligned_cols=20  Identities=20%  Similarity=0.388  Sum_probs=16.3

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|+-+.+.+|+|+|||..
T Consensus        20 i~~G~~~~lvGpsGsGKSTL   39 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTL   39 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            45788999999999999974

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=90.55  E-value=0.14  Score=34.16  Aligned_cols=21  Identities=24%  Similarity=0.338  Sum_probs=16.5

Q ss_pred             HHhcCCcEEEEccCCchHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+..|+-+.+.+|+|+|||..
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTL   36 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTV   36 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHH
Confidence            567889999999999999974

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=90.45  E-value=0.12  Score=36.65  Aligned_cols=16  Identities=19%  Similarity=0.121  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.||+|+|||..
T Consensus        37 ~~lLl~GppGtGKT~l   52 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQ   52 (293)
T ss_dssp             SEEEEEECTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            5789999999999974

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=90.43  E-value=0.14  Score=33.29  Aligned_cols=18  Identities=22%  Similarity=0.233  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++.+++.|++|||||...
T Consensus         5 ~~~i~l~G~~GsGKst~a   22 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVG   22 (185)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            567999999999999743

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=90.40  E-value=0.13  Score=32.69  Aligned_cols=15  Identities=27%  Similarity=0.426  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.|++|||||..
T Consensus         3 ~I~l~G~~GsGKsT~   17 (179)
T 3lw7_A            3 VILITGMPGSGKSEF   17 (179)
T ss_dssp             EEEEECCTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=90.40  E-value=0.12  Score=35.87  Aligned_cols=17  Identities=35%  Similarity=0.255  Sum_probs=14.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.||+|+|||...
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            58999999999999753

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=90.40  E-value=0.37  Score=32.19  Aligned_cols=28  Identities=14%  Similarity=0.132  Sum_probs=19.5

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .|+=.++.++.|||||... +-++.++..
T Consensus         7 ~g~i~v~~G~mgsGKTT~l-l~~a~r~~~   34 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEEL-IRRIRRAKI   34 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHH-HHHHHHHHH
T ss_pred             CCEEEEEECCCCCcHHHHH-HHHHHHHHH
Confidence            3566788999999999765 444555443

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=90.39  E-value=0.17  Score=33.73  Aligned_cols=20  Identities=20%  Similarity=0.433  Sum_probs=17.0

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...|+-+++.||+|||||..
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl   28 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTL   28 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHH
T ss_pred             cccCCEEEEECCCCCCHHHH
Confidence            44678999999999999974

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=90.34  E-value=0.23  Score=35.46  Aligned_cols=18  Identities=28%  Similarity=0.471  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+.++++.+++|+|||..
T Consensus        24 ~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             TTSCEEEESCTTSCHHHH
T ss_pred             CCCcEEEECCCCchHHHH
Confidence            567999999999999974

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=90.16  E-value=0.3  Score=32.32  Aligned_cols=15  Identities=27%  Similarity=0.395  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.||+|+|||..
T Consensus        47 ~~ll~G~~G~GKT~l   61 (250)
T 1njg_A           47 AYLFSGTRGVGKTSI   61 (250)
T ss_dssp             EEEEECSTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            689999999999964

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=90.08  E-value=0.16  Score=33.64  Aligned_cols=18  Identities=39%  Similarity=0.556  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+.+.+++|||||..
T Consensus        28 ~g~~i~l~G~~GsGKSTl   45 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTI   45 (200)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            578899999999999974

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.08  E-value=0.42  Score=43.76  Aligned_cols=47  Identities=13%  Similarity=0.229  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHH-HHHH---hHHhcCCcEEEEccCCchHHHHH
Q psy3307          18 MTEIITNNIALARYDKPTPVQ-KYAI---PVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q-~~~i---~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +.+.+.+.+.+.++ .+++.+ ..++   ..+.....+++.||||||||.++
T Consensus       890 l~~~i~~~~~~~~l-~~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~  940 (2695)
T 4akg_A          890 IVQCLKDAGQRSGF-SMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATW  940 (2695)
T ss_dssp             HHHHHHHHHHHHTC-CCCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHHHHcCC-cccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHH
Confidence            44556677777887 456654 2222   23345678999999999999976

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=90.02  E-value=0.15  Score=38.50  Aligned_cols=19  Identities=42%  Similarity=0.655  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .++.+++.+|+|+|||...
T Consensus        62 ~~~~iLl~GppGtGKT~la   80 (456)
T 2c9o_A           62 AGRAVLLAGPPGTGKTALA   80 (456)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCcCCHHHHH
Confidence            3468999999999999754

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=90.01  E-value=0.17  Score=34.58  Aligned_cols=21  Identities=24%  Similarity=0.422  Sum_probs=16.4

Q ss_pred             HHhcCCcEEEEccCCchHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~   64 (130)
                      +.-.|+-+.+.||+|+|||..
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTL   32 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSL   32 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHH
T ss_pred             cCCCCcEEEEECCCCCCHHHH
Confidence            355788999999999999974

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=89.95  E-value=0.39  Score=44.58  Aligned_cols=47  Identities=15%  Similarity=0.204  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHH-HHHh---HHhcCCcEEEEccCCchHHHHH
Q psy3307          18 MTEIITNNIALARYDKPTPVQK-YAIP---VIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~-~~i~---~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      |.+.+.+.+.+.|+ .+++.+. +++.   .+.-...+++.||+|||||.++
T Consensus       873 l~~ai~~~~~~~~L-~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~  923 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHL-VTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSW  923 (3245)
T ss_dssp             HHHHHHHHHHHTTC-CCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHH
T ss_pred             HHHHHHHHHHHcCC-ccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHH
Confidence            44667777788888 4666443 3332   2234467999999999999976

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=89.87  E-value=0.18  Score=33.65  Aligned_cols=16  Identities=25%  Similarity=0.596  Sum_probs=14.0

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      |-+++.||+|+|||..
T Consensus         2 RpIVi~GPSG~GK~Tl   17 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            5689999999999973

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=89.85  E-value=0.16  Score=36.67  Aligned_cols=18  Identities=33%  Similarity=0.482  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.||+|+|||..
T Consensus        43 ~~~~vll~G~~G~GKT~l   60 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAV   60 (387)
T ss_dssp             CCCCEEECBCTTSSHHHH
T ss_pred             CCCcEEEECCCCCCHHHH
Confidence            457899999999999975

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=89.79  E-value=0.48  Score=34.81  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=16.3

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .+.++++.++||+|||...
T Consensus        34 ~~~~~~i~G~~G~GKs~~~   52 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTA   52 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHH
Confidence            4679999999999999754

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=89.67  E-value=0.19  Score=36.72  Aligned_cols=52  Identities=17%  Similarity=0.271  Sum_probs=29.3

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh-----cCCcEEEEccCCchHHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII-----SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~-----~g~~~l~~aptGsGKT~~~   65 (130)
                      .+..+|+++.-.+...+.+.+.=.   .+..   .+.++     ..+.+++.||+|+|||...
T Consensus        45 ~~~~~~~di~G~~~~~~~l~~~v~---~~~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           45 KPNVKWEDVAGLEGAKEALKEAVI---LPVK---FPHLFKGNRKPTSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             --CCCGGGSCCGGGHHHHHHHHTH---HHHH---CGGGGCSSCCCCCCEEEECSTTSCHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHH---HHHh---CHHHHhcCCCCCceEEEECCCCCcHHHHH
Confidence            455677777665666666544210   1110   11222     2357999999999999753

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=89.65  E-value=0.18  Score=33.07  Aligned_cols=18  Identities=28%  Similarity=0.602  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.+++|||||..
T Consensus         9 ~~~~I~l~G~~GsGKSTv   26 (184)
T 1y63_A            9 KGINILITGTPGTGKTSM   26 (184)
T ss_dssp             SSCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999975

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=89.57  E-value=0.25  Score=32.98  Aligned_cols=18  Identities=28%  Similarity=0.342  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+.+.+|+|||||..
T Consensus        21 ~g~~v~I~G~sGsGKSTl   38 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTL   38 (208)
T ss_dssp             SCEEEEEECCTTSCTHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            466788999999999973

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=89.53  E-value=0.18  Score=32.38  Aligned_cols=16  Identities=25%  Similarity=0.306  Sum_probs=13.4

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.|++|||||...
T Consensus         4 ~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEecCCCCCHHHHH
Confidence            4789999999999743

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=89.49  E-value=0.15  Score=32.83  Aligned_cols=19  Identities=26%  Similarity=0.267  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|..+++.+++|||||...
T Consensus         7 ~g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3567899999999999743

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=89.42  E-value=0.19  Score=35.92  Aligned_cols=17  Identities=24%  Similarity=0.366  Sum_probs=14.9

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.||+|+|||...
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            58999999999999753

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=89.32  E-value=0.21  Score=33.72  Aligned_cols=19  Identities=11%  Similarity=0.316  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|+-+++.||+|+|||..
T Consensus        17 ~~g~~ivl~GPSGaGKsTL   35 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHI   35 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHH
T ss_pred             CCCCEEEEECcCCCCHHHH
Confidence            4788999999999999973

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=89.31  E-value=0.21  Score=36.44  Aligned_cols=18  Identities=33%  Similarity=0.449  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ..++++.||+|+|||...
T Consensus        72 ~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            468999999999999753

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=89.31  E-value=0.18  Score=34.99  Aligned_cols=16  Identities=31%  Similarity=0.158  Sum_probs=13.2

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+|+|||||...
T Consensus         3 li~I~G~~GSGKSTla   18 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMA   18 (253)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            3688999999999743

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=89.16  E-value=0.2  Score=32.51  Aligned_cols=17  Identities=24%  Similarity=0.401  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      |.-+++.+++|||||..
T Consensus         3 ~~~I~i~G~~GsGKsT~   19 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTS   19 (192)
T ss_dssp             CCEEEEECCTTSCHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            56789999999999974

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=89.15  E-value=0.3  Score=35.19  Aligned_cols=27  Identities=15%  Similarity=0.118  Sum_probs=20.3

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      -.|+-+.+.+|+|+|||.  ++-+|..++
T Consensus       124 ~~Ge~vaIvGpsGsGKST--Ll~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSM--LCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHH--HHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHH--HHHHHhhhc
Confidence            378899999999999997  344444444

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=88.99  E-value=0.32  Score=34.73  Aligned_cols=17  Identities=24%  Similarity=0.483  Sum_probs=14.6

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        59 ~~~ll~G~~G~GKT~la   75 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTI   75 (353)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46999999999999653

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=88.85  E-value=0.19  Score=35.36  Aligned_cols=17  Identities=29%  Similarity=0.311  Sum_probs=14.6

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.||+|+|||...
T Consensus        48 ~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             EEEEEESCSSSSHHHHH
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            37999999999999754

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=88.84  E-value=0.18  Score=38.62  Aligned_cols=19  Identities=26%  Similarity=0.427  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+.+++.||+|+|||+..
T Consensus       237 ~~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          237 PPRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CCCEEEEECSTTSSHHHHH
T ss_pred             CCCcEEEECcCCCCHHHHH
Confidence            3468999999999999753

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=88.75  E-value=0.21  Score=31.81  Aligned_cols=15  Identities=7%  Similarity=-0.086  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.|+.|||||..
T Consensus         3 ~i~l~G~~GsGKsT~   17 (173)
T 3kb2_A            3 LIILEGPDCCFKSTV   17 (173)
T ss_dssp             EEEEECSSSSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=88.71  E-value=0.84  Score=32.63  Aligned_cols=43  Identities=14%  Similarity=0.199  Sum_probs=28.3

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .+|+++--++.+.+.+++.=...            -+...+++.||+|+|||...
T Consensus        11 ~~~~~~vg~~~~~~~l~~~~~~~------------~~~~~~ll~Gp~G~GKTtl~   53 (354)
T 1sxj_E           11 KSLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRC   53 (354)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHhhC------------CCCCeEEEECCCCCCHHHHH
Confidence            45777777777777776431110            12235999999999999753

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=88.68  E-value=0.69  Score=33.13  Aligned_cols=27  Identities=33%  Similarity=0.617  Sum_probs=19.1

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .|.-+.+.+|+|+|||..  +..+..++.
T Consensus       101 ~g~vi~lvG~nGsGKTTl--l~~Lagll~  127 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTT--IAKLGRYYQ  127 (304)
T ss_dssp             SSSEEEEECSTTSSHHHH--HHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHH--HHHHHHHHH
Confidence            356788999999999974  444444444

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=88.55  E-value=0.2  Score=34.12  Aligned_cols=18  Identities=28%  Similarity=0.518  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+-+++.+|||+|||..
T Consensus        33 ~g~~ilI~GpsGsGKStL   50 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSET   50 (205)
T ss_dssp             TTEEEEEECCCTTTTHHH
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            567899999999999853

>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=88.54  E-value=0.61  Score=39.29  Aligned_cols=38  Identities=21%  Similarity=0.270  Sum_probs=25.1

Q ss_pred             EEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcH
Q psy3307          52 MACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR  105 (130)
Q Consensus        52 l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~  105 (130)
                      ++.|..|||||...+-=+...+.....                +.+++++||..
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~~~----------------~~~il~lVP~q   42 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRAPF----------------GKPIIFLVPDQ   42 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHCTT----------------SSCEEEECCGG
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCC----------------CCcEEEEecCc
Confidence            678899999998765444444443211                14688888865

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=88.48  E-value=0.18  Score=35.66  Aligned_cols=18  Identities=22%  Similarity=0.248  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ...+++.||+|+|||...
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            378999999999999753

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=88.45  E-value=0.37  Score=37.76  Aligned_cols=15  Identities=13%  Similarity=0.408  Sum_probs=13.9

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      ++++.||+|+|||..
T Consensus       329 ~vLL~GppGtGKT~L  343 (595)
T 3f9v_A          329 HILIIGDPGTAKSQM  343 (595)
T ss_dssp             CEEEEESSCCTHHHH
T ss_pred             ceEEECCCchHHHHH
Confidence            899999999999974

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=88.33  E-value=0.16  Score=32.91  Aligned_cols=18  Identities=28%  Similarity=0.484  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|..+++.|++|||||..
T Consensus         3 ~g~~I~l~G~~GsGKST~   20 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQ   20 (186)
T ss_dssp             CEEEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            356789999999999974

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=88.32  E-value=0.52  Score=31.32  Aligned_cols=18  Identities=33%  Similarity=0.512  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |.-+.+.+|+|+|||...
T Consensus         1 G~~i~i~G~nG~GKTTll   18 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLI   18 (189)
T ss_dssp             CCCEEEESCCSSCHHHHH
T ss_pred             CCEEEEECCCCChHHHHH
Confidence            456789999999999743

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=88.20  E-value=0.25  Score=35.85  Aligned_cols=16  Identities=38%  Similarity=0.397  Sum_probs=13.3

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+|||||||...
T Consensus        12 ~i~i~GptgsGKt~la   27 (316)
T 3foz_A           12 AIFLMGPTASGKTALA   27 (316)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCccCHHHHH
Confidence            4788999999999643

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=88.16  E-value=0.23  Score=36.44  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++-+++.||||||||...
T Consensus        40 ~~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             CEEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            346899999999999643

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=88.06  E-value=0.16  Score=36.39  Aligned_cols=18  Identities=28%  Similarity=0.447  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      ...++++.||+|+|||..
T Consensus        44 ~~~~vLl~G~~GtGKT~l   61 (350)
T 1g8p_A           44 GIGGVLVFGDRGTGKSTA   61 (350)
T ss_dssp             GGCCEEEECCGGGCTTHH
T ss_pred             CCceEEEECCCCccHHHH
Confidence            345799999999999974

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=88.05  E-value=0.26  Score=35.87  Aligned_cols=17  Identities=29%  Similarity=0.249  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.||||||||...
T Consensus         4 ~~i~i~GptgsGKt~la   20 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTS   20 (322)
T ss_dssp             EEEEEECCTTSCHHHHH
T ss_pred             cEEEEECCCcCCHHHHH
Confidence            35788999999999643

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=87.96  E-value=0.18  Score=32.98  Aligned_cols=17  Identities=18%  Similarity=0.335  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .-+++.+|+|+|||...
T Consensus         3 ~ii~l~G~~GaGKSTl~   19 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTC   19 (189)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            45688999999999743

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=87.80  E-value=0.87  Score=34.37  Aligned_cols=27  Identities=26%  Similarity=0.194  Sum_probs=19.1

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.|++|+|||... +-+.....
T Consensus       196 ~G~liiIaG~pG~GKTtla-l~ia~~~a  222 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFA-LKQAKNMS  222 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHH-HHHHHHHH
T ss_pred             CCcEEEEEeCCCCChHHHH-HHHHHHHH
Confidence            4578899999999999654 44444443

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=87.71  E-value=0.3  Score=33.63  Aligned_cols=18  Identities=33%  Similarity=0.434  Sum_probs=16.0

Q ss_pred             hcCCcEEEEccCCchHHH
Q psy3307          46 ISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~   63 (130)
                      ..|.-+.+.+|+|||||.
T Consensus        29 ~~Ge~~~iiG~nGsGKST   46 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKST   46 (235)
T ss_dssp             CTTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCcHHH
Confidence            367888999999999997

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=87.58  E-value=0.94  Score=32.39  Aligned_cols=19  Identities=32%  Similarity=0.240  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.|++|+|||...
T Consensus        67 ~G~l~li~G~pG~GKTtl~   85 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFA   85 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHH
Confidence            4578999999999999643

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=87.48  E-value=0.3  Score=32.13  Aligned_cols=15  Identities=27%  Similarity=0.543  Sum_probs=12.8

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+.+.+|+|+|||..
T Consensus         2 ~i~l~G~nGsGKTTL   16 (178)
T 1ye8_A            2 KIIITGEPGVGKTTL   16 (178)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            467899999999974

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=87.46  E-value=0.43  Score=34.44  Aligned_cols=16  Identities=25%  Similarity=0.453  Sum_probs=14.2

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999753

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=87.38  E-value=0.37  Score=31.94  Aligned_cols=19  Identities=26%  Similarity=0.179  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.+|+|+|||...
T Consensus        19 ~G~~~~i~G~~GsGKTtl~   37 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLA   37 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4678899999999999754

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=87.33  E-value=0.33  Score=34.83  Aligned_cols=18  Identities=33%  Similarity=0.532  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +..+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            578999999999999753

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=87.29  E-value=1.5  Score=33.68  Aligned_cols=52  Identities=19%  Similarity=0.202  Sum_probs=31.6

Q ss_pred             ccCCCcCCCCCHHHHHHHHHCCC--CCCcHHHHHHHhHH--hcCCcEEEEccCCchHHHHH
Q psy3307           9 KKQGFDDIQMTEIITNNIALARY--DKPTPVQKYAIPVI--ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         9 ~~~~f~~l~l~~~i~~~l~~~~~--~~~t~~Q~~~i~~~--~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..+|+++.-.++....+++.-.  ..+     ..+..+  .-.+.+++.+|+|+|||+..
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~-----~~~~~lg~~ip~GvLL~GppGtGKTtLa   81 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNP-----SRFHEMGARIPKGVLLVGPPGVGKTHLA   81 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCG-----GGTTTTSCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhch-----hhhhhccCCCCceEEEECCCCCCHHHHH
Confidence            66789999877777777654311  010     011111  01245999999999999743

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=87.28  E-value=0.27  Score=32.59  Aligned_cols=19  Identities=26%  Similarity=0.375  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+++|||||..
T Consensus        23 ~~g~~i~l~G~sGsGKSTl   41 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTL   41 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4577899999999999974

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=87.24  E-value=0.26  Score=32.01  Aligned_cols=17  Identities=18%  Similarity=0.286  Sum_probs=14.5

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +.-+++.|+.|||||..
T Consensus         5 ~~~I~l~G~~GsGKST~   21 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTL   21 (193)
T ss_dssp             CEEEEEEESTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45689999999999974

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=87.20  E-value=0.65  Score=35.87  Aligned_cols=28  Identities=25%  Similarity=0.414  Sum_probs=19.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .+.++++.+.||||||.+.-.-++..+.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~sLl~  193 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILSMLY  193 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4579999999999999865333333333

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=87.14  E-value=0.95  Score=32.24  Aligned_cols=19  Identities=26%  Similarity=0.513  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|+-+.+.+++|+|||...
T Consensus       104 ~g~vi~lvG~~GsGKTTl~  122 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTL  122 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3567889999999999754

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=87.10  E-value=0.48  Score=34.93  Aligned_cols=23  Identities=35%  Similarity=0.602  Sum_probs=17.7

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.|  ++.-+.||||||++.
T Consensus        98 ~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           98 SQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHhCCCCEEEEEeCCCCCCccEEe
Confidence            34568864  677889999999874

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=87.04  E-value=0.45  Score=33.15  Aligned_cols=19  Identities=37%  Similarity=0.499  Sum_probs=16.8

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|+.+++.+++|+|||...
T Consensus        47 ~g~~i~l~G~~GsGKSTl~   65 (250)
T 3nwj_A           47 NGRSMYLVGMMGSGKTTVG   65 (250)
T ss_dssp             TTCCEEEECSTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4999999999999999753

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=87.03  E-value=1.2  Score=31.05  Aligned_cols=42  Identities=14%  Similarity=0.226  Sum_probs=26.4

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|+++--.+...+.+.+.= ..            -....+++.||+|+|||...
T Consensus        14 ~~~~~~~g~~~~~~~l~~~l-~~------------~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGYV-ER------------KNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTTT-TT------------TCCCCEEEESSSSSSHHHHH
T ss_pred             CCHHHHhCCHHHHHHHHHHH-hC------------CCCCeEEEECcCCcCHHHHH
Confidence            35666666666666665421 00            01236999999999999653

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=86.95  E-value=0.32  Score=32.12  Aligned_cols=16  Identities=25%  Similarity=0.526  Sum_probs=14.2

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +-+++.|++|||||..
T Consensus        19 ~~I~l~G~~GsGKSTl   34 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSV   34 (202)
T ss_dssp             SCEEEECSTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4799999999999974

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=86.92  E-value=0.34  Score=34.89  Aligned_cols=16  Identities=31%  Similarity=0.464  Sum_probs=14.4

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ..+++.+|+|+|||..
T Consensus        52 ~~~ll~Gp~G~GKTTL   67 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTL   67 (334)
T ss_dssp             CCEEEESSTTSSHHHH
T ss_pred             CeEEEECCCCCcHHHH
Confidence            6799999999999974

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=86.88  E-value=0.32  Score=32.47  Aligned_cols=19  Identities=26%  Similarity=0.191  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+.+.+|+|+|||...
T Consensus        24 ~G~~~~l~G~nGsGKSTll   42 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLA   42 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5678899999999999743

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=86.86  E-value=0.25  Score=35.03  Aligned_cols=17  Identities=35%  Similarity=0.431  Sum_probs=14.4

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +.-+++.||+|||||..
T Consensus        33 ~~livl~G~sGsGKSTl   49 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSL   49 (287)
T ss_dssp             CEEEEEECCTTSCTHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            35689999999999974

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=86.85  E-value=0.25  Score=33.45  Aligned_cols=19  Identities=26%  Similarity=0.394  Sum_probs=12.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|+-+.+.||+|+|||..
T Consensus        25 ~~G~ii~l~Gp~GsGKSTl   43 (231)
T 3lnc_A           25 SVGVILVLSSPSGCGKTTV   43 (231)
T ss_dssp             ECCCEEEEECSCC----CH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4678889999999999974

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=86.78  E-value=0.54  Score=31.59  Aligned_cols=16  Identities=31%  Similarity=0.405  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -.++.|++|||||+..
T Consensus         7 i~l~tG~pGsGKT~~a   22 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKM   22 (199)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEEeCCCCCHHHHH
Confidence            4578999999999854

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=86.78  E-value=0.53  Score=34.19  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=18.0

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.|  ++.-++||||||++.
T Consensus        71 ~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           71 KDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCeEEEEEECCCCCCCceEe
Confidence            34568865  677899999999875

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=86.72  E-value=0.29  Score=32.48  Aligned_cols=18  Identities=28%  Similarity=0.152  Sum_probs=14.7

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+.+.||+|||||..
T Consensus         5 ~~~~i~i~G~~GsGKSTl   22 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTL   22 (211)
T ss_dssp             CCEEEEEEESTTSSHHHH
T ss_pred             CcEEEEEECCCCCCHHHH
Confidence            455678999999999974

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=86.68  E-value=0.42  Score=32.18  Aligned_cols=19  Identities=21%  Similarity=0.205  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+.+.+|+|+|||...
T Consensus        23 ~G~~~~i~G~~GsGKTtl~   41 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQIC   41 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHH
Confidence            5678899999999999754

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=86.68  E-value=5.9  Score=28.93  Aligned_cols=19  Identities=37%  Similarity=0.326  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|+-+++.+++|+|||...
T Consensus        62 ~G~ii~I~G~pGsGKTtLa   80 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLT   80 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3478899999999999754

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=86.65  E-value=0.57  Score=34.54  Aligned_cols=19  Identities=47%  Similarity=0.574  Sum_probs=16.1

Q ss_pred             cCCc--EEEEccCCchHHHHH
Q psy3307          47 SGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~--~l~~aptGsGKT~~~   65 (130)
                      .|.+  ++.-+.||||||++.
T Consensus        82 ~G~n~tifAYGqTGSGKTyTM  102 (360)
T 1ry6_A           82 NGCVCSCFAYGQTGSGKTYTM  102 (360)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             CCceeEEEeeCCCCCCCCEEE
Confidence            4776  689999999999875

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=86.43  E-value=0.41  Score=31.92  Aligned_cols=31  Identities=16%  Similarity=0.087  Sum_probs=22.3

Q ss_pred             CcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          34 PTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        34 ~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .++.+... ..+..|.-+++.++.|||||...
T Consensus        12 ~~~~~r~~-~~~~~~~~i~~~G~~GsGKsT~~   42 (211)
T 1m7g_A           12 LTRSERTE-LRNQRGLTIWLTGLSASGKSTLA   42 (211)
T ss_dssp             CCHHHHHH-HHTSSCEEEEEECSTTSSHHHHH
T ss_pred             cCHHHhhc-ccCCCCCEEEEECCCCCCHHHHH
Confidence            34555544 34557788999999999999743

>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=86.42  E-value=0.36  Score=34.86  Aligned_cols=18  Identities=28%  Similarity=0.183  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            357999999999999753

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=86.34  E-value=0.53  Score=34.51  Aligned_cols=23  Identities=30%  Similarity=0.553  Sum_probs=17.5

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.+  ++.-++||||||++.
T Consensus        88 ~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           88 DKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hHhhCCCceEEEEecCCCCCCCeEE
Confidence            34467865  577899999999874

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=86.28  E-value=0.39  Score=31.53  Aligned_cols=18  Identities=28%  Similarity=0.259  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+++.|+.|||||..
T Consensus         3 ~~~~I~l~G~~GsGKsT~   20 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQ   20 (204)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            467899999999999974

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=86.26  E-value=0.58  Score=32.88  Aligned_cols=16  Identities=31%  Similarity=0.463  Sum_probs=14.1

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.||+|+|||...
T Consensus        48 ~~ll~G~~G~GKT~la   63 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAA   63 (327)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             eEEEECcCCCCHHHHH
Confidence            6999999999999753

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=86.25  E-value=0.32  Score=31.52  Aligned_cols=18  Identities=22%  Similarity=0.233  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +.-+++.+++|||||...
T Consensus         3 ~~~I~l~G~~GsGKsT~a   20 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQC   20 (196)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            456889999999999753

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=86.22  E-value=0.39  Score=32.39  Aligned_cols=18  Identities=22%  Similarity=0.215  Sum_probs=14.9

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.|++|||||..
T Consensus         6 ~~~~I~l~G~~GsGKsT~   23 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTV   23 (227)
T ss_dssp             -CCEEEEEECTTSSHHHH
T ss_pred             cCcEEEEECCCCCCHHHH
Confidence            456799999999999974

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=86.19  E-value=0.38  Score=31.33  Aligned_cols=19  Identities=21%  Similarity=0.277  Sum_probs=16.1

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..+.-+++.|+.|||||..
T Consensus         7 ~~~~~I~l~G~~GsGKsT~   25 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQ   25 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3567899999999999964

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=86.18  E-value=0.47  Score=30.92  Aligned_cols=19  Identities=21%  Similarity=0.263  Sum_probs=16.0

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..+.-+++.|++|||||..
T Consensus        10 ~~~~~I~l~G~~GsGKsT~   28 (199)
T 2bwj_A           10 RKCKIIFIIGGPGSGKGTQ   28 (199)
T ss_dssp             HHSCEEEEEECTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3567899999999999964

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=86.14  E-value=0.36  Score=32.35  Aligned_cols=18  Identities=17%  Similarity=0.298  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.|+.|||||..
T Consensus         3 ~~~~I~l~G~~GsGKsT~   20 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQ   20 (220)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            356789999999999964

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=86.11  E-value=0.57  Score=33.54  Aligned_cols=26  Identities=23%  Similarity=0.302  Sum_probs=17.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+.+.+|+|+|||..  +..+..+.
T Consensus        99 ~g~vi~lvG~nGsGKTTl--l~~Lag~l  124 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTS--LGKLAHRL  124 (302)
T ss_dssp             SCEEEEEECCTTSCHHHH--HHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHH--HHHHHHHH
Confidence            345678999999999984  33344443

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=86.09  E-value=0.46  Score=32.29  Aligned_cols=19  Identities=32%  Similarity=0.288  Sum_probs=16.5

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        33 ~~Ge~~~iiG~NGsGKSTL   51 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTL   51 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4778889999999999973

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=86.05  E-value=0.41  Score=32.93  Aligned_cols=19  Identities=32%  Similarity=0.414  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|||||..
T Consensus        29 ~~Ge~~~i~G~nGsGKSTL   47 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSL   47 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4778889999999999973

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=85.73  E-value=0.69  Score=36.19  Aligned_cols=23  Identities=22%  Similarity=0.281  Sum_probs=19.1

Q ss_pred             hHHhcCCcEEEEccCCchHHHHH
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+..|..+++.+|+|+|||...
T Consensus        55 ~~i~~g~~vll~Gp~GtGKTtla   77 (604)
T 3k1j_A           55 TAANQKRHVLLIGEPGTGKSMLG   77 (604)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHH
T ss_pred             ccccCCCEEEEEeCCCCCHHHHH
Confidence            34568899999999999999743

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=85.70  E-value=0.38  Score=34.95  Aligned_cols=16  Identities=25%  Similarity=0.318  Sum_probs=13.7

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.+|||||||...
T Consensus         7 ~i~i~GptGsGKTtla   22 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLA   22 (323)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5889999999999743

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=85.67  E-value=0.65  Score=33.98  Aligned_cols=23  Identities=43%  Similarity=0.596  Sum_probs=17.4

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.|  ++.-++||||||++.
T Consensus        77 ~~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           77 EAFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHhhcCeeEEEecccCCCceEee
Confidence            34568865  577889999999874

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=85.66  E-value=0.61  Score=34.33  Aligned_cols=22  Identities=41%  Similarity=0.658  Sum_probs=17.2

Q ss_pred             HHhcCCc--EEEEccCCchHHHHH
Q psy3307          44 VIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+++|.+  ++.-+.||||||++.
T Consensus        75 ~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           75 DILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCcceEEEECCCCCCcceEe
Confidence            4567864  577899999999875

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=85.61  E-value=0.64  Score=34.46  Aligned_cols=22  Identities=36%  Similarity=0.658  Sum_probs=17.0

Q ss_pred             HHhcCCc--EEEEccCCchHHHHH
Q psy3307          44 VIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+++|.|  ++.-+.||||||++.
T Consensus        96 ~~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           96 SVLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHhCCCeeeEEeecCCCCCCCEeE
Confidence            4568864  567889999999874

>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=85.61  E-value=2.3  Score=32.25  Aligned_cols=17  Identities=29%  Similarity=0.411  Sum_probs=14.3

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .-+++.+++|+|||...
T Consensus       101 ~vIlivG~~G~GKTTt~  117 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTV  117 (443)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46789999999999864

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=85.57  E-value=0.66  Score=34.28  Aligned_cols=22  Identities=36%  Similarity=0.602  Sum_probs=17.4

Q ss_pred             HHhcCCc--EEEEccCCchHHHHH
Q psy3307          44 VIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+++|.|  ++.-+.||||||++.
T Consensus        79 ~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           79 DVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCceEEEeecCCCCCCceEE
Confidence            4568864  577899999999885

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=85.57  E-value=0.49  Score=33.01  Aligned_cols=22  Identities=18%  Similarity=0.265  Sum_probs=18.5

Q ss_pred             HHhcCCcEEEEccCCchHHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      -+..|.-+++.+|+|+|||...
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~   47 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLA   47 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHH
Confidence            3557889999999999999754

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=85.52  E-value=0.57  Score=33.63  Aligned_cols=20  Identities=25%  Similarity=0.524  Sum_probs=15.5

Q ss_pred             hcCC--cEEEEccCCchHHHHH
Q psy3307          46 ISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ..|+  ++++.||+|+|||...
T Consensus        42 ~~g~~~~~ll~Gp~G~GKTtla   63 (340)
T 1sxj_C           42 DEGKLPHLLFYGPPGTGKTSTI   63 (340)
T ss_dssp             HTTCCCCEEEECSSSSSHHHHH
T ss_pred             hcCCCceEEEECCCCCCHHHHH
Confidence            3454  3899999999999754

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=85.50  E-value=0.38  Score=31.10  Aligned_cols=18  Identities=33%  Similarity=0.483  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|..+.+.++.|||||..
T Consensus         4 ~g~~i~l~G~~GsGKST~   21 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTV   21 (179)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            466789999999999974

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=85.49  E-value=0.67  Score=34.04  Aligned_cols=22  Identities=36%  Similarity=0.614  Sum_probs=17.2

Q ss_pred             HHhcCC--cEEEEccCCchHHHHH
Q psy3307          44 VIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      .+++|.  .++.-+.||||||+..
T Consensus        84 ~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           84 AVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCceeEEeecCCCCCCCEEe
Confidence            346786  4577899999999875

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=85.47  E-value=0.46  Score=32.48  Aligned_cols=19  Identities=32%  Similarity=0.457  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        32 ~~Ge~~~i~G~nGsGKSTL   50 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTSL   50 (229)
T ss_dssp             ETTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3778889999999999973

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=85.45  E-value=0.66  Score=34.72  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=19.2

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-+.||||||++.
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            3455678875  477889999999875

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=85.42  E-value=0.45  Score=32.43  Aligned_cols=19  Identities=32%  Similarity=0.386  Sum_probs=16.1

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        28 ~~Ge~~~iiG~nGsGKSTL   46 (224)
T 2pcj_A           28 KKGEFVSIIGASGSGKSTL   46 (224)
T ss_dssp             ETTCEEEEEECTTSCHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3677888999999999973

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=85.40  E-value=0.47  Score=32.44  Aligned_cols=18  Identities=22%  Similarity=0.209  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+.-+.+.||+|||||..
T Consensus        26 ~~~~i~l~G~~GsGKSTl   43 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTV   43 (246)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            356899999999999974

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=85.37  E-value=0.45  Score=33.65  Aligned_cols=19  Identities=21%  Similarity=0.267  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|||||..
T Consensus        32 ~~Ge~~~iiGpnGsGKSTL   50 (275)
T 3gfo_A           32 KRGEVTAILGGNGVGKSTL   50 (275)
T ss_dssp             ETTSEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3678889999999999973

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=85.31  E-value=0.7  Score=33.65  Aligned_cols=25  Identities=36%  Similarity=0.565  Sum_probs=19.3

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-++||||||++.
T Consensus        72 lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           72 LVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            3455678875  577899999999875

>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=85.31  E-value=1.3  Score=32.60  Aligned_cols=26  Identities=27%  Similarity=0.290  Sum_probs=18.4

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      |+-+++.+++|+|||... +.++....
T Consensus        74 G~li~I~G~pGsGKTtla-l~la~~~~   99 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLA-LAIVAQAQ   99 (366)
T ss_dssp             TSEEEEEESTTSSHHHHH-HHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHH-HHHHHHHH
Confidence            467899999999999643 44444433

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=85.31  E-value=0.69  Score=34.17  Aligned_cols=23  Identities=30%  Similarity=0.530  Sum_probs=17.6

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.+  ++.-+.||||||++.
T Consensus        83 ~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           83 QHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhcCCeeEEEEeCCCCCCCceEe
Confidence            34568864  577899999999875

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=85.31  E-value=0.44  Score=31.94  Aligned_cols=17  Identities=29%  Similarity=0.313  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.|+.|||||..
T Consensus         5 ~~~I~l~G~~GsGKsT~   21 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQ   21 (222)
T ss_dssp             SCCEEEEESTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            46789999999999974

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=85.30  E-value=0.68  Score=33.99  Aligned_cols=23  Identities=39%  Similarity=0.491  Sum_probs=17.7

Q ss_pred             hHHhcCC--cEEEEccCCchHHHHH
Q psy3307          43 PVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ..+++|.  .++.-++||||||+..
T Consensus        71 ~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           71 DSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHcCCccceeeecCCCCCCCeEE
Confidence            3456886  4577899999999885

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=85.29  E-value=0.43  Score=36.95  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=16.2

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|..+++.+|+|+|||...
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999743

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=85.29  E-value=1.2  Score=32.82  Aligned_cols=33  Identities=30%  Similarity=0.335  Sum_probs=22.1

Q ss_pred             HHhHHhc------CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          41 AIPVIIS------GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        41 ~i~~~~~------g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .++.++.      |.-+++.+|+|+|||.. ++.++..+.
T Consensus        48 ~LD~~Lg~GGi~~G~i~~I~GppGsGKSTL-al~la~~~~   86 (356)
T 3hr8_A           48 AIDIATGVGGYPRGRIVEIFGQESSGKTTL-ALHAIAEAQ   86 (356)
T ss_dssp             HHHHHTSSSSEETTEEEEEEESTTSSHHHH-HHHHHHHHH
T ss_pred             HHHHHhccCCccCCcEEEEECCCCCCHHHH-HHHHHHHHH
Confidence            3455565      46789999999999964 344444433

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=85.28  E-value=0.43  Score=33.57  Aligned_cols=21  Identities=24%  Similarity=0.395  Sum_probs=17.3

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      +..|.-+++.||+|+|||...
T Consensus        32 l~~G~~~~i~G~~G~GKTTl~   52 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTFV   52 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHH
Confidence            346788999999999999754

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=85.28  E-value=0.75  Score=33.74  Aligned_cols=25  Identities=36%  Similarity=0.569  Sum_probs=19.2

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-+.||||||++.
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            4455678875  567899999999875

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=85.25  E-value=0.42  Score=35.00  Aligned_cols=16  Identities=31%  Similarity=0.287  Sum_probs=13.6

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.||||||||...
T Consensus         9 lI~I~GptgSGKTtla   24 (340)
T 3d3q_A            9 LIVIVGPTASGKTELS   24 (340)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             eEEEECCCcCcHHHHH
Confidence            5789999999999643

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=85.23  E-value=0.47  Score=33.01  Aligned_cols=19  Identities=26%  Similarity=0.386  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        31 ~~Ge~~~liG~nGsGKSTL   49 (257)
T 1g6h_A           31 NKGDVTLIIGPNGSGKSTL   49 (257)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             eCCCEEEEECCCCCCHHHH
Confidence            3778889999999999973

>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=85.19  E-value=0.65  Score=33.43  Aligned_cols=31  Identities=23%  Similarity=0.371  Sum_probs=21.9

Q ss_pred             cHHHHHHHhHHh----cCC---cEEEEccCCchHHHHH
Q psy3307          35 TPVQKYAIPVII----SGR---DVMACAQTGSGKTAAF   65 (130)
Q Consensus        35 t~~Q~~~i~~~~----~g~---~~l~~aptGsGKT~~~   65 (130)
                      .|+|..++..+.    +|+   .+++.||.|+|||...
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a   41 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH
Confidence            466666665443    444   4899999999999754

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=85.17  E-value=0.6  Score=34.55  Aligned_cols=25  Identities=36%  Similarity=0.577  Sum_probs=18.9

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-+.||||||++.
T Consensus        71 lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           71 LVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hhHhhhcCCceEEEEECCCCCCCeEee
Confidence            3445678875  567889999999875

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=85.17  E-value=0.38  Score=31.10  Aligned_cols=15  Identities=20%  Similarity=0.253  Sum_probs=12.9

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.|+.|||||..
T Consensus         3 ~I~i~G~~GsGKsT~   17 (194)
T 1nks_A            3 IGIVTGIPGVGKSTV   17 (194)
T ss_dssp             EEEEEECTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=85.11  E-value=0.52  Score=30.32  Aligned_cols=15  Identities=27%  Similarity=0.452  Sum_probs=13.4

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.+++|||||..
T Consensus         6 ~i~i~G~~GsGKsTl   20 (175)
T 1via_A            6 NIVFIGFMGSGKSTL   20 (175)
T ss_dssp             CEEEECCTTSCHHHH
T ss_pred             EEEEEcCCCCCHHHH
Confidence            689999999999974

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=85.11  E-value=0.42  Score=36.12  Aligned_cols=17  Identities=24%  Similarity=0.411  Sum_probs=14.5

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            36999999999999743

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=85.09  E-value=0.41  Score=36.59  Aligned_cols=55  Identities=16%  Similarity=0.250  Sum_probs=32.7

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCC--CCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALAR--YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~--~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .+..+|+|+.-.++..+.+++.-  +..+..++...   +.-.+.+++.+|+|+|||+..
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g---~~~p~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIG---ARMPKGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTT---CCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcC---CCCCCeEEEECCCCCCHHHHH
Confidence            35678999987777777765421  11111111100   012256999999999999753

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=85.08  E-value=0.7  Score=34.04  Aligned_cols=23  Identities=39%  Similarity=0.588  Sum_probs=17.6

Q ss_pred             hHHhcCC--cEEEEccCCchHHHHH
Q psy3307          43 PVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ..+++|.  .++.-+.||||||++.
T Consensus        82 ~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           82 DEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHhCCCceEEEEeCCCCCCCceEE
Confidence            3456886  4577899999999864

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=85.05  E-value=0.71  Score=33.96  Aligned_cols=24  Identities=33%  Similarity=0.563  Sum_probs=18.3

Q ss_pred             HhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          42 IPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      +..+++|.|  ++.-+.||||||.+.
T Consensus        85 v~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           85 LQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHhCCceeEEEeeCCCCCCCceEE
Confidence            344568875  477889999999885

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=85.05  E-value=0.48  Score=33.27  Aligned_cols=19  Identities=32%  Similarity=0.447  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        35 ~~Ge~~~liG~nGsGKSTL   53 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTL   53 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3678889999999999973

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=85.03  E-value=0.49  Score=32.56  Aligned_cols=19  Identities=32%  Similarity=0.422  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        30 ~~Ge~~~l~G~nGsGKSTL   48 (240)
T 1ji0_A           30 PRGQIVTLIGANGAGKTTT   48 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3678889999999999973

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=84.98  E-value=0.69  Score=33.90  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=18.9

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-+.||||||+..
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            3445678875  577899999999875

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=84.96  E-value=4.7  Score=36.33  Aligned_cols=25  Identities=32%  Similarity=0.421  Sum_probs=20.1

Q ss_pred             HhHHhc------CCcEEEEccCCchHHHHHH
Q psy3307          42 IPVIIS------GRDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        42 i~~~~~------g~~~l~~aptGsGKT~~~~   66 (130)
                      ++.++.      |+.+++.+|+|+|||....
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ 1445 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTL 1445 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHH
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHH
Confidence            555665      6899999999999997653

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=84.92  E-value=0.47  Score=30.66  Aligned_cols=22  Identities=18%  Similarity=0.120  Sum_probs=15.7

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      -.++.+|+|+|||..  +-++..+
T Consensus        28 ~~~i~G~NGsGKStl--l~ai~~~   49 (182)
T 3kta_A           28 FTAIVGANGSGKSNI--GDAILFV   49 (182)
T ss_dssp             EEEEEECTTSSHHHH--HHHHHHH
T ss_pred             cEEEECCCCCCHHHH--HHHHHHH
Confidence            567899999999974  3444443

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=84.90  E-value=1.1  Score=32.47  Aligned_cols=27  Identities=26%  Similarity=0.316  Sum_probs=18.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .|.-+.+.+|+|+|||..  +..+..+..
T Consensus       128 ~g~vi~lvG~nGaGKTTl--l~~Lag~l~  154 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTT--IAKLANWLK  154 (328)
T ss_dssp             SSEEEEEECCTTSSHHHH--HHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHH--HHHHHHHHH
Confidence            356789999999999974  344444443

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=84.89  E-value=0.56  Score=30.70  Aligned_cols=24  Identities=17%  Similarity=0.223  Sum_probs=16.0

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      -+.+.+++|||||..  +-.|..++.
T Consensus         4 ~v~IvG~SGsGKSTL--~~~L~~~~~   27 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTL--ITRMMPILR   27 (171)
T ss_dssp             EEEEEESCHHHHHHH--HHHHHHHHH
T ss_pred             EEEEECCCCCCHHHH--HHHHHHHhh
Confidence            466889999999974  334444443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=84.88  E-value=0.42  Score=31.09  Aligned_cols=19  Identities=37%  Similarity=0.347  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.++.|||||...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~   30 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIA   30 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4667899999999999753

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=84.87  E-value=0.9  Score=32.57  Aligned_cols=18  Identities=28%  Similarity=0.180  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |.-+++.+++|+|||...
T Consensus       107 G~i~~i~G~~GsGKT~la  124 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLC  124 (324)
T ss_dssp             TSEEEEEESTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHhHHH
Confidence            467899999999999754

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=84.86  E-value=0.82  Score=34.35  Aligned_cols=23  Identities=43%  Similarity=0.614  Sum_probs=17.6

Q ss_pred             hHHhcCC--cEEEEccCCchHHHHH
Q psy3307          43 PVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ..+++|.  .++.-|.||||||++.
T Consensus       148 ~~~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          148 QTIFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHhcCCceeEEeecCCCCCCCeEe
Confidence            3456786  4577889999999874

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=84.86  E-value=0.64  Score=34.93  Aligned_cols=25  Identities=40%  Similarity=0.594  Sum_probs=19.1

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-|.||||||++.
T Consensus       130 lv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          130 LIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            4455678875  577789999999874

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=84.85  E-value=0.51  Score=32.71  Aligned_cols=19  Identities=26%  Similarity=0.422  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        33 ~~Ge~~~i~G~nGsGKSTL   51 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTL   51 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3778889999999999973

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=84.83  E-value=0.45  Score=34.93  Aligned_cols=16  Identities=25%  Similarity=0.451  Sum_probs=13.3

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -.++.+|||+|||..+
T Consensus        25 ~~~i~G~NGaGKTTll   40 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLF   40 (365)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5678999999999743

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=84.81  E-value=0.48  Score=31.51  Aligned_cols=15  Identities=20%  Similarity=0.459  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.|+.|||||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQ   16 (216)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999975

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=84.80  E-value=0.7  Score=33.98  Aligned_cols=22  Identities=36%  Similarity=0.652  Sum_probs=17.1

Q ss_pred             HHhcCCc--EEEEccCCchHHHHH
Q psy3307          44 VIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+++|.|  ++.-++||||||++.
T Consensus       100 ~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A          100 SFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHhCCCceEEEEeCCCCCCceeee
Confidence            4457864  577899999999875

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=84.78  E-value=0.45  Score=36.08  Aligned_cols=19  Identities=26%  Similarity=0.351  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      ...++++.||+|+|||...
T Consensus       200 ~~~~~LL~G~pG~GKT~la  218 (468)
T 3pxg_A          200 TKNNPVLIGEPGVGKTAIA  218 (468)
T ss_dssp             SSCEEEEESCTTTTTHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH
Confidence            3468999999999999753

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=84.77  E-value=0.59  Score=30.20  Aligned_cols=16  Identities=25%  Similarity=0.397  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ..+++.+++|||||..
T Consensus         3 ~~I~l~G~~GsGKsT~   18 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTI   18 (184)
T ss_dssp             CSEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4588999999999975

>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=84.69  E-value=0.52  Score=35.44  Aligned_cols=17  Identities=24%  Similarity=0.237  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.||+|+|||..
T Consensus       130 ~~~lll~Gp~G~GKTtL  146 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHL  146 (440)
T ss_dssp             SCCEEEECSSSSSHHHH
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            46899999999999974

>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=84.67  E-value=0.47  Score=36.37  Aligned_cols=17  Identities=41%  Similarity=0.497  Sum_probs=15.0

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +.+++.||+|+|||...
T Consensus        78 ~~lLL~GppGtGKTtla   94 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAA   94 (516)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            68999999999999753

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=84.66  E-value=0.9  Score=36.29  Aligned_cols=60  Identities=20%  Similarity=0.205  Sum_probs=41.4

Q ss_pred             CCcHHHHHHHhHHhc--CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHH
Q psy3307          33 KPTPVQKYAIPVIIS--GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ  110 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~--g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q  110 (130)
                      .+|.-|.+++..+..  ..-.++.|+.|.|||.+.-+.+-.  ..                    ..++|.+|+.+-+..
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~--~~--------------------~~~~vtAP~~~a~~~  232 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISR--IA--------------------GRAIVTAPAKASTDV  232 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHH--SS--------------------SCEEEECSSCCSCHH
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHH--HH--------------------hCcEEECCCHHHHHH
Confidence            578999999988775  234689999999999654333321  11                    126888899887776


Q ss_pred             HHHH
Q psy3307         111 IYDE  114 (130)
Q Consensus       111 ~~~~  114 (130)
                      +.+.
T Consensus       233 l~~~  236 (671)
T 2zpa_A          233 LAQF  236 (671)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>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=84.66  E-value=1.8  Score=31.03  Aligned_cols=16  Identities=25%  Similarity=0.322  Sum_probs=13.7

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIA   55 (373)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4799999999999753

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=84.65  E-value=0.52  Score=32.91  Aligned_cols=19  Identities=37%  Similarity=0.496  Sum_probs=16.6

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        44 ~~Ge~~~i~G~nGsGKSTL   62 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTI   62 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3778899999999999973

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=84.60  E-value=0.52  Score=32.93  Aligned_cols=19  Identities=26%  Similarity=0.396  Sum_probs=16.2

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        30 ~~Ge~~~liG~nGsGKSTL   48 (262)
T 1b0u_A           30 RAGDVISIIGSSGSGKSTF   48 (262)
T ss_dssp             CTTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3677889999999999973

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=84.59  E-value=0.41  Score=31.49  Aligned_cols=18  Identities=28%  Similarity=0.324  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+++.|+.|||||..
T Consensus         3 ~~~~I~i~G~~GsGKsT~   20 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQ   20 (213)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCeEEEEEcCCCCCHHHH
Confidence            356789999999999974

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=84.59  E-value=0.46  Score=30.20  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=15.7

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      -.++.+|+|+|||..  +-.+....
T Consensus        25 ~~~I~G~NGsGKSti--l~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSL--LDAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHH--HHHHHHHH
T ss_pred             eEEEECCCCCCHHHH--HHHHHHHH
Confidence            457899999999974  34444333

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=84.53  E-value=1.1  Score=32.88  Aligned_cols=26  Identities=23%  Similarity=0.318  Sum_probs=17.9

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      |.-+.+.+|+|+|||...  ..|..++.
T Consensus       157 g~vi~lvG~nGsGKTTll--~~Lag~l~  182 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSL--GKLAHRLK  182 (359)
T ss_dssp             SEEEEEECCTTSCHHHHH--HHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHH--HHHHhhcc
Confidence            456789999999999843  33444443

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=84.52  E-value=0.5  Score=31.18  Aligned_cols=18  Identities=22%  Similarity=0.300  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+++.|+.|||||..
T Consensus         9 ~~~~I~l~G~~GsGKST~   26 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQ   26 (212)
T ss_dssp             CSCEEEEEESTTSSHHHH
T ss_pred             cCCEEEEEcCCCCCHHHH
Confidence            567899999999999974

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=84.42  E-value=0.73  Score=34.12  Aligned_cols=22  Identities=41%  Similarity=0.702  Sum_probs=17.1

Q ss_pred             HHhcCCc--EEEEccCCchHHHHH
Q psy3307          44 VIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+++|.+  ++.-+.||||||++.
T Consensus        95 ~~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           95 EVLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCceEEEEeecCCCCCcceec
Confidence            4567864  577899999999874

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=84.40  E-value=0.29  Score=32.48  Aligned_cols=21  Identities=24%  Similarity=-0.023  Sum_probs=16.6

Q ss_pred             HHhcCCcEEEEccCCchHHHH
Q psy3307          44 VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        44 ~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+.-+.+.+++|||||..
T Consensus        17 ~~~~~~~i~i~G~~GsGKSTl   37 (207)
T 2qt1_A           17 RGSKTFIIGISGVTNSGKTTL   37 (207)
T ss_dssp             CSCCCEEEEEEESTTSSHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHH
Confidence            344566788999999999974

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=84.38  E-value=0.57  Score=30.83  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=14.5

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.+++|||||..
T Consensus        20 ~~~I~l~G~~GsGKST~   36 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQ   36 (201)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45789999999999964

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=84.38  E-value=0.46  Score=30.65  Aligned_cols=27  Identities=26%  Similarity=0.129  Sum_probs=19.4

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..|.-+.+.+|+|+|||.  ++-++..+.
T Consensus        31 ~~Ge~v~L~G~nGaGKTT--Llr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTT--LTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHH--HHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHH--HHHHHHHhC
Confidence            467778899999999997  344444443

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=84.36  E-value=0.58  Score=35.52  Aligned_cols=18  Identities=28%  Similarity=0.464  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      .+++++.+|+|+|||...
T Consensus        50 ~~~iLl~GppGtGKT~la   67 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIA   67 (444)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            468999999999999743

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=84.32  E-value=0.55  Score=32.63  Aligned_cols=19  Identities=21%  Similarity=0.359  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        24 ~~Ge~~~liG~NGsGKSTL   42 (249)
T 2qi9_C           24 RAGEILHLVGPNGAGKSTL   42 (249)
T ss_dssp             ETTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3678889999999999974

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=84.24  E-value=0.53  Score=31.06  Aligned_cols=18  Identities=17%  Similarity=0.244  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+++.|+.|||||..
T Consensus         8 ~~~~I~l~G~~GsGKsT~   25 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQ   25 (215)
T ss_dssp             CCCEEEEEESTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            467899999999999974

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=84.22  E-value=0.53  Score=31.35  Aligned_cols=16  Identities=19%  Similarity=0.295  Sum_probs=13.4

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.|++|||||...
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQG   17 (216)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999753

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=84.18  E-value=0.57  Score=32.47  Aligned_cols=19  Identities=21%  Similarity=0.282  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        27 ~~Ge~~~l~G~nGsGKSTL   45 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTL   45 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3678889999999999974

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=84.16  E-value=0.56  Score=32.82  Aligned_cols=19  Identities=32%  Similarity=0.520  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        31 ~~Ge~~~liG~nGsGKSTL   49 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTL   49 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3678889999999999973

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=84.15  E-value=0.51  Score=43.22  Aligned_cols=20  Identities=40%  Similarity=0.697  Sum_probs=17.6

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..++.+++.||+|+|||..
T Consensus      1264 l~~~~~vLL~GPpGtGKT~l 1283 (2695)
T 4akg_A         1264 LNSKRGIILCGPPGSGKTMI 1283 (2695)
T ss_dssp             HHHTCEEEEECSTTSSHHHH
T ss_pred             HHCCCeEEEECCCCCCHHHH
Confidence            44789999999999999974

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=84.12  E-value=0.83  Score=34.04  Aligned_cols=23  Identities=43%  Similarity=0.614  Sum_probs=17.6

Q ss_pred             hHHhcCC--cEEEEccCCchHHHHH
Q psy3307          43 PVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ..+++|.  .++.-+.||||||++.
T Consensus       128 ~~~l~G~N~tifAYGQTGSGKTyTM  152 (387)
T 2heh_A          128 QTIFEGGKATCFAYGQTGSGKTHTM  152 (387)
T ss_dssp             HHHHTTCEEEEEEESCTTSSHHHHH
T ss_pred             HHHhcCCceEEEEecCCCCCCCeEe
Confidence            3456786  4677899999999874

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=84.07  E-value=0.57  Score=32.59  Aligned_cols=19  Identities=26%  Similarity=0.363  Sum_probs=16.2

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        29 ~~Ge~~~l~G~nGsGKSTL   47 (253)
T 2nq2_C           29 NKGDILAVLGQNGCGKSTL   47 (253)
T ss_dssp             ETTCEEEEECCSSSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3677888999999999973

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=84.00  E-value=0.58  Score=32.82  Aligned_cols=19  Identities=26%  Similarity=0.321  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        44 ~~Ge~~~l~G~NGsGKSTL   62 (267)
T 2zu0_C           44 HPGEVHAIMGPNGSGKSTL   62 (267)
T ss_dssp             CTTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3678889999999999974

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=83.92  E-value=0.59  Score=32.64  Aligned_cols=19  Identities=26%  Similarity=0.300  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        39 ~~Gei~~l~G~NGsGKSTL   57 (256)
T 1vpl_A           39 EEGEIFGLIGPNGAGKTTT   57 (256)
T ss_dssp             CTTCEEEEECCTTSSHHHH
T ss_pred             cCCcEEEEECCCCCCHHHH
Confidence            3678889999999999973

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=83.91  E-value=0.6  Score=29.72  Aligned_cols=16  Identities=19%  Similarity=0.395  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.++.|||||..
T Consensus         3 ~~I~l~G~~GsGKsT~   18 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTV   18 (173)
T ss_dssp             CCEEEESCTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            4688999999999974

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=83.90  E-value=2.1  Score=33.62  Aligned_cols=27  Identities=22%  Similarity=0.413  Sum_probs=19.7

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..++++.+.||||||.+.-.-+++.++
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~  240 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILF  240 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHH
Confidence            468999999999999875444444443

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=83.87  E-value=0.53  Score=31.57  Aligned_cols=17  Identities=24%  Similarity=0.433  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.++.|||||..
T Consensus         5 ~~~I~l~G~~GsGKsT~   21 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQ   21 (217)
T ss_dssp             CCEEEEEECTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            46789999999999964

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=83.87  E-value=0.55  Score=35.30  Aligned_cols=15  Identities=27%  Similarity=0.446  Sum_probs=12.7

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.||||||||..
T Consensus         4 ~i~i~GptgsGKttl   18 (409)
T 3eph_A            4 VIVIAGTTGVGKSQL   18 (409)
T ss_dssp             EEEEEECSSSSHHHH
T ss_pred             EEEEECcchhhHHHH
Confidence            367899999999964

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=83.84  E-value=0.47  Score=32.69  Aligned_cols=19  Identities=16%  Similarity=0.272  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        26 ~~Ge~~~i~G~nGsGKSTL   44 (243)
T 1mv5_A           26 QPNSIIAFAGPSGGGKSTI   44 (243)
T ss_dssp             CTTEEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3677889999999999973

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=83.84  E-value=0.83  Score=32.83  Aligned_cols=27  Identities=11%  Similarity=0.161  Sum_probs=18.6

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      .|.-+.+.||+|||||..  +-+|..+..
T Consensus        89 ~g~ivgI~G~sGsGKSTL--~~~L~gll~  115 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTT--ARVLQALLA  115 (312)
T ss_dssp             CCEEEEEECCTTSCHHHH--HHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHH--HHHHHhhcc
Confidence            455678999999999974  344444443

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=83.77  E-value=0.53  Score=30.41  Aligned_cols=16  Identities=31%  Similarity=0.387  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +-+++.++.|||||..
T Consensus         7 ~~I~l~G~~GsGKsT~   22 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQ   22 (194)
T ss_dssp             EEEEEEESTTSSHHHH
T ss_pred             cEEEEECCCCCCHHHH
Confidence            3588999999999975

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=83.65  E-value=0.56  Score=30.86  Aligned_cols=16  Identities=19%  Similarity=0.306  Sum_probs=13.3

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+.+.|++|||||...
T Consensus         3 ~i~i~G~~GsGKSTl~   18 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVA   18 (204)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            4788999999999753

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=83.60  E-value=0.61  Score=32.69  Aligned_cols=18  Identities=33%  Similarity=0.529  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+.+.+|+|+|||..
T Consensus        49 ~Gei~~liG~NGsGKSTL   66 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTF   66 (263)
T ss_dssp             TTCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEEcCCCCcHHHH
Confidence            677889999999999973

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=83.52  E-value=2.1  Score=28.01  Aligned_cols=15  Identities=27%  Similarity=0.113  Sum_probs=12.4

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+.+.++.|||||..
T Consensus         6 ~i~i~G~sGsGKTTl   20 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTL   20 (169)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            467889999999964

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=83.50  E-value=0.7  Score=34.45  Aligned_cols=21  Identities=38%  Similarity=0.768  Sum_probs=16.7

Q ss_pred             HhcCCc--EEEEccCCchHHHHH
Q psy3307          45 IISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      +++|.+  ++.-+.||||||++.
T Consensus        94 ~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           94 LLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             HTTTCCEEEEEESCTTSSHHHHH
T ss_pred             hhcCceeeEeeecCCCCCCCeEe
Confidence            457864  577899999999875

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=83.50  E-value=1.8  Score=32.50  Aligned_cols=27  Identities=22%  Similarity=0.250  Sum_probs=19.2

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.|++|+|||... +-+...+.
T Consensus       202 ~G~liiI~G~pG~GKTtl~-l~ia~~~~  228 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFA-LNIAQNVA  228 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHH-HHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            5578899999999999644 44444333

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=83.50  E-value=0.62  Score=32.74  Aligned_cols=19  Identities=26%  Similarity=0.454  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        43 ~~Ge~~~i~G~nGsGKSTL   61 (271)
T 2ixe_A           43 YPGKVTALVGPNGSGKSTV   61 (271)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4778889999999999973

>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=83.49  E-value=1.6  Score=30.91  Aligned_cols=16  Identities=25%  Similarity=0.434  Sum_probs=12.2

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+|+|+|||...
T Consensus        50 ~~L~~G~~G~GKT~la   65 (324)
T 3u61_B           50 IILHSPSPGTGKTTVA   65 (324)
T ss_dssp             EEEECSSTTSSHHHHH
T ss_pred             EEEeeCcCCCCHHHHH
Confidence            4566777999999753

>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=83.46  E-value=1.9  Score=31.37  Aligned_cols=18  Identities=33%  Similarity=0.403  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      |+-+++.+++|+|||...
T Consensus        61 G~iv~I~G~pGsGKTtLa   78 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVA   78 (349)
T ss_dssp             TSEEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            467899999999999754

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=83.41  E-value=0.63  Score=32.92  Aligned_cols=19  Identities=26%  Similarity=0.407  Sum_probs=16.2

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        45 ~~Ge~~~liG~NGsGKSTL   63 (279)
T 2ihy_A           45 AKGDKWILYGLNGAGKTTL   63 (279)
T ss_dssp             ETTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3677889999999999973

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=83.41  E-value=0.59  Score=31.21  Aligned_cols=16  Identities=19%  Similarity=0.258  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ..+.+.|++|||||..
T Consensus         6 ~~i~i~G~~GsGKSTl   21 (227)
T 1cke_A            6 PVITIDGPSGAGKGTL   21 (227)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4688999999999964

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=83.37  E-value=0.57  Score=31.77  Aligned_cols=18  Identities=22%  Similarity=0.383  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.+++|||||..
T Consensus        15 ~~~~I~l~G~~GsGKsT~   32 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQ   32 (233)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            456899999999999964

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=83.30  E-value=1.3  Score=34.09  Aligned_cols=26  Identities=23%  Similarity=0.339  Sum_probs=17.8

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      |.-+.+.|++|+|||...  -.|..++.
T Consensus       293 GeVI~LVGpNGSGKTTLl--~~LAgll~  318 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTI--GKLARQFE  318 (503)
T ss_dssp             TEEEEEECCTTSSHHHHH--HHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHH--HHHHHHhh
Confidence            446789999999999843  33444443

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=83.20  E-value=1.8  Score=32.40  Aligned_cols=27  Identities=26%  Similarity=0.252  Sum_probs=18.8

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.|++|+|||.. ++-+.....
T Consensus       199 ~G~l~ii~G~pg~GKT~l-al~ia~~~a  225 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAF-ALTIAQNAA  225 (444)
T ss_dssp             TTCEEEEEECTTSCHHHH-HHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHH-HHHHHHHHH
Confidence            456789999999999964 344444443

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=83.19  E-value=0.6  Score=32.36  Aligned_cols=18  Identities=17%  Similarity=0.097  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      +.-+++.|++|||||...
T Consensus         4 ~~lIvl~G~pGSGKSTla   21 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFS   21 (260)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHH
Confidence            346899999999999743

>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=83.13  E-value=2  Score=29.36  Aligned_cols=40  Identities=18%  Similarity=0.261  Sum_probs=25.4

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRE  106 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  106 (130)
                      |+=.++.++-|+|||... +-.+.+.....                  -+++++.|..+
T Consensus        28 G~l~vitG~MgsGKTT~l-L~~a~r~~~~g------------------~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEEL-IRRVRRTQFAK------------------QHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHH-HHHHHHHHHTT------------------CCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHH-HHHHHHHHHCC------------------CEEEEEEeccC
Confidence            455567898899999764 44444544433                  35888877754

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=83.13  E-value=0.46  Score=30.56  Aligned_cols=19  Identities=21%  Similarity=0.151  Sum_probs=11.2

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .+.-+++.++.|||||...
T Consensus         4 ~~~~I~l~G~~GsGKST~a   22 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTA   22 (183)
T ss_dssp             -CCEEEEECCC----CHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3567899999999999753

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=83.02  E-value=0.96  Score=34.30  Aligned_cols=22  Identities=36%  Similarity=0.516  Sum_probs=17.3

Q ss_pred             HHhcCCc--EEEEccCCchHHHHH
Q psy3307          44 VIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        44 ~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+++|.|  ++.-+.||||||++.
T Consensus       131 ~~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          131 HNFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HhhcCCceEEEEeCCCCCCCCEEe
Confidence            4468864  577889999999875

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=82.94  E-value=0.63  Score=30.70  Aligned_cols=15  Identities=40%  Similarity=0.317  Sum_probs=12.7

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+.+.|+.|||||..
T Consensus         4 ~i~l~G~~GsGKST~   18 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTI   18 (206)
T ss_dssp             EEEEECSTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            367899999999974

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=82.75  E-value=0.41  Score=33.02  Aligned_cols=17  Identities=29%  Similarity=0.450  Sum_probs=14.5

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +..+++.|++|||||..
T Consensus        32 ~~~i~l~G~~GsGKSTl   48 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTI   48 (253)
T ss_dssp             CEEEEEESCGGGTTHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45789999999999974

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=82.74  E-value=0.62  Score=30.62  Aligned_cols=17  Identities=18%  Similarity=0.311  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.|+.|||||...
T Consensus        16 ~~I~l~G~~GsGKsT~~   32 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQC   32 (203)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            46889999999999753

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=82.68  E-value=0.87  Score=33.79  Aligned_cols=24  Identities=38%  Similarity=0.581  Sum_probs=18.0

Q ss_pred             HhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          42 IPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      +..+++|.|  ++.-+.||||||++.
T Consensus       108 v~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          108 VQSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HHGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhcCCCceEEEEeCCCCCCCceEe
Confidence            344568864  577789999999875

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=82.68  E-value=0.59  Score=37.47  Aligned_cols=19  Identities=26%  Similarity=0.351  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      ...++++.||+|+|||...
T Consensus       200 ~~~~vLL~G~pGtGKT~la  218 (758)
T 3pxi_A          200 TKNNPVLIGEPGVGKTAIA  218 (758)
T ss_dssp             SSCEEEEESCTTTTTHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH
Confidence            3469999999999999753

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=82.59  E-value=0.58  Score=30.55  Aligned_cols=15  Identities=20%  Similarity=0.459  Sum_probs=12.8

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.|+.|||||..
T Consensus         2 ~I~i~G~~GsGKsT~   16 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTI   16 (205)
T ss_dssp             EEEEECCTTSCHHHH
T ss_pred             EEEEECCCccCHHHH
Confidence            478899999999974

>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=82.31  E-value=1.7  Score=31.16  Aligned_cols=17  Identities=29%  Similarity=0.436  Sum_probs=13.9

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.+++|+|||...
T Consensus       105 ~vi~ivG~~GsGKTTl~  121 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSC  121 (306)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEEcCCCChHHHHH
Confidence            45789999999999753

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=82.29  E-value=0.74  Score=31.77  Aligned_cols=19  Identities=16%  Similarity=0.197  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+.+.+|+|||||...
T Consensus        26 ~g~~I~I~G~~GsGKSTl~   44 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLC   44 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4678999999999999753

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=82.26  E-value=0.68  Score=29.46  Aligned_cols=16  Identities=25%  Similarity=0.424  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      .++++.++.|||||..
T Consensus         8 ~~i~l~G~~GsGKSTv   23 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSL   23 (168)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            5789999999999974

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=82.01  E-value=1.3  Score=29.57  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=15.8

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      -.++.+|+|+|||..  +-++..+.
T Consensus        25 ~~~I~G~NgsGKSti--l~ai~~~l   47 (203)
T 3qks_A           25 INLIIGQNGSGKSSL--LDAILVGL   47 (203)
T ss_dssp             EEEEECCTTSSHHHH--HHHHHHHH
T ss_pred             eEEEEcCCCCCHHHH--HHHHHHHh
Confidence            457889999999974  33444433

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=81.92  E-value=0.77  Score=31.49  Aligned_cols=18  Identities=22%  Similarity=0.281  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+++.|+.|||||..
T Consensus        28 ~~~~I~l~G~~GsGKsT~   45 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQ   45 (243)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            445799999999999964

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=81.79  E-value=1.3  Score=32.33  Aligned_cols=21  Identities=24%  Similarity=0.240  Sum_probs=15.8

Q ss_pred             cEEEEccCCchHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      -.++.|+||+|||..  +-.+..
T Consensus        27 l~vi~G~NGaGKT~i--leAI~~   47 (371)
T 3auy_A           27 IVAIIGENGSGKSSI--FEAVFF   47 (371)
T ss_dssp             EEEEEECTTSSHHHH--HHHHHH
T ss_pred             eEEEECCCCCCHHHH--HHHHHH
Confidence            457899999999974  555555

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=81.76  E-value=0.83  Score=32.83  Aligned_cols=26  Identities=23%  Similarity=0.617  Sum_probs=19.3

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+.+.+|+|+|||.  ++-++..++
T Consensus        79 ~Ge~vaivG~sGsGKST--Ll~ll~gl~  104 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKST--ILRLLFRFY  104 (306)
T ss_dssp             TTCEEEEESSSCHHHHH--HHHHHTTSS
T ss_pred             CCCEEEEECCCCchHHH--HHHHHHcCC
Confidence            67788999999999997  344444433

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=81.72  E-value=0.66  Score=31.29  Aligned_cols=15  Identities=20%  Similarity=0.290  Sum_probs=12.4

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.+|+||||+.-
T Consensus         2 ~Iil~GpPGsGKgTq   16 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQ   16 (206)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999853

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=81.52  E-value=2.6  Score=29.02  Aligned_cols=17  Identities=47%  Similarity=0.556  Sum_probs=14.8

Q ss_pred             cEEEEccCCchHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFL   66 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~   66 (130)
                      ++++.++.|+|||...+
T Consensus         8 ~I~~~~kgGvGKTt~a~   24 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAML   24 (228)
T ss_dssp             EEEEESSTTSSHHHHHH
T ss_pred             EEEEECCCCCcHHHHHH
Confidence            68999999999998753

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=81.50  E-value=4.1  Score=30.73  Aligned_cols=17  Identities=35%  Similarity=0.358  Sum_probs=14.2

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +-+++.+++|+|||...
T Consensus        98 ~vI~lvG~~GsGKTTt~  114 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTA  114 (433)
T ss_dssp             EEEEECCCTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            46788999999999754

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=81.49  E-value=0.73  Score=29.78  Aligned_cols=15  Identities=33%  Similarity=0.295  Sum_probs=12.7

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.|+.|||||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQ   16 (195)
T ss_dssp             EEEEECSTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            368899999999974

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=81.45  E-value=0.8  Score=32.59  Aligned_cols=18  Identities=33%  Similarity=0.532  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|.-+.+.+|+|+|||..
T Consensus        63 ~Ge~~~i~G~NGsGKSTL   80 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSL   80 (290)
T ss_dssp             TTCEEEEEESTTSSHHHH
T ss_pred             CCCEEEEECCCCCcHHHH
Confidence            677889999999999973

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=81.44  E-value=2.3  Score=30.76  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=17.2

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      -+.+.||+|||||..  +-.|..+..
T Consensus        94 iigI~GpsGSGKSTl--~~~L~~ll~  117 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTT--SRVLKALLS  117 (321)
T ss_dssp             EEEEECCTTSSHHHH--HHHHHHHHT
T ss_pred             EEEEECCCCCCHHHH--HHHHHHHhc
Confidence            478899999999974  344555443

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=81.42  E-value=0.75  Score=29.15  Aligned_cols=15  Identities=20%  Similarity=0.220  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.++.|||||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTV   16 (168)
T ss_dssp             EEEEESCTTSCHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            478999999999974

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=81.15  E-value=0.68  Score=30.65  Aligned_cols=18  Identities=22%  Similarity=0.038  Sum_probs=14.7

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+.-+.+.+++|||||..
T Consensus        21 ~~~~i~i~G~~GsGKstl   38 (201)
T 1rz3_A           21 GRLVLGIDGLSRSGKTTL   38 (201)
T ss_dssp             SSEEEEEEECTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            345688999999999974

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=81.07  E-value=0.82  Score=32.03  Aligned_cols=17  Identities=41%  Similarity=0.636  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      |.-+.+.+|+|+|||..
T Consensus        30 Ge~~~i~G~NGsGKSTL   46 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTL   46 (263)
T ss_dssp             SSEEEEECCTTSSHHHH
T ss_pred             CEEEEEECCCCCCHHHH
Confidence            77888999999999974

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=80.98  E-value=0.73  Score=37.57  Aligned_cols=17  Identities=29%  Similarity=0.501  Sum_probs=15.0

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +.+++.+|+|+|||+..
T Consensus       239 ~GILL~GPPGTGKT~LA  255 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLIA  255 (806)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            68999999999999743

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=80.75  E-value=0.78  Score=30.55  Aligned_cols=15  Identities=13%  Similarity=0.222  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.|+.|||||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQ   16 (214)
T ss_dssp             EEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>4h1g_A Maltose binding protein-cakar3 motor domain fusio; kinesin motor domain, motor protein, chimera; HET: MTT ADP EDO; 2.15A {Escherichia coli}

Probab=80.51  E-value=1.2  Score=35.59  Aligned_cols=25  Identities=44%  Similarity=0.618  Sum_probs=19.5

Q ss_pred             HHhHHhcCCc--EEEEccCCchHHHHH
Q psy3307          41 AIPVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.|  ++.-+.||||||.+.
T Consensus       454 ~v~~~~~G~n~~i~ayGqtgsGKT~Tm  480 (715)
T 4h1g_A          454 LIQCSLDGTNVCVFAYGQTGSGKTFTM  480 (715)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhCCceEEEEccCCCCCchhhcc
Confidence            4566788875  566789999999874

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=80.48  E-value=0.75  Score=31.46  Aligned_cols=19  Identities=21%  Similarity=0.120  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+.+.+|+|||||...
T Consensus        24 ~g~iigI~G~~GsGKSTl~   42 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVC   42 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4556789999999999753

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=80.48  E-value=1.1  Score=32.59  Aligned_cols=25  Identities=28%  Similarity=0.422  Sum_probs=18.7

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      |+-+.+.+|+|+|||.  ++-+|..++
T Consensus       170 g~k~~IvG~nGsGKST--Llk~L~gl~  194 (365)
T 1lw7_A          170 AKTVAILGGESSGKSV--LVNKLAAVF  194 (365)
T ss_dssp             CEEEEEECCTTSHHHH--HHHHHHHHT
T ss_pred             hCeEEEECCCCCCHHH--HHHHHHHHh
Confidence            7788999999999997  344444443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=80.47  E-value=3.3  Score=30.17  Aligned_cols=27  Identities=22%  Similarity=0.297  Sum_probs=19.0

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.|++|+|||... +-+...+.
T Consensus        45 ~G~LiiIaG~pG~GKTt~a-l~ia~~~a   71 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLM-MNMVLSAL   71 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHH-HHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHH-HHHHHHHH
Confidence            5577899999999999644 44444333

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=80.02  E-value=0.85  Score=42.49  Aligned_cols=19  Identities=37%  Similarity=0.688  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|+.++++||||+|||.
T Consensus      1301 l~~~~pvLL~GptGtGKT~ 1319 (3245)
T 3vkg_A         1301 LSEHRPLILCGPPGSGKTM 1319 (3245)
T ss_dssp             HHTTCCCEEESSTTSSHHH
T ss_pred             HHCCCcEEEECCCCCCHHH
Confidence            4478999999999999995

---

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	130
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	7e-18
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-15
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	1e-14
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	3e-14
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-14
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-13
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-13
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	2e-12
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-12
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-11
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-11
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	5e-11
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-08
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	4e-06

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 74.2 bits (181), Expect = 7e-18
 Identities = 59/117 (50%), Positives = 78/117 (66%), Gaps = 7/117 (5%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD++++   I NNI LA Y +PTP+QK AIP I+  RD+MACAQTGSGKTAAFL+PI+N 
Sbjct: 23  FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINH 82

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +  +       +       K  +P  L+LAPTRELA QI  E++KF+  + LR CVV
Sbjct: 83  LVCQDLNQQRYS-------KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVV 132

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 68.4 bits (166), Expect = 1e-15
 Identities = 22/117 (18%), Positives = 37/117 (31%), Gaps = 21/117 (17%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
            +D  + E +          +P  +QK     I+      A A TG GKT+  L   L  
Sbjct: 25  PEDFLLKEFV--EFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLF- 81

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
                                      V+ PT  L  Q  +  +K+A ++ +    +
Sbjct: 82  ------------------LALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENL 120

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.3 bits (158), Expect = 1e-14
 Identities = 38/115 (33%), Positives = 52/115 (45%), Gaps = 16/115 (13%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FDD+ ++E +   I    ++KP+ +Q+ AI   I G DV+A AQ+G+GKTA F + IL Q
Sbjct: 14  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 73

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPC 127
           +                         LVLAPTRELA QI                
Sbjct: 74  IE----------------LDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCH 112

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.5 bits (156), Expect = 3e-14
 Identities = 35/117 (29%), Positives = 54/117 (46%), Gaps = 16/117 (13%)

Query: 13  FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
           FD + + E +   I    ++KP+ +Q+ AI  II GRDV+A +Q+G+GKTA F + +L  
Sbjct: 19  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 78

Query: 73  MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 129
           +                  +      L+LAPTRELA QI            ++    
Sbjct: 79  LD----------------IQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC 119

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 64.9 bits (157), Expect = 4e-14
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 18/84 (21%)

Query: 44  VIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAP 103
           +    R  +     G+GKT  +L  I+ +  +RG               +     L+LAP
Sbjct: 5   IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGL--------------RT----LILAP 46

Query: 104 TRELATQIYDEAKKFAYRSQLRPC 127
           TR +A ++ +  +    R Q    
Sbjct: 47  TRVVAAEMEEALRGLPIRYQTPAI 70

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 62.3 bits (150), Expect = 1e-13
 Identities = 18/108 (16%), Positives = 42/108 (38%), Gaps = 21/108 (19%)

Query: 13  FDDIQ--MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 70
            +++   ++      +     ++  P Q  A+  + SG++++    T +GKT    + ++
Sbjct: 3   VEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMV 62

Query: 71  NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF 118
            +  + G                     L + P R LA + Y+  KK+
Sbjct: 63  REAIKGGK-------------------SLYVVPLRALAGEKYESFKKW 91

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (150), Expect = 2e-13
 Identities = 23/68 (33%), Positives = 45/68 (66%)

Query: 9  KKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVP 68
          K   F+D  +   +   I    ++KP+P+Q+ +IP+ +SGRD++A A+ G+GK+ A+L+P
Sbjct: 1  KGNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIP 60

Query: 69 ILNQMYER 76
          +L ++  +
Sbjct: 61 LLERLDLK 68

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 59.2 bits (142), Expect = 2e-12
 Identities = 27/64 (42%), Positives = 45/64 (70%)

Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
          F+D  +   +   I  A ++KP+P+Q+ AIPV I+GRD++A A+ G+GKTAAF++P L +
Sbjct: 3  FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 62

Query: 73 MYER 76
          +  +
Sbjct: 63 VKPK 66

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.1 bits (142), Expect = 2e-12
 Identities = 22/63 (34%), Positives = 33/63 (52%)

Query: 12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILN 71
          GF D  +   +   I    ++ P+ VQ   IP  I G DV+  A++G GKTA F++  L 
Sbjct: 2  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 72 QMY 74
          Q+ 
Sbjct: 62 QLE 64

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.1 bits (137), Expect = 1e-11
 Identities = 23/71 (32%), Positives = 40/71 (56%)

Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
          FDD+++ E +   +    +++P+ +Q+ AI  II G DV+A AQ+G+GKT  F +  L +
Sbjct: 12 FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQR 71

Query: 73 MYERGPLPTPP 83
          +      P   
Sbjct: 72 IDTSVKAPQAL 82

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 55.8 bits (133), Expect = 4e-11
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 31 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQM 73
          Y +  P Q+  I  ++SGRD +    TG GK+  + +P L   
Sbjct: 23 YQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN 65

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 55.4 bits (132), Expect = 5e-11
 Identities = 21/63 (33%), Positives = 34/63 (53%)

Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 72
          F        I   I   R+ KPT +Q+  IP  + G  ++  +QTG+GKT A+L+PI+ +
Sbjct: 3  FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEK 62

Query: 73 MYE 75
          +  
Sbjct: 63 IKP 65

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 21/63 (33%), Positives = 42/63 (66%), Gaps = 1/63 (1%)

Query: 13 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGR-DVMACAQTGSGKTAAFLVPILN 71
          F+++ +++ I N I    ++KPT +Q   IP+ ++   +++A A+TGSGKTA+F +P++ 
Sbjct: 6  FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE 65

Query: 72 QMY 74
           + 
Sbjct: 66 LVN 68

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 42.1 bits (97), Expect = 4e-06
 Identities = 8/46 (17%), Positives = 17/46 (36%), Gaps = 1/46 (2%)

Query: 33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGP 78
          +P   Q+          + +    TG GKT   ++    ++ + G 
Sbjct: 9  QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG 53

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	130
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.97
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.97
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.97
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.96
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.96
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.96
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.94
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.94
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.92
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.84
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.81
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.79
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.63
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.4
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.39
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.36
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.29
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.21
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.02
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.69
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.36
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	98.15
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.84
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.8
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	97.77
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.74
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.63
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	97.48
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	97.29
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.51
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	96.49
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.84
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.63
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	95.52
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.49
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	95.46
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.42
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	95.27
d1ls1a2	207	GTPase domain of the signal sequence recognition p	95.25
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.09
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.97
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.92
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.77
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	94.75
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	94.7
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.69
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	94.55
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.49
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.46
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.45
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	94.43
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.42
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	94.15
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	93.95
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.9
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.83
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	93.77
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	93.45
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	93.41
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	93.27
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	93.22
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	93.19
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.19
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	93.16
d1okkd2	207	GTPase domain of the signal recognition particle r	93.15
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	93.01
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	92.9
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	92.46
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	92.36
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	92.34
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	92.21
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.08
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	91.98
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	91.92
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	91.92
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	91.82
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	91.65
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.52
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	91.44
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.24
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	91.16
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	91.13
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	91.05
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	90.96
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	90.37
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	90.34
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	90.23
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	90.23
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	90.12
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	90.1
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	90.09
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	89.96
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	89.8
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	89.79
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	89.32
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	89.25
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	89.25
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	89.13
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	89.08
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	89.04
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	89.0
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	88.94
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	88.92
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	88.62
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	88.6
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	88.59
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	88.53
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	88.32
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	87.76
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	87.63
d1tuea_	205	Replication protein E1 helicase domain {Human papi	87.51
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	87.49
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	87.49
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	87.38
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	87.13
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	86.59
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	86.57
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	86.54
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	86.51
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	86.47
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	86.4
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	86.22
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	86.05
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	85.67
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	85.65
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	85.22
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	84.74
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	84.72
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	84.58
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	84.39
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	84.35
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	84.07
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	83.94
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	83.86
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.86
d2awna2	232	Maltose transport protein MalK, N-terminal domain	83.84
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	83.65
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	83.55
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	83.42
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	83.23
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.19
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	83.05
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	82.69
d1g2912	240	Maltose transport protein MalK, N-terminal domain	82.67
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	82.3
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	82.26
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	82.17
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	81.9
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	81.75
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	81.64
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	81.47
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	80.62
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	80.61
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	80.5
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	80.24
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	80.07

>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=99.97  E-value=1.9e-31  Score=185.09  Aligned_cols=107  Identities=33%  Similarity=0.434  Sum_probs=98.2

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG   87 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~   87 (130)
                      ....+|++|+|++.++++|+++||+.|||+|.++||.+++|+|++++||||||||+||++|+++++.....         
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~---------   84 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR---------   84 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSC---------
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccccc---------
Confidence            44568999999999999999999999999999999999999999999999999999999999998754432         


Q ss_pred             CCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          88 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        88 ~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                             .++++|++|||||+.|+++.+++++++.++++.+++
T Consensus        85 -------~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~  120 (222)
T d2j0sa1          85 -------ETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI  120 (222)
T ss_dssp             -------SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEEC
T ss_pred             -------CceeEEecchHHHHHHHHHHHHHHhCccceeEEEEe
Confidence                   278999999999999999999999999999988764

>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=99.97  E-value=3.4e-31  Score=183.40  Aligned_cols=111  Identities=35%  Similarity=0.407  Sum_probs=102.2

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      |...++++.+|++++|++.++++|+++||+.||++|.++||.+++|+|++++||||||||++|++|+++++.....    
T Consensus         4 ~~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~----   79 (218)
T d2g9na1           4 ESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLK----   79 (218)
T ss_dssp             CCCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC----
T ss_pred             CCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccccc----
Confidence            5567889999999999999999999999999999999999999999999999999999999999999999854322    


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                  +++++|++||++||.|+++.++++....+.++.++
T Consensus        80 ------------~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~  114 (218)
T d2g9na1          80 ------------ATQALVLAPTRELAQQIQKVVMALGDYMGASCHAC  114 (218)
T ss_dssp             ------------SCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEE
T ss_pred             ------------CccEEEEcccchhhhhHHHHHhhhccccceeEEee
Confidence                        38899999999999999999999999999887665

>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=99.97  E-value=6.3e-31  Score=184.14  Aligned_cols=121  Identities=49%  Similarity=0.791  Sum_probs=105.2

Q ss_pred             ccccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCC
Q psy3307           3 ECLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTP   82 (130)
Q Consensus         3 ~~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~   82 (130)
                      +...+.+..+|+|++|+++++++|++.||+.|||+|.++||.+++|+|++++||||||||++|++|+++++........ 
T Consensus        13 ~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~-   91 (238)
T d1wrba1          13 DYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQ-   91 (238)
T ss_dssp             SSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----
T ss_pred             CCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccc-
Confidence            4566778899999999999999999999999999999999999999999999999999999999999999976542211 


Q ss_pred             CCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          83 PAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        83 ~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                            ......+++++|++||++|+.|+++.++.++.+.++++..++
T Consensus        92 ------~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~  133 (238)
T d1wrba1          92 ------RYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVY  133 (238)
T ss_dssp             ---------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEEC
T ss_pred             ------cccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEe
Confidence                  112334589999999999999999999999999999888763

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=5.4e-30  Score=176.01  Aligned_cols=102  Identities=33%  Similarity=0.435  Sum_probs=91.8

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      ++|+||+|++++++++++.||+.|||+|.++||.+++|+|++++||||||||++|++|+++++.....            
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~------------   68 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG------------   68 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTT------------
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCC------------
Confidence            47999999999999999999999999999999999999999999999999999999999987654332            


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCC-ceEE
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQL-RPCV  128 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~-~~~~  128 (130)
                          +++++|++|||+|+.|+.+.++.++..++. ++++
T Consensus        69 ----~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~  103 (207)
T d1t6na_          69 ----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAV  103 (207)
T ss_dssp             ----CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEE
T ss_pred             ----CceEEEEeccchhhHHHHHHHHHHHhhCCCceeEE
Confidence                378999999999999999999999988653 4443

>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=99.96  E-value=1.1e-29  Score=175.01  Aligned_cols=110  Identities=32%  Similarity=0.457  Sum_probs=100.5

Q ss_pred             cccccccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCC
Q psy3307           4 CLVSLKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPP   83 (130)
Q Consensus         4 ~~~~~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~   83 (130)
                      ...+.+..+|++|+|+++++++|+++||+.||++|.++||.+++|+|++++||||||||++|++|+++++.....     
T Consensus         3 ~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~-----   77 (212)
T d1qdea_           3 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK-----   77 (212)
T ss_dssp             BSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC-----
T ss_pred             CCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCC-----
Confidence            467888999999999999999999999999999999999999999999999999999999999999998754332     


Q ss_pred             CCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          84 AGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        84 ~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                                 +++++|++||++++.|+...+..+.....+.+..+
T Consensus        78 -----------~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~  112 (212)
T d1qdea_          78 -----------APQALMLAPTRELALQIQKVVMALAFHMDIKVHAC  112 (212)
T ss_dssp             -----------SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEE
T ss_pred             -----------CcceEEEcccHHHhhhhhhhhcccccccccceeeE
Confidence                       38999999999999999999999998888776654

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=2.8e-29  Score=172.26  Aligned_cols=98  Identities=31%  Similarity=0.544  Sum_probs=89.7

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ..+|+|++|+++++++|+++||+.|||+|.++||.+++|+|++++||||||||++|++|+++++.....           
T Consensus         2 ~~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~-----------   70 (206)
T d1veca_           2 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKD-----------   70 (206)
T ss_dssp             CSSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSC-----------
T ss_pred             CCChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccccc-----------
Confidence            468999999999999999999999999999999999999999999999999999999999998654432           


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCC
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ  123 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~  123 (130)
                           +++++|++||++|+.|+++.++.+.+...
T Consensus        71 -----~~~~lil~pt~el~~q~~~~~~~~~~~~~   99 (206)
T d1veca_          71 -----NIQAMVIVPTRELALQVSQICIQVSKHMG   99 (206)
T ss_dssp             -----SCCEEEECSCHHHHHHHHHHHHHHTTTSS
T ss_pred             -----CcceEEEeecchhhHHHHHHHHHHhhccc
Confidence                 37899999999999999999999877543

>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=99.94  E-value=5.8e-27  Score=160.76  Aligned_cols=102  Identities=32%  Similarity=0.551  Sum_probs=93.0

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCC-cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGR-DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~-~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      .+|+|++|++++++++.+.||..|||+|.++||.+++|+ |++++||||||||++|++|+++.....             
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-------------   70 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-------------   70 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-------------
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-------------
Confidence            489999999999999999999999999999999999885 999999999999999999999864332             


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                          .+++++|++||++|+.|+.+.++.+....+.++.+.
T Consensus        71 ----~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~  106 (208)
T d1hv8a1          71 ----NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKI  106 (208)
T ss_dssp             ----SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEE
T ss_pred             ----cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEe
Confidence                237899999999999999999999999998887765

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.94  E-value=2.7e-26  Score=157.07  Aligned_cols=104  Identities=35%  Similarity=0.548  Sum_probs=95.6

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      .+|++|+|++.++++|++.||..|||+|.++||.+++|+|+++.||||||||++|++|+++.+.....            
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~------------   68 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLN------------   68 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSC------------
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccc------------
Confidence            37999999999999999999999999999999999999999999999999999999999998654432            


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEeC
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVL  130 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~~  130 (130)
                          ++++++++|+++++.|....+..+....++++.+++
T Consensus        69 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (206)
T d1s2ma1          69 ----KIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTT  104 (206)
T ss_dssp             ----SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEEC
T ss_pred             ----cccceeeccchhhhhhhhhhhhhcccccCeeEEeec
Confidence                277999999999999999999999999999987753

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.92  E-value=7.1e-25  Score=149.85  Aligned_cols=97  Identities=35%  Similarity=0.538  Sum_probs=87.6

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPS   90 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~   90 (130)
                      .+|++++|+++++++|++.||+.|||+|.++||.+++|+|++++||||||||++|++|+++........           
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~-----------   69 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAE-----------   69 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCS-----------
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeecccccccccc-----------
Confidence            479999999999999999999999999999999999999999999999999999999999987654322           


Q ss_pred             CCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCC
Q psy3307          91 RKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ  123 (130)
Q Consensus        91 ~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~  123 (130)
                           +..++++|+++++.+....+........
T Consensus        70 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (209)
T d1q0ua_          70 -----VQAVITAPTRELATQIYHETLKITKFCP   97 (209)
T ss_dssp             -----CCEEEECSSHHHHHHHHHHHHHHHTTSC
T ss_pred             -----ccccccccccchhHHHHHHHHhhhcccc
Confidence                 6789999999999999999888766643

>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=99.84  E-value=2e-21  Score=134.87  Aligned_cols=95  Identities=22%  Similarity=0.176  Sum_probs=78.8

Q ss_pred             CCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCC
Q psy3307          12 GFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSR   91 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~   91 (130)
                      .|.+..+.+.+ +++.+.++.+|+++|..+++.++.|+|++++||||+|||++++++++......               
T Consensus        23 ~~~~~~~~~~~-~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~---------------   86 (237)
T d1gkub1          23 LFPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKG---------------   86 (237)
T ss_dssp             CCTTHHHHHHH-HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTS---------------
T ss_pred             cCccchhHHHH-HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhc---------------
Confidence            34444444444 44556688899999999999999999999999999999999999988765432               


Q ss_pred             CCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCce
Q psy3307          92 KKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRP  126 (130)
Q Consensus        92 ~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~  126 (130)
                          .+++|++||++|+.|++++++++.+.+++++
T Consensus        87 ----~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~  117 (237)
T d1gkub1          87 ----KRCYVIFPTSLLVIQAAETIRKYAEKAGVGT  117 (237)
T ss_dssp             ----CCEEEEESCHHHHHHHHHHHHHHHTTTCCSG
T ss_pred             ----CeEEEEeccHHHHHHHHHHHHHHHHHcCCce
Confidence                4799999999999999999999999887764

>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=99.81  E-value=1.7e-20  Score=127.44  Aligned_cols=89  Identities=21%  Similarity=0.323  Sum_probs=80.1

Q ss_pred             CCCcCCCCCHHHHHHHHHC-CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q psy3307          11 QGFDDIQMTEIITNNIALA-RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYP   89 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~-~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~   89 (130)
                      ...+.++|++.+.+.+++. ||+.++|+|.++++.+++|+|+++++|||||||++|.+|++..    .            
T Consensus         2 ~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~----~------------   65 (206)
T d1oywa2           2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL----N------------   65 (206)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS----S------------
T ss_pred             CchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc----c------------
Confidence            4678899999999999887 9999999999999999999999999999999999999998642    1            


Q ss_pred             CCCCCCceEEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          90 SRKKVFPLGLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        90 ~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                            .++++++|+++|+.|..+.++.+...
T Consensus        66 ------~~~~~v~P~~~L~~q~~~~l~~~~~~   91 (206)
T d1oywa2          66 ------GLTVVVSPLISLMKDQVDQLQANGVA   91 (206)
T ss_dssp             ------SEEEEECSCHHHHHHHHHHHHHTTCC
T ss_pred             ------CceEEeccchhhhhhHHHHHHhhccc
Confidence                  46999999999999999999887554

>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=99.79  E-value=4.3e-20  Score=125.25  Aligned_cols=85  Identities=20%  Similarity=0.293  Sum_probs=74.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCce
Q psy3307          18 MTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL   97 (130)
Q Consensus        18 l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (130)
                      +++.++..|++.||++++|+|.++++.+.+|+|+++++|||||||+++.++++..+...                   .+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~-------------------~~   70 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG-------------------GK   70 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT-------------------CC
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhcc-------------------Cc
Confidence            67888999999999999999999999999999999999999999999999998877543                   46


Q ss_pred             EEEEcCcHHHHHHHHHHHHHHHhc
Q psy3307          98 GLVLAPTRELATQIYDEAKKFAYR  121 (130)
Q Consensus        98 ~lil~Pt~~La~q~~~~~~~l~~~  121 (130)
                      +|+++|+++|+.|..+.++++...
T Consensus        71 vl~l~P~~~L~~q~~~~~~~~~~~   94 (202)
T d2p6ra3          71 SLYVVPLRALAGEKYESFKKWEKI   94 (202)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTTTT
T ss_pred             ceeecccHHHHHHHHHHHHHHhhc
Confidence            999999999999999999877654

>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=99.63  E-value=1.2e-15  Score=102.32  Aligned_cols=77  Identities=19%  Similarity=0.184  Sum_probs=65.2

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      +|+++|.+++..+. ++|+++++|||+|||+++++++...+.+..                  .++++++|+++|+.|..
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~------------------~~il~i~P~~~L~~q~~   69 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYG------------------GKVLMLAPTKPLVLQHA   69 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSC------------------SCEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcC------------------CcEEEEcCchHHHHHHH
Confidence            79999999998775 567999999999999999888877765543                  46999999999999999


Q ss_pred             HHHHHHHhcCCCceEE
Q psy3307         113 DEAKKFAYRSQLRPCV  128 (130)
Q Consensus       113 ~~~~~l~~~~~~~~~~  128 (130)
                      +.++++....+.++..
T Consensus        70 ~~~~~~~~~~~~~v~~   85 (200)
T d1wp9a1          70 ESFRRLFNLPPEKIVA   85 (200)
T ss_dssp             HHHHHHBCSCGGGEEE
T ss_pred             HHHHHhhcccccceee
Confidence            9999998777666653

>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=99.40  E-value=3e-12  Score=89.61  Aligned_cols=87  Identities=23%  Similarity=0.195  Sum_probs=74.7

Q ss_pred             HHHHHHCCCCCCcHHHHHHHhHHhc----C--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCc
Q psy3307          23 TNNIALARYDKPTPVQKYAIPVIIS----G--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFP   96 (130)
Q Consensus        23 ~~~l~~~~~~~~t~~Q~~~i~~~~~----g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (130)
                      -+-++.+.| .+|+-|.+++..+..    +  .+.+++|.+|||||..|+..+...+...                   .
T Consensus        74 ~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g-------------------~  133 (264)
T d1gm5a3          74 EEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG-------------------F  133 (264)
T ss_dssp             HHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT-------------------S
T ss_pred             HHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcc-------------------c
Confidence            334567788 799999999998862    2  4789999999999999999998888765                   3


Q ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          97 LGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        97 ~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ++++++||..|+.|.++.++++...++++++.+
T Consensus       134 q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l  166 (264)
T d1gm5a3         134 QTAFMVPTSILAIQHYRRTVESFSKFNIHVALL  166 (264)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTCSSCCEEEC
T ss_pred             ceeEEeehHhhhHHHHHHHHHhhhhccccceee
Confidence            699999999999999999999999988887764

>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=99.39  E-value=5.4e-12  Score=86.82  Aligned_cols=94  Identities=22%  Similarity=0.233  Sum_probs=77.1

Q ss_pred             CCCCHHHHHHHHH-CCCCCCcHHHHHHHhHHh----cC--CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q psy3307          16 IQMTEIITNNIAL-ARYDKPTPVQKYAIPVII----SG--RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY   88 (130)
Q Consensus        16 l~l~~~i~~~l~~-~~~~~~t~~Q~~~i~~~~----~g--~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~   88 (130)
                      +..+.+..+.+.+ +.| .+|+-|..++..+.    ++  .+.+++|.||||||..|+..+...+...            
T Consensus        38 ~~~~~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g------------  104 (233)
T d2eyqa3          38 FKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH------------  104 (233)
T ss_dssp             CCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT------------
T ss_pred             CCCCHHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcC------------
Confidence            3445666666544 566 78999999998875    23  4889999999999999999888877543            


Q ss_pred             CCCCCCCceEEEEcCcHHHHHHHHHHHHHHHhcCCCceEEe
Q psy3307          89 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus        89 ~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~~~~~~~~~~  129 (130)
                             .++++++||..|+.|.++.++++...++++++++
T Consensus       105 -------~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l  138 (233)
T d2eyqa3         105 -------KQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMI  138 (233)
T ss_dssp             -------CEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEE
T ss_pred             -------CceEEEccHHHhHHHHHHHHHHHHhhCCCEEEec
Confidence                   4799999999999999999999999988888764

>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=99.36  E-value=1.1e-13  Score=97.52  Aligned_cols=57  Identities=28%  Similarity=0.440  Sum_probs=48.7

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA  119 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~  119 (130)
                      +..|+++++.||||||||++|+.+++.......                  .++||++||++||.|+++.++.+.
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~------------------~~~lvi~Ptr~La~q~~~~l~~~~   62 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRG------------------LRTLILAPTRVVAAEMEEALRGLP   62 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHT------------------CCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcC------------------CEEEEEccHHHHHHHHHHHHhcCC
Confidence            457899999999999999999888887766543                  579999999999999998876553

>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=99.29  E-value=7.4e-12  Score=88.38  Aligned_cols=72  Identities=22%  Similarity=0.200  Sum_probs=58.6

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .|+++|.+++..++..+..++.+|||+|||+.... ++..+.....                 .++||++|+++|+.|..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~~~-----------------~k~Liivp~~~Lv~Q~~  174 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQAL-LARYYLENYE-----------------GKILIIVPTTALTTQMA  174 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHH-HHHHHHHHCS-----------------SEEEEECSSHHHHHHHH
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHH-HHHHhhhccc-----------------ceEEEEEcCchhHHHHH
Confidence            69999999999999988999999999999987543 3333333321                 47999999999999999


Q ss_pred             HHHHHHHhcC
Q psy3307         113 DEAKKFAYRS  122 (130)
Q Consensus       113 ~~~~~l~~~~  122 (130)
                      +.+.+++...
T Consensus       175 ~~f~~~~~~~  184 (282)
T d1rifa_         175 DDFVDYRLFS  184 (282)
T ss_dssp             HHHHHHTSCC
T ss_pred             HHHHHhhccc
Confidence            9999886543

>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=99.21  E-value=2.3e-11  Score=81.97  Aligned_cols=67  Identities=24%  Similarity=0.247  Sum_probs=55.1

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++++|.+++..+++++..++.+|||+|||+..+.. +..   ..                  .++||++|+++|+.|..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~-~~~---~~------------------~~~Liv~p~~~L~~q~~  127 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAA-INE---LS------------------TPTLIVVPTLALAEQWK  127 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHH-HHH---SC------------------SCEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhH-HHH---hc------------------CceeEEEcccchHHHHH
Confidence            689999999999999989999999999999876432 222   11                  35999999999999999


Q ss_pred             HHHHHHHhc
Q psy3307         113 DEAKKFAYR  121 (130)
Q Consensus       113 ~~~~~l~~~  121 (130)
                      +.++++...
T Consensus       128 ~~~~~~~~~  136 (206)
T d2fz4a1         128 ERLGIFGEE  136 (206)
T ss_dssp             HHHGGGCGG
T ss_pred             HHHHhhccc
Confidence            999877543

>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=99.02  E-value=1.1e-10  Score=72.77  Aligned_cols=54  Identities=31%  Similarity=0.387  Sum_probs=44.8

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK  117 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~  117 (130)
                      ..|+++++++|||||||..++..++.......                  .++++++|+++++.|..+.+..
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~------------------~~vli~~p~~~l~~q~~~~~~~   58 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARRR------------------LRTLVLAPTRVVLSEMKEAFHG   58 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHTT------------------CCEEEEESSHHHHHHHHHHTTT
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhcC------------------ceeeeeecchhHHHHHHHHhhh
Confidence            47899999999999999888777776665543                  5699999999999999887643

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.69  E-value=1.5e-08  Score=63.34  Aligned_cols=51  Identities=24%  Similarity=0.100  Sum_probs=38.2

Q ss_pred             CCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHHHHHh
Q psy3307          48 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAY  120 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~l~~  120 (130)
                      .+..++.+|||||||+.+...    +....                  .+++|++|+++|++|..+.+.+...
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~----~~~~~------------------~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAA----YAAQG------------------YKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHH----HHTTT------------------CCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCEEEEEeCCCCCHHHHHHHH----HHHcC------------------CcEEEEcChHHHHHHHHHHHHHHhh
Confidence            356799999999999754222    12211                  4699999999999999999877643

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=98.36  E-value=9.6e-07  Score=61.18  Aligned_cols=71  Identities=18%  Similarity=0.111  Sum_probs=50.5

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .++|-|.+++..  ....+++.|+.|||||.+.+--+...+......               ..+++++++|+.++..+.
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~---------------~~~ILvlt~tn~a~~~i~   63 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQ---------------ARHIAAVTFTNKAAREMK   63 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCC---------------GGGEEEEESSHHHHHHHH
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCC---------------hhHEEEEeCcHHHHHHHH
Confidence            368899999954  345689999999999987543333333332210               146999999999999998


Q ss_pred             HHHHHHHh
Q psy3307         113 DEAKKFAY  120 (130)
Q Consensus       113 ~~~~~l~~  120 (130)
                      ..+.++..
T Consensus        64 ~~~~~~~~   71 (306)
T d1uaaa1          64 ERVGQTLG   71 (306)
T ss_dssp             HHHHHHSC
T ss_pred             HHHHHhcC
Confidence            88876543

>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=98.15  E-value=7.3e-06  Score=57.10  Aligned_cols=71  Identities=20%  Similarity=0.125  Sum_probs=51.3

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      .+++-|.+++..  .+..++|.|+.|||||.+.+--+...+.....               ..-+++++++|+..+..+.
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~---------------~p~~il~lt~t~~aa~~~~   73 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV---------------APWNILAITFTNKAAREMR   73 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC---------------CGGGEEEEESSHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCC---------------CHHHeEeEeccHHHHHHHH
Confidence            478999999964  24569999999999998764444433332211               1136999999999999998


Q ss_pred             HHHHHHHh
Q psy3307         113 DEAKKFAY  120 (130)
Q Consensus       113 ~~~~~l~~  120 (130)
                      ..+.....
T Consensus        74 ~~~~~~~~   81 (318)
T d1pjra1          74 ERVQSLLG   81 (318)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHhhcc
Confidence            88865543

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.84  E-value=3.7e-05  Score=51.44  Aligned_cols=71  Identities=21%  Similarity=0.276  Sum_probs=51.3

Q ss_pred             CCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          33 KPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      .+.|+|.+++..+.    .+..+++.-+.|.|||+.. +.++..+......                .++||++| ..+.
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~-i~~~~~~~~~~~~----------------~~~LIv~p-~~l~   73 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT-IAVFSDAKKENEL----------------TPSLVICP-LSVL   73 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH-HHHHHHHHHTTCC----------------SSEEEEEC-STTH
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHH-HHhhhhhhhcccc----------------cccceecc-hhhh
Confidence            57899999986442    4567899999999999986 4444444433221                35899998 5778


Q ss_pred             HHHHHHHHHHHhc
Q psy3307         109 TQIYDEAKKFAYR  121 (130)
Q Consensus       109 ~q~~~~~~~l~~~  121 (130)
                      .|..+++.++...
T Consensus        74 ~~W~~e~~~~~~~   86 (230)
T d1z63a1          74 KNWEEELSKFAPH   86 (230)
T ss_dssp             HHHHHHHHHHCTT
T ss_pred             hHHHHHHHhhccc
Confidence            8888888877654

>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=97.80  E-value=8.3e-05  Score=53.28  Aligned_cols=71  Identities=21%  Similarity=0.185  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHH
Q psy3307          33 KPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIY  112 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~  112 (130)
                      ..++.|..|+..++.++-.++.||+|||||... ..++..+.....              ..+.++++.+||..-+..+.
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~~~--------------~~~~~I~l~ApTgkAA~~L~  212 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQMAD--------------GERCRIRLAAPTGKAAARLT  212 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH-HHHHHHHHHTCS--------------SCCCCEEEEBSSHHHHHHHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehH-HHHHHHHHHHHh--------------ccCCeEEEecCcHHHHHHHH
Confidence            456789999999999999999999999999864 233333332211              11257999999999888887


Q ss_pred             HHHHHH
Q psy3307         113 DEAKKF  118 (130)
Q Consensus       113 ~~~~~l  118 (130)
                      +.....
T Consensus       213 e~~~~~  218 (359)
T d1w36d1         213 ESLGKA  218 (359)
T ss_dssp             HHHTHH
T ss_pred             HHHHHH
Confidence            776544

>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=97.77  E-value=0.00019  Score=49.37  Aligned_cols=79  Identities=20%  Similarity=0.108  Sum_probs=66.1

Q ss_pred             CCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHH
Q psy3307          29 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA  108 (130)
Q Consensus        29 ~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La  108 (130)
                      +|. .++++|...--.+..|+  ++...||-|||++..+|+.-.....+                   .+-|++.+--||
T Consensus        77 lG~-RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~-------------------~vhvvTvNdyLA  134 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGK-------------------GVHVVTVNEYLA  134 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSS-------------------CEEEEESSHHHH
T ss_pred             hce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCC-------------------CceEEecCcccc
Confidence            465 78899988776677774  77999999999998888876655443                   488999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEe
Q psy3307         109 TQIYDEAKKFAYRSQLRPCVV  129 (130)
Q Consensus       109 ~q~~~~~~~l~~~~~~~~~~~  129 (130)
                      ..=.+++..+-+.+|++|.++
T Consensus       135 ~RDae~m~~iy~~lGlsvg~~  155 (273)
T d1tf5a3         135 SRDAEQMGKIFEFLGLTVGLN  155 (273)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEC
T ss_pred             chhhhHHhHHHHHcCCCcccc
Confidence            999999999999999999875

>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=97.63  E-value=0.00032  Score=48.48  Aligned_cols=76  Identities=18%  Similarity=0.296  Sum_probs=51.7

Q ss_pred             CCcHHHHHHHhHHh---------cCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcC
Q psy3307          33 KPTPVQKYAIPVII---------SGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAP  103 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~---------~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~P  103 (130)
                      .+.|+|.+++.-+.         .+...++.-..|.|||+.. +.++..+.......           .....++||++|
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qa-ia~l~~l~~~~~~~-----------~~~~~~~LIV~P  122 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQC-ITLIWTLLKQSPDC-----------KPEIDKVIVVSP  122 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHH-HHHHHHHHHCCTTS-----------SCSCSCEEEEEC
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHH-HHHHHHHHHhcccc-----------cCCCCcEEEEcc
Confidence            57899999986432         3457888999999999864 34444444433210           001135899999


Q ss_pred             cHHHHHHHHHHHHHHHhc
Q psy3307         104 TRELATQIYDEAKKFAYR  121 (130)
Q Consensus       104 t~~La~q~~~~~~~l~~~  121 (130)
                      . .+..|..++++++...
T Consensus       123 ~-sl~~qW~~Ei~k~~~~  139 (298)
T d1z3ix2         123 S-SLVRNWYNEVGKWLGG  139 (298)
T ss_dssp             H-HHHHHHHHHHHHHHGG
T ss_pred             c-hhhHHHHHHHHhhcCC
Confidence            8 4889999999887653

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=97.48  E-value=0.00016  Score=52.68  Aligned_cols=67  Identities=31%  Similarity=0.448  Sum_probs=49.4

Q ss_pred             CCcHHHHHHHhHHh----cC-CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVII----SG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g-~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|+.-|=++|..+.    +| ++.++.|-||||||+.. ..++...   .                  ..+|||+|+..+
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~i-A~l~~~~---~------------------rp~LVVt~n~~~   68 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTI-SNVIAQV---N------------------KPTLVIAHNKTL   68 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHH-HHHHHHH---T------------------CCEEEECSSHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHH-HHHHHHh---C------------------CCEEEEeCCHHH
Confidence            57777877776665    34 67899999999999643 2222221   1                  238999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy3307         108 ATQIYDEAKKFAYR  121 (130)
Q Consensus       108 a~q~~~~~~~l~~~  121 (130)
                      |.|+++.++.+...
T Consensus        69 A~qL~~dL~~~l~~   82 (413)
T d1t5la1          69 AGQLYSELKEFFPH   82 (413)
T ss_dssp             HHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHcCC
Confidence            99999999988643

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=96.51  E-value=0.0019  Score=45.36  Aligned_cols=30  Identities=40%  Similarity=0.537  Sum_probs=22.1

Q ss_pred             cHHHHHHHh-HHhcCCcEEEEccCCchHHHH
Q psy3307          35 TPVQKYAIP-VIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        35 t~~Q~~~i~-~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+-+...+. .+..+++++++|+||||||..
T Consensus       152 ~~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         152 KEQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             HHHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            344444443 455889999999999999974

>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=96.49  E-value=0.0042  Score=44.90  Aligned_cols=67  Identities=30%  Similarity=0.340  Sum_probs=47.5

Q ss_pred             CCcHHHHHHHhHHh----cCC-cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHH
Q psy3307          33 KPTPVQKYAIPVII----SGR-DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL  107 (130)
Q Consensus        33 ~~t~~Q~~~i~~~~----~g~-~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L  107 (130)
                      .|+.-|-++|..+.    +|. ...+.+-+||+|++  +++.+..-..                    ..+|||+|+.+.
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~--~~A~l~~~~~--------------------rp~LvVt~~~~~   65 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTV--TMAKVIEALG--------------------RPALVLAPNKIL   65 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHH--HHHHHHHHHT--------------------CCEEEEESSHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHH--HHHHHHHHhC--------------------CCEEEEeCCHHH
Confidence            45556666666543    554 57889999999985  3444433221                    138999999999


Q ss_pred             HHHHHHHHHHHHhc
Q psy3307         108 ATQIYDEAKKFAYR  121 (130)
Q Consensus       108 a~q~~~~~~~l~~~  121 (130)
                      |.++++.++.+...
T Consensus        66 A~~l~~dL~~~l~~   79 (408)
T d1c4oa1          66 AAQLAAEFRELFPE   79 (408)
T ss_dssp             HHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHhcCc
Confidence            99999999988643

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.84  E-value=0.0082  Score=37.14  Aligned_cols=27  Identities=22%  Similarity=0.292  Sum_probs=19.9

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      |++++.+|+|+|||.. +-.++..+...
T Consensus         2 k~v~ItG~~GtGKTtl-~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL-IHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHH-HHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHH-HHHHHHHHHHC
Confidence            6899999999999983 34555555443

>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=95.63  E-value=0.014  Score=38.44  Aligned_cols=16  Identities=31%  Similarity=0.530  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+|||+|||.+.
T Consensus        13 vi~lvGptGvGKTTTi   28 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSC   28 (213)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4677999999999874

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=95.52  E-value=0.0096  Score=39.13  Aligned_cols=44  Identities=14%  Similarity=0.181  Sum_probs=29.4

Q ss_pred             cCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHh----cCCcEEEEccCCchHHHHH
Q psy3307          10 KQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVII----SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        10 ~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~----~g~~~l~~aptGsGKT~~~   65 (130)
                      ..+|+|+--.+.+.+.|+..            +....    .-.++++.||+|+|||...
T Consensus         5 P~~~ddivGq~~~~~~L~~~------------i~~~~~~~~~~~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2           5 PKTLDEYIGQERLKQKLRVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCSGGGSCSCHHHHHHHHHH------------HHHHTTSSSCCCCEEEECCTTSCHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHH------------HHHHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            34788887677777766532            11111    1258999999999999754

>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=95.49  E-value=0.018  Score=37.89  Aligned_cols=15  Identities=27%  Similarity=0.552  Sum_probs=13.0

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.+|||+|||.+.
T Consensus        12 i~lvGptGvGKTTTi   26 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTI   26 (211)
T ss_dssp             EEEECCTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567999999999875

>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=95.46  E-value=0.0026  Score=42.91  Aligned_cols=54  Identities=17%  Similarity=0.129  Sum_probs=32.9

Q ss_pred             cccCCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHH--hcCCcEEEEccCCchHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVI--ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~--~~g~~~l~~aptGsGKT~~   64 (130)
                      .|..+|+|+.-.+...+.|.+. + .+ -.+...+...  ..-+.+++.||+|+|||+.
T Consensus         3 ~p~~~~~di~G~~~~k~~l~~~-i-~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~l   58 (247)
T d1ixza_           3 APKVTFKDVAGAEEAKEELKEI-V-EF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHH-H-HH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CCCCcHHHHccHHHHHHHHHHH-H-HH-HHCHHHHHHcCCCCCceEEEecCCCCChhHH
Confidence            4668999998788777776531 0 00 0011111111  1225799999999999975

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.42  E-value=0.0083  Score=39.52  Aligned_cols=43  Identities=14%  Similarity=0.183  Sum_probs=30.7

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      ++|+|+-.++.+.+.|+..--.            -.....+++.||+|+|||...
T Consensus         8 ~~~~diig~~~~~~~L~~~~~~------------~~~~~~lll~Gp~G~GKTt~~   50 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLSDQ------------PRDLPHLLLYGPNGTGKKTRC   50 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTC------------TTCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHHHc------------CCCCCeEEEECCCCCCHHHHH
Confidence            3688998899999888753110            011235899999999999754

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=95.27  E-value=0.0039  Score=45.54  Aligned_cols=17  Identities=29%  Similarity=0.536  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      .+|+++.+|||+|||+-
T Consensus        49 ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             cccEEEECCCCCCHHHH
Confidence            46999999999999974

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=95.25  E-value=0.014  Score=38.26  Aligned_cols=16  Identities=31%  Similarity=0.266  Sum_probs=13.1

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      -+++.+|||+|||.+.
T Consensus        12 vi~lvGp~GvGKTTTi   27 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTA   27 (207)
T ss_dssp             EEEEECCTTTTHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3567999999999764

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.09  E-value=0.021  Score=37.15  Aligned_cols=42  Identities=31%  Similarity=0.298  Sum_probs=28.8

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .+|+|+-.++.+.+.|...       ++.      ..-.++++.||+|+|||...
T Consensus        21 ~~~~diig~~~~~~~l~~~-------i~~------~~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          21 QRLDDIVGQEHIVKRLKHY-------VKT------GSMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CSTTTCCSCHHHHHHHHHH-------HHH------TCCCEEEEESCTTSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH-------HHc------CCCCeEEEECCCCCcHHHHH
Confidence            3688888888777776542       000      01246999999999999754

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=94.97  E-value=0.0034  Score=42.55  Aligned_cols=54  Identities=22%  Similarity=0.260  Sum_probs=32.9

Q ss_pred             cccCCCcCCCCCHHHHHHHHHC--CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307           8 LKKQGFDDIQMTEIITNNIALA--RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus         8 ~~~~~f~~l~l~~~i~~~l~~~--~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      .+..+|+|.+-.+...+.+.+.  -+..+..+|...   +...+.+++.+|+|+|||+.
T Consensus         6 ~~~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_           6 QIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHH
T ss_pred             CCCCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHH
Confidence            4567899999888887777542  011111111110   11236799999999999975

>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=94.92  E-value=0.017  Score=41.09  Aligned_cols=48  Identities=19%  Similarity=0.323  Sum_probs=31.7

Q ss_pred             hHHhcCCcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHH
Q psy3307          43 PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELAT  109 (130)
Q Consensus        43 ~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~  109 (130)
                      |.=...+++++.|+||||||.+. ..++..+....                  ..++|+=|..++..
T Consensus        45 ~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~g------------------~~~iiiD~kge~~~   92 (433)
T d1e9ra_          45 PRDAEPRHLLVNGATGTGKSVLL-RELAYTGLLRG------------------DRMVIVDPNGDMLS   92 (433)
T ss_dssp             CGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHHTT------------------CEEEEEEETTHHHH
T ss_pred             CCCcccceEEEEeCCCCcHHHHH-HHHHHHHHhCC------------------CCEEEEeCChhHHH
Confidence            34455689999999999999764 44555544432                  34666667766543

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=94.77  E-value=0.0073  Score=41.79  Aligned_cols=18  Identities=28%  Similarity=0.464  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      .+.+++.+|||+|||+..
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            579999999999999854

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.75  E-value=0.025  Score=36.66  Aligned_cols=40  Identities=15%  Similarity=0.323  Sum_probs=28.5

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~   65 (130)
                      .+|+|+-.++++.+.|++.               +.++  .++++.||+|+|||...
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i~~~~~~~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------VDEGKLPHLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------HHTTCCCCEEEECSSSSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCChhHHH
Confidence            4788887788877776542               1122  25899999999999653

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=94.70  E-value=0.0076  Score=39.58  Aligned_cols=44  Identities=20%  Similarity=0.317  Sum_probs=29.6

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhc---CCcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIIS---GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~---g~~~l~~aptGsGKT~~~   65 (130)
                      .+|+|+--.+.+.+.|+..       ++.    ....   ..++++.||+|+|||...
T Consensus         6 ~~~~divGqe~~~~~l~~~-------i~~----~~~~~~~~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLA-------LEA----AKMRGEVLDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-------HHH----HHHHTCCCCCEEEESSTTSSHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHH-------HHH----HHhcCCCCCeEEEECCCCCcHHHHH
Confidence            4788888788877766532       000    1112   247999999999999854

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.69  E-value=0.035  Score=36.39  Aligned_cols=15  Identities=27%  Similarity=0.503  Sum_probs=9.0

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.+|||+|||.+.
T Consensus        15 i~lvGptGvGKTTTi   29 (211)
T d1j8yf2          15 IMLVGVQGTGKATTA   29 (211)
T ss_dssp             EEEECSCCC----HH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567899999999864

>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=94.55  E-value=0.074  Score=34.26  Aligned_cols=31  Identities=23%  Similarity=0.371  Sum_probs=22.6

Q ss_pred             cHHHHHHHhHHh----cCC---cEEEEccCCchHHHHH
Q psy3307          35 TPVQKYAIPVII----SGR---DVMACAQTGSGKTAAF   65 (130)
Q Consensus        35 t~~Q~~~i~~~~----~g~---~~l~~aptGsGKT~~~   65 (130)
                      +|+|..++..+.    +++   .+++.||.|+|||...
T Consensus         4 yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a   41 (207)
T d1a5ta2           4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI   41 (207)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH
T ss_pred             CcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHH
Confidence            467777666543    443   4899999999999754

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=94.49  E-value=0.013  Score=38.54  Aligned_cols=17  Identities=24%  Similarity=0.409  Sum_probs=14.9

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        44 ~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            68999999999999653

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=94.46  E-value=0.03  Score=40.08  Aligned_cols=39  Identities=21%  Similarity=0.278  Sum_probs=25.3

Q ss_pred             cHHHHHHHhHHhcC--CcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          35 TPVQKYAIPVIISG--RDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        35 t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .+.|.+.|..+...  -=+++.||||||||.+. ..++..+.
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            34455555555433  35789999999999764 45566554

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=94.45  E-value=0.011  Score=35.78  Aligned_cols=18  Identities=22%  Similarity=0.420  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      .+++++.||+|||||...
T Consensus         2 ~k~I~l~G~~GsGKSTva   19 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG   19 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999743

>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=94.43  E-value=0.027  Score=36.58  Aligned_cols=40  Identities=20%  Similarity=0.266  Sum_probs=26.8

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC--CcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG--RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g--~~~l~~aptGsGKT~~~   65 (130)
                      .+|+|+-.++.+.+.|+..               +.++  .++++.||+|+|||.+.
T Consensus        12 ~~~~d~ig~~~~~~~L~~~---------------~~~~~~~~~ll~Gp~G~GKTt~a   53 (224)
T d1sxjb2          12 QVLSDIVGNKETIDRLQQI---------------AKDGNMPHMIISGMPGIGKTTSV   53 (224)
T ss_dssp             SSGGGCCSCTHHHHHHHHH---------------HHSCCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH---------------HHcCCCCeEEEECCCCCCchhhH
Confidence            4567776666666665431               1222  26899999999999764

>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=94.42  E-value=0.0039  Score=42.08  Aligned_cols=50  Identities=20%  Similarity=0.326  Sum_probs=28.1

Q ss_pred             CCcCCCCCHHHHHHHHHC---CCCCCcHHHHHHHhHHhcCCcEEEEccCCchHHHH
Q psy3307          12 GFDDIQMTEIITNNIALA---RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        12 ~f~~l~l~~~i~~~l~~~---~~~~~t~~Q~~~i~~~~~g~~~l~~aptGsGKT~~   64 (130)
                      +|+|.+--+...+.+++.   .+..+--++...   +.-.+.+++.||+|+|||+.
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~l   54 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIG---VKPPRGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCC---CCCCCEEEEECCTTSSHHHH
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCC---CCCCceeEEecCCCCCchHH
Confidence            577777555666666542   111111111110   11236899999999999974

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.15  E-value=0.13  Score=36.36  Aligned_cols=60  Identities=18%  Similarity=0.167  Sum_probs=37.2

Q ss_pred             cEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCceEEEEcCcHHHHHHHHHHHH
Q psy3307          50 DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAK  116 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~  116 (130)
                      ..+|.|.-|||||.+..-=++..+.........       ......-.+|+|+=|+.-|.++.+.+.
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~-------~~~~~~~~IL~lTFT~kAA~Emk~RI~   77 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAF-------PRPLTVEELLVVTFTEAATAELRGRIR   77 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSC-------SSCCCGGGEEEEESCHHHHHHHHHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHHHHhhCcccccc-------cCCCCcccEeEeccHHHHHHHHHHHHH
Confidence            578899999999987655555544432211000       011112458999999888888766653

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=93.95  E-value=0.013  Score=35.44  Aligned_cols=15  Identities=27%  Similarity=0.377  Sum_probs=12.8

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      =+++.|++|||||..
T Consensus         4 lIii~G~pGsGKTTl   18 (152)
T d1ly1a_           4 IILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            368899999999974

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.90  E-value=0.0099  Score=36.72  Aligned_cols=18  Identities=28%  Similarity=0.532  Sum_probs=15.7

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+-+++.||+|||||..
T Consensus         3 ~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             TTEEEEEEECTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            577789999999999984

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=93.83  E-value=0.015  Score=35.80  Aligned_cols=17  Identities=29%  Similarity=0.636  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      +.++++.||+|||||..
T Consensus         5 ~~~I~i~G~~GsGKTT~   21 (174)
T d1y63a_           5 GINILITGTPGTGKTSM   21 (174)
T ss_dssp             SCEEEEECSTTSSHHHH
T ss_pred             CCEEEEEeCCCCCHHHH
Confidence            56799999999999974

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=93.77  E-value=0.01  Score=36.64  Aligned_cols=17  Identities=24%  Similarity=0.311  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      -+.+++.|++|||||..
T Consensus         7 ~K~I~i~G~~GsGKTTl   23 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVL   23 (192)
T ss_dssp             CEEEEEECCTTSHHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            35799999999999973

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=93.45  E-value=0.018  Score=35.18  Aligned_cols=15  Identities=20%  Similarity=0.337  Sum_probs=13.1

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.||+|||||..
T Consensus         4 lI~i~G~~GsGKTTv   18 (176)
T d2bdta1           4 LYIITGPAGVGKSTT   18 (176)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999975

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.41  E-value=0.0022  Score=43.58  Aligned_cols=17  Identities=29%  Similarity=0.464  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      .+.+++.||+|+|||+.
T Consensus        41 ~~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CCEEEEBCCTTSSHHHH
T ss_pred             CCeEEEECCCCCcchhH
Confidence            46899999999999974

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=93.27  E-value=0.017  Score=38.24  Aligned_cols=16  Identities=38%  Similarity=0.491  Sum_probs=14.0

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +.+++.||+|+|||..
T Consensus        33 ~~ilL~GpPGtGKT~l   48 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSL   48 (273)
T ss_dssp             EEEEEECCTTSCTHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            3599999999999974

>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=93.22  E-value=0.23  Score=31.70  Aligned_cols=28  Identities=18%  Similarity=0.090  Sum_probs=20.6

Q ss_pred             HHHHHhHHh---cCCcEEEEccCCchHHHHH
Q psy3307          38 QKYAIPVII---SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        38 Q~~~i~~~~---~g~~~l~~aptGsGKT~~~   65 (130)
                      |.+.+..+.   .+.++++.||+|+|||...
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a   32 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVS   32 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHH
Confidence            455555554   3458999999999999754

>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=93.19  E-value=0.019  Score=37.72  Aligned_cols=53  Identities=15%  Similarity=-0.024  Sum_probs=31.6

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHH-HHHHhH-----HhcCCcEEEEccCCchHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQ-KYAIPV-----IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q-~~~i~~-----~~~g~~~l~~aptGsGKT~~~   65 (130)
                      .+|+|+-.++...+.|++.=  ...... ...+..     ....+.+++.||+|+|||...
T Consensus        11 ~~~~dlig~~~~~~~L~~~l--~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNWL--ANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHHH--HTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHH--HhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            47999999999888876520  000000 001100     112257999999999999754

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=93.19  E-value=0.022  Score=34.89  Aligned_cols=16  Identities=25%  Similarity=0.488  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      ..+++.||+|||||..
T Consensus         5 ~~I~i~G~pGsGKTTi   20 (173)
T d1rkba_           5 PNILLTGTPGVGKTTL   20 (173)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4689999999999964

>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=93.16  E-value=0.016  Score=38.75  Aligned_cols=17  Identities=35%  Similarity=0.255  Sum_probs=14.6

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +.+++.||+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999753

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=93.15  E-value=0.13  Score=33.39  Aligned_cols=18  Identities=39%  Similarity=0.636  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCchHHHHH
Q psy3307          48 GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~~   65 (130)
                      ++-+++.+|||+|||.+.
T Consensus         6 ~~vi~lvGptGvGKTTTi   23 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTI   23 (207)
T ss_dssp             SSEEEEECSTTSSHHHHH
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            456788999999999874

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=93.01  E-value=0.078  Score=32.14  Aligned_cols=25  Identities=28%  Similarity=0.448  Sum_probs=17.0

Q ss_pred             EEEEccCCchHHHHHHHHHHHHHHhc
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQMYER   76 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~~~~   76 (130)
                      +.+.++.|||||.. +--++..+..+
T Consensus         5 i~itG~~GSGKTTL-~~~L~~~l~~~   29 (170)
T d1np6a_           5 LAFAAWSGTGKTTL-LKKLIPALCAR   29 (170)
T ss_dssp             EEEECCTTSCHHHH-HHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHH-HHHHHHHHHHC
Confidence            57899999999963 34455554443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=92.90  E-value=0.088  Score=34.48  Aligned_cols=41  Identities=24%  Similarity=0.298  Sum_probs=29.8

Q ss_pred             CCCcCCCCCHHHHHHHHHCCCCCCcHHHHHHHhHHhcC---CcEEEEccCCchHHHHHH
Q psy3307          11 QGFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISG---RDVMACAQTGSGKTAAFL   66 (130)
Q Consensus        11 ~~f~~l~l~~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g---~~~l~~aptGsGKT~~~~   66 (130)
                      .+|+|+-.++++.+.|+..               +.++   ..+++.||+|+|||....
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~   52 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIAR   52 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHH
Confidence            5888988888888877532               1122   248999999999997643

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.46  E-value=0.056  Score=33.27  Aligned_cols=15  Identities=27%  Similarity=0.543  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.+|+|+|||..
T Consensus         2 ki~I~G~~G~GKSTL   16 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL   16 (178)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCcHHHHH
Confidence            378999999999973

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=92.36  E-value=0.023  Score=34.90  Aligned_cols=21  Identities=24%  Similarity=0.241  Sum_probs=17.1

Q ss_pred             HhcCCcEEEEccCCchHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~   65 (130)
                      -..|.-+++.|++|||||...
T Consensus         3 ~~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           3 ATQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TTCCEEEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            346778899999999999754

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=92.34  E-value=0.033  Score=34.41  Aligned_cols=16  Identities=25%  Similarity=0.480  Sum_probs=14.1

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +++++.|++|+|||..
T Consensus         1 k~I~liG~~GsGKsTi   16 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTL   16 (161)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5789999999999964

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.21  E-value=0.033  Score=34.98  Aligned_cols=16  Identities=31%  Similarity=0.422  Sum_probs=13.6

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      .=++++|++|||||..
T Consensus        15 ~liil~G~pGsGKST~   30 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTF   30 (172)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            3578999999999964

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=92.08  E-value=0.036  Score=39.21  Aligned_cols=17  Identities=35%  Similarity=0.497  Sum_probs=14.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.+|||+|||...
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999754

>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=91.98  E-value=0.18  Score=32.56  Aligned_cols=25  Identities=24%  Similarity=0.300  Sum_probs=17.0

Q ss_pred             CcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      +.+++.||+|+|||-- +-++.+.+.
T Consensus        37 n~l~l~G~~G~GKTHL-l~A~~~~~~   61 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHL-LQAAGNEAK   61 (213)
T ss_dssp             SSEEEECSSSSSHHHH-HHHHHHHHH
T ss_pred             CcEEEECCCCCcHHHH-HHHHHHHhc
Confidence            3489999999999952 234444443

>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=91.92  E-value=0.036  Score=35.93  Aligned_cols=17  Identities=24%  Similarity=0.483  Sum_probs=14.2

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      .++++.||+|+|||...
T Consensus        34 ~~lll~Gp~G~GKTtl~   50 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTI   50 (237)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCChHHHH
Confidence            35899999999999653

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=91.92  E-value=0.036  Score=34.92  Aligned_cols=19  Identities=21%  Similarity=0.323  Sum_probs=15.5

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|..+++.||+|||||...
T Consensus         2 ~~~riil~G~pGSGKsT~a   20 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQA   20 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CccEEEEECCCCCCHHHHH
Confidence            3667889999999999743

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=91.82  E-value=0.04  Score=33.66  Aligned_cols=19  Identities=16%  Similarity=0.323  Sum_probs=15.1

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      +.+=+++.|++|||||...
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456889999999999643

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=91.65  E-value=0.021  Score=37.75  Aligned_cols=15  Identities=27%  Similarity=0.259  Sum_probs=12.2

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.||+|+|||...
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999763

>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=91.52  E-value=0.16  Score=33.65  Aligned_cols=27  Identities=22%  Similarity=0.239  Sum_probs=19.0

Q ss_pred             HhcCCcEEEEccCCchHHHHHHHHHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAAFLVPILNQ   72 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~~~l~~l~~   72 (130)
                      +..|.-+++.|++|+|||... +-+...
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~-~~la~~   58 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFV-RQQALQ   58 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHH-HHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHH-HHHHHh
Confidence            345678899999999999643 334333

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=91.44  E-value=0.045  Score=33.43  Aligned_cols=17  Identities=29%  Similarity=0.315  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +=+++.|++|||||...
T Consensus         7 ~iivl~G~~GsGKsT~a   23 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVA   23 (171)
T ss_dssp             EEEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            34678999999999754

>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=91.24  E-value=0.15  Score=32.86  Aligned_cols=27  Identities=22%  Similarity=0.325  Sum_probs=18.9

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      .|.-+++.+++|+|||... +-++....
T Consensus        25 ~gsl~li~G~pGsGKT~l~-~qia~~~~   51 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLV-SRFVENAC   51 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHH-HHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH-HHHHHHHH
Confidence            3478899999999999754 33333333

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.16  E-value=0.028  Score=35.18  Aligned_cols=19  Identities=32%  Similarity=0.408  Sum_probs=15.4

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.|++|||||...
T Consensus        18 ~g~vI~L~G~pGSGKTTiA   36 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVS   36 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3567889999999999753

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.13  E-value=0.049  Score=34.40  Aligned_cols=15  Identities=27%  Similarity=0.663  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHH
Q psy3307          49 RDVMACAQTGSGKTA   63 (130)
Q Consensus        49 ~~~l~~aptGsGKT~   63 (130)
                      |.+++.||+|+|||.
T Consensus         2 rpIvl~GpsG~GK~t   16 (186)
T d1gkya_           2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            568999999999997

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=91.05  E-value=0.19  Score=31.93  Aligned_cols=19  Identities=32%  Similarity=0.511  Sum_probs=16.0

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.|++|+|||...
T Consensus        25 ~G~~~~I~G~~G~GKT~la   43 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFS   43 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH
Confidence            4578899999999999653

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=90.96  E-value=0.094  Score=36.94  Aligned_cols=35  Identities=20%  Similarity=0.096  Sum_probs=22.8

Q ss_pred             CCCCcHHHHHHHhHHhcC----CcEEEEccCCchHHHHH
Q psy3307          31 YDKPTPVQKYAIPVIISG----RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        31 ~~~~t~~Q~~~i~~~~~g----~~~l~~aptGsGKT~~~   65 (130)
                      +......-..++..++.|    +.+++.||+|+|||...
T Consensus       133 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~  171 (362)
T d1svma_         133 LPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA  171 (362)
T ss_dssp             STTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHH
T ss_pred             ccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHH
Confidence            433333333445445544    68999999999999743

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=90.37  E-value=0.05  Score=37.49  Aligned_cols=18  Identities=28%  Similarity=0.447  Sum_probs=15.8

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .+.++++.+++|+|||..
T Consensus        27 ~~h~vLl~G~pG~GKT~l   44 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTA   44 (333)
T ss_dssp             GGCCEEEECCGGGCTTHH
T ss_pred             CCCeEEEECCCCccHHHH
Confidence            457899999999999975

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.34  E-value=0.057  Score=33.73  Aligned_cols=18  Identities=22%  Similarity=0.232  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+-+++.+|+|+|||..
T Consensus        22 ~G~v~~i~G~~GsGKT~l   39 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQI   39 (242)
T ss_dssp             TTSEEEEECCTTSSHHHH
T ss_pred             CCEEEEEEeCCCCCHHHH
Confidence            357889999999999964

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.23  E-value=0.064  Score=33.55  Aligned_cols=17  Identities=29%  Similarity=0.503  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      |+=+++.||+|+||+..
T Consensus         2 G~iivl~GpsG~GK~tl   18 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTV   18 (182)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            67789999999999974

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.23  E-value=0.056  Score=33.69  Aligned_cols=15  Identities=27%  Similarity=0.454  Sum_probs=13.2

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      ++++.||+|||||.-
T Consensus         2 ~I~i~G~pGsGKsT~   16 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQ   16 (181)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999974

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=90.12  E-value=0.06  Score=33.84  Aligned_cols=15  Identities=33%  Similarity=0.439  Sum_probs=13.1

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.||+|||||..
T Consensus         5 ~I~i~GppGsGKsT~   19 (189)
T d1zaka1           5 KVMISGAPASGKGTQ   19 (189)
T ss_dssp             CEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            588999999999864

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=90.10  E-value=0.058  Score=33.40  Aligned_cols=16  Identities=19%  Similarity=0.355  Sum_probs=13.5

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.||+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~a   17 (182)
T d1zina1           2 NLVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999743

>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=90.09  E-value=0.22  Score=32.76  Aligned_cols=33  Identities=18%  Similarity=0.334  Sum_probs=22.6

Q ss_pred             HhHHhcCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          42 IPVIISGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        42 i~~~~~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      |+-++.|.-.++.|++|+|||... +-+...+..
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~-l~la~~ia~   55 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLA-LQLAAQIAG   55 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHH-HHHHHHHHT
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHH-HHHHHHHHc
Confidence            444556788899999999999654 333334443

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=89.96  E-value=0.12  Score=36.12  Aligned_cols=23  Identities=39%  Similarity=0.619  Sum_probs=17.9

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.+  ++.-|+||||||++.
T Consensus        73 ~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          73 DDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhhccCceeEEecccCCCCcceee
Confidence            44568875  677899999999874

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.80  E-value=0.087  Score=33.36  Aligned_cols=16  Identities=31%  Similarity=0.586  Sum_probs=13.7

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      |.+++.||+|+|||..
T Consensus         1 rpIvl~GPsGsGK~tl   16 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTL   16 (190)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999973

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.79  E-value=0.084  Score=33.86  Aligned_cols=24  Identities=13%  Similarity=0.250  Sum_probs=18.5

Q ss_pred             HHhHHh-----cCCcEEEEccCCchHHHH
Q psy3307          41 AIPVII-----SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        41 ~i~~~~-----~g~~~l~~aptGsGKT~~   64 (130)
                      .++.++     .|+-+++.+++|+|||..
T Consensus        22 ~LD~ll~GGi~~G~~~li~G~pGsGKT~l   50 (251)
T d1szpa2          22 NLDTLLGGGVETGSITELFGEFRTGKSQL   50 (251)
T ss_dssp             HHHHHHTSSEESSSEEEEEESTTSSHHHH
T ss_pred             HHHhhhCCCCcCCeEEEEEcCCCCCHHHH
Confidence            345555     447899999999999964

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.32  E-value=0.14  Score=35.25  Aligned_cols=24  Identities=33%  Similarity=0.544  Sum_probs=18.9

Q ss_pred             HhHHhcCC--cEEEEccCCchHHHHH
Q psy3307          42 IPVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      ++.+++|.  .++.-|+||||||...
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHcCCCcceeeecccCCCCceec
Confidence            34557886  5688999999999875

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.25  E-value=0.077  Score=32.95  Aligned_cols=15  Identities=13%  Similarity=0.222  Sum_probs=13.0

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.+|+|||||..
T Consensus         2 ~I~i~G~pGSGKsT~   16 (179)
T d1e4va1           2 RIILLGAPVAGKGTQ   16 (179)
T ss_dssp             EEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999975

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=89.25  E-value=0.1  Score=32.16  Aligned_cols=17  Identities=18%  Similarity=0.270  Sum_probs=14.3

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      +.+++.|++|||||...
T Consensus         3 ~~Iil~G~~GsGKSTia   19 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVG   19 (170)
T ss_dssp             CCEEEESCTTSSHHHHH
T ss_pred             CCEEEECCCCCCHHHHH
Confidence            57889999999998643

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=89.13  E-value=0.078  Score=33.31  Aligned_cols=15  Identities=33%  Similarity=0.406  Sum_probs=12.8

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.||+|||||..
T Consensus         8 iI~i~G~pGSGKsT~   22 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQ   22 (194)
T ss_dssp             EEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            468899999999964

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=89.08  E-value=0.082  Score=32.94  Aligned_cols=15  Identities=20%  Similarity=0.459  Sum_probs=12.9

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      .+++.||+|||||..
T Consensus         2 ~I~i~G~pGSGKsT~   16 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQ   16 (182)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999974

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.04  E-value=0.082  Score=33.30  Aligned_cols=15  Identities=20%  Similarity=0.375  Sum_probs=12.6

Q ss_pred             cEEEEccCCchHHHH
Q psy3307          50 DVMACAQTGSGKTAA   64 (130)
Q Consensus        50 ~~l~~aptGsGKT~~   64 (130)
                      -+++.||+|||||.-
T Consensus        10 iI~i~GppGSGKsT~   24 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQ   24 (196)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999854

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.00  E-value=0.085  Score=34.20  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=18.4

Q ss_pred             HhHHhc-----CCcEEEEccCCchHHHHH
Q psy3307          42 IPVIIS-----GRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~-----g~~~l~~aptGsGKT~~~   65 (130)
                      ++.++.     |+-+++.+++|+|||...
T Consensus        25 LD~ll~GGlp~G~~~li~G~pGsGKT~~~   53 (254)
T d1pzna2          25 LDKLLGGGIETQAITEVFGEFGSGKTQLA   53 (254)
T ss_dssp             HHHHHTSSEESSEEEEEEESTTSSHHHHH
T ss_pred             HHHhhcCCccCCEEEEEEcCCCCCHHHHH
Confidence            455554     468899999999999754

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.94  E-value=0.34  Score=29.39  Aligned_cols=23  Identities=17%  Similarity=0.131  Sum_probs=15.5

Q ss_pred             EEEccCCchHHHHHHHHHHHHHHh
Q psy3307          52 MACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        52 l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      -+.++.|||||.. +--++..+..
T Consensus         5 ~I~G~~gSGKTTl-i~~l~~~L~~   27 (165)
T d1xjca_           5 QVVGYKHSGKTTL-MEKWVAAAVR   27 (165)
T ss_dssp             EEECCTTSSHHHH-HHHHHHHHHH
T ss_pred             EEEeCCCCCHHHH-HHHHHHHHHh
Confidence            4899999999973 2344444444

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=88.92  E-value=0.092  Score=32.14  Aligned_cols=16  Identities=25%  Similarity=0.418  Sum_probs=13.5

Q ss_pred             CcEEEEccCCchHHHH
Q psy3307          49 RDVMACAQTGSGKTAA   64 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~   64 (130)
                      +-+++.|++|||||..
T Consensus         2 kiI~i~G~~GsGKsT~   17 (190)
T d1khta_           2 KVVVVTGVPGVGSTTS   17 (190)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4578999999999973

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=88.62  E-value=0.13  Score=33.11  Aligned_cols=19  Identities=32%  Similarity=0.288  Sum_probs=16.5

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        25 ~~Gei~~l~G~NGsGKSTL   43 (200)
T d1sgwa_          25 EKGNVVNFHGPNGIGKTTL   43 (200)
T ss_dssp             ETTCCEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCChHHHH
Confidence            3778889999999999973

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=88.60  E-value=0.11  Score=33.40  Aligned_cols=18  Identities=28%  Similarity=0.497  Sum_probs=15.3

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .|+=++++||+|+||+..
T Consensus         1 ~G~livi~GPSG~GK~tl   18 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSL   18 (205)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            367789999999999974

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.59  E-value=0.1  Score=32.46  Aligned_cols=17  Identities=18%  Similarity=0.259  Sum_probs=13.8

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.||+|||||...
T Consensus         3 mrIvl~G~pGSGKtT~a   19 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQA   19 (180)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45788999999999643

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=88.53  E-value=0.13  Score=32.42  Aligned_cols=20  Identities=20%  Similarity=0.375  Sum_probs=16.3

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..++-+++.||+||||+..
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~   24 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQ   24 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHH
Confidence            44567789999999999964

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=88.32  E-value=0.098  Score=33.09  Aligned_cols=17  Identities=24%  Similarity=0.217  Sum_probs=14.2

Q ss_pred             CcEEEEccCCchHHHHH
Q psy3307          49 RDVMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~~l~~aptGsGKT~~~   65 (130)
                      ..+++.||+|||||...
T Consensus         7 mrIiliG~PGSGKtT~a   23 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVS   23 (189)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             eeEEEECCCCCCHHHHH
Confidence            47889999999999643

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=87.76  E-value=0.26  Score=32.53  Aligned_cols=20  Identities=20%  Similarity=0.312  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      ...+..+++.|++||||+..
T Consensus        20 a~~~~pvlI~Ge~GtGK~~~   39 (247)
T d1ny5a2          20 SCAECPVLITGESGVGKEVV   39 (247)
T ss_dssp             TTCCSCEEEECSTTSSHHHH
T ss_pred             hCCCCCEEEECCCCcCHHHH
Confidence            34678999999999999864

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.63  E-value=0.12  Score=32.43  Aligned_cols=15  Identities=27%  Similarity=0.428  Sum_probs=12.6

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +++.||+|||||.-.
T Consensus         4 I~i~GppGSGKsT~a   18 (194)
T d1teva_           4 VFVLGGPGAGKGTQC   18 (194)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999643

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=87.51  E-value=1  Score=29.03  Aligned_cols=51  Identities=12%  Similarity=0.201  Sum_probs=33.0

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcC----CcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISG----RDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g----~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ..|++-|+-.+++ +-+. ..++..++.|    +-+++.+|+++|||+. ...++..+
T Consensus        23 ~~I~~~l~~q~i~-~~~F-l~~l~~~l~~~PKkn~i~~~GP~~TGKS~f-~~sl~~~l   77 (205)
T d1tuea_          23 RPIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYF-GMSFIHFI   77 (205)
T ss_dssp             HHHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHH-HHHHHHHH
T ss_pred             HHHHHHHHhcCcc-HHHH-HHHHHHHHcCCCCceEEEEECCCCccHHHH-HHHHHHHh
Confidence            5677777777764 2332 2334445555    5889999999999974 34455554

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=87.49  E-value=0.39  Score=30.98  Aligned_cols=18  Identities=11%  Similarity=0.147  Sum_probs=15.2

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      .++.+++.||.|+|||..
T Consensus        28 ~~~~i~i~G~~G~GKTsL   45 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSI   45 (283)
T ss_dssp             CSSEEEEEESTTSSHHHH
T ss_pred             cCCEEEEEcCCCCcHHHH
Confidence            356889999999999964

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=87.49  E-value=0.14  Score=32.19  Aligned_cols=15  Identities=20%  Similarity=0.220  Sum_probs=12.9

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      ++++|.+|||||..+
T Consensus         5 i~l~GlpgsGKSTla   19 (213)
T d1bifa1           5 IVMVGLPARGKTYIS   19 (213)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999754

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=87.38  E-value=0.24  Score=34.64  Aligned_cols=23  Identities=43%  Similarity=0.621  Sum_probs=17.3

Q ss_pred             hHHhcCCc--EEEEccCCchHHHHH
Q psy3307          43 PVIISGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~~--~l~~aptGsGKT~~~   65 (130)
                      ..+++|.+  ++.-|+||||||...
T Consensus       107 ~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         107 QTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHhccCceEEeeccCCCCCceee
Confidence            44568864  456699999999875

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=87.13  E-value=0.14  Score=31.61  Aligned_cols=18  Identities=39%  Similarity=0.444  Sum_probs=13.4

Q ss_pred             cCCcEE-EEccCCchHHHH
Q psy3307          47 SGRDVM-ACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l-~~aptGsGKT~~   64 (130)
                      .|+-++ +.|++|||||..
T Consensus        20 ~~~~iIgI~G~~GSGKSTl   38 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTL   38 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHH
T ss_pred             CCCEEEEEECCCCCCHHHH
Confidence            344444 899999999964

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=86.59  E-value=0.14  Score=31.44  Aligned_cols=14  Identities=21%  Similarity=0.361  Sum_probs=11.9

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +++.|++|||||..
T Consensus         4 ivi~G~~GsGKTT~   17 (194)
T d1nksa_           4 GIVTGIPGVGKSTV   17 (194)
T ss_dssp             EEEEECTTSCHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            56789999999974

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=86.57  E-value=0.25  Score=34.20  Aligned_cols=24  Identities=38%  Similarity=0.602  Sum_probs=18.5

Q ss_pred             HhHHhcCC--cEEEEccCCchHHHHH
Q psy3307          42 IPVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      +..+++|.  .++.-|+||||||...
T Consensus        73 v~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          73 LDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHHhccCCceEEeeeeccccceEEe
Confidence            45567886  4578899999999773

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.54  E-value=0.17  Score=30.95  Aligned_cols=16  Identities=25%  Similarity=0.308  Sum_probs=13.4

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.|++|+|||...
T Consensus         3 ~IvliG~~G~GKSTig   18 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIG   18 (165)
T ss_dssp             SEEEECSTTSSHHHHH
T ss_pred             cEEEECCCCCCHHHHH
Confidence            5788899999999753

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.51  E-value=0.18  Score=31.55  Aligned_cols=17  Identities=12%  Similarity=0.305  Sum_probs=14.4

Q ss_pred             CCcEEEEccCCchHHHH
Q psy3307          48 GRDVMACAQTGSGKTAA   64 (130)
Q Consensus        48 g~~~l~~aptGsGKT~~   64 (130)
                      .+-+++.||+|+||+..
T Consensus         3 ~k~ivl~Gpsg~GK~tl   19 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHI   19 (178)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CCcEEEECCCCCCHHHH
Confidence            35689999999999974

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.47  E-value=0.13  Score=33.20  Aligned_cols=25  Identities=20%  Similarity=0.092  Sum_probs=19.0

Q ss_pred             HHhHHh-----cCCcEEEEccCCchHHHHH
Q psy3307          41 AIPVII-----SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~-----~g~~~l~~aptGsGKT~~~   65 (130)
                      .++.++     .|+-+++.+++|+|||...
T Consensus        25 ~LD~~lgGGip~G~~~~i~G~~GsGKT~la   54 (258)
T d1v5wa_          25 EFDKLLGGGIESMAITEAFGEFRTGKTQLS   54 (258)
T ss_dssp             HHHHHTTSSBCSSEEEEEECCTTCTHHHHH
T ss_pred             HHHHhhcCCCcCCEEEEEECCCCCCHHHHH
Confidence            445555     4478899999999999754

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=86.40  E-value=0.15  Score=34.98  Aligned_cols=16  Identities=31%  Similarity=0.422  Sum_probs=13.9

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.+|||+|||...
T Consensus        54 ~~lf~Gp~GvGKT~la   69 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVT   69 (315)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCcchhHHHH
Confidence            6899999999999754

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=86.22  E-value=0.24  Score=34.68  Aligned_cols=24  Identities=38%  Similarity=0.542  Sum_probs=18.9

Q ss_pred             HhHHhcCC--cEEEEccCCchHHHHH
Q psy3307          42 IPVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        42 i~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      +..+++|.  .++.-|+||||||.+.
T Consensus        67 v~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          67 VQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCceeeeccccCCCCccccc
Confidence            45667886  4577899999999885

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=86.05  E-value=0.25  Score=34.66  Aligned_cols=25  Identities=40%  Similarity=0.522  Sum_probs=19.3

Q ss_pred             HHhHHhcCC--cEEEEccCCchHHHHH
Q psy3307          41 AIPVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      .++.+++|.  .++.-|+||||||+..
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            345567886  5688899999999874

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=85.67  E-value=0.3  Score=33.84  Aligned_cols=23  Identities=30%  Similarity=0.452  Sum_probs=18.2

Q ss_pred             hHHhcCC--cEEEEccCCchHHHHH
Q psy3307          43 PVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        43 ~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      +.+++|.  .++.-|+||||||.+.
T Consensus        80 ~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          80 QHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhccCceeeeeccCCCCCceee
Confidence            4457886  5688899999999875

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=85.65  E-value=0.19  Score=33.36  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=16.2

Q ss_pred             hcCCcEEEEccCCchHHH
Q psy3307          46 ISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~   63 (130)
                      ..|.-+.+.+|+|||||.
T Consensus        27 ~~Ge~vaIvG~sGsGKST   44 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKST   44 (241)
T ss_dssp             ETTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            478899999999999996

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.22  E-value=0.21  Score=33.31  Aligned_cols=27  Identities=26%  Similarity=0.528  Sum_probs=20.0

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..|.-+.+.+|+|||||.  ++-++..++
T Consensus        38 ~~Ge~vaivG~sGsGKST--Ll~li~gl~   64 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKST--VAALLQNLY   64 (251)
T ss_dssp             CTTCEEEEECSTTSSHHH--HHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHH--HHHHHhccc
Confidence            478899999999999997  344444433

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=84.74  E-value=0.22  Score=33.23  Aligned_cols=19  Identities=32%  Similarity=0.574  Sum_probs=16.7

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|||||..
T Consensus        39 ~~Ge~iaivG~sGsGKSTL   57 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTI   57 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHH
T ss_pred             cCCCEEEEECCCCChHHHH
Confidence            4788999999999999973

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=84.72  E-value=0.21  Score=31.86  Aligned_cols=19  Identities=32%  Similarity=0.226  Sum_probs=15.9

Q ss_pred             cCCcEEEEccCCchHHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~   65 (130)
                      .|.-+++.|++|+|||...
T Consensus        33 ~G~l~~i~G~~G~GKT~~~   51 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIM   51 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH
Confidence            3578899999999999754

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=84.58  E-value=0.35  Score=33.43  Aligned_cols=25  Identities=36%  Similarity=0.496  Sum_probs=19.2

Q ss_pred             HHhHHhcCC--cEEEEccCCchHHHHH
Q psy3307          41 AIPVIISGR--DVMACAQTGSGKTAAF   65 (130)
Q Consensus        41 ~i~~~~~g~--~~l~~aptGsGKT~~~   65 (130)
                      .+..+++|.  .++.-++||||||...
T Consensus        74 ~v~~~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          74 LVQSSLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             hhcchhcccccceeeeeccCCcccccc
Confidence            445567887  4567899999999876

>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=84.39  E-value=3.4  Score=26.13  Aligned_cols=28  Identities=18%  Similarity=0.303  Sum_probs=19.3

Q ss_pred             cCCcEEEEccCCchHHHHHHHHHHHHHHh
Q psy3307          47 SGRDVMACAQTGSGKTAAFLVPILNQMYE   75 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~~~l~~l~~~~~   75 (130)
                      ...++++.+++|.|||... -.+.+++..
T Consensus        42 ~k~n~lLvG~pGVGKTalv-~~LA~ri~~   69 (195)
T d1jbka_          42 TKNNPVLIGEPGVGKTAIV-EGLAQRIIN   69 (195)
T ss_dssp             SSCEEEEECCTTSCHHHHH-HHHHHHHHH
T ss_pred             CCCCeEEEecCCcccHHHH-HHHHHHHHh
Confidence            3369999999999999642 334444444

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.35  E-value=0.2  Score=33.46  Aligned_cols=19  Identities=26%  Similarity=0.413  Sum_probs=16.6

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+++|||||..
T Consensus        42 ~~Ge~vaivG~sGsGKSTL   60 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTL   60 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            4788999999999999973

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.07  E-value=0.25  Score=31.31  Aligned_cols=14  Identities=29%  Similarity=0.406  Sum_probs=11.3

Q ss_pred             EEEEccCCchHHHH
Q psy3307          51 VMACAQTGSGKTAA   64 (130)
Q Consensus        51 ~l~~aptGsGKT~~   64 (130)
                      +-+.|++|||||..
T Consensus         5 IgI~G~~gSGKSTl   18 (213)
T d1uj2a_           5 IGVSGGTASGKSSV   18 (213)
T ss_dssp             EEEECSTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            34789999999964

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=83.94  E-value=0.21  Score=33.12  Aligned_cols=19  Identities=21%  Similarity=0.382  Sum_probs=16.5

Q ss_pred             HhcCCcEEEEccCCchHHH
Q psy3307          45 IISGRDVMACAQTGSGKTA   63 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~   63 (130)
                      +..|.-+.+.+|+|||||.
T Consensus        28 i~~Ge~~~iiG~sGsGKST   46 (240)
T d3dhwc1          28 VPAGQIYGVIGASGAGKST   46 (240)
T ss_dssp             ECSSCEEEEEESTTSSHHH
T ss_pred             EcCCCEEEEECCCCCCHHH
Confidence            3478889999999999996

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=83.86  E-value=0.23  Score=31.38  Aligned_cols=15  Identities=20%  Similarity=0.341  Sum_probs=11.6

Q ss_pred             EEEEccCCchHHHHH
Q psy3307          51 VMACAQTGSGKTAAF   65 (130)
Q Consensus        51 ~l~~aptGsGKT~~~   65 (130)
                      +.+.||+||||+.-.
T Consensus         6 I~I~GppGSGKgT~a   20 (225)
T d1ckea_           6 ITIDGPSGAGKGTLC   20 (225)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            455699999999743

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=83.86  E-value=0.1  Score=32.12  Aligned_cols=21  Identities=14%  Similarity=0.268  Sum_probs=14.8

Q ss_pred             EEEccCCchHHHHHHHHHHHHHH
Q psy3307          52 MACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        52 l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ++.|++|||||.  ++-++..+.
T Consensus        28 vi~G~NGsGKSt--il~Ai~~~L   48 (222)
T d1qhla_          28 TLSGGNGAGKST--TMAAFVTAL   48 (222)
T ss_dssp             HHHSCCSHHHHH--HHHHHHHHH
T ss_pred             EEECCCCCCHHH--HHHHHHHHh
Confidence            457899999997  445555544

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.84  E-value=0.22  Score=32.84  Aligned_cols=27  Identities=19%  Similarity=0.340  Sum_probs=19.6

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..|.-+.+.+|+|+|||..  +-++..+.
T Consensus        24 ~~Gei~~liGpsGsGKSTL--l~~i~Gl~   50 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTL--LRMIAGLE   50 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHH--HHHHHTSS
T ss_pred             cCCCEEEEECCCCChHHHH--HHHHhcCC
Confidence            4778899999999999963  44444433

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=83.65  E-value=0.25  Score=31.23  Aligned_cols=20  Identities=25%  Similarity=0.456  Sum_probs=16.9

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|+-+++.++.|+|||...
T Consensus        13 ~~g~gvli~G~sG~GKS~la   32 (177)
T d1knxa2          13 VFGVGVLLTGRSGIGKSECA   32 (177)
T ss_dssp             ETTEEEEEEESSSSSHHHHH
T ss_pred             ECCEEEEEEcCCCCCHHHHH
Confidence            36789999999999998654

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=83.55  E-value=0.3  Score=32.15  Aligned_cols=26  Identities=27%  Similarity=0.446  Sum_probs=19.7

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ..|.-+.+.+|+|||||.  ++-++..+
T Consensus        29 ~~Ge~~~iiG~sGsGKST--Ll~~i~gl   54 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKST--MLNIIGCL   54 (230)
T ss_dssp             CTTCEEEEECSTTSSHHH--HHHHHTTS
T ss_pred             cCCCEEEEECCCCCCcch--hhHhccCC
Confidence            478899999999999996  34444444

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=83.42  E-value=0.26  Score=31.09  Aligned_cols=20  Identities=30%  Similarity=0.494  Sum_probs=17.0

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|+-+++.++.|+|||...
T Consensus        12 ~~g~gvl~~G~sG~GKStla   31 (176)
T d1kkma_          12 IYGLGVLITGDSGVGKSETA   31 (176)
T ss_dssp             ETTEEEEEECCTTSCHHHHH
T ss_pred             ECCEEEEEEeCCCCCHHHHH
Confidence            36789999999999998654

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=83.23  E-value=0.22  Score=32.84  Aligned_cols=19  Identities=37%  Similarity=0.394  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        24 ~~Ge~~~liGpsGaGKSTl   42 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLF   42 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHH
Confidence            4778899999999999973

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=83.05  E-value=0.23  Score=32.87  Aligned_cols=27  Identities=19%  Similarity=0.471  Sum_probs=20.1

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..|.-+.+.+|+|||||.  ++-++..++
T Consensus        26 ~~Ge~vaivG~sGsGKST--Ll~ll~gl~   52 (242)
T d1mv5a_          26 QPNSIIAFAGPSGGGKST--IFSLLERFY   52 (242)
T ss_dssp             CTTEEEEEECCTTSSHHH--HHHHHTTSS
T ss_pred             cCCCEEEEECCCCCCHHH--HHHHHHHhh
Confidence            367888999999999997  444454444

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.69  E-value=0.29  Score=33.07  Aligned_cols=17  Identities=41%  Similarity=0.575  Sum_probs=14.9

Q ss_pred             cCCcEEEEccCCchHHH
Q psy3307          47 SGRDVMACAQTGSGKTA   63 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~   63 (130)
                      .|.-+.+.+|+|+|||.
T Consensus        61 ~Ge~vaivG~nGsGKST   77 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTS   77 (281)
T ss_dssp             TTCEEEEEESTTSSHHH
T ss_pred             CCCEEEEECCCCChHHH
Confidence            56778899999999997

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=82.67  E-value=0.34  Score=32.10  Aligned_cols=19  Identities=26%  Similarity=0.427  Sum_probs=16.3

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        27 ~~Ge~~~liG~sGaGKSTl   45 (240)
T d1g2912          27 KDGEFMILLGPSGCGKTTT   45 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCChHHHH
Confidence            3678889999999999963

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=82.30  E-value=0.27  Score=33.74  Aligned_cols=16  Identities=31%  Similarity=0.351  Sum_probs=13.6

Q ss_pred             cEEEEccCCchHHHHH
Q psy3307          50 DVMACAQTGSGKTAAF   65 (130)
Q Consensus        50 ~~l~~aptGsGKT~~~   65 (130)
                      .+++.+|||+|||...
T Consensus        55 ~~lf~Gp~G~GKt~la   70 (315)
T d1qvra3          55 SFLFLGPTGVGKTELA   70 (315)
T ss_dssp             EEEEBSCSSSSHHHHH
T ss_pred             EEEEECCCcchHHHHH
Confidence            5788999999999754

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=82.26  E-value=0.31  Score=30.52  Aligned_cols=20  Identities=25%  Similarity=0.469  Sum_probs=16.9

Q ss_pred             hcCCcEEEEccCCchHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAF   65 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~   65 (130)
                      ..|+-+++.++.|+|||...
T Consensus        13 ~~g~gvli~G~sg~GKS~la   32 (169)
T d1ko7a2          13 VYGVGVLITGDSGIGKSETA   32 (169)
T ss_dssp             ETTEEEEEEESTTSSHHHHH
T ss_pred             ECCEEEEEEeCCCCCHHHHH
Confidence            46789999999999998643

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=82.17  E-value=0.36  Score=31.93  Aligned_cols=27  Identities=19%  Similarity=0.354  Sum_probs=19.9

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQMY   74 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~~   74 (130)
                      ..|.-+.+.+|+|+|||..  +-++..+.
T Consensus        30 ~~Ge~~~liGpsGaGKSTL--l~~i~Gl~   56 (239)
T d1v43a3          30 KDGEFLVLLGPSGCGKTTT--LRMIAGLE   56 (239)
T ss_dssp             CTTCEEEEECCTTSSHHHH--HHHHHTSS
T ss_pred             CCCCEEEEECCCCChHHHH--HHHHHcCC
Confidence            4678889999999999973  44444443

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=81.90  E-value=0.31  Score=33.71  Aligned_cols=17  Identities=29%  Similarity=0.401  Sum_probs=12.9

Q ss_pred             Cc-EEEEccCCchHHHHH
Q psy3307          49 RD-VMACAQTGSGKTAAF   65 (130)
Q Consensus        49 ~~-~l~~aptGsGKT~~~   65 (130)
                      +. +++.+|+|+|||+..
T Consensus       123 ~g~~l~~G~pG~GKT~la  140 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLV  140 (321)
T ss_dssp             SEEEEEECSSSSCHHHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            44 455899999999753

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=81.75  E-value=0.38  Score=31.72  Aligned_cols=19  Identities=32%  Similarity=0.422  Sum_probs=16.4

Q ss_pred             hcCCcEEEEccCCchHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~   64 (130)
                      ..|.-+.+.+|+|+|||..
T Consensus        30 ~~Gei~~liGpnGaGKSTl   48 (240)
T d1ji0a_          30 PRGQIVTLIGANGAGKTTT   48 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCcHHHH
Confidence            3678889999999999974

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=81.64  E-value=1  Score=28.48  Aligned_cols=13  Identities=46%  Similarity=0.654  Sum_probs=11.6

Q ss_pred             EEEEccCCchHHH
Q psy3307          51 VMACAQTGSGKTA   63 (130)
Q Consensus        51 ~l~~aptGsGKT~   63 (130)
                      +++.|+.|||||.
T Consensus         3 i~v~G~~GsGKTT   15 (244)
T d1yrba1           3 VVFVGTAGSGKTT   15 (244)
T ss_dssp             EEEECSTTSSHHH
T ss_pred             EEEEcCCCCcHHH
Confidence            5789999999996

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=81.47  E-value=0.34  Score=30.67  Aligned_cols=18  Identities=28%  Similarity=0.423  Sum_probs=15.6

Q ss_pred             cCCcEEEEccCCchHHHH
Q psy3307          47 SGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        47 ~g~~~l~~aptGsGKT~~   64 (130)
                      +|+-+++.|+-|||||..
T Consensus         1 rgkfIviEG~dGsGKsT~   18 (210)
T d4tmka_           1 RSKYIVIEGLEGAGKTTA   18 (210)
T ss_dssp             CCCEEEEEECTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            477889999999999974

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=80.62  E-value=0.42  Score=32.84  Aligned_cols=19  Identities=47%  Similarity=0.574  Sum_probs=15.4

Q ss_pred             cCCc--EEEEccCCchHHHHH
Q psy3307          47 SGRD--VMACAQTGSGKTAAF   65 (130)
Q Consensus        47 ~g~~--~l~~aptGsGKT~~~   65 (130)
                      +|.+  ++.-++||||||.+.
T Consensus        82 ~G~n~~i~aYGqTGSGKTyTm  102 (330)
T d1ry6a_          82 NGCVCSCFAYGQTGSGKTYTM  102 (330)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             cCCCeEEEeeeccccccceee
Confidence            5875  577789999999885

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=80.61  E-value=3.5  Score=27.20  Aligned_cols=100  Identities=13%  Similarity=0.075  Sum_probs=52.6

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHhHHhcC-----CcEEEEccCCchHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Q psy3307          20 EIITNNIALARYDKPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV   94 (130)
Q Consensus        20 ~~i~~~l~~~~~~~~t~~Q~~~i~~~~~g-----~~~l~~aptGsGKT~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~   94 (130)
                      +++.+-|+..++ .+-.+.. ++-.++.+     .-+++.+|.++|||..  +-++..+.... ....+....++-....
T Consensus        73 ~~i~~~l~~q~~-~~~~f~~-~l~~~L~~~~~k~n~~~l~G~~~tGKS~f--~~~i~~~lg~~-~~~~~~~~~f~l~~l~  147 (267)
T d1u0ja_          73 NRIYKILELNGY-DPQYAAS-VFLGWATKKFGKRNTIWLFGPATTGKTNI--AEAIAHTVPFY-GCVNWTNENFPFNDCV  147 (267)
T ss_dssp             CHHHHHHHHTTC-CHHHHHH-HHHHHHTTCSTTCCEEEEECSTTSSHHHH--HHHHHHHSSCE-EECCTTCSSCTTGGGS
T ss_pred             HHHHHHHHHcCc-CHHHHHH-HHHHHHcCCCCccEEEEEEcCCCCCHHHH--HHHHHHHhcch-hhccccCCCccccccC
Confidence            357777777777 4555554 44455543     4678899999999974  33444444211 1111111122222333


Q ss_pred             CceEEEEc-CcHHHHHHHHHHHHHHHhcCCCce
Q psy3307          95 FPLGLVLA-PTRELATQIYDEAKKFAYRSQLRP  126 (130)
Q Consensus        95 ~~~~lil~-Pt~~La~q~~~~~~~l~~~~~~~~  126 (130)
                      +.+++++- |+..  ......++.+..+-.+.+
T Consensus       148 ~k~~~~~~e~~~~--~~~~~~~K~l~gGd~i~v  178 (267)
T d1u0ja_         148 DKMVIWWEEGKMT--AKVVESAKAILGGSKVRV  178 (267)
T ss_dssp             SCSEEEECSCCEE--TTTHHHHHHHHTTCCEEC
T ss_pred             CCEEEEEeCCCcc--ccHHHHHHHhcCCCceEe
Confidence            44555554 3321  223446788877765554

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=80.50  E-value=0.23  Score=32.63  Aligned_cols=20  Identities=20%  Similarity=0.393  Sum_probs=17.2

Q ss_pred             HhcCCcEEEEccCCchHHHH
Q psy3307          45 IISGRDVMACAQTGSGKTAA   64 (130)
Q Consensus        45 ~~~g~~~l~~aptGsGKT~~   64 (130)
                      +..|.-+-+.+|+|+|||..
T Consensus        22 I~~Gei~~iiG~nGaGKSTL   41 (231)
T d1l7vc_          22 VRAGEILHLVGPNGAGKSTL   41 (231)
T ss_dssp             EETTCEEECBCCTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCcHHHH
Confidence            44788899999999999974

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.24  E-value=0.57  Score=32.30  Aligned_cols=21  Identities=19%  Similarity=0.310  Sum_probs=14.7

Q ss_pred             EEEEccCCchHHHHHHHHHHHHH
Q psy3307          51 VMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        51 ~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      -++.|++|||||..  +-++.++
T Consensus        28 ~~i~G~NGsGKS~i--leAi~~~   48 (427)
T d1w1wa_          28 TSIIGPNGSGKSNM--MDAISFV   48 (427)
T ss_dssp             EEEECSTTSSHHHH--HHHHHHH
T ss_pred             EEEECCCCCCHHHH--HHHHHHH
Confidence            46789999999973  4444443

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=80.07  E-value=0.3  Score=32.38  Aligned_cols=26  Identities=23%  Similarity=0.364  Sum_probs=19.5

Q ss_pred             hcCCcEEEEccCCchHHHHHHHHHHHHH
Q psy3307          46 ISGRDVMACAQTGSGKTAAFLVPILNQM   73 (130)
Q Consensus        46 ~~g~~~l~~aptGsGKT~~~~l~~l~~~   73 (130)
                      ..|.-+.+.+|+|+|||..  +-++..+
T Consensus        29 ~~Ge~~~iiG~sGsGKSTl--l~~i~gl   54 (242)
T d1oxxk2          29 ENGERFGILGPSGAGKTTF--MRIIAGL   54 (242)
T ss_dssp             CTTCEEEEECSCHHHHHHH--HHHHHTS
T ss_pred             CCCCEEEEECCCCCcHHHH--HHHHHcC
Confidence            4788999999999999973  4444443