RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1621
(224 letters)
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 299 bits (768), Expect = e-101
Identities = 126/175 (72%), Positives = 152/175 (86%), Gaps = 2/175 (1%)
Query: 52 RRVLIVGDSMTR--IRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTES 109
+R+L+ D +T IRQFY+ +E+E+WKFDTLCDLY TL+ITQA+I+CNTRRKVD+LT+
Sbjct: 227 KRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKK 286
Query: 110 MLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPS 169
M +++FTVS MHGDMDQ RD+IMR+FRSGS+RVLITTDLLARGIDVQQVSLVINYDLP+
Sbjct: 287 MHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPA 346
Query: 170 NRENYIHRIGRGGRFGRKGVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVADLI 224
+ ENYIHRIGR GRFGRKGVAINFVT +D LK+ E+ YNT+IEEMPM VAD +
Sbjct: 347 SPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL 401
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 184 bits (470), Expect = 8e-56
Identities = 69/154 (44%), Positives = 101/154 (65%), Gaps = 1/154 (0%)
Query: 63 RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHG 122
+I+QFY+ +E E+ K + L L + ++F T+R V+ L ES+ K+ F V+A+HG
Sbjct: 246 KIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHG 305
Query: 123 DMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGG 182
D+ Q RD + +F+ G RVL+ TD+ ARG+D+ VS VINYDLP + E+Y+HRIGR G
Sbjct: 306 DLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTG 365
Query: 183 RFGRKGVAINFVTA-EDKRTLKDTEQFYNTRIEE 215
R GRKGVAI+FVT E+ + LK E+ ++
Sbjct: 366 RAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPS 399
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 143 bits (363), Expect = 5e-44
Identities = 52/129 (40%), Positives = 77/129 (59%), Gaps = 2/129 (1%)
Query: 67 FYIYIEREDWKFDTLCDLY--GTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDM 124
+ ED K + L +L + +IFC +++ +D L E + K V+A+HGD
Sbjct: 3 KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62
Query: 125 DQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRF 184
Q R+ +++ FR G VL+ TD++ARGID+ VS+VINYDLP + +Y+ RIGR GR
Sbjct: 63 SQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRA 122
Query: 185 GRKGVAINF 193
G+KG AI
Sbjct: 123 GQKGTAILL 131
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 140 bits (356), Expect = 2e-39
Identities = 47/153 (30%), Positives = 87/153 (56%), Gaps = 1/153 (0%)
Query: 62 TRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMH 121
I Q + + ++ + L L V+FCNT+++ + +++ + F+ A+H
Sbjct: 215 PAIEQRFYEVSPDE-RLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALH 273
Query: 122 GDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRG 181
GD++Q RD ++ +F + S VL+ TD+ ARG+D++ + VINY+L + E ++HRIGR
Sbjct: 274 GDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRT 333
Query: 182 GRFGRKGVAINFVTAEDKRTLKDTEQFYNTRIE 214
GR G KG+A++ V E+ + E + ++
Sbjct: 334 GRAGSKGLALSLVAPEEMQRANAIEDYLGRKLN 366
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 127 bits (322), Expect = 8e-35
Identities = 53/140 (37%), Positives = 79/140 (56%)
Query: 63 RIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHG 122
+I Q+Y + + K LC L +T++++F TR +V L + K + G
Sbjct: 218 KIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEG 277
Query: 123 DMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGG 182
+M Q R+ +++ G VL+ TD+ ARGID+ VS VIN+D+P + + Y+HRIGR G
Sbjct: 278 EMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTG 337
Query: 183 RFGRKGVAINFVTAEDKRTL 202
R GRKG AI+ V A D L
Sbjct: 338 RAGRKGTAISLVEAHDHLLL 357
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 105 bits (264), Expect = 1e-29
Identities = 38/78 (48%), Positives = 52/78 (66%)
Query: 108 ESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDL 167
+ + K V+ +HG + Q R+ I+ FR+G S+VL+ TD+ RGID+ V+LVINYDL
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 168 PSNRENYIHRIGRGGRFG 185
P N +YI RIGR GR G
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 101 bits (254), Expect = 3e-28
Identities = 34/82 (41%), Positives = 51/82 (62%)
Query: 104 DWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVI 163
+ L E + + V+ +HG + Q R+ I+ +F +G +VL+ TD+ RG+D+ V LVI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 164 NYDLPSNRENYIHRIGRGGRFG 185
YDLP + +YI RIGR GR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 111 bits (278), Expect = 3e-28
Identities = 49/144 (34%), Positives = 82/144 (56%), Gaps = 3/144 (2%)
Query: 63 RIRQFYIYIEREDWKFDTLCDLYGTL--SITQAVIFCNTRRKVDWLTESMLKKEFTVSAM 120
I+Q +++ E K L L + + +IF T++ D+LT+ + + +
Sbjct: 349 NIKQ-EVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCI 407
Query: 121 HGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGR 180
HGD Q R ++ +F++G S ++I TD+ +RG+DV+ V VIN+D P+ E+Y+HRIGR
Sbjct: 408 HGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGR 467
Query: 181 GGRFGRKGVAINFVTAEDKRTLKD 204
GR G KG + F+T + R +D
Sbjct: 468 TGRAGAKGASYTFLTPDKYRLARD 491
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 106 bits (267), Expect = 1e-26
Identities = 50/132 (37%), Positives = 86/132 (65%)
Query: 93 AVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLAR 152
A+IF T+ + E++ + + +A++GDM+Q R+ + + + G +LI TD+ AR
Sbjct: 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAAR 307
Query: 153 GIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTAEDKRTLKDTEQFYNTR 212
G+DV+++SLV+NYD+P + E+Y+HRIGR GR GR G A+ FV ++R L++ E+
Sbjct: 308 GLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLT 367
Query: 213 IEEMPMNVADLI 224
I E+ + A+L+
Sbjct: 368 IPEVELPNAELL 379
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 103 bits (259), Expect = 6e-26
Identities = 48/140 (34%), Positives = 81/140 (57%)
Query: 77 KFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQF 136
K + L + G + Q ++F T+ + L E + K +A+HG+ Q AR + F
Sbjct: 232 KRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADF 291
Query: 137 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTA 196
+SG RVL+ TD+ ARG+D++++ V+NY+LP+ E+Y+HRIGR GR G A++ V
Sbjct: 292 KSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCV 351
Query: 197 EDKRTLKDTEQFYNTRIEEM 216
++ + L+D E+ I +
Sbjct: 352 DEHKLLRDIEKLLKKEIPRI 371
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 101 bits (254), Expect = 3e-25
Identities = 49/142 (34%), Positives = 79/142 (55%), Gaps = 1/142 (0%)
Query: 77 KFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQF 136
K+ L +L + ++F N + +V + E ++K + + GD+ Q+ R + F
Sbjct: 322 KYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGF 381
Query: 137 RSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTA 196
R G RVL+ TD+ RGI + +S VIN+ LP + ++Y+HRIGR GR G GV+I+F
Sbjct: 382 REGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGE 441
Query: 197 EDKRTLKDTEQFYNTRIE-EMP 217
+D L + E+ +I EMP
Sbjct: 442 DDAFQLPEIEELLGRKISCEMP 463
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 97.7 bits (243), Expect = 1e-23
Identities = 50/157 (31%), Positives = 84/157 (53%), Gaps = 1/157 (0%)
Query: 62 TRIRQFYIYIEREDWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMH 121
R+RQ IY ++ K L L + ++F NT+ V+ + ++ + + V +
Sbjct: 230 ARVRQ-RIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLS 288
Query: 122 GDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRG 181
GD+ Q R+ ++ +F+ G +L+ TD+ ARG+ + V V NYDLP + E+Y+HRIGR
Sbjct: 289 GDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRT 348
Query: 182 GRFGRKGVAINFVTAEDKRTLKDTEQFYNTRIEEMPM 218
R G +G AI+F +L D E + +I P+
Sbjct: 349 ARLGEEGDAISFACERYAMSLPDIEAYIEQKIPVEPV 385
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 92.7 bits (231), Expect = 4e-22
Identities = 38/101 (37%), Positives = 59/101 (58%)
Query: 93 AVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLAR 152
A+IF NT+ + + + + V + GD+ Q R I+ +F G +L+ TD+ AR
Sbjct: 258 AIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAAR 317
Query: 153 GIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINF 193
G+ + V+ V NYDLP + E+Y+HRIGR GR G G +I+
Sbjct: 318 GLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 84.5 bits (209), Expect = 6e-19
Identities = 39/113 (34%), Positives = 62/113 (54%), Gaps = 1/113 (0%)
Query: 93 AVIFCNTRRKVDWLTESMLK-KEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLA 151
AV+F ++R D L ++ ++HG+ R +M+ F G V++ T +L
Sbjct: 370 AVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLG 429
Query: 152 RGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTAEDKRTLKD 204
RG+D+ +V VI +D+P+ + YIH+IGR R G KG AI FV ED+ +
Sbjct: 430 RGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPE 482
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 78.5 bits (194), Expect = 7e-17
Identities = 37/111 (33%), Positives = 57/111 (51%)
Query: 93 AVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLAR 152
+I+C TR+KV+ L E + K + A H + R+ + + F + +V++ T+
Sbjct: 233 GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGM 292
Query: 153 GIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTAEDKRTLK 203
GID V VI+YDLP + E+Y GR GR G AI + ED R +
Sbjct: 293 GIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 69.8 bits (171), Expect = 6e-14
Identities = 32/110 (29%), Positives = 53/110 (48%)
Query: 94 VIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARG 153
+I+C +R+K + +T S+ A H ++ +ARD + +F+ +V++ T G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 154 IDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTAEDKRTLK 203
I+ V VI+Y LP + E+Y GR GR G F D L+
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLR 339
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 64.7 bits (158), Expect = 3e-12
Identities = 42/169 (24%), Positives = 71/169 (42%), Gaps = 7/169 (4%)
Query: 35 INVEACADVDVNAAELRRRVLIVG-----DSMTRIRQFYIYIEREDWKFDTLCDLYGTLS 89
I + A AD + ++R + + S R + +++ + K L D
Sbjct: 166 IALTATADAET-RQDIRELLRLADANEFITSFDRPNLRFSVVKKNN-KQKFLLDYLKKHR 223
Query: 90 ITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDL 149
+I+ ++R+KV+ L E + + + A H + R F +V++ T+
Sbjct: 224 GQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNA 283
Query: 150 LARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTAED 198
GID V VI+YD+P N E+Y GR GR G AI + D
Sbjct: 284 FGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPAD 332
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 60.5 bits (147), Expect = 8e-11
Identities = 28/100 (28%), Positives = 51/100 (51%)
Query: 94 VIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARG 153
+I+CN+R KV+ + + + +A H +D + R + F+ ++++ T G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299
Query: 154 IDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINF 193
I+ V V+++D+P N E+Y GR GR G A+ F
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLF 339
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 51.1 bits (123), Expect = 1e-07
Identities = 31/106 (29%), Positives = 47/106 (44%), Gaps = 4/106 (3%)
Query: 95 IFCNTRRKVDWLTESMLKKEFTVSAM--HGDMDQNARDVIMRQFRSGSSRVLITTDLLAR 152
IF NTR + L LKK HG + + R + + + G + ++ T L
Sbjct: 258 IFTNTRSGAERLAFR-LKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLEL 316
Query: 153 GIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAINFVTAED 198
GID+ + LVI P + ++ RIGR G V+ + AED
Sbjct: 317 GIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH-RLGEVSKGIIIAED 361
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 50.9 bits (122), Expect = 1e-07
Identities = 25/93 (26%), Positives = 47/93 (50%), Gaps = 1/93 (1%)
Query: 91 TQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLL 150
+ +IF + + + L V A+ G+ + R+ I+ +FR+G +VL+T +L
Sbjct: 284 DKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVL 342
Query: 151 ARGIDVQQVSLVINYDLPSNRENYIHRIGRGGR 183
G+D+ ++I +R +I R+GRG R
Sbjct: 343 DEGVDIPDADVLIILRPTGSRRLFIQRLGRGLR 375
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 50.5 bits (121), Expect = 2e-07
Identities = 28/112 (25%), Positives = 46/112 (41%), Gaps = 11/112 (9%)
Query: 96 FCNTRRKVDWLTESMLKKEF--------TVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
F +R++V+ L S ++ VS + + R I +F+ G +I T
Sbjct: 312 FFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIAT 371
Query: 148 DLLARGIDVQQVSLVINYDLPSNRE-NYIHRIGRGGRFGRKGVAINFVTAED 198
+ L GID+ + VI Y P ++ R GR GR R ++ V
Sbjct: 372 NALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGR--RGQESLVLVVLRS 421
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 47.0 bits (112), Expect = 3e-06
Identities = 35/98 (35%), Positives = 50/98 (51%), Gaps = 5/98 (5%)
Query: 124 MDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGR 183
M Q + I+ QFR G VL+ T + G+D+ +V LVI Y+ + I R GR GR
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGR 468
Query: 184 FGRKGVAINFVTAEDKRTLKDTEQFYNTRIEEMPMNVA 221
RKG + VT E R D +Y++R +E M +
Sbjct: 469 -KRKGRVVVLVT-EGTR---DEAYYYSSRRKEQKMIES 501
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 46.3 bits (110), Expect = 5e-06
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 6/97 (6%)
Query: 92 QAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLA 151
Q ++F +RR+ L +++ K + H + R + R F + ++TT LA
Sbjct: 442 QTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALA 501
Query: 152 RGID--VQQV---SLVINYDLPSNRENYIHRIGRGGR 183
G+D QV SL + + S RE + +GR GR
Sbjct: 502 AGVDFPASQVIFESLAMGIEWLSVRE-FQQMLGRAGR 537
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 46.4 bits (111), Expect = 5e-06
Identities = 36/110 (32%), Positives = 53/110 (48%), Gaps = 11/110 (10%)
Query: 106 LTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINY 165
LTE + + V +H D+D R I+R R G VL+ +LL G+D+ +VSLV
Sbjct: 462 LTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAIL 521
Query: 166 D------LPSNRENYIHRIGRGGRFGRKGVAI---NFVTAEDKRTLKDTE 206
D L S R + I IGR R G I + +T ++ + +TE
Sbjct: 522 DADKEGFLRSER-SLIQTIGRAAR-NVNGKVILYADKITDSMQKAIDETE 569
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 45.3 bits (107), Expect = 1e-05
Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 9/111 (8%)
Query: 121 HGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGR 180
HG + + R + + +SG R ++ T L GID+ V LVI P + + + RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
Query: 181 GG-RFGRKGVAINFVTAEDKRTLKDT----EQFYNTRIEEM--PMNVADLI 224
G + G GV+ +R L D+ E + R+E + P N D++
Sbjct: 368 AGHQVG--GVSKGLFFPRTRRDLVDSAVIVECMFAGRLENLTPPHNPLDVL 416
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 44.9 bits (106), Expect = 2e-05
Identities = 25/94 (26%), Positives = 44/94 (46%)
Query: 94 VIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARG 153
+I+C +R + + E + + + HG MD R + +Q+ ++ T G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743
Query: 154 IDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRK 187
I+ V VI++ LP + E Y GR GR G++
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQR 777
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 41.1 bits (97), Expect = 3e-04
Identities = 30/91 (32%), Positives = 46/91 (50%), Gaps = 7/91 (7%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
T++ + LT+ + + V +H ++D R I+R R G VL+ +LL G+D+ +
Sbjct: 451 TKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPE 510
Query: 159 VSLVINYD------LPSNRENYIHRIGRGGR 183
VSLV D L S R + I IGR R
Sbjct: 511 VSLVAILDADKEGFLRSER-SLIQTIGRAAR 540
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 39.7 bits (93), Expect = 6e-04
Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 13/104 (12%)
Query: 92 QAVIFCNTRRKV----DWLTESMLKKEFTVSAMHGDMDQNAR----DVIMRQFRSGSSRV 143
I NT + L E E + +H + R ++ +F+ V
Sbjct: 220 SVAIIVNTVDRAQEFYQQLKEKG--PEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFV 277
Query: 144 LITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRK 187
++ T ++ +D+ V ++I P + I R+GR R+G K
Sbjct: 278 IVATQVIEASLDI-SVDVMITELAPIDS--LIQRLGRLHRYGEK 318
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 39.7 bits (93), Expect = 7e-04
Identities = 21/104 (20%), Positives = 42/104 (40%), Gaps = 13/104 (12%)
Query: 92 QAVIFCNTRRKV----DWLTESMLKKEFTVSAMHGDMDQNAR----DVIMRQFRSGSSRV 143
+ I NT + L E+ E + +H + R ++ + + V
Sbjct: 224 KIAIIVNTVDRAQEFYQQLKENA--PEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFV 281
Query: 144 LITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRK 187
++ T ++ +D+ ++I P + I R+GR R+GRK
Sbjct: 282 IVATQVIEASLDI-SADVMITELAPIDS--LIQRLGRLHRYGRK 322
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 39.2 bits (92), Expect = 0.001
Identities = 22/87 (25%), Positives = 45/87 (51%), Gaps = 4/87 (4%)
Query: 109 SMLKK---EFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINY 165
LKK ++ V +HG M + ++ +M +FR G +L+ T ++ G+DV ++++
Sbjct: 474 ERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIE 533
Query: 166 DLPSNRENYIHRI-GRGGRFGRKGVAI 191
D + +H++ GR GR + +
Sbjct: 534 DAERFGLSQLHQLRGRVGRGDHQSYCL 560
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 39.5 bits (93), Expect = 0.001
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 114 EFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYD 166
E V +HG M +D +M F+ G +L+ T ++ G+DV ++++ +
Sbjct: 507 ELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIEN 559
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. 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) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 38.5 bits (90), Expect = 0.002
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 126 QNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSL--VINYD----LPSNRE-----NY 174
+ A + ++ QF +G + +LI T ++A+G V+L V++ D P R
Sbjct: 298 KGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQL 357
Query: 175 IHRI-GRGGRFGRKGVAI 191
+ ++ GR GR G I
Sbjct: 358 LTQVAGRAGRAEDPGQVI 375
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 37.5 bits (88), Expect = 0.004
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 132 IMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYD-LPSNRENYIHRIGRGGRFGRKG 188
I+ +FR+G VL++T + G+D+ V LVI Y+ +PS I I R GR GR+
Sbjct: 415 ILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSE----IRSIQRKGRTGRQE 468
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 36.6 bits (86), Expect = 0.007
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 106 LTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLV 162
LT+ + + V +H D+D R I+R R G VL+ +LL G+D+ +VSLV
Sbjct: 462 LTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLV 518
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 35.7 bits (83), Expect = 0.010
Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 5/77 (6%)
Query: 119 AMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRI 178
A+ GD ++ R+ S + LA G+D ++ +V N D + +
Sbjct: 48 AIIGDPSKSE----ERKLLSREEVLENAKAQLACGLDPEKSEIVNNSDWLEH-LELAWLL 102
Query: 179 GRGGRFGRKGVAINFVT 195
G + F
Sbjct: 103 RDLGNHFSLNRMLQFKD 119
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 36.0 bits (84), Expect = 0.014
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 6/107 (5%)
Query: 95 IFCNTRRKVDWLTESMLKK--EFT-VSAM-HGDMDQNARDVIMRQFRSGSSRVLITTDLL 150
+F NTR + + +++ + EF A+ HG +D+ R + +G R ++ T L
Sbjct: 252 VFTNTRSQAELWFQALWEANPEFALPIALHHGSLDREQRRWVEAAMAAGRLRAVVCTSSL 311
Query: 151 ARGIDVQQVSLVINYDLPSNRENYIHRIGRGG-RFGRKGVAINFVTA 196
G+D V LVI P + R GR R G A+ V
Sbjct: 312 DLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGEPSRAL-LVPT 357
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 35.8 bits (83), Expect = 0.016
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 19/102 (18%)
Query: 132 IMRQFRSGSSRVLITTDLLARGIDVQQVSLV--INYDLPSNR------ENYIHRI----G 179
++ QF +G + +LI T ++A+G D V+LV ++ D E + G
Sbjct: 526 LLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAG 585
Query: 180 RGGRFGRKGVAINFVTAE----DKRTLK--DTEQFYNTRIEE 215
R GR G+ G + T + LK D E FY + E
Sbjct: 586 RAGRAGKPGEVV-IQTYNPDHPAIQALKRGDYEAFYEQELAE 626
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 35.5 bits (82), Expect = 0.017
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 10/84 (11%)
Query: 109 SMLKKEF---TVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINY 165
+ LKK+ T++++H + DQ+ R + FR G +LITT +L RG+ V + +
Sbjct: 323 AALKKKLPKETIASVHSE-DQH-RKEKVEAFRDGKITLLITTTILERGVTFPNVDVFV-- 378
Query: 166 DLPSNRENYIHR--IGRGGRFGRK 187
L + + + GR GR
Sbjct: 379 -LGAEHRVFTESALVQIAGRVGRS 401
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 34.7 bits (79), Expect = 0.038
Identities = 25/142 (17%), Positives = 45/142 (31%), Gaps = 19/142 (13%)
Query: 84 LYGTLSITQAVIFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRV 143
L + +IF +D L + + + G R ++ +F +
Sbjct: 705 LLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEK 764
Query: 144 LITTDLLA--RGIDVQQVSLVINYDLPSNR------ENYIHRIGR-----------GGRF 184
+ L A G+++ VI +D N + HRIG+ G
Sbjct: 765 VFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTI 824
Query: 185 GRKGVAINFVTAEDKRTLKDTE 206
K + + E +L D E
Sbjct: 825 EEKILELQEKKQELLDSLIDAE 846
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 34.4 bits (80), Expect = 0.041
Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 21/103 (20%)
Query: 132 IMRQFRSGSSRVLITTDLLARGIDVQQVSLV--INYDLPSNRENY---------IHRI-G 179
++ QF G + +LI T +LA+G D V+LV ++ DL ++ + ++ G
Sbjct: 472 LLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAG 531
Query: 180 RGGRFGRKGVAI-------NFVTAEDKRTLKDTEQFYNTRIEE 215
R GR + G + + V +D + F +EE
Sbjct: 532 RAGRAEKPGEVLIQTYHPEHPVIQALLA--QDYDAFAEQELEE 572
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 33.9 bits (78), Expect = 0.067
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 129 RDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKG 188
R + R R G + TT+ L G+D+ + V+ P R + + GR GR G+
Sbjct: 318 RRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGA 377
Query: 189 VAINFVTAED 198
+ + V +D
Sbjct: 378 LVV-LVARDD 386
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 33.2 bits (77), Expect = 0.091
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 110 MLKKEF---TVSAMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDV 156
L++ F V +HG M +D +M F++G +L+ T ++ G+DV
Sbjct: 498 ELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDV 547
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 32.7 bits (75), Expect = 0.16
Identities = 27/120 (22%), Positives = 45/120 (37%), Gaps = 33/120 (27%)
Query: 108 ESMLKKEFTVSAM---------HGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQ 158
ES+ K + + HG M +N + +M +F G +VL+ T ++ GID+
Sbjct: 671 ESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPN 730
Query: 159 VSLVINYDLPSNRENYIHRI------------GRGGRFGRKGVAINFVTAEDKRTLKDTE 206
+ +I I R GR GR +K A + K +D +
Sbjct: 731 ANTII-----------IERADKFGLAQLYQLRGRVGRSKKKAYAY-LLYPHQKALTEDAQ 778
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 31.0 bits (71), Expect = 0.55
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 8/95 (8%)
Query: 95 IFCNTR----RKVDWLTESMLKKEFTVS---AMHGDMDQNARDVIMRQFRSGSSRVLITT 147
IF NTR R + L + +E+ A H + + R + + + G +V++++
Sbjct: 289 IFTNTRSGAERVLYNLRK-RFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSS 347
Query: 148 DLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGG 182
L GID+ + LV+ P + + RIGR G
Sbjct: 348 TSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 29.5 bits (67), Expect = 1.5
Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 24/99 (24%)
Query: 121 HGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRI-- 178
HG M + + +M F +G VL+ T ++ GID+ + +I I R
Sbjct: 836 HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTII-----------IERADK 884
Query: 179 ----------GRGGRFGRKGVAINFVTAEDKRTLKDTEQ 207
GR GR ++ A F+ K +D E+
Sbjct: 885 FGLAQLYQLRGRVGRSNKQAYAY-FLYPPQKALTEDAEK 922
>gnl|CDD|213816 TIGR03470, HpnH, hopanoid biosynthesis associated radical SAM
protein HpnH. The sequences represented by this model
are members of the radical SAM superfamily of enzymes
(pfam04055). These enzymes utilize an iron-sulfur redox
cluster and S-adenosylmethionine to carry out diverse
radical mediated reactions. The members of this clade
are frequently found in the same locus as
squalene-hopene cyclase (SHC, TIGR01507) and other genes
associated with the biosynthesis of hopanoid natural
products. The linkage between SHC and this radical SAM
enzyme is strong; one is nearly always observed in the
same genome where the other is found. A hopanoid
biosynthesis locus was described in Zymomonas mobilis
consisting of the genes HpnA-E and SHC (HpnF).
Continuing past SHC are found a phosphorylase enzyme
(ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM
enzyme (ZMO0874) which we name here HpnH. Granted, in Z.
mobilis, HpnH is in a convergent orientation with
respect to HpnA-G, but one gene beyond HpnH and running
in the same convergent direction is IspH (ZM0875,
4-hydroxy-3-methylbut-2-enyl diphosphate reductase), an
essential enzyme of IPP biosynthesis and therefore
essential for the biosynthesis of hopanoids. One of the
well-described hopanoid intermediates is
bacteriohopanetetrol. In the conversion from hopene
several reactions must occur in the side chain for which
a radical mechanism might be reasonable. These include
the four (presumably anaerobic) hydroxylations and a
methyl shift.
Length = 318
Score = 29.3 bits (66), Expect = 1.5
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 9/103 (8%)
Query: 120 MHGDMDQNARDVIMRQFRSGSSRVLITTD--LLARGIDVQQVS--LVINYDLPSNRENYI 175
+H ++D+ R ++ R+ V + T+ LL + +D + S L + L RE++
Sbjct: 85 LHPEIDEIVRGLVARK-----KFVYLCTNALLLEKKLDKFEPSPYLTFSVHLDGLREHHD 139
Query: 176 HRIGRGGRFGRKGVAINFVTAEDKRTLKDTEQFYNTRIEEMPM 218
+ R G F R AI A R +T F +T EE+
Sbjct: 140 ASVCREGVFDRAVEAIREAKARGFRVTTNTTLFNDTDPEEVAE 182
>gnl|CDD|177633 PHA03397, vlf-1, very late expression factor 1; Provisional.
Length = 363
Score = 29.2 bits (66), Expect = 1.7
Identities = 12/49 (24%), Positives = 28/49 (57%)
Query: 133 MRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRG 181
M + RS R + +++ G+ +Q+VS ++N++ S +Y+++ G
Sbjct: 295 MDRPRSNMIRHYLASNMYNSGVPLQKVSKLMNHESVSATRHYLNKYHPG 343
>gnl|CDD|218229 pfam04722, Ssu72, Ssu72-like protein. The highly conserved and
essential protein Ssu72 has intrinsic phosphatase
activity and plays an essential role in the
transcription cycle. Ssu72 was originally identified in
a yeast genetic screen as enhancer of a defect caused by
a mutation in the transcription initiation factor TFIIB.
It binds to TFIIB and is also involved in mRNA
elongation. Ssu72 is further involved in both poly(A)
dependent and independent termination. It is a subunit
of the yeast cleavage and polyadenylation factor (CPF),
which is part of the machinery for mRNA 3'-end
formation. Ssu72 is also essential for transcription
termination of snRNAs.
Length = 193
Score = 28.7 bits (65), Expect = 1.8
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 148 DLLARGIDVQQVSLVINYDLPSNREN 173
DL+ RG + Q VIN D+ N E
Sbjct: 119 DLMNRGSSLNQPVHVINVDIKDNHEE 144
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 29.1 bits (66), Expect = 2.1
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 14/73 (19%)
Query: 95 IFCNTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVI----------MRQFRSGS-SRV 143
IF T D + +LK+ F +G ++ +A I +R+F++ +
Sbjct: 703 IFAATDAHADMVVR-LLKEAFK--KKYGQVEDDAVIKITGSIDKPDQLIRRFKNERLPNI 759
Query: 144 LITTDLLARGIDV 156
++T DLL GIDV
Sbjct: 760 VVTVDLLTTGIDV 772
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 29.0 bits (65), Expect = 2.4
Identities = 36/157 (22%), Positives = 55/157 (35%), Gaps = 45/157 (28%)
Query: 92 QAVIFCNTRRKVD-----------------------WLTESM--------LKKEFT--VS 118
A++F NTRR + L +S+ LKK V+
Sbjct: 240 GALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVA 299
Query: 119 AMHGDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRI 178
H + + R +I FR G +V+ T L+ GI++ ++I D I
Sbjct: 300 FHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIR-DTKRYSNFGWEDI 358
Query: 179 ---------GRGGR--FGRKGVAINFVTAEDKRTLKD 204
GR GR + G AI T E+ L +
Sbjct: 359 PVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLME 395
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 28.9 bits (65), Expect = 2.4
Identities = 28/132 (21%), Positives = 44/132 (33%), Gaps = 23/132 (17%)
Query: 99 TRRKVDWLTESMLKKEFTVSAMH-GDMDQNARDVIMRQFRSGSSRVLITTDLLARGIDVQ 157
T D ++ + A H + + R ++ FR G +VL++T LA G
Sbjct: 301 TPTSEDEELAELVLRGV---AFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAG---- 353
Query: 158 QVSL----VINYDL----------PSNRENYIHRIGRGGRFGRKGVAINFVTAEDKRTLK 203
V+L VI D + + GR GR G + A L+
Sbjct: 354 -VNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELE 412
Query: 204 DTEQFYNTRIEE 215
+ Y E
Sbjct: 413 YLAELYIQSEPE 424
>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
Length = 251
Score = 28.5 bits (64), Expect = 2.5
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 75 DWKFDTLCDLYGTLSITQAVIFCNTRRKVDWLTESMLKK 113
D KFDT Y + I A+I + RK DWL SM +K
Sbjct: 75 DLKFDT----YASFRIRGAII--DGLRKEDWLPRSMREK 107
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 28.9 bits (65), Expect = 2.7
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 142 RVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGR-----FGRKGVAINFV 194
R+ IT DLL G+DV +V ++ ++ + +GRG R G + F
Sbjct: 483 RIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRLCPDLGGPEQDKEFFT 540
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 27.9 bits (63), Expect = 2.9
Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 93 AVIFCNTRRK----VDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITTD 148
++ + + L +L+K + + +R+ ++ +F+ G +L
Sbjct: 12 VLVLFPSYSLLEQVAELLASELLEKGIELLVQ----GEGSREKLLERFKKGKGAILFGVG 67
Query: 149 LLARGIDVQ--QVSLVI 163
GID + LVI
Sbjct: 68 SFWEGIDFPGDALRLVI 84
>gnl|CDD|233953 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3, subtype
Dpsyc. 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 [Mobile and extrachromosomal element functions,
Other].
Length = 862
Score = 28.4 bits (63), Expect = 3.5
Identities = 27/112 (24%), Positives = 45/112 (40%), Gaps = 20/112 (17%)
Query: 94 VIFCNTRRKVDWLTESMLKKEF-------TVSAMHGDMDQNARDVIMR---QFRSGS--- 140
++FCNT V + + K+ TV M DM ++ +R +R+GS
Sbjct: 285 LVFCNTVDTVKKVVAKLPKQARKLEELTGTVRGMERDMLARRSEIFVRFLPPYRTGSEGR 344
Query: 141 ----SRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKG 188
+ ++ T G D+ LV + E+ + R GR RFG +
Sbjct: 345 PQQGTVYVVATSTGEVGADLDFDHLVTDL---CPFESLVQRFGRVNRFGERP 393
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 28.3 bits (63), Expect = 4.4
Identities = 11/50 (22%), Positives = 18/50 (36%)
Query: 98 NTRRKVDWLTESMLKKEFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
K+ L E + A H + + M + +G +LITT
Sbjct: 136 QVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITT 185
>gnl|CDD|173585 PTZ00394, PTZ00394, glucosamine-fructose-6-phosphate
aminotransferase; Provisional.
Length = 670
Score = 27.9 bits (62), Expect = 5.6
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 110 MLKK-----EFTVSAMHGDMDQNARDVIMRQFRSGSSRVLITT 147
MLK+ E +S+MHG +D ++ V + F S R ++T+
Sbjct: 312 MLKEIYEQPESVISSMHGRIDFSSGTVQLSGFTQQSIRAILTS 354
>gnl|CDD|131155 TIGR02100, glgX_debranch, glycogen debranching enzyme GlgX. This
family consists of the GlgX protein from the E. coli
glycogen operon and probable equivalogs from other
prokaryotic species. GlgX is not required for glycogen
biosynthesis, but instead acts as a debranching enzyme
for glycogen catabolism. This model distinguishes GlgX
from pullanases and other related proteins that also
operate on alpha-1,6-glycosidic linkages. In the wide
band between the trusted and noise cutoffs are
functionally similar enzymes, mostly from plants, that
act similarly but usually are termed isoamylase [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 688
Score = 27.7 bits (62), Expect = 5.8
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 180 RGGRFGRKGVAINFVTAEDKRTLKDT 205
GR R +INFVTA D TL+D
Sbjct: 433 HNGR--RPWASINFVTAHDGFTLRDL 456
>gnl|CDD|180368 PRK06048, PRK06048, acetolactate synthase 3 catalytic subunit;
Reviewed.
Length = 561
Score = 27.4 bits (61), Expect = 6.4
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 18/74 (24%)
Query: 17 ADVHVNVGARIG-------AGF--NADINVEACADVDVNAAEL----RRRVLIVGDSMTR 63
+D+ + VGAR A F NA I +D++ AE+ + V IVGD+
Sbjct: 274 SDLIIAVGARFDDRVTGKLASFAPNAKI-----IHIDIDPAEISKNVKVDVPIVGDAKQV 328
Query: 64 IRQFYIYIEREDWK 77
++ Y++ D K
Sbjct: 329 LKSLIKYVQYCDRK 342
>gnl|CDD|132354 TIGR03311, Se_dep_Molyb_1, selenium-dependent molybdenum
hydroxylase 1. Members of this protein family show full
length homology to the molybdenum-containing aldehyde
oxido-reductase of Desulfovibrio gigas. Members,
however, are found only within species that have, and
near those genes that encode, a set of predicted
accessory proteins for selenium-dependent molybdenum
hydroxylases. The best known examples of such enzymes
are forms of xanthine dehydrogenase and purine
hydroxylase; this family appears to be another such
enzyme.
Length = 848
Score = 27.5 bits (61), Expect = 7.1
Identities = 24/99 (24%), Positives = 37/99 (37%), Gaps = 27/99 (27%)
Query: 136 FRSGSSRVLITTDLLARGIDVQQ-------VSLVINYDLPSNRENYIHRI---------- 178
RS R L+ + ID+ V+++ D+P NR I I
Sbjct: 196 LRSKYPRALV------KSIDITVALKHPGVVAVLTAKDIPGNR--KIGHIFKDWPALIAV 247
Query: 179 GRGGRFGRKGVAINFVTAEDKRTLKDTEQFYNTRIEEMP 217
G R+ VA+ V A+ K L++ EE+P
Sbjct: 248 GEITRYVGDAVAL--VAAKSKEALREALNLIKVDYEELP 284
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 27.5 bits (61), Expect = 7.3
Identities = 29/141 (20%), Positives = 62/141 (43%), Gaps = 19/141 (13%)
Query: 59 DSMTRIRQFYIYIEREDWKFDTLCDL-YGTLSITQAVIFC---NTRRKVDWLTESM---- 110
D +++I + + + + + + L ++ T + +A+ F T +++ E++
Sbjct: 428 DDVSKIVGCWNGLAKRNGEDNDLKNIKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAY 487
Query: 111 ---LKKEF---TVSAMHGDMDQNARD-----VIMRQFRSGSSRVLITTDLLARGIDVQQV 159
LKK+F +S H D NA + + F ++L L+ G+DV +
Sbjct: 488 DEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPAL 547
Query: 160 SLVINYDLPSNRENYIHRIGR 180
VI +D S+ + + +GR
Sbjct: 548 DSVIFFDPRSSMVDIVQAVGR 568
>gnl|CDD|238283 cd00512, MM_CoA_mutase, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM)-like family; contains
proteins similar to MCM, and the large subunit of
Streptomyces coenzyme B12-dependent isobutyryl-CoA
mutase (ICM). MCM catalyzes the isomerization of
methylmalonyl-CoA to succinyl-CoA. The reaction proceeds
via radical intermediates beginning with a
substrate-induced homolytic cleavage of the Co-C bond of
coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
higher animals, MCM is involved in the breakdown of
odd-chain fatty acids, several amino acids, and
cholesterol. Methylobacterium extorquens MCM
participates in the glyoxylate regeneration pathway. In
M. extorquens, MCM forms a complex with MeaB; MeaB may
protect MCM from irreversible inactivation. In some
bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Examples include Propionbacterium
shermanni MCM during propionic acid fermentation, E.coli
MCM in a pathway for the conversion of succinate to
propionate and Streptomyces MCM in polyketide
biosynthesis. P. shermanni and Streptomyces
cinnamonensis MCMs are alpha/beta heterodimers, with
both subunits being homologous members of this family.
It has been shown for P. shermanni MCM that only the
alpha subunit binds coenzyme B12 and substrates. Human
MCM is a homodimer with two active sites. Mouse and
E.coli MCMs are also homodimers. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA (intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis). In humans, impaired activity of MCM results
in methylmalonic aciduria, a disorder of propionic acid
metabolism.
Length = 399
Score = 27.0 bits (60), Expect = 8.4
Identities = 24/87 (27%), Positives = 32/87 (36%), Gaps = 4/87 (4%)
Query: 133 MRQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSNRENYIHRIGRGGRFGRKGVAIN 192
RQ +G T R + Q L + +DLP+ R G G GVAI+
Sbjct: 4 QRQL-AGFGTAEETNKRYRRNLAAGQTGLSVAFDLPTLRGYDSDNPRDAGEVGMCGVAID 62
Query: 193 FVTAEDKRTLKDTEQFYNTRIEEMPMN 219
T ED L T + M +N
Sbjct: 63 --TLEDMDELFQGIPLEQTSV-SMTIN 86
>gnl|CDD|235935 PRK07109, PRK07109, short chain dehydrogenase; Provisional.
Length = 334
Score = 26.8 bits (60), Expect = 9.6
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 38 EACADVDVNAAELRRRVLIVGDS 60
E AD + AAE RR L VG
Sbjct: 218 EVVADAILYAAEHPRRELWVGGP 240
>gnl|CDD|235704 PRK06126, PRK06126, hypothetical protein; Provisional.
Length = 545
Score = 26.9 bits (60), Expect = 10.0
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 17 ADVHVNVGARIGAGFNADINVEACADVDVNAAEL------RRRVLIVGDS 60
V+ A + G DI+ E + V L R RV + GD+
Sbjct: 262 TIDDVDARAFVRRGVGEDIDYEVLSVVPWTGRRLVADSYRRGRVFLAGDA 311
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.138 0.410
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,607,042
Number of extensions: 1101008
Number of successful extensions: 1357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1348
Number of HSP's successfully gapped: 75
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.6 bits)