RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10478
(451 letters)
>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 = 324 bits (831), Expect = e-106
Identities = 139/369 (37%), Positives = 191/369 (51%), Gaps = 49/369 (13%)
Query: 41 FKGSSVTMAESQVPPDKCCDNCRQVVYMTPEYVTNNTSFLSRIPRIVLIAIDEAHCVSQW 100
F SS + + + D +++Y+TPE + + L + E
Sbjct: 80 FLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTL---------EER----- 125
Query: 101 GHDFRPSYRCLSELRLPLPDVPILFLSRIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSEL 160
I LIA+DEAHC+SQWGHDFRP Y+ L L
Sbjct: 126 -----------------------------KGITLIAVDEAHCISQWGHDFRPDYKALGSL 156
Query: 161 RLPLPDVPILAVTATATPVVIDDICTSLMLRDPNIINTGFDRPNLYLAASVKQDDIMADL 220
+ P+VPI+A+TATA+P V +DI L L++P I T FDRPNLY K I+ DL
Sbjct: 157 KQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTPKILEDL 216
Query: 221 RKLTNFENQFEG-STIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVK 279
+ E F+G S IIYCP++ E+V L GI YHA + + R ++H F +
Sbjct: 217 LRFIRKE--FKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQR 274
Query: 280 DLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTAD 339
D I+VVVAT AFGMGI+KPDVR VIHY PK + +YYQE GRAGRDGL S C+ FY AD
Sbjct: 275 DEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPAD 334
Query: 340 FTKN-NMIFQPNLNDSEIQEHSKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTVAESQVP 398
+ ++ + D + + + + + +E L TCRR LL+HF + + +
Sbjct: 335 INRLRRLLME--EPDGQQRTYKLKLYEMMEYCLNSSTCRRLILLSHFGEKQLNKSFGIMG 392
Query: 399 PDKCCDNCR 407
+KCCDNC
Sbjct: 393 TEKCCDNCC 401
Score = 57.1 bits (138), Expect = 9e-09
Identities = 21/85 (24%), Positives = 38/85 (44%)
Query: 8 NDSEIQEHSKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTMAESQVPPDKCCDNCRQVVY 67
D + + + + + +E L TCRR LL+HF + + + +KCCDNC + +
Sbjct: 346 PDGQQRTYKLKLYEMMEYCLNSSTCRRLILLSHFGEKQLNKSFGIMGTEKCCDNCCKRLD 405
Query: 68 MTPEYVTNNTSFLSRIPRIVLIAID 92
+ VT+ + L A+
Sbjct: 406 YKTKDVTDKVYDFGPQAQKALSAVG 430
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 307 bits (789), Expect = 6e-99
Identities = 128/284 (45%), Positives = 165/284 (58%), Gaps = 9/284 (3%)
Query: 125 FLSRIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDI 184
L R+ I L+AIDEAHC+SQWGHDFRP YR L LR LP+ P+LA+TATATP V DDI
Sbjct: 126 LLKRL-PISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPRVRDDI 184
Query: 185 CTSLMLRDPNIINTGFDRPNLYLAASVKQDDIMADLRKLTNFENQFEGSTIIYCPTKVIC 244
L L+D NI FDRPNL L V++ + L L Q S IIYC T+
Sbjct: 185 REQLGLQDANIFRGSFDRPNLALKV-VEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKV 243
Query: 245 EKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVI 304
E++ + L +NGI YHA +S ++R+ + F+ D IKV+VAT AFGMGIDKPDVR VI
Sbjct: 244 EELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVI 303
Query: 305 HYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTKNNMIFQPNLNDSEIQEHSKTMM 364
HY P + +YYQE GRAGRDGL + Y D + + + D E ++ +
Sbjct: 304 HYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQSKPDEEQKQIELAKL 363
Query: 365 KRVEKYLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNCRH 408
+++ Y E +TCRR LL +F E + P CDNC
Sbjct: 364 RQMIAYCETQTCRRLVLLKYF-------GEDEPEPCGNCDNCLD 400
Score = 40.7 bits (96), Expect = 0.001
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 8 NDSEIQEHSKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTMAESQVPPDKCCDNCR 63
D E ++ ++++ Y E +TCRR LL +F E + P CDNC
Sbjct: 351 PDEEQKQIELAKLRQMIAYCETQTCRRLVLLKYF-------GEDEPEPCGNCDNCL 399
>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 = 273 bits (699), Expect = 1e-85
Identities = 123/292 (42%), Positives = 157/292 (53%), Gaps = 25/292 (8%)
Query: 125 FLSRIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDI 184
L RIP I L+A+DEAHCVSQWGHDFRP Y+ L L P VP +A+TATA DI
Sbjct: 122 MLQRIP-IALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAETRQDI 180
Query: 185 CTSLMLRDPNIINTGFDRPNLYLAASVK---QDDIMADLRKLTNFENQFEGSTIIYCPTK 241
L L D N T FDRPNL + K Q ++ L+K S IIY ++
Sbjct: 181 RELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDYLKK------HRGQSGIIYASSR 234
Query: 242 VICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVR 301
E++ + L GI YHA +S K R E F+ D +KV+VAT AFGMGIDKP+VR
Sbjct: 235 KKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVR 294
Query: 302 CVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTKNNMIFQPNLNDSEIQEHSK 361
VIHY P +L +YYQE GRAGRDGL + Y AD + + + SE + K
Sbjct: 295 FVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIA----LLKRRIEQSEADDDYK 350
Query: 362 -TMMKRVEK---YLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNCRHN 409
+++ Y E +TCRR Y+L +F E++V P CDNC
Sbjct: 351 QIEREKLRAMIAYCETQTCRRAYILRYF-------GENEVEPCGNCDNCLDP 395
Score = 35.8 bits (83), Expect = 0.047
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 26 YLELRTCRRKYLLNHFKGSSVTMAESQVPPDKCCDNC 62
Y E +TCRR Y+L +F E++V P CDNC
Sbjct: 363 YCETQTCRRAYILRYF-------GENEVEPCGNCDNC 392
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 219 bits (559), Expect = 7e-65
Identities = 111/287 (38%), Positives = 151/287 (52%), Gaps = 22/287 (7%)
Query: 125 FLSRIP--RIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVID 182
FL + L+A+DEAHC+SQWGHDFRP Y L +LR P +P +A+TATA
Sbjct: 131 FLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQ 190
Query: 183 DICTSLMLRDPNIINTGFDRPNLYLAASVKQDDIMADLRKLTNF-ENQFEGSTIIYCPTK 241
DI L L DP I + FDRPN+ K L +L + + Q S IIYC ++
Sbjct: 191 DIVRLLGLNDPLIQISSFDRPNIRYTLVEK----FKPLDQLMRYVQEQRGKSGIIYCNSR 246
Query: 242 VICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVR 301
E L GI YHA + R ++ F +D +++VVAT AFGMGI+KP+VR
Sbjct: 247 AKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVR 306
Query: 302 CVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFT--KNNMIFQPNLNDSEIQEH 359
V+H+ P+++ +YYQE GRAGRDGL + FY AD + + +P +I+ H
Sbjct: 307 FVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERH 366
Query: 360 SKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNC 406
M + E +TCRR LLN+F E + P C NC
Sbjct: 367 KLNAMG---AFAEAQTCRRLVLLNYF-------GEGRQEP---CGNC 400
Score = 28.9 bits (65), Expect = 6.5
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 13/52 (25%)
Query: 11 EIQEHSKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTMAESQVPPDKCCDNC 62
+I+ H M + E +TCRR LLN+F E + P C NC
Sbjct: 362 DIERHKLNAMG---AFAEAQTCRRLVLLNYF-------GEGRQEP---CGNC 400
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 208 bits (531), Expect = 7e-59
Identities = 118/307 (38%), Positives = 163/307 (53%), Gaps = 21/307 (6%)
Query: 135 IAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDICTSLMLRDPN 194
IDEAHCVSQWGHDFRP Y+ L L+ P++P+LA+TATAT V +D+ +L L +
Sbjct: 585 FVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCV 644
Query: 195 IINTGFDRPNLYLAASVKQDDIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRN 254
+ F+RPNL+ + K + D+ K EN F+ IIYC +++ CEKV + L
Sbjct: 645 VFRQSFNRPNLWYSVVPKTKKCLEDIDKFIK-ENHFDECGIIYCLSRMDCEKVAERLQEF 703
Query: 255 GIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSA 314
G + YH + QR + + KD I ++ AT AFGMGI+KPDVR VIH+ PK +
Sbjct: 704 GHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEG 763
Query: 315 YYQEIGRAGRDGLSSVCYTFYKTADFTK-NNMIFQPNLNDSE-------------IQEHS 360
Y+QE GRAGRDG S C +Y +D+ + +MI Q + S I E +
Sbjct: 764 YHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMAMGYNRMASSGRILETN 823
Query: 361 KTMMKRVEKYLELRT-CRRKYLLNHFKGSSVTVAESQVPPDKCCDNCRHNEMLELEQVPR 419
+ R+ Y E CRR L HF G + K CDNC ++ L + V
Sbjct: 824 TENLLRMVSYCENEVDCRRFLQLVHF-GEKFDSTNCK----KTCDNCSSSKSLIDKDVTE 878
Query: 420 GGRMVVE 426
R +VE
Sbjct: 879 IARQLVE 885
>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 = 111 bits (280), Expect = 2e-29
Identities = 40/124 (32%), Positives = 65/124 (52%)
Query: 211 VKQDDIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQR 270
+D+ + L +L + G +I+CP+K + +++ ++L + GI+ H S ++R
Sbjct: 8 PVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEER 67
Query: 271 KEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSV 330
+E+ F + I V+VAT GID P+V VI+Y P S+Y Q IGRAGR G
Sbjct: 68 EEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGT 127
Query: 331 CYTF 334
Sbjct: 128 AILL 131
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 90.7 bits (226), Expect = 2e-22
Identities = 33/82 (40%), Positives = 46/82 (56%)
Query: 245 EKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVI 304
E++ ++L GI+ H +S ++R+EI F IKV+VAT G+D P V VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 305 HYGAPKDLSAYYQEIGRAGRDG 326
Y P ++Y Q IGRAGR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>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 = 86.0 bits (214), Expect = 7e-21
Identities = 34/76 (44%), Positives = 45/76 (59%)
Query: 251 LSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPK 310
L + GI+ H +S ++R+EI F KV+VAT G GID PDV VI+Y P
Sbjct: 3 LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPW 62
Query: 311 DLSAYYQEIGRAGRDG 326
+ ++Y Q IGRAGR G
Sbjct: 63 NPASYIQRIGRAGRAG 78
>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 = 85.6 bits (212), Expect = 7e-18
Identities = 45/155 (29%), Positives = 66/155 (42%), Gaps = 13/155 (8%)
Query: 190 LRDPNIINTGFDRPNLYLAAS-VKQDDIMAD--------LRKLTNFENQFEGSTIIYCPT 240
L DP I L +KQ + + L KL E+ EG I++ T
Sbjct: 227 LNDPVEIE--VSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDED--EGRVIVFVRT 282
Query: 241 KVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDV 300
K + E++ + L + G + H + ++R F ++V+VAT G+D PDV
Sbjct: 283 KRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDV 342
Query: 301 RCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFY 335
VI+Y P D Y IGR GR G V +F
Sbjct: 343 SHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFV 377
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 64.8 bits (158), Expect = 4e-11
Identities = 29/104 (27%), Positives = 52/104 (50%), Gaps = 10/104 (9%)
Query: 230 FEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATC 289
+ G TI++ ++ C ++ D L+ G++ PYHA + K+RK + F + VV T
Sbjct: 439 YRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTA 498
Query: 290 AFGMGIDKPDVRCV-------IHYGAPKDLSAYYQEIGRAGRDG 326
A G+D P + + I + + ++ + Q +GRAGR
Sbjct: 499 ALAAGVDFPASQVIFESLAMGIEWLSVRE---FQQMLGRAGRPD 539
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 61.0 bits (148), Expect = 6e-10
Identities = 55/208 (26%), Positives = 102/208 (49%), Gaps = 28/208 (13%)
Query: 132 IVLIAIDEAHCVSQWGHDFRPS----YRCLSELRLPLPDVPILAVTATATPVVIDDICTS 187
+ ++ +DE C+ + G FR ++ LS+ P V L +AT +P V + +S
Sbjct: 271 VSVLVLDEVDCMLERG--FRDQVMQIFQALSQ-----PQV--LLFSATVSPEV-EKFASS 320
Query: 188 LMLRDPNIINTGF-DRPNLYLAASVKQDDIMADLR--KLTNFE-----NQFEGSTIIYCP 239
+ +D +I+ G +RPN +VKQ I + + K F+ F+ +++
Sbjct: 321 -LAKDIILISIGNPNRPN----KAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVS 375
Query: 240 TKVICEKVCDVLSR-NGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKP 298
+++ + + + ++ G++ H S+K+R+E+ F+ + V+VAT G G+D
Sbjct: 376 SRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLL 435
Query: 299 DVRCVIHYGAPKDLSAYYQEIGRAGRDG 326
VR VI + P + Y +IGRA R G
Sbjct: 436 RVRQVIIFDMPNTIKEYIHQIGRASRMG 463
>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 = 54.1 bits (131), Expect = 9e-08
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIG 320
+H + +QR+ + ++ VV T + +G+D V VI G+PK ++ Q G
Sbjct: 281 HHGSLDREQRRWVEAAMAAGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAG 340
Query: 321 RAG 323
R+
Sbjct: 341 RSN 343
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 52.3 bits (126), Expect = 3e-07
Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 5/95 (5%)
Query: 233 STIIYCPTKVICEKVCDVLSRNGIQNRPYHAH---ISLKQRKEIHGLFVKDLIKVVVATC 289
+T+I+ T+ E++ L + G H +S + R E+ + +K VVAT
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLG--PDIIEVHHGSLSRELRLEVEERLKEGELKAVVATS 312
Query: 290 AFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGR 324
+ +GID D+ VI G+PK ++ + Q IGRAG
Sbjct: 313 SLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 51.8 bits (124), Expect = 4e-07
Identities = 56/190 (29%), Positives = 78/190 (41%), Gaps = 22/190 (11%)
Query: 161 RLPLPDVPILAVTATATPVVIDDICTSLMLRDPNIINTGFDRPNLYLAASVKQDDIMADL 220
+LP PDV + +AT P I ++ T M RDP I D L ++Q + +
Sbjct: 197 KLP-PDVQVALFSAT-MPNEILELTTKFM-RDPKRILVKKDELTL---EGIRQFYVAVEK 250
Query: 221 R--KLTNFENQFEGSTI----IYCPTKVICEKVCDVLSRNGIQNRPY-----HAHISLKQ 269
K + +E TI IYC T+ KV D L++ + R + H + K
Sbjct: 251 EEWKFDTLCDLYETLTITQAIIYCNTR---RKV-DYLTKK-MHERDFTVSCMHGDMDQKD 305
Query: 270 RKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSS 329
R I F +V++ T GID V VI+Y P Y IGR+GR G
Sbjct: 306 RDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKG 365
Query: 330 VCYTFYKTAD 339
V F D
Sbjct: 366 VAINFVTPDD 375
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. 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
Score = 46.5 bits (111), Expect = 5e-06
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 10/68 (14%)
Query: 64 QVVYMTPE----YVTNNTSFLSRIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLP 119
++ TP + L + + L+ +DEAH + G F + L P
Sbjct: 98 DILVGTPGRLLDLLRRGKLKLLKNLK--LLVLDEAHRLLDMG--FGDDLEEI--LSRLPP 151
Query: 120 DVPILFLS 127
D IL LS
Sbjct: 152 DRQILLLS 159
Score = 44.2 bits (105), Expect = 2e-05
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 134 LIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVID 182
L+ +DEAH + G F + L PD IL ++AT + D
Sbjct: 124 LLVLDEAHRLLDMG--FGDDLEEI--LSRLPPDRQILLLSATLPRNLED 168
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 48.2 bits (115), Expect = 5e-06
Identities = 61/228 (26%), Positives = 94/228 (41%), Gaps = 32/228 (14%)
Query: 126 LSRIPRIVLIAIDEAHCVSQWGHDFRPSYRCL-SELRLPLPDVPILAVTATATPVVIDDI 184
L R+ +VL DEA + G F P R + S++R PD L +AT P + +
Sbjct: 275 LRRVTYLVL---DEADRMLDMG--FEPQIRKIVSQIR---PDRQTLMWSAT-WPKEVQSL 325
Query: 185 CTSLMLRDPNIINTGFDRPNLYLAAS--VKQDDIMADLR----KLTNFENQFEGST---I 235
L +P +N G +L L A +KQ+ + + KL + +
Sbjct: 326 ARDLCKEEPVHVNVG----SLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKIL 381
Query: 236 IYCPTKVICEKVCDVLSR----NGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAF 291
I+ TK K D L++ +G H ++R + F +++AT
Sbjct: 382 IFVETK----KGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVA 437
Query: 292 GMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTAD 339
G+D DV+ VI++ P + Y IGR GR G YTF T D
Sbjct: 438 SRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFL-TPD 484
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 48.0 bits (115), Expect = 6e-06
Identities = 38/160 (23%), Positives = 62/160 (38%), Gaps = 22/160 (13%)
Query: 214 DDIMADLRKLTNFENQFE-GSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKE 272
DD+ L + Q E +I++ T+ ++ L + GI + +R E
Sbjct: 227 DDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNE 286
Query: 273 IHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCY 332
+ V+VAT GID DV VI++ P+ Y IGR GR G
Sbjct: 287 AIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG------ 340
Query: 333 TFYKTADFTKNNMIFQPNLNDSEIQEHSKTMMKRVEKYLE 372
K I S ++ H ++ ++E+Y+E
Sbjct: 341 --------RKGTAI-------SLVEAHDHLLLGKIERYIE 365
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 47.1 bits (113), Expect = 1e-05
Identities = 31/116 (26%), Positives = 51/116 (43%), Gaps = 4/116 (3%)
Query: 233 STIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVAT--CA 290
S +++C TK C++V D L+ G H + + R ++ F V+VAT A
Sbjct: 244 SCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAA 303
Query: 291 FGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCYTFYKTADFTKNNMI 346
G+ I + VI+Y +D + IGR GR G + + + + N I
Sbjct: 304 RGLDIKALEA--VINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAI 357
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 44.6 bits (106), Expect = 1e-05
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 64 QVVYMTPEYVTNNTSFLS-RIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVP 122
+V TP + + L + ++ L+ +DEAH + G L L D
Sbjct: 81 DIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLG----LKILLKLPKDRQ 136
Query: 123 ILFLS 127
+L LS
Sbjct: 137 VLLLS 141
Score = 38.9 bits (91), Expect = 0.001
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 130 PRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTAT 175
++ L+ +DEAH + G L L D +L ++AT
Sbjct: 102 KKLDLLILDEAHRLLNQGFGLLG----LKILLKLPKDRQVLLLSAT 143
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 47.6 bits (113), Expect = 1e-05
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 259 RPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQE 318
R +H +S +QR ++ VVAT + +GID V VI P +++ Q
Sbjct: 305 RSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQR 364
Query: 319 IGRAGRD--GLSS 329
IGRAG G+S
Sbjct: 365 IGRAGHQVGGVSK 377
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 45.3 bits (108), Expect = 4e-05
Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 2/122 (1%)
Query: 213 QDDIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKE 272
++ M L T E ++ II+ TK CE++ L+ +G + ++ K+R
Sbjct: 239 NEEKMRLL--QTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLR 296
Query: 273 IHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDGLSSVCY 332
I F + + ++VAT G+ P V V +Y P D Y IGR GR G S
Sbjct: 297 ILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSI 356
Query: 333 TF 334
+
Sbjct: 357 SL 358
>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 = 45.5 bits (108), Expect = 6e-05
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKD-LSAYYQEI 319
Y A + ++R+ I F + + V+AT A +GID + VI YG P + ++ Q
Sbjct: 344 YRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRA 403
Query: 320 GRAGRDGLSS 329
GRAGR G S
Sbjct: 404 GRAGRRGQES 413
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 44.6 bits (105), Expect = 9e-05
Identities = 34/109 (31%), Positives = 53/109 (48%), Gaps = 10/109 (9%)
Query: 231 EGS-TIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVAT- 288
EG+ T+++ TK E+V L R+G + + K+R+ + F K ++++VAT
Sbjct: 256 EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD 315
Query: 289 -CAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGR-----DGLSSVC 331
A G+ ID V+ V +Y P D Y IGR R D +S C
Sbjct: 316 VAARGLHID--GVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC 362
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 44.3 bits (105), Expect = 1e-04
Identities = 26/108 (24%), Positives = 36/108 (33%), Gaps = 16/108 (14%)
Query: 262 HAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSA------- 314
HA + + R+ + F K IKV+V+T G++ P R VI +
Sbjct: 321 HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLP-ARTVIIKDTRRYDPKGGIVDIP 379
Query: 315 ---YYQEIGRAGRDGLSSVCYTFYKTADFTKNNMIFQPNLNDSEIQEH 359
Q GRAGR G A L + IQ
Sbjct: 380 VLDVLQMAGRAGRPGYDDYGEAII-LATSHDELEY----LAELYIQSE 422
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 40.9 bits (96), Expect = 5e-04
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 11/71 (15%)
Query: 61 NCRQVVYMTPE----YVTNNTSFLSRIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRL 116
++ TP + N+ LS + ++ +DEAH + G F L L+L
Sbjct: 104 GKTDILVTTPGRLLDLLENDKLSLSNVDLVI---LDEAHRLLDGG--FGDQLEKL--LKL 156
Query: 117 PLPDVPILFLS 127
+V +L LS
Sbjct: 157 LPKNVQLLLLS 167
Score = 40.2 bits (94), Expect = 8e-04
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 134 LIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDICTSLMLRDP 193
L+ +DEAH + G F L L+L +V +L ++AT + + L L DP
Sbjct: 132 LVILDEAHRLLDGG--FGDQLEKL--LKLLPKNVQLLLLSATPPEEIENL--LELFLNDP 185
Query: 194 NIINTGFDRPNLY 206
I+ GF
Sbjct: 186 VFIDVGFTPLEPI 198
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 41.1 bits (96), Expect = 0.001
Identities = 32/90 (35%), Positives = 45/90 (50%), Gaps = 8/90 (8%)
Query: 249 DVLSRNGIQNRPYHAHIS--LKQRKEIHGL--FVKDLIKVVVATCAFGMGIDKPDVRCVI 304
+ L ++GI A +S + Q K I L F + I+V+VAT G GI + VI
Sbjct: 353 ERLVKDGINA----AQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVI 408
Query: 305 HYGAPKDLSAYYQEIGRAGRDGLSSVCYTF 334
++ P+D Y IGR GR G S V +F
Sbjct: 409 NFTLPEDPDDYVHRIGRTGRAGASGVSISF 438
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 40.5 bits (95), Expect = 0.002
Identities = 28/70 (40%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 267 LKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPK-------DLSA--YYQ 317
+K+ E LF + L+KVV AT F +GI+ P R V+ K LS Y Q
Sbjct: 458 IKELVEE--LFQEGLVKVVFATETFAIGINMP-ARTVVFTSLSKFDGNGHRWLSPGEYTQ 514
Query: 318 EIGRAGRDGL 327
GRAGR GL
Sbjct: 515 MSGRAGRRGL 524
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 39.8 bits (93), Expect = 0.003
Identities = 39/137 (28%), Positives = 57/137 (41%), Gaps = 29/137 (21%)
Query: 201 DRPNLYLAASVKQDDIMADLRKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRP 260
++ L LA +K+ +LR L + E + PT EK+ L R G+
Sbjct: 252 EKEALELAKKIKRFLTKPELRALKELADSLEEN-----PTN---EKLKKAL-RGGVAF-- 300
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAY----- 315
+HA + +R I F + LIKV+ AT GI+ P R +I +D Y
Sbjct: 301 HHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVII-----RDTKRYSNFGW 355
Query: 316 --------YQEIGRAGR 324
Q +GRAGR
Sbjct: 356 EDIPVLEIQQMMGRAGR 372
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 39.6 bits (93), Expect = 0.003
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIH--------YG-APKD 311
+HA +S + R+ + F LIKV+ +T G++ P R +I G P
Sbjct: 309 HHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIP 368
Query: 312 LSAYYQEIGRAGRDGL 327
+ Y+Q GRAGR GL
Sbjct: 369 VLEYHQMAGRAGRPGL 384
>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 = 39.3 bits (92), Expect = 0.004
Identities = 40/166 (24%), Positives = 72/166 (43%), Gaps = 14/166 (8%)
Query: 167 VPILAVTATATPVVIDDICTSLMLRDPNIIN-TGFDRPNLYLAASVKQDDIMADL----- 220
P++AVT +P ++ L +P + TG + + +AS + D++ADL
Sbjct: 217 APVVAVTEDGSP----RGARTVALWEPPLTELTGENGAPVRRSASAEAADLLADLVAEGA 272
Query: 221 RKLTNFENQFEGSTIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKD 280
R LT F G+ ++ + + +V + Y A + R+E+
Sbjct: 273 RTLT-FVRSRRGAELVAAIAR---RLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDG 328
Query: 281 LIKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDG 326
+ V T A +G+D + V+ G P ++ +Q+ GRAGR G
Sbjct: 329 ELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG 374
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 39.1 bits (92), Expect = 0.004
Identities = 18/42 (42%), Positives = 27/42 (64%)
Query: 282 IKVVVATCAFGMGIDKPDVRCVIHYGAPKDLSAYYQEIGRAG 323
+KVVV++ + +GID + V+ G+PK +S Q IGRAG
Sbjct: 341 LKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 38.7 bits (90), Expect = 0.006
Identities = 28/76 (36%), Positives = 37/76 (48%), Gaps = 12/76 (15%)
Query: 261 YHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPD----VRCVIHYGAPKDLSAYY 316
+HA +S +QR+ I +F IKV+VAT G++ P VR + YG Y
Sbjct: 291 HHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYG--NGGIRYL 348
Query: 317 ------QEIGRAGRDG 326
Q IGRAGR G
Sbjct: 349 SNMEIKQMIGRAGRPG 364
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 38.6 bits (90), Expect = 0.006
Identities = 27/140 (19%), Positives = 48/140 (34%), Gaps = 14/140 (10%)
Query: 189 MLRDPNIINTGFDRPNLYLAASVKQDDIMADLRKLTNFENQFEGSTIIYCPTKVICEKVC 248
+LR + + + +A+ K + L K + T+I+ ++
Sbjct: 246 LLRARGTLRAENEARRIAIASERKIAAVRGLLLKHARGD-----KTLIFASDVEHAYEIA 300
Query: 249 DVLSRNGIQNRPYHAHI----SLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVI 304
+ GI I ++R+ I F IKV+V G+D PD +I
Sbjct: 301 KLFLAPGI-----VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLI 355
Query: 305 HYGAPKDLSAYYQEIGRAGR 324
+ Q +GR R
Sbjct: 356 ILRPTGSRRLFIQRLGRGLR 375
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 37.1 bits (86), Expect = 0.016
Identities = 25/94 (26%), Positives = 44/94 (46%)
Query: 233 STIIYCPTKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFG 292
+ II+ TK +V + L RNG + + ++ R++ + +++AT
Sbjct: 247 AAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAA 306
Query: 293 MGIDKPDVRCVIHYGAPKDLSAYYQEIGRAGRDG 326
G+D + V++Y P D +Y IGR GR G
Sbjct: 307 RGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 37.3 bits (87), Expect = 0.017
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 245 EKVCDVLSRNGIQ---------NRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGI 295
E++ + L + GI+ +R +S K++KEI F K V+VAT G+
Sbjct: 380 EEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGL 439
Query: 296 DKPDVRCVIHYGAPKDLSAYYQEIGRAGRD 325
D P+V VI Y Q GR GR
Sbjct: 440 DIPEVDLVIFYEPVPSEIRSIQRKGRTGRK 469
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 35.6 bits (82), Expect = 0.054
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 251 LSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVRCVIHYGAPK 310
L+++GI++ H + S R F I+V+VAT G+D ++ V++Y P
Sbjct: 265 LNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPN 324
Query: 311 DLSAYYQEIGRAGR-----DGLSSVC 331
Y IGR GR + LS VC
Sbjct: 325 VPEDYVHRIGRTGRAAATGEALSLVC 350
>gnl|CDD|165451 PHA03180, PHA03180, helicase-primase primase subunit; Provisional.
Length = 1071
Score = 32.9 bits (75), Expect = 0.42
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 356 IQEHSKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTVAESQVPPDKCCDNCRHNEMLELE 415
I E + + KR++K LE + + + + G ++ P D D R + + +LE
Sbjct: 447 ICECATVIAKRLDK-LEAKLQKYGWPESRPDGPNLMSDNQNDPSDSSYDRDRCDGL-QLE 504
Query: 416 Q---VPRGGRMVVENSEVWMSTEARPG 439
Q PRGG M+V+ +S + R G
Sbjct: 505 QPDTHPRGGPMIVKRLLALVSADPRAG 531
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 31.9 bits (73), Expect = 0.66
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 284 VVVATCAFGMGIDKPDVRCVIHYGAPK-DLSAYYQEIGRAGRDGLSSVCYTFYKT 337
++VAT +G+D P+ ++ A + LS +Q GR GR S C YK
Sbjct: 511 ILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKN 565
>gnl|CDD|216590 pfam01590, GAF, GAF domain. This domain is present in
cGMP-specific phosphodiesterases, adenylyl and guanylyl
cyclases, phytochromes, FhlA and NifA. Adenylyl and
guanylyl cyclases catalyze ATP and GTP to the second
messengers cAMP and cGMP, respectively, these products
up-regulating catalytic activity by binding to the
regulatory GAF domain(s). The opposite hydrolysis
reaction is catalyzed by phosphodiesterase.
cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes
the conversion of guanosine 3',5'-cyclic phosphate to
guanosine 5'-phosphate. Here too, cGMP regulates
catalytic activity by GAF-domain binding. Phytochromes
are regulatory photoreceptors in plants and bacteria
which exist in two thermally-stable states that are
reversibly inter-convertible by light: the Pr state
absorbs maximally in the red region of the spectrum,
while the Pfr state absorbs maximally in the far-red
region. This domain is also found in FhlA (formate
hydrogen lyase transcriptional activator) and NifA, a
transcriptional activator which is required for
activation of most Nif operons which are directly
involved in nitrogen fixation. NifA interacts with
sigma-54.
Length = 143
Score = 29.8 bits (67), Expect = 1.3
Identities = 19/89 (21%), Positives = 30/89 (33%), Gaps = 3/89 (3%)
Query: 130 PRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPVVIDDICTSLM 189
R ++ D + S L+ RLPL + V A P+V+ D+
Sbjct: 20 DRCAILLADADGLLLYLVAGDGLSDIPLAARRLPLGGGIVGEVIAGGRPIVVPDVQDDPR 79
Query: 190 LRDPNIINTGFDR---PNLYLAASVKQDD 215
D + + F R LA +K
Sbjct: 80 FSDLTALASDFLRGLGIRSCLAVPLKGGG 108
>gnl|CDD|184207 PRK13648, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 269
Score = 30.5 bits (69), Expect = 1.4
Identities = 22/84 (26%), Positives = 32/84 (38%), Gaps = 19/84 (22%)
Query: 214 DDIMADLRK-----LTNFENQFEGSTIIY----------CPTKVICEKVCDVLSRNGIQN 258
DD LRK N +NQF GS + Y P + +V + L + +
Sbjct: 75 DDNFEKLRKHIGIVFQNPDNQFVGSIVKYDVAFGLENHAVPYDEMHRRVSEALKQVDMLE 134
Query: 259 RPYHAHISL----KQRKEIHGLFV 278
R + +L KQR I G+
Sbjct: 135 RADYEPNALSGGQKQRVAIAGVLA 158
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 30.5 bits (69), Expect = 2.0
Identities = 15/116 (12%), Positives = 26/116 (22%), Gaps = 23/116 (19%)
Query: 3 FQPNLNDSEIQEH-SKTMMKRVEKYLELRTCRRKYLLNHFKGSSVTMAESQVPPDKC--- 58
+D +Q K + + E +T + L D C
Sbjct: 117 QLGGDDDDYLQSLALKALADLLVWLTETKTGDLREL-TPKALDDPLWTLVTDDKDSCLGE 175
Query: 59 -CDNCR--------------QVVYMTPEYVT---NNTSFLSRIPRIVLIAIDEAHC 96
C +V + +P ++ DEAH
Sbjct: 176 DCPYYTECFYFPARKEAENADLVVTNHALLLADVALEESRILLPENDVVVFDEAHN 231
>gnl|CDD|213278 cd05910, FACL_like_1, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 455
Score = 30.4 bits (69), Expect = 2.3
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 281 LIKVVVATCAFGMGIDKPDVRCVIHYGAP---KDLSAYYQEI 319
L+K V C GI P +R V+ GAP L + +
Sbjct: 183 LLKNVARYCE-ENGIQLPSLRRVLSAGAPVPPDLLRRFVANL 223
>gnl|CDD|180298 PRK05870, PRK05870, enoyl-CoA hydratase; Provisional.
Length = 249
Score = 30.1 bits (68), Expect = 2.3
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 298 PDVRCVIHYGAPK------DLSAYYQEIGRAGRDGLSSVCYTFYKTAD 339
PDV ++ GA K DL+A GR DGL + F A
Sbjct: 46 PDVHALVVTGAGKAFCAGADLTALGAAPGRPAEDGLRRIYDGFLAVAS 93
>gnl|CDD|180835 PRK07094, PRK07094, biotin synthase; Provisional.
Length = 323
Score = 29.8 bits (68), Expect = 2.8
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 145 QWGHDFRPSYRCLSELRLPLPDVPILAVTATAT 177
+ G + + L+ LRL LPD I A TA T
Sbjct: 228 EKGGSLELTLKVLALLRLLLPDANIPATTALGT 260
>gnl|CDD|169423 PRK08392, PRK08392, hypothetical protein; Provisional.
Length = 215
Score = 29.0 bits (65), Expect = 4.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 304 IHYGAPKDLSAYYQEIGRAGRD 325
IHY P +AY EI + G +
Sbjct: 37 IHYFTPSKFNAYINEIRQWGEE 58
>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 = 29.6 bits (67), Expect = 4.3
Identities = 27/90 (30%), Positives = 37/90 (41%), Gaps = 5/90 (5%)
Query: 240 TKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPD 299
TK + E + D L GI+ R H+ I +R EI V+V G+D P+
Sbjct: 451 TKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPE 510
Query: 300 VRCVI-----HYGAPKDLSAYYQEIGRAGR 324
V V G + + Q IGRA R
Sbjct: 511 VSLVAILDADKEGFLRSERSLIQTIGRAAR 540
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 29.5 bits (67), Expect = 4.7
Identities = 29/94 (30%), Positives = 41/94 (43%), Gaps = 13/94 (13%)
Query: 240 TKVICEKVCDVLSRNGIQNRPYHAHISLKQRKEIHGLFVKDL----IKVVVATCAFGMGI 295
TK + E + + L GI+ R H+ I +R EI ++DL V+V G+
Sbjct: 455 TKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEI----IRDLRLGEFDVLVGINLLREGL 510
Query: 296 DKPDVRCVIHYGAPK-----DLSAYYQEIGRAGR 324
D P+V V A K + Q IGRA R
Sbjct: 511 DLPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 544
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 29.5 bits (67), Expect = 4.8
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 282 IKVVVATCAFGMGIDKPDVRCVIHYGAPK-DLSAYYQEIGRAGRDGLSSVCYTFYK 336
I ++VAT +G+D P+ ++ A + L+ +Q GR GR L S C YK
Sbjct: 534 IDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYK 589
>gnl|CDD|179559 PRK03321, PRK03321, putative aminotransferase; Provisional.
Length = 352
Score = 29.2 bits (66), Expect = 5.0
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 78 SFLSRIPRIVLIAIDEAHC 96
FL +P VL+ +DEA+
Sbjct: 169 RFLDAVPADVLVVLDEAYV 187
Score = 28.8 bits (65), Expect = 6.6
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 125 FLSRIPRIVLIAIDEAHC 142
FL +P VL+ +DEA+
Sbjct: 170 FLDAVPADVLVVLDEAYV 187
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 28.8 bits (65), Expect = 6.0
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 255 GIQNRPYHAHISLKQRKEIHGLFVKDLIKVVVATCAFGMGIDKPDVR 301
G++ + A S ++R+E+ F L++ +VA G+D P R
Sbjct: 313 GMRVNTFTAEESKEEREELLRQFESGLLQGLVAIRCLDEGVDIPATR 359
>gnl|CDD|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7.
Length = 393
Score = 28.1 bits (63), Expect = 9.1
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 56 DKCCDNCRQVVYMTPEY---VTNNTSFLSRIPRIVLIAIDEAHCVSQWG 101
DKC D C + EY +T N FL R+ + +I +EA WG
Sbjct: 173 DKCLDFCDYFLTGVAEYQKLITRNPIFLERVEGVGIIGGEEA---INWG 218
>gnl|CDD|185037 PRK15079, PRK15079, oligopeptide ABC transporter ATP-binding
protein OppF; Provisional.
Length = 331
Score = 28.1 bits (63), Expect = 9.2
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 2 IFQPNLNDSEIQEHSKTMMKRV 23
+ P L+ E+++ K MM +V
Sbjct: 127 TYHPKLSRQEVKDRVKAMMLKV 148
Score = 28.1 bits (63), Expect = 9.2
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 346 IFQPNLNDSEIQEHSKTMMKRV 367
+ P L+ E+++ K MM +V
Sbjct: 127 TYHPKLSRQEVKDRVKAMMLKV 148
>gnl|CDD|215386 PLN02727, PLN02727, NAD kinase.
Length = 986
Score = 28.3 bits (63), Expect = 9.3
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 10/49 (20%)
Query: 34 RKYLLNHFKGSSVTMAESQVPP--------DKCCDNCRQVV--YMTPEY 72
R +++ F+GS V+ E ++PP +CC++ + Y+TP+
Sbjct: 157 RSSIMSSFRGSEVSAMEDKLPPLAIFRGEMKRCCESLHVALENYLTPDD 205
>gnl|CDD|223655 COG0582, XerC, Integrase [DNA replication, recombination, and
repair].
Length = 309
Score = 28.3 bits (61), Expect = 9.8
Identities = 19/98 (19%), Positives = 31/98 (31%)
Query: 82 RIPRIVLIAIDEAHCVSQWGHDFRPSYRCLSELRLPLPDVPILFLSRIPRIVLIAIDEAH 141
R R V ++ + ++ RP LR P L ++R+ R A EA
Sbjct: 186 RKERRVPLSEQALEALKKYLLIRRPREYLFLSLRGPRLSRSALTINRLLRARAKAAKEAG 245
Query: 142 CVSQWGHDFRPSYRCLSELRLPLPDVPILAVTATATPV 179
H R ++ L + L A+
Sbjct: 246 IRKITPHGLRHTFATLLLAGGDERVIQKLLGHASLNTT 283
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
0.323 0.138 0.425
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: 23,023,452
Number of extensions: 2218246
Number of successful extensions: 1860
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1838
Number of HSP's successfully gapped: 75
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.2 bits)