RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9509
(231 letters)
>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 = 125 bits (315), Expect = 2e-33
Identities = 56/213 (26%), Positives = 97/213 (45%), Gaps = 35/213 (16%)
Query: 20 PSRPQRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAGTGDTQPTSSEAGADNLSSGFI 79
P Q LLFSAT+ D + E A P E + L
Sbjct: 203 PPDRQTLLFSATMPDD-----------------IRELARRYLNDPVEIEVSVEKLER--- 242
Query: 80 GKFTTPAELSEKLTTCST-NLKPLVLYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDN 138
T ++ + + K +L +L++ V+ FV T + LA L
Sbjct: 243 ----TLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKR-- 296
Query: 139 VATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINY 198
+A ++ DL ++R++ +++F+ ++ ++VA+D ARG+D+ ++ VINY
Sbjct: 297 --------GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINY 348
Query: 199 EAPDNIKKYIHRIGRTARGGRQGTSVTLVTTHE 231
+ P + + Y+HRIGRT R GR+G +++ VT E
Sbjct: 349 DLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEE 381
>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 = 109 bits (275), Expect = 1e-30
Identities = 43/133 (32%), Positives = 76/133 (57%), Gaps = 12/133 (9%)
Query: 96 STNLKPLVLYQLIRKHAMQG--VLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEV 153
+ K L +L+++H +G VL F + + LA LL + +A +
Sbjct: 9 VEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPG----------IKVAAL 58
Query: 154 YSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGR 213
+ D ++R +++++FR +I ++VA+D +ARGID+ N+ VVINY+ P + Y+ RIGR
Sbjct: 59 HGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGR 118
Query: 214 TARGGRQGTSVTL 226
R G++GT++ L
Sbjct: 119 AGRAGQKGTAILL 131
>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 = 87.2 bits (217), Expect = 1e-22
Identities = 28/72 (38%), Positives = 47/72 (65%)
Query: 147 KMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKK 206
+ +A ++ L ++R +I+++FR K ++VA+D RGID+ ++++VINY+ P N
Sbjct: 7 GIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPAS 66
Query: 207 YIHRIGRTARGG 218
YI RIGR R G
Sbjct: 67 YIQRIGRAGRAG 78
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 90.8 bits (226), Expect = 3e-21
Identities = 62/219 (28%), Positives = 98/219 (44%), Gaps = 54/219 (24%)
Query: 22 RPQRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAGTGDTQPTSSEAG--------ADN 73
R Q LLFSATL D + F +L VE + +P+ E AD+
Sbjct: 178 RKQTLLFSATLEGD-----AVQDFAERLLNDPVEV----EAEPSRRERKKIHQWYYRADD 228
Query: 74 LSSGFIGKFTTPAELSEKLTTCSTNLKPLVLYQLIRKHAMQGVLCFVNTAQGAHRLARLL 133
L K +L L+++ + + FV T + H LA L
Sbjct: 229 L-----------------------EHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWL 265
Query: 134 HHIDNVATKGAGTKMNIAEVY--SDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVEN 191
K I Y ++ +RN+ I+ +++++VA+D ARGID+++
Sbjct: 266 R------------KAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDD 313
Query: 192 IDVVINYEAPDNIKKYIHRIGRTARGGRQGTSVTLVTTH 230
+ VIN++ P + Y+HRIGRT R GR+GT+++LV H
Sbjct: 314 VSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAH 352
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 83.8 bits (208), Expect = 3e-21
Identities = 26/72 (36%), Positives = 44/72 (61%)
Query: 147 KMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKK 206
+ +A ++ L ++R +I+ +F KI ++VA+D RG+D+ +D+VI Y+ P +
Sbjct: 11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPAS 70
Query: 207 YIHRIGRTARGG 218
YI RIGR R G
Sbjct: 71 YIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 81.7 bits (202), Expect = 5e-18
Identities = 39/113 (34%), Positives = 66/113 (58%), Gaps = 10/113 (8%)
Query: 116 VLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKID 175
+L FV T +GA L + L +D ++ D K ++R ++ EF+ K
Sbjct: 380 ILIFVETKKGADFLTKELR-LDGWPA---------LCIHGDKKQEERTWVLNEFKTGKSP 429
Query: 176 LVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQGTSVTLVT 228
+++A+D +RG+DV+++ VIN++ P+ I+ Y+HRIGRT R G +G S T +T
Sbjct: 430 IMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLT 482
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 81.4 bits (201), Expect = 7e-18
Identities = 64/212 (30%), Positives = 95/212 (44%), Gaps = 36/212 (16%)
Query: 20 PSRPQRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAGTGDTQPTSSEAGADNLSSGFI 79
P++ Q LLFSAT S D + L + KL + P E N +S +
Sbjct: 178 PAKRQNLLFSATFSDDIKALAE------KLLHN-----------PLEIEVARRNTASEQV 220
Query: 80 GKFTTPAELSEKLTTCSTNLKPLVLYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDNV 139
+ +K K +L Q+I K Q VL F T GA+ LA L+
Sbjct: 221 TQHV---HFVDK------KRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIR 271
Query: 140 ATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYE 199
+ G K A R + + +F+ I ++VA+D ARG+D+E + V+NYE
Sbjct: 272 SAAIHGNKSQGA----------RTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYE 321
Query: 200 APDNIKKYIHRIGRTARGGRQGTSVTLVTTHE 231
P+ + Y+HRIGRT R G +++LV E
Sbjct: 322 LPNVPEDYVHRIGRTGRAAATGEALSLVCVDE 353
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 80.3 bits (198), Expect = 2e-17
Identities = 58/205 (28%), Positives = 91/205 (44%), Gaps = 42/205 (20%)
Query: 24 QRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAG-TGDT--QPTSSEAGADNLSSGFIG 80
Q LLFSAT + D L + P + +EP DT Q + AG+D
Sbjct: 272 QTLLFSATFTDDVMNLAKQWTTDPAIVE--IEPENVASDTVEQHVYAVAGSD-------- 321
Query: 81 KFTTPAELSEKLTTCSTNLKPLVLYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDNVA 140
K +LY L+ ++ + V+ F N R+ + +
Sbjct: 322 -------------------KYKLLYNLVTQNPWERVMVFANRKDEVRRIE------ERLV 356
Query: 141 TKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEA 200
G +N A++ D+ +R K ++ FR KI ++VA+D RGI ++ I VIN+
Sbjct: 357 KDG----INAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTL 412
Query: 201 PDNIKKYIHRIGRTARGGRQGTSVT 225
P++ Y+HRIGRT R G G S++
Sbjct: 413 PEDPDDYVHRIGRTGRAGASGVSIS 437
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 79.1 bits (195), Expect = 4e-17
Identities = 65/229 (28%), Positives = 104/229 (45%), Gaps = 39/229 (17%)
Query: 1 MRRRGVGGLVIMWDTFLTYPSRPQRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAGTG 60
M RG G + +D F P Q LFSAT+ ++ +L + PK +V+
Sbjct: 182 MLSRGFKGQI--YDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPK--RILVK----- 232
Query: 61 DTQPTSSEAGADNLSSGFIGKFTTPAELSE-KLTTCSTNLKPLVLYQLIRKHAMQGVLCF 119
D L+ I +F E E K T + L + Q I +
Sbjct: 233 ----------KDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAI---------IY 273
Query: 120 VNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVA 179
NT + L + +H D ++ ++ D+ R+ I++EFR +++
Sbjct: 274 CNTRRKVDYLTKKMHERD----------FTVSCMHGDMDQKDRDLIMREFRSGSTRVLIT 323
Query: 180 SDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQGTSVTLVT 228
+D LARGIDV+ + +VINY+ P + + YIHRIGR+ R GR+G ++ VT
Sbjct: 324 TDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVT 372
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 72.1 bits (178), Expect = 1e-14
Identities = 38/127 (29%), Positives = 66/127 (51%), Gaps = 14/127 (11%)
Query: 107 LIRKHAMQGVLCFVNTAQGAHRLARLLHH--IDNVATKGAGTKMNIAEVYSDLKFDQRNK 164
L+ H + + F NT + +A L+ +A G DL+ R++
Sbjct: 236 LLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHG------------DLEQRDRDQ 283
Query: 165 IIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQGTSV 224
++ F R ++VA+D ARG+D++ ++ VINYE + + ++HRIGRT R G +G ++
Sbjct: 284 VLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLAL 343
Query: 225 TLVTTHE 231
+LV E
Sbjct: 344 SLVAPEE 350
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 71.1 bits (174), Expect = 2e-14
Identities = 55/204 (26%), Positives = 96/204 (47%), Gaps = 38/204 (18%)
Query: 24 QRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAGTGDTQPTSSEAGADNLSSGFI-GKF 82
Q LLFSATLSH V+E A +P + +++ + +
Sbjct: 194 QTLLFSATLSH-----------------RVLELAYEHMNEPEKLVVETETITAARVRQRI 236
Query: 83 TTPAELSEKLTTCSTNLKPLVLYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDNVATK 142
PA+ EK L+L L R + + FVNT R+AR L
Sbjct: 237 YFPAD-EEKQ--------TLLLGLLSRSEGAR-TMVFVNTKAFVERVARTLER------- 279
Query: 143 GAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPD 202
G ++ + + D+ +R ++ F++ +++++VA+D ARG+ ++ + V NY+ P
Sbjct: 280 -HGYRVGV--LSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPF 336
Query: 203 NIKKYIHRIGRTARGGRQGTSVTL 226
+ + Y+HRIGRTAR G +G +++
Sbjct: 337 DAEDYVHRIGRTARLGEEGDAISF 360
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 69.1 bits (169), Expect = 1e-13
Identities = 31/83 (37%), Positives = 52/83 (62%)
Query: 149 NIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYI 208
N A + D+ R + ++ + ++D+++A+D ARG+DVE I +V+NY+ P + + Y+
Sbjct: 271 NSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYV 330
Query: 209 HRIGRTARGGRQGTSVTLVTTHE 231
HRIGRT R GR G ++ V E
Sbjct: 331 HRIGRTGRAGRAGRALLFVENRE 353
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 68.1 bits (167), Expect = 2e-13
Identities = 29/65 (44%), Positives = 45/65 (69%)
Query: 162 RNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQG 221
R +I++EF R +D++VA+D ARG+ + + V NY+ PD+ + Y+HRIGRT R G G
Sbjct: 294 RLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASG 353
Query: 222 TSVTL 226
S++L
Sbjct: 354 HSISL 358
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 67.7 bits (166), Expect = 4e-13
Identities = 32/110 (29%), Positives = 57/110 (51%), Gaps = 11/110 (10%)
Query: 104 LYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQRN 163
+ +L++KH + L F NT GA RLA L + I + L + R
Sbjct: 246 IAELVKKH--RTTLIFTNTRSGAERLAFRLKKLGPD---------IIEVHHGSLSRELRL 294
Query: 164 KIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGR 213
++ + + ++ VVA+ +L GID+ +ID+VI +P ++ +++ RIGR
Sbjct: 295 EVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGR 344
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 65.2 bits (159), Expect = 2e-12
Identities = 55/209 (26%), Positives = 98/209 (46%), Gaps = 37/209 (17%)
Query: 21 SRPQRLLFSATLSHDPEKLHQLSLFQPKLFTSVVEPAGTGDTQPTSSEAGADNLSSGFIG 80
S+PQ LLFSAT+S + EK SL + + S+ P +P +
Sbjct: 299 SQPQVLLFSATVSPEVEKFAS-SLAKDIILISIGNP-----NRPNKA------------- 339
Query: 81 KFTTPAELSEKLTTCSTNLKPLVLYQLI--RKHAMQGVLCFVNTAQGAHRLARLLHHIDN 138
+ + T K L+ ++ ++H + FV++ GA LA N
Sbjct: 340 -------VKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLA-------N 385
Query: 139 VATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINY 198
T G K ++ + +R ++++ F ++ ++VA+ L RG+D+ + VI +
Sbjct: 386 AITVVTGLK--ALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIF 443
Query: 199 EAPDNIKKYIHRIGRTARGGRQGTSVTLV 227
+ P+ IK+YIH+IGR +R G +GT++ V
Sbjct: 444 DMPNTIKEYIHQIGRASRMGEKGTAIVFV 472
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 50.4 bits (121), Expect = 2e-07
Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 3/70 (4%)
Query: 160 DQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEA-PDNIKKYIHRIGRTARGG 218
++ +II +FR+ + +++VA+ G+D+ +D+VI YE P I+ I R GRT R
Sbjct: 412 KEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIR-SIQRKGRTGR-K 469
Query: 219 RQGTSVTLVT 228
R+G V LVT
Sbjct: 470 RKGRVVVLVT 479
>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 = 3e-07
Identities = 26/107 (24%), Positives = 50/107 (46%), Gaps = 3/107 (2%)
Query: 116 VLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKID 175
L F + + L L + +G ++ + L ++R +I EF+ ++
Sbjct: 309 TLVFFRSRKQVELLY--LSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELL 366
Query: 176 LVVASDNLARGIDVENIDVVINYEAP-DNIKKYIHRIGRTARGGRQG 221
V+A++ L GID+ ++D VI Y P ++ + R GR R G++
Sbjct: 367 GVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQES 413
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 49.1 bits (118), Expect = 7e-07
Identities = 37/134 (27%), Positives = 70/134 (52%), Gaps = 20/134 (14%)
Query: 83 TTPAELSEKLTTCSTNLKPLVLYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDNVATK 142
T E+SE L L++LI++H + L F NT GA R+ L+++ K
Sbjct: 264 TPAEEISEALYE--------TLHELIKEH--RTTLIFTNTRSGAERV---LYNL----RK 306
Query: 143 GAGTKMNIAEV---YSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYE 199
+ + + +S L + R ++ ++ +R ++ +VV+S +L GID+ ID+V+
Sbjct: 307 RFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLG 366
Query: 200 APDNIKKYIHRIGR 213
+P ++ + + RIGR
Sbjct: 367 SPKSVSRLLQRIGR 380
>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 = 47.1 bits (112), Expect = 3e-06
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 157 LKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTAR 216
L+ R+ + +F+R +I +VVA+ GI+ ++ VI+Y P +++ Y GR R
Sbjct: 260 LEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGR 319
Query: 217 GGRQGTSVTLVTTHE 231
G +
Sbjct: 320 DGLPSECHLFYAPAD 334
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 44.7 bits (106), Expect = 1e-05
Identities = 28/134 (20%), Positives = 55/134 (41%), Gaps = 17/134 (12%)
Query: 103 VLYQLIRKHAMQ-GVLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQ 161
+ L+ KHA L F + + A+ +A+L + + + ++
Sbjct: 272 AVRGLLLKHARGDKTLIFASDVEHAYEIAKLF-----------LAPGIVEAITGETPKEE 320
Query: 162 RNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKK-YIHRIG---RTARG 217
R I++ FR I ++V L G+D+ + DV+I P ++ +I R+G R A G
Sbjct: 321 REAILERFRTGGIKVLVTVKVLDEGVDIPDADVLI-ILRPTGSRRLFIQRLGRGLRPAEG 379
Query: 218 GRQGTSVTLVTTHE 231
++ +
Sbjct: 380 KEDTLALDYSLVPD 393
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 44.6 bits (106), Expect = 2e-05
Identities = 26/113 (23%), Positives = 51/113 (45%), Gaps = 10/113 (8%)
Query: 114 QGVLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRK 173
+ + + T + LA L G ++ ++ L ++R ++ Q F +
Sbjct: 231 KSGIIYCLTRKKVEELAEWLR------KNG----ISAGAYHAGLSNEERERVQQAFLNDE 280
Query: 174 IDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQGTSVTL 226
I ++VA++ GID ++ VI+Y+ P +I+ Y GR R G ++ L
Sbjct: 281 IKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILL 333
>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 = 44.1 bits (105), Expect = 3e-05
Identities = 32/129 (24%), Positives = 53/129 (41%), Gaps = 12/129 (9%)
Query: 104 LYQLIRKHAMQGVLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLKFDQRN 163
+Y I + L F NT A + L + + A IA + L +QR
Sbjct: 240 VYAEIDQART--TLVFTNTRSQAELWFQALWEAN---PEFALP---IALHHGSLDREQRR 291
Query: 164 KIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTA-RGGRQGT 222
+ ++ VV + +L G+D +D+VI +P + + + R GR+ R G
Sbjct: 292 WVEAAMAAGRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPGE--P 349
Query: 223 S-VTLVTTH 230
S LV T+
Sbjct: 350 SRALLVPTN 358
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 43.2 bits (102), Expect = 6e-05
Identities = 32/137 (23%), Positives = 66/137 (48%), Gaps = 7/137 (5%)
Query: 87 ELSEKLTTCSTNLKPLVLYQLIRKHA-MQGVLCFVNTAQGAHRL----ARLLHHIDNVAT 141
L++ L S+ +P + Y L+ K + ++ +V +G + +R +++ A
Sbjct: 197 GLNDPLIQISSFDRPNIRYTLVEKFKPLDQLMRYVQEQRGKSGIIYCNSR--AKVEDTAA 254
Query: 142 KGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAP 201
+ ++ A ++ L D R + + F+R + +VVA+ GI+ N+ V++++ P
Sbjct: 255 RLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIP 314
Query: 202 DNIKKYIHRIGRTARGG 218
NI+ Y GR R G
Sbjct: 315 RNIESYYQETGRAGRDG 331
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 42.6 bits (101), Expect = 1e-04
Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 164 KIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEA-PDNIKKYIHRIGRTARGGRQGT 222
+I+ +FR + +++V++ G+D+ ++D+VI YE P I + I R GRT R +G
Sbjct: 414 EILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEI-RSIQRKGRTGR-QEEGR 471
Query: 223 SVTLVT 228
V L+
Sbjct: 472 VVVLIA 477
>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 = 41.3 bits (97), Expect = 2e-04
Identities = 34/120 (28%), Positives = 54/120 (45%), Gaps = 14/120 (11%)
Query: 101 PLVLYQLIRKHAMQG--VLCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVYSDLK 158
PL L + + K G VL F + ++A L K K IA V+S+ +
Sbjct: 291 PLKLKRWLEKQRKTGRPVLIFFPEIETMEQVAAAL--------KKKLPKETIASVHSEDQ 342
Query: 159 FDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDV-VINYEAPDNIKKYIHRI-GRTAR 216
R + ++ FR KI L++ + L RG+ N+DV V+ E + + +I GR R
Sbjct: 343 H--RKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGR 400
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 38.1 bits (89), Expect = 0.003
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 147 KMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIK- 205
K N+ ++ +K D++ +++EFR ++D++VA+ + G+DV N V++ E +
Sbjct: 482 KYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMV-IEDAERFGL 540
Query: 206 KYIHRI-GRTARGGRQG 221
+H++ GR RG Q
Sbjct: 541 SQLHQLRGRVGRGDHQS 557
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 37.6 bits (87), Expect = 0.005
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 160 DQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGR 213
+QR Q + ++ VVA+ +L GID+ +D+VI P ++ + RIGR
Sbjct: 314 EQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
>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 = 37.4 bits (87), Expect = 0.005
Identities = 19/67 (28%), Positives = 34/67 (50%)
Query: 160 DQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGR 219
R + ++F + ++VA++ GID N+ VI+Y+ P N++ Y GR R G
Sbjct: 261 KVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGL 320
Query: 220 QGTSVTL 226
++ L
Sbjct: 321 PAEAILL 327
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 37.2 bits (86), Expect = 0.006
Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 28/136 (20%)
Query: 106 QLIRKHAMQG--VLCFVNTAQGAHRLAR-LLHHIDNVATKGAGTKMN------------- 149
LI++ G VL FV++ + A A L+ H ++ N
Sbjct: 227 SLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPH 286
Query: 150 -IAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGID-------VENI----DVVIN 197
+A ++ L +QR I + FR R I ++VA+ LA G++ V +I + I
Sbjct: 287 GVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIR 346
Query: 198 YEAPDNIKKYIHRIGR 213
Y + IK+ I R GR
Sbjct: 347 YLSNMEIKQMIGRAGR 362
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 35.9 bits (83), Expect = 0.017
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 12/73 (16%)
Query: 117 LCFVNTAQGAHRLARLLHHIDNVATKGAGTKMNIAEVY-SDLKFDQRNKIIQEFRRRKID 175
+ F + + H LA L G G K A Y + L + +R + + F +++
Sbjct: 444 IVFTYSRRRCHELADAL--------TGKGLK---AAPYHAGLPYKERKSVERAFAAQELA 492
Query: 176 LVVASDNLARGID 188
VV + LA G+D
Sbjct: 493 AVVTTAALAAGVD 505
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 34.1 bits (79), Expect = 0.058
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 155 SDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEA-----PDNIKKYIH 209
SD+ +R +II++ R + D++V + L G+D+ + +V +A + + I
Sbjct: 478 SDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQ 537
Query: 210 RIGRTAR 216
IGR AR
Sbjct: 538 TIGRAAR 544
>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 = 33.1 bits (76), Expect = 0.12
Identities = 14/69 (20%), Positives = 32/69 (46%)
Query: 148 MNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKY 207
M + ++ ++R +++++F + +VA L G+D+ + N +++
Sbjct: 314 MRVNTFTAEESKEEREELLRQFESGLLQGLVAIRCLDEGVDIPATRTAYILASSSNPRQF 373
Query: 208 IHRIGRTAR 216
I R GR R
Sbjct: 374 IQRRGRVLR 382
>gnl|CDD|234549 TIGR04332, gamma_Glu_sys, poly-gamma-glutamate system protein.
Poly(gamma-glutamic acid), or PGA, is an extracellular
structural polymer found in Bacillus subtilis and a
number of other species. PGA is sometimes
capsule-forming, sometimes secretory, and may be
produced by Gram-positive (single plasma membrane) and
Gram-negative (inner and outer membranes), so export
and/or attachment machinery may differ from system to
system. Members of this family occur in a subset of PGA
operons, in lineages that include Francisella,
Leptospira, Treponema, Thermotoga, Fusobacterium, and
Clostridium, among others. Because gene symbols pgsWXYZ
are not yet in use, we suggest pgsW, as one of a series
of poly-gamma-glutamate synthesis auxiliary proteins.
Length = 307
Score = 31.0 bits (71), Expect = 0.42
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 71 ADNLSSGFIGKF-----TTPAELSEKLTTCSTNLKPLVLYQLIRKHAMQG 115
D +G IG+ TT L K T+ + + LV+ + +G
Sbjct: 61 LDPNRTGLIGEEWSPITTTLGSLEAKRTSANPDFAALVVRWFKKAGLKEG 110
>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 = 31.2 bits (71), Expect = 0.46
Identities = 12/70 (17%), Positives = 30/70 (42%), Gaps = 12/70 (17%)
Query: 164 KIIQEFRRRKIDLVVASDNLARGIDVENIDVVI-----------NYEAPDNIKKYIHRI- 211
++ +F K D+++ + +A+G N+ +V ++ A + + + ++
Sbjct: 303 ALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVA 362
Query: 212 GRTARGGRQG 221
GR R G
Sbjct: 363 GRAGRAEDPG 372
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 31.0 bits (71), Expect = 0.52
Identities = 14/59 (23%), Positives = 34/59 (57%)
Query: 142 KGAGTKMNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEA 200
K ++ + V+ +K +++ +++ F+ +ID++VA+ + G+DV N V++ A
Sbjct: 502 KSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENA 560
>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 = 30.7 bits (70), Expect = 0.58
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 153 VYSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEA-----PDNIKKY 207
++S++ +R +II++ R + D++V + L G+D+ + +V +A + +
Sbjct: 472 LHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSL 531
Query: 208 IHRIGRTAR 216
I IGR AR
Sbjct: 532 IQTIGRAAR 540
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 31.0 bits (70), Expect = 0.64
Identities = 16/64 (25%), Positives = 36/64 (56%)
Query: 161 QRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQ 220
QR + +++ + +I+++ A+ GI+ ++ VI++ P +I+ Y GR R G++
Sbjct: 718 QRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQR 777
Query: 221 GTSV 224
+ V
Sbjct: 778 SSCV 781
>gnl|CDD|205365 pfam13184, KH_5, NusA-like KH domain.
Length = 67
Score = 27.6 bits (62), Expect = 1.2
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 163 NKIIQEFRRRKIDLVVASDNLAR 185
I E KID+V S+++
Sbjct: 29 RAISDELNGEKIDVVEYSEDIKE 51
>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 = 29.3 bits (66), Expect = 1.5
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 154 YSDLKFDQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGR 213
D + + ++++E ++ + ++VA+ + +D+ + DV+I AP I I R+GR
Sbjct: 260 EKD-RAKKEAELLEEMKKNEKFVIVATQVIEASLDI-SADVMITELAP--IDSLIQRLGR 315
Query: 214 TARGGR 219
R GR
Sbjct: 316 LHRYGR 321
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 29.5 bits (67), Expect = 1.5
Identities = 11/72 (15%), Positives = 33/72 (45%), Gaps = 17/72 (23%)
Query: 161 QRNKIIQEFRRRKIDLVVA------SDNLARGIDVENIDVVI---------NYEAPDNIK 205
+R ++ +E++ R +++ N+ +D+ + ++ N+ D ++
Sbjct: 122 ERERVYEEYKDRVGEIITGVVKRVERGNII--VDLGRAEAILPRKEQIPRENFRPGDRVR 179
Query: 206 KYIHRIGRTARG 217
Y++ + + ARG
Sbjct: 180 AYVYEVRKEARG 191
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 29.0 bits (65), Expect = 1.5
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 20 PSRPQRLLFSATLSHDPEKLHQLSLFQPKLFTS 52
P Q LL SAT + E L +L L P
Sbjct: 158 PKNVQLLLLSATPPEEIENLLELFLNDPVFIDV 190
>gnl|CDD|152725 pfam12290, DUF3802, Protein of unknown function (DUF3802). This
family of proteins is found in bacteria. Proteins in
this family are typically between 114 and 143 amino
acids in length. There is a conserved KNLFD sequence
motif.
Length = 114
Score = 28.0 bits (63), Expect = 2.1
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 5/32 (15%)
Query: 148 MNIAEVYSDLKFDQRNKIIQEFRRRKIDLVVA 179
M + E +L F QR +I+E +D +V
Sbjct: 48 MMVCEQNPELSFAQRFDVIRE-----VDAIVY 74
>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 = 28.9 bits (65), Expect = 2.2
Identities = 33/120 (27%), Positives = 50/120 (41%), Gaps = 21/120 (17%)
Query: 117 LCFVNTAQGAHRLA----RLLHHID-----NVATKGAGTKMNIAEVYSDLKFDQRNKIIQ 167
L FV + +GA +A RLL +D VA AG + E R ++ +
Sbjct: 275 LTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGY---LPE--------DRRELER 323
Query: 168 EFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGRQGTSVTLV 227
R ++ V ++ L G+D+ +D V+ P + GR R G QG V LV
Sbjct: 324 ALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG-QGALVVLV 382
>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 = 28.4 bits (64), Expect = 2.4
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 20 PSRPQRLLFSATLSHDPEKL 39
P Q LL SATL + E L
Sbjct: 150 PPDRQILLLSATLPRNLEDL 169
>gnl|CDD|179479 PRK02821, PRK02821, hypothetical protein; Provisional.
Length = 77
Score = 26.9 bits (60), Expect = 2.8
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 175 DLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGRTARGGR 219
D+ V S RG ++V ++ PD++ K I R GRTA R
Sbjct: 19 DVRVDSHTNRRG---RTLEVRVH---PDDLGKVIGRGGRTATALR 57
>gnl|CDD|149395 pfam08321, PPP5, PPP5 TPR repeat region. This region is specific
to the PPP5 subfamily of serine/threonine phosphatases
and contains TPR repeats.
Length = 95
Score = 26.9 bits (60), Expect = 3.4
Identities = 10/45 (22%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 158 KFDQRNKIIQEFR-RRKIDLVVASDNLARGIDVENIDVVINYEAP 201
K + K++++ I + ++A ID+EN+ + +Y+ P
Sbjct: 1 KLKECEKLVKQIAFEEAIAVPEQKRSVADSIDIENMTIEDDYDGP 45
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 28.5 bits (64), Expect = 3.7
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 160 DQRNKIIQEFRRRKIDLVVASDNLARGI 187
+ R + FR+ KI ++V++ LA G+
Sbjct: 327 EDRQLVEDAFRKGKIKVLVSTPTLAAGV 354
>gnl|CDD|232958 TIGR00399, metG_C_term, methionyl-tRNA synthetase C-terminal
region/beta chain. The methionyl-tRNA synthetase (metG)
is a class I amino acyl-tRNA ligase. This model
describes a region of the methionyl-tRNA synthetase that
is present at the C-terminus of MetG in some species (E.
coli, B. subtilis, Thermotoga maritima, Methanobacterium
thermoautotrophicum), and as a separate beta chain in
Aquifex aeolicus. It is absent in a number of other
species (e.g. Mycoplasma genitalium, Mycobacterium
tuberculosis), while Pyrococcus horikoshii has both a
full length MetG and a second protein homologous to the
beta chain only. Proteins hit by This model should
called methionyl-tRNA synthetase beta chain if and only
if the model metG hits a separate protein not also hit
by This model [Protein synthesis, tRNA aminoacylation].
Length = 137
Score = 27.4 bits (61), Expect = 4.3
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 76 SGFIGKFTTPAELSEKLTTCSTNLKP 101
SG G +T P EL K NLKP
Sbjct: 75 SGIAGYYT-PEELVGKKVIVVANLKP 99
>gnl|CDD|151983 pfam11547, E3_UbLigase_EDD, E3 ubiquitin ligase EDD. EDD, the ER
ubiquitin ligase from the HECT ligases, contains an
N-terminal ubiquitin-associated domain which binds
ubiquitin. Ubiquitin is recognised by helices alpha-1
and -3 in in the UBA domain. EDD is involved in DNA
damage repair pathways and binds to mono-ubiquitinated
proteins.
Length = 51
Score = 25.7 bits (56), Expect = 5.0
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 150 IAEVYSDLKFDQRNKIIQEFRRRKIDLVVASDNL 183
I + L+ RN II+E +R +D+ +A +NL
Sbjct: 11 INQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNL 44
>gnl|CDD|227644 COG5339, COG5339, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 479
Score = 27.8 bits (62), Expect = 5.0
Identities = 11/46 (23%), Positives = 14/46 (30%), Gaps = 2/46 (4%)
Query: 21 SRPQRLLFSATLSHDPEKLHQL--SLFQPKLFTSVVEPAGTGDTQP 64
Q + F + H P L L P L + TQP
Sbjct: 83 KPGQPVTFVNHVEHGPFPLAALVKLNLIPALASVQTSLVNNEVTQP 128
>gnl|CDD|239199 cd02800, tRNA_bind_EcMetRS_like, tRNA-binding-domain-containing
Escherichia coli methionyl-tRNA synthetase
(EcMetRS)-like proteins. This family includes EcMetRS
and Aquifex aeolicus Trbp111 (AaTrbp111). This domain
has general tRNA binding properties. MetRS
aminoacylates methionine transfer RNAs (tRNAmet).
AaTrbp111 is structure-specific molecular chaperone
recognizing the L-shape of the tRNA fold. AaTrbp111
plays a role in nuclear trafficking of tRNAs. The
functional unit of EcMetRs and AaTrbp111 is a homodimer,
this domain acts as the dimerization domain.
Length = 105
Score = 26.7 bits (60), Expect = 5.0
Identities = 13/26 (50%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 76 SGFIGKFTTPAELSEKLTTCSTNLKP 101
SG I KF P EL K NLKP
Sbjct: 44 SG-IAKFYPPEELVGKKVVVVANLKP 68
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 27.6 bits (62), Expect = 5.2
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 160 DQRNKIIQEFRRRKIDLVVASDNLARGIDVENIDVVINYEAPDNIK 205
D ++ R+ L A LA G+D E ++V N + ++++
Sbjct: 52 DPSKSEERKLLSREEVLENAKAQLACGLDPEKSEIVNNSDWLEHLE 97
>gnl|CDD|188595 TIGR04080, rSAM_pep_cyc, KxxxW cyclic peptide radical SAM maturase.
Members of this family are radical SAM enzymes that
appear to perform a cyclization on an adjacent cognate
peptide from family TIGR04079. Genomes with the complete
system include Streptococcus thermophilus LMD-9 and
Lactococcus lactis subsp. cremoris MG1363, among others.
The gene symbol assigned is kwcM, for KxxxW Cyclic
peptide Maturase [Protein fate, Protein modification and
repair].
Length = 440
Score = 28.0 bits (62), Expect = 5.3
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 167 QEFRRRKIDLVVASDNLARGIDVENIDVVINYE----APD---NIKKYIHRIGRTAR 216
QE ++ ID++ SD + I +E+ID N+E PD + K H G+ R
Sbjct: 189 QEIKKSTIDIIAKSDYITPVISLESIDDFKNFELMGTRPDRGIELAKLFHERGKKCR 245
>gnl|CDD|238702 cd01411, SIR2H, SIR2H: Uncharacterized prokaryotic Sir2 homologs
from several gram positive bacterial species and
Fusobacteria; and are members of the SIR2 family of
proteins, silent information regulator 2 (Sir2) enzymes
which catalyze NAD+-dependent protein/histone
deacetylation. Sir2 proteins have been shown to
regulate gene silencing, DNA repair, metabolic enzymes,
and life span.
Length = 225
Score = 27.3 bits (61), Expect = 6.6
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 4 RGVGGLVIMWDTFLTYPSRPQRLLFSATLSHDPEKLHQ 41
R GL ++ Y P+ LL L +PEK +Q
Sbjct: 29 RSKNGL---YNEIYKY--SPEYLLSHDFLEREPEKFYQ 61
>gnl|CDD|99905 cd05563, PTS_IIB_ascorbate, PTS_IIB_ascorbate: subunit IIB of
enzyme II (EII) of the L-ascorbate-specific
phosphoenolpyruvate:carbohydrate phosphotransferase
system (PTS). In this system, EII is an
L-ascorbate-specific permease with two cytoplasmic
subunits (IIA and IIB) and a transmembrane channel IIC
subunit. Subunits IIA, IIB, and IIC are encoded by the
sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon.
In some bacteria, the IIB (SgaB) domain is fused
C-terminal to the IIA (SgaT) domain. The IIB domain fold
includes a central four-stranded parallel open twisted
beta-sheet flanked by alpha-helices on both sides. The
seven major PTS systems with this IIB fold include
ascorbate, chitobiose/lichenan, lactose, galactitol,
mannitol, fructose, and a sensory system with similarity
to the bacterial bgl system.
Length = 86
Score = 25.6 bits (57), Expect = 8.1
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 12/73 (16%)
Query: 143 GAGT----KMNIAEVYSDLKFDQRNKI----IQEFRRRKIDLVVASDNLARGIDVENIDV 194
G G+ KMN+ +V +L + ++ + + D++V S +LA + V
Sbjct: 9 GLGSSLMLKMNVEKVLKELGIE--AEVEHTDLGSAKASSADIIVTSKDLASLLADGGAKV 66
Query: 195 VI--NYEAPDNIK 205
+ N + IK
Sbjct: 67 IGLKNIMDKNEIK 79
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 27.3 bits (61), Expect = 8.1
Identities = 29/100 (29%), Positives = 38/100 (38%), Gaps = 25/100 (25%)
Query: 119 FVNTAQGAHRLARLLHHIDNVA----TKG-AGTKMNIAEVYSDLKFDQRNKIIQEFRRRK 173
FV GA L L I A TKG AGT N+ E ++ KI E RR
Sbjct: 127 FVC---GARNLGEALRRISEGAAMIRTKGEAGTG-NVVEAVRHMR-----KINGEIRR-- 175
Query: 174 IDLVVASDNLARGIDVENIDVVINYEAPDNIKKYIHRIGR 213
L + E V +AP + K + ++GR
Sbjct: 176 ---------LQSMTEDELYVVAKELQAPYELVKEVAKLGR 206
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
0.320 0.135 0.390
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,785,238
Number of extensions: 1108160
Number of successful extensions: 1321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1311
Number of HSP's successfully gapped: 77
Length of query: 231
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 137
Effective length of database: 6,768,326
Effective search space: 927260662
Effective search space used: 927260662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.5 bits)