RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7790
(367 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 = 144 bits (366), Expect = 6e-39
Identities = 59/155 (38%), Positives = 87/155 (56%), Gaps = 2/155 (1%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVE 262
+D+ I RQTLLFSATMP I+ AR L P+ I V + Q
Sbjct: 193 DDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYL 252
Query: 263 YVK-QEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEER 320
V+ +E K+ LL+ L+ + V++F K+ V+ + E L +G + A+HG QEER
Sbjct: 253 EVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEER 312
Query: 321 TRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
R++E F+ G+ V+VATDVA++GLD ++ HVIN
Sbjct: 313 DRALEKFKDGELRVLVATDVAARGLDIPDVSHVIN 347
Score = 42.9 bits (101), Expect = 2e-04
Identities = 40/209 (19%), Positives = 71/209 (33%), Gaps = 72/209 (34%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS-EDVRTIFSFFRGQRQ-----TLL 220
F + L L++AL+ G ++PTPIQ+ IP L+ DV GQ Q T
Sbjct: 30 EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDV-------LGQAQTGTGKTAA 82
Query: 221 FSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLECLQKT 280
F + + +L+ +++
Sbjct: 83 FLLPL--------------------------------------------LQKILKSVERK 98
Query: 281 EPPVLIFAEKKQDVDAIHE-----YLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVM 335
LI A ++ I E L G+ ++GG ++ ++ K D++
Sbjct: 99 YVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL----KRGVDIV 154
Query: 336 VATD------VASKGLDFEEIKHVINTEA 358
VAT + LD ++ ++ EA
Sbjct: 155 VATPGRLLDLIKRGKLDLSGVETLVLDEA 183
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 131 bits (331), Expect = 7e-34
Identities = 64/155 (41%), Positives = 93/155 (60%), Gaps = 5/155 (3%)
Query: 205 VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALV-KPITINVGRAGKIMPSMNVVQEVEY 263
+R I S R RQTL++SAT PK++Q+ AR +P+ +NVG + N+ QEV
Sbjct: 298 IRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSL-DLTACHNIKQEVFV 356
Query: 264 VKQEAKIVYLLECLQKTEPP---VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEER 320
V++ K L LQ+ +LIF E K+ D + + L L G A+ IHG K QEER
Sbjct: 357 VEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEER 416
Query: 321 TRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
T + F+ G+ +M+ATDVAS+GLD +++K+VIN
Sbjct: 417 TWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVIN 451
Score = 59.8 bits (145), Expect = 8e-10
Identities = 24/58 (41%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 146 DIIRRNLRI-LVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS 202
D IR+ I ++ G++VP SF P+ ++++L+ G +PTPIQVQG P ALS
Sbjct: 109 DEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALS 166
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 97.6 bits (243), Expect = 2e-22
Identities = 58/155 (37%), Positives = 84/155 (54%), Gaps = 3/155 (1%)
Query: 204 DVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEY 263
D+R + + +RQ LLFSAT I+ A L P+ I V R + S V Q V +
Sbjct: 169 DIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVAR--RNTASEQVTQHVHF 226
Query: 264 VKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTR 322
V ++ K L + + K VL+F K + + E L G+ + AIHG K Q RTR
Sbjct: 227 VDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTR 286
Query: 323 SVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
++ F+ G V+VATD+A++GLD EE+ HV+N E
Sbjct: 287 ALADFKSGDIRVLVATDIAARGLDIEELPHVVNYE 321
Score = 37.5 bits (87), Expect = 0.009
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS 202
SF + L ++RA+ +G ++PTPIQ Q IPA L
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLE 37
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 92.6 bits (231), Expect = 1e-20
Identities = 44/158 (27%), Positives = 79/158 (50%), Gaps = 6/158 (3%)
Query: 202 SEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEV 261
+ + I +RQTLLFSAT P+ I ++ P+ + V + +++
Sbjct: 165 QDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVEST----HDLPAIEQR 220
Query: 262 EY-VKQEAKIVYLLECLQKTEP-PVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEE 319
Y V + ++ L L +P ++F K++ + + L +G A+A+HG +Q +
Sbjct: 221 FYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRD 280
Query: 320 RTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTE 357
R + + F V+VATDVA++GLD + ++ VIN E
Sbjct: 281 RDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYE 318
Score = 30.5 bits (70), Expect = 1.6
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS-EDVR 206
+F + LP +L+ L G + TPIQ Q +PA L+ +DV
Sbjct: 5 AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVI 45
>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 = 85.8 bits (213), Expect = 2e-20
Identities = 36/105 (34%), Positives = 58/105 (55%), Gaps = 2/105 (1%)
Query: 256 NVVQEVEYVK--QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHG 313
+ Q V V+ + ++ LL+ K VLIF K+ +D + E L G++ A+HG
Sbjct: 1 PIKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 314 GKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEA 358
QEER ++ FR+G+ V+VATDV ++G+D + VIN +
Sbjct: 61 DGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDL 105
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 89.6 bits (222), Expect = 1e-19
Identities = 52/145 (35%), Positives = 75/145 (51%), Gaps = 5/145 (3%)
Query: 213 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVY 272
+ +RQTLLFSAT + N A+ P + + S V Q V V K
Sbjct: 268 KEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV--ASDTVEQHVYAVAGSDK-YK 324
Query: 273 LLECLQKTEP--PVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKG 330
LL L P V++FA +K +V I E L+ G+ A + G Q +R +++E FR+G
Sbjct: 325 LLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREG 384
Query: 331 QKDVMVATDVASKGLDFEEIKHVIN 355
+ V+VATDVA +G+ + I HVIN
Sbjct: 385 KIRVLVATDVAGRGIHIDGISHVIN 409
>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 = 74.1 bits (183), Expect = 9e-17
Identities = 25/60 (41%), Positives = 37/60 (61%)
Query: 299 EYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINTEA 358
+ L G++ +HGG QEER +E FR G+ V+VATDVA +G+D ++ VIN +
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 72.2 bits (178), Expect = 3e-16
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 295 DAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
+ + E L G++ +HGG QEER ++ F G+ V+VATDVA +GLD + VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 355 NTEA 358
+
Sbjct: 61 IYDL 64
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 78.8 bits (195), Expect = 4e-16
Identities = 45/160 (28%), Positives = 83/160 (51%), Gaps = 11/160 (6%)
Query: 202 SEDVRTIFSFFRGQRQTLLFSATMP-KKIQNFARSALVKPITINVGRA----GKIMPSMN 256
++D+ TI + R ++QTLLFSAT+ +Q+FA L P+ + + KI
Sbjct: 165 AQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYY 224
Query: 257 VVQEVEYVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK 315
++E+ K L L++ E ++F ++ V + +L G+ + G
Sbjct: 225 RADDLEH-----KTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEM 279
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
Q +R +++ G+ +V+VATDVA++G+D +++ HVIN
Sbjct: 280 VQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVIN 319
Score = 39.5 bits (93), Expect = 0.002
Identities = 16/29 (55%), Positives = 20/29 (68%)
Query: 173 LPESLVRALEAKGIKKPTPIQVQGIPAAL 201
L ESL+ AL+ KG +PT IQ + IP AL
Sbjct: 8 LDESLLEALQDKGYTRPTAIQAEAIPPAL 36
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 79.1 bits (195), Expect = 5e-16
Identities = 45/144 (31%), Positives = 81/144 (56%), Gaps = 6/144 (4%)
Query: 215 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYV---KQEAKIV 271
Q Q LLFSAT+ +++ FA S I I++G + P+ V Q +V +++ K+
Sbjct: 300 QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNR--PNKAVKQLAIWVETKQKKQKLF 357
Query: 272 YLLECLQKTEPPVLIFAEKKQDVDAIHEYL-LLKGVEAVAIHGGKDQEERTRSVESFRKG 330
+L+ Q +PP ++F + D + + ++ G++A++IHG K +ER ++SF G
Sbjct: 358 DILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVG 417
Query: 331 QKDVMVATDVASKGLDFEEIKHVI 354
+ V+VAT V +G+D ++ VI
Sbjct: 418 EVPVIVATGVLGRGVDLLRVRQVI 441
Score = 62.5 bits (152), Expect = 1e-10
Identities = 30/65 (46%), Positives = 38/65 (58%)
Query: 138 LSLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRALEAKGIKKPTPIQVQGI 197
L +++RR L I V+G+ VPP SF LP L+ LE G + PTPIQ+Q I
Sbjct: 93 SGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAI 152
Query: 198 PAALS 202
PAALS
Sbjct: 153 PAALS 157
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 70.3 bits (172), Expect = 4e-13
Identities = 53/157 (33%), Positives = 79/157 (50%), Gaps = 9/157 (5%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKP----ITINVGRAGKIMPSMNVV 258
EDV TI + QT LFSATMP+ I+ R + +P I +V I S V
Sbjct: 168 EDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTV 227
Query: 259 QEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQE 318
+ K EA +V LE + +IF K + E L G + A++G +Q
Sbjct: 228 WGMR--KNEA-LVRFLEA--EDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQA 282
Query: 319 ERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
R +++E + G+ D+++ATDVA++GLD E I V+N
Sbjct: 283 LREQTLERLKDGRLDILIATDVAARGLDVERISLVVN 319
Score = 29.4 bits (66), Expect = 3.0
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALS 202
+F + L ++ AL G +KP+PIQ + IP L+
Sbjct: 7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLN 42
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 66.9 bits (163), Expect = 4e-12
Identities = 45/144 (31%), Positives = 75/144 (52%), Gaps = 3/144 (2%)
Query: 213 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVY 272
RG RQTLLFSAT+ ++ A + +P + V + + + V Q + + E K
Sbjct: 190 RGTRQTLLFSATLSHRVLELAYEHMNEPEKLVV--ETETITAARVRQRIYFPADEEKQTL 247
Query: 273 LLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQ 331
LL L ++E ++F K V+ + L G + G Q++R + F+KGQ
Sbjct: 248 LLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQ 307
Query: 332 KDVMVATDVASKGLDFEEIKHVIN 355
+++VATDVA++GL + +K+V N
Sbjct: 308 LEILVATDVAARGLHIDGVKYVYN 331
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 65.8 bits (161), Expect = 8e-12
Identities = 42/142 (29%), Positives = 70/142 (49%), Gaps = 3/142 (2%)
Query: 215 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLL 274
QR +LFSAT+ +++ A + P + V + + +E+ Y E K+ L
Sbjct: 190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEV--EPEQKTGHRIKEELFYPSNEEKMRLLQ 247
Query: 275 ECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKD 333
+++ P +IFA K + I +L G + G Q++R R +E F +G D
Sbjct: 248 TLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLD 307
Query: 334 VMVATDVASKGLDFEEIKHVIN 355
++VATDVA++GL + HV N
Sbjct: 308 ILVATDVAARGLHIPAVTHVFN 329
Score = 28.4 bits (64), Expect = 6.6
Identities = 19/47 (40%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 173 LPESLVRALEAKGIKKPTPIQVQGIPAALS-EDVRTIFSFFRGQRQT 218
L +V ALE KG TPIQ +P L+ DV GQ QT
Sbjct: 15 LHPQVVEALEKKGFHNCTPIQALALPLTLAGRDV-------AGQAQT 54
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 59.8 bits (146), Expect = 1e-10
Identities = 19/42 (45%), Positives = 26/42 (61%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITIN 244
+ +R I RQTLLFSATMPK++++ AR L P+ I
Sbjct: 162 DQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
Score = 47.9 bits (115), Expect = 2e-06
Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 168 FRLMKLPESLVRALEAKGIKKPTPIQVQGIPAALSE-DV 205
F + L L+R + A G +KPTPIQ + IP LS DV
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDV 39
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 52.1 bits (125), Expect = 2e-07
Identities = 37/143 (25%), Positives = 69/143 (48%), Gaps = 8/143 (5%)
Query: 217 QTLLFSATMPKKIQNFARSALVKPITINVGRAGKIMPSMN----VVQEVEYVKQEAKIVY 272
Q LFSATMP +I + P I V + + + V++ E+ + +
Sbjct: 203 QVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEW--KFDTLCD 260
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQK 332
L E L T+ +I+ ++ VD + + + + +HG DQ++R + FR G
Sbjct: 261 LYETLTITQ--AIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGST 318
Query: 333 DVMVATDVASKGLDFEEIKHVIN 355
V++ TD+ ++G+D +++ VIN
Sbjct: 319 RVLITTDLLARGIDVQQVSLVIN 341
Score = 31.0 bits (70), Expect = 1.0
Identities = 14/31 (45%), Positives = 21/31 (67%)
Query: 167 SFRLMKLPESLVRALEAKGIKKPTPIQVQGI 197
SF +KL E L+R + + G +KP+ IQ +GI
Sbjct: 29 SFDALKLNEDLLRGIYSYGFEKPSAIQQRGI 59
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 52.1 bits (125), Expect = 2e-07
Identities = 28/91 (30%), Positives = 39/91 (42%), Gaps = 3/91 (3%)
Query: 266 QEAKIVYLLECLQKTEP--PVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRS 323
E KI + L K LIFA + I + L G+ AI G +EER
Sbjct: 266 SERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVE-AITGETPKEEREAI 324
Query: 324 VESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
+E FR G V+V V +G+D + +I
Sbjct: 325 LERFRTGGIKVLVTVKVLDEGVDIPDADVLI 355
>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 = 52.4 bits (126), Expect = 2e-07
Identities = 29/92 (31%), Positives = 48/92 (52%), Gaps = 1/92 (1%)
Query: 264 VKQEAKIVYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTR 322
VK+ K +LL+ L+K +I+A ++ V+ + E L +G+ A+A H G + R
Sbjct: 206 VKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAE 265
Query: 323 SVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
+ E F VMVAT+ G+D ++ VI
Sbjct: 266 NQEDFLYDDVKVMVATNAFGMGIDKPNVRFVI 297
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 46.9 bits (112), Expect = 1e-05
Identities = 23/78 (29%), Positives = 39/78 (50%)
Query: 261 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEER 320
VE + ++ +L L + +I+ ++ V+ + E+L G+ A A H G EER
Sbjct: 210 VEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEER 269
Query: 321 TRSVESFRKGQKDVMVAT 338
R ++F + VMVAT
Sbjct: 270 ERVQQAFLNDEIKVMVAT 287
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 44.4 bits (105), Expect = 2e-05
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 202 SEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRA 248
+ + + Q LL SAT P++I+N L P+ I+VG
Sbjct: 147 GDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFT 193
Score = 28.2 bits (63), Expect = 6.2
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 181 LEAKGIKKPTPIQVQGIPAALSEDVRTI 208
+E G + P Q + I A LS I
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVI 28
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 42.2 bits (100), Expect = 4e-04
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHG--------GKDQEERTRSVESFRKGQKDVM 335
+++F + + + I + L +G++AV G G Q+E+ ++ FR G+ +V+
Sbjct: 368 IIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVL 427
Query: 336 VATDVASKGLDFEEIKHVI 354
V+T VA +GLD + VI
Sbjct: 428 VSTSVAEEGLDIPSVDLVI 446
>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 = 39.2 bits (92), Expect = 0.001
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATMPKKIQNF 232
+D+ I S RQ LL SAT+P+ +++
Sbjct: 140 DDLEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 40.0 bits (94), Expect = 0.002
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAI---------HGGKDQEERTRSVESFRKGQKDV 334
V++F E + + I +L G++A G Q+E+ ++ FRKG+ +V
Sbjct: 369 VIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNV 428
Query: 335 MVATDVASKGLDFEEIKHVINTEA 358
+VAT V +GLD E+ VI E
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEP 452
>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 = 39.0 bits (91), Expect = 0.003
Identities = 37/153 (24%), Positives = 70/153 (45%), Gaps = 13/153 (8%)
Query: 218 TLLFSATMPKKIQNFARSALVKPITINVGRAGKIMP------SMNVVQEVEYVKQEAKIV 271
T+ +AT KK++ ++ + + GK +P N ++++ K K+
Sbjct: 236 TIYLTATPTKKLERKILKGNLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLK 295
Query: 272 YLLECLQKTEPPVLIFA---EKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFR 328
LE +KT PVLIF E + V A + L K ++H + + R VE+FR
Sbjct: 296 RWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPK-ETIASVHS--EDQHRKEKVEAFR 352
Query: 329 KGQKDVMVATDVASKGLDFEEIK-HVINTEAKI 360
G+ +++ T + +G+ F + V+ E ++
Sbjct: 353 DGKITLLITTTILERGVTFPNVDVFVLGAEHRV 385
>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 = 37.1 bits (86), Expect = 0.013
Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 13/106 (12%)
Query: 254 SMNVVQEVE--YVKQEAKIVYLLECLQKTEPPVLIFAEK---KQDVDAIHEYLLLKGVEA 308
+ ++ V YV+ E LLE ++K +++ K+ + I E+L GV+A
Sbjct: 297 GSDTLRNVVDVYVEDEDLKETLLEIVKKLGTGGIVYVSIDYGKEKAEEIAEFLENHGVKA 356
Query: 309 VAIHGGKDQEERTRSVESFRKGQKDVMVAT----DVASKGLDFEEI 350
VA H K +E+ E F +G+ DV++ +GLD E
Sbjct: 357 VAYHATKPKED----YEKFAEGEIDVLIGVASYYGTLVRGLDLPER 398
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 36.2 bits (84), Expect = 0.025
Identities = 24/90 (26%), Positives = 43/90 (47%), Gaps = 13/90 (14%)
Query: 273 LLECLQKTEPPVLIFAEK---KQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRK 329
++E ++K LIF ++ + + EYL G+ A IH K+ ++E F +
Sbjct: 327 VVELVKKLGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKE-----EALEDFEE 381
Query: 330 GQKDVMVAT----DVASKGLDF-EEIKHVI 354
G+ DV+V V +GLD I++ +
Sbjct: 382 GEVDVLVGVASYYGVLVRGLDLPHRIRYAV 411
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 35.3 bits (82), Expect = 0.054
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 283 PVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGK-DQEERTRSVESFRKGQKDVMVATDVA 341
LIF + + + L G + + +H G +E R E ++G+ +VAT
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314
Query: 342 SKGLDFEEIKHVI 354
G+D +I VI
Sbjct: 315 ELGIDIGDIDLVI 327
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 35.1 bits (81), Expect = 0.058
Identities = 15/63 (23%), Positives = 29/63 (46%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
++F ++ + + L KG++A H G +ER +F + +V T + G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503
Query: 345 LDF 347
+DF
Sbjct: 504 VDF 506
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 34.8 bits (80), Expect = 0.084
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 263 YVKQEAK---IVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEE 319
Y K IV + + KT PVL+ + + + + E LL GV ++ D EE
Sbjct: 404 YATAAEKNDAIVEEIAEVHKTGQPVLVGTQDVAESEELAEALLEAGVPCNVLNAKNDAEE 463
Query: 320 RTRSVESFRKGQKDVMVATDVASKGLD 346
E+ G V V+T +A +G D
Sbjct: 464 AAIIAEAGDIGA--VTVSTQMAGRGTD 488
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 34.4 bits (79), Expect = 0.11
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 273 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRK 329
LL L++ + VLIF++ + +D + +YL+ +G + I G E+R S+++F K
Sbjct: 479 LLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNK 535
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 34.3 bits (78), Expect = 0.11
Identities = 14/70 (20%), Positives = 32/70 (45%)
Query: 278 QKTEPPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVA 337
+ VLIF++ +D + +YL G++ V + G + R ++ F +++ +
Sbjct: 708 EGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFL 767
Query: 338 TDVASKGLDF 347
+ + GL
Sbjct: 768 LSLKAGGLGL 777
>gnl|CDD|179606 PRK03606, PRK03606, ureidoglycolate hydrolase; Provisional.
Length = 162
Score = 32.5 bits (75), Expect = 0.14
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 203 EDVRTIFSFFRGQRQTLLFSATM 225
E R + S FR Q + L M
Sbjct: 50 EGGRALISIFRAQPRALPLEIRM 72
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 33.5 bits (77), Expect = 0.15
Identities = 23/112 (20%), Positives = 44/112 (39%), Gaps = 10/112 (8%)
Query: 36 EEKKKLVLSDDEDNNKDSTDEENDESKVWGRMSNISLLDQHSELKKMAEAKKESAKEKQL 95
+ K + + + S + + S+ +++ S E K E+KK+S K+K+
Sbjct: 18 KSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKE-DKNNESKKKSEKKKKK 76
Query: 96 KEEEKILRSVAETKALMGVAELAKGIQYNDPIKTSWRAPRCILSLPDQVHDI 147
K+E+K +S ETK G + K + + P D +
Sbjct: 77 KKEKKEPKSEGETK---------LGFKTPKKSKKTKKKPPKPKPNEDVDNAF 119
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 33.8 bits (78), Expect = 0.19
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 17/102 (16%)
Query: 263 YVKQEAKIVYLLECLQKTEPPVLIFA---EKKQDVDAIHEYLLLKGVEAVAIHGGKDQEE 319
Y+ E + L+E +++ LIF + K+ + + EYL G+ A
Sbjct: 310 YIVDEDSVEKLVELVKRLGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAI-----SG 364
Query: 320 RTRSVESFRKGQKDVMVATDVAS------KGLDF-EEIKHVI 354
R E F +G+ DV+V VAS +G+D E I++ I
Sbjct: 365 FERKFEKFEEGEVDVLVG--VASYYGVLVRGIDLPERIRYAI 404
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 33.6 bits (77), Expect = 0.20
Identities = 34/160 (21%), Positives = 74/160 (46%), Gaps = 11/160 (6%)
Query: 200 ALSEDVRTIFSFFRGQRQTLLFSATMP-KKIQNFARSALVKPITINVGRAGKIMPSMNVV 258
AL+ DV+ S R + L SAT+ +++ + A P+ + GR+ + +
Sbjct: 134 ALALDVQ---SSLREDLKILAMSATLDGERLSSLLPDA---PVVESEGRSFPVEIRYLPL 187
Query: 259 QEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYL---LLKGVEAVAIHGGK 315
+ + + ++A + L +L+F + ++ + E L L V ++G
Sbjct: 188 RGDQRL-EDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGEL 246
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVIN 355
+ R+++ +G++ V++AT++A L E I+ VI+
Sbjct: 247 SLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVID 286
>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 = 32.8 bits (75), Expect = 0.24
Identities = 30/137 (21%), Positives = 57/137 (41%), Gaps = 9/137 (6%)
Query: 219 LLFSATMPKKIQNFARSAL--VKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLEC 276
LL SAT+PK ++ +A +++ + + E + V + + + LLE
Sbjct: 159 LLMSATLPKFLKEYAEKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEF 218
Query: 277 LQKTEPPVLIFAEKKQDVDAIHEYLLLKG--VEAVAIHGG---KDQEERT-RSVESFRKG 330
++K + I ++ L E + +H KD+ ++ +E +K
Sbjct: 219 IKK-GGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKN 277
Query: 331 QKDVMVATDVASKGLDF 347
+K V+VAT V LD
Sbjct: 278 EKFVIVATQVIEASLDI 294
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 32.4 bits (74), Expect = 0.38
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVAT 338
+I+ + V+ L +G+ A A H G D + R E+F++ ++VAT
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVAT 293
>gnl|CDD|178439 PLN02847, PLN02847, triacylglycerol lipase.
Length = 633
Score = 32.5 bits (74), Expect = 0.42
Identities = 27/125 (21%), Positives = 58/125 (46%), Gaps = 2/125 (1%)
Query: 2 SNESDDEHYVPYVSVKERKKQKLIQLGRLAQERHEEKKKLVLSDDEDNNKDSTDEENDES 61
++ + E V V + + K +E+++ L ++ S +EE E
Sbjct: 438 TSSVNSESLVTEVKTTKSVEHKSESSSSDGSGHDDEEEEEPLLSEDRVITSSVEEEVTEG 497
Query: 62 KVWGRMSNISLLDQHSELKKMAEAKKESAKEKQLKEEEKILRSVAETKALMGVAELAKGI 121
++W + L Q +E+ A+ ++E+A K++ EEE +L E+K + ++L++
Sbjct: 498 ELWYELEK-ELQRQETEVDAQAQ-EEEAAAAKEITEEENVLAKAVESKTSITSSDLSESQ 555
Query: 122 QYNDP 126
Q+ P
Sbjct: 556 QFYPP 560
>gnl|CDD|212055 cd11486, SLC5sbd_SGLT1, Na(+)/glucose cotransporter SGLT1;solute
binding domain. Human SGLT1 (hSGLT1) is a
high-affinity/low-capacity glucose transporter, which
can also transport galactose. In the transport
mechanism, two Na+ ions first bind to the extracellular
side of the transporter and induce a conformational
change in the glucose binding site. This results in an
increased affinity for glucose. A second conformational
change in the transporter follows, bringing the Na+ and
glucose binding sites to the inner surface of the
membrane. Glucose is then released, followed by the Na+
ions. In the process, hSGLT1 is also able to transport
water and urea and may be a major pathway for transport
of these across the intestinal brush-border membrane.
hSGLT1 is encoded by the SLC5A1 gene and expressed
mostly in the intestine, but also in the trachea,
kidney, heart, brain, testis, and prostate. The
WHO/UNICEF oral rehydration solution (ORS) for the
treatment of secretory diarrhea contains salt and
glucose. The glucose, along with sodium ions, is
transported by hSGLT1 and water is either co-transported
along with these or follows by osmosis. Mutations in
SGLT1 are associated with intestinal glucose galactose
malabsorption (GGM). Up-regulation of intestinal SGLT1
may protect against enteric infections. SGLT1 is
expressed in colorectal, head and neck, and prostate
tumors. Epidermal growth factor receptor (EGFR)
functions in cell survival by stabilizing SGLT1, and
thereby maintaining intracellular glucose levels. SGLT1
is predicted to have 14 membrane-spanning regions. This
subgroup belongs to the solute carrier 5
(SLC5)transporter family.
Length = 635
Score = 31.8 bits (72), Expect = 0.60
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 6/85 (7%)
Query: 36 EEKKKLVLSD---DEDNNKDSTDEENDESKVWGRMSNISL-LDQHSELKKMAEAKKESAK 91
EE+ L D DED N+ TDEE + + N DQ K+ E ++ + K
Sbjct: 542 EERIDLDADDWTEDEDENEMETDEERKKPGCCRKAYNWFCGFDQGKA-PKLTEEEEAALK 600
Query: 92 EKQLKEEEKIL-RSVAETKALMGVA 115
K EK L R+V ++ +
Sbjct: 601 MKMTDTSEKPLWRNVVNINGIILLT 625
>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Length = 75
Score = 29.2 bits (66), Expect = 0.64
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATD 339
VLI E D A+ + +G VA+ G +E+ + ++ K + +V++ATD
Sbjct: 2 VLIIVEGPADAIALEKAGGKRGN-VVALGGHLLSKEQIKLLKKLAK-KAEVILATD 55
>gnl|CDD|220958 pfam11055, Gsf2, Glucose signalling factor 2. Gsf2 is localised to
the ER and functions to promote the secretion of certain
hexose transporters.
Length = 376
Score = 31.6 bits (72), Expect = 0.68
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 9/74 (12%)
Query: 36 EEKKKLVLSDD-----EDNNKDSTDEEN-DESKVWG---RMSNISLLDQHSELKKMAEAK 86
EE +K LS++ E+N K++ ++ + D SK+ + LL+ ++KK+ + +
Sbjct: 302 EEDEKFKLSEEYFAQLENNLKENIEKCDGDISKMNAEIRQFRRYGLLESDEKIKKLVQLR 361
Query: 87 KESAKEKQLKEEEK 100
K ++ EE+K
Sbjct: 362 KGVGDSEEPVEEKK 375
>gnl|CDD|237060 PRK12326, PRK12326, preprotein translocase subunit SecA; Reviewed.
Length = 764
Score = 31.9 bits (73), Expect = 0.70
Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 11/90 (12%)
Query: 263 YVKQEAK---IVYLLECLQKTEPPVLIFAEKKQDV---DAIHEYLLLKGVEAVAIHGGKD 316
Y K IV + + +T PVL+ DV + + E L GV AV ++ D
Sbjct: 406 YATAAEKNDAIVEHIAEVHETGQPVLV---GTHDVAESEELAERLRAAGVPAVVLNAKND 462
Query: 317 QEERTRSVESFRKGQKDVMVATDVASKGLD 346
EE E+ + G V V+T +A +G D
Sbjct: 463 AEEARIIAEAGKYGA--VTVSTQMAGRGTD 490
>gnl|CDD|217335 pfam03044, Herpes_UL16, Herpesvirus UL16/UL94 family. This family
groups together HSV-1 UL16, HSV-6 ORF11R, EHV-1 46, HCMV
UL94, EBV BGLF2 and VZV 44. UL16 protein may play a role
in capsid maturation including DNA packaging/cleavage.
In immunofluorescence studies, UL16 was localised to the
nucleus of infected cells in areas containing high
concentrations of HSV capsid proteins. These nuclear
compartments have been described previously as viral
assemblons and are distinct from compartments containing
replicating DNA. Localisation within assemblons argues
for a role of UL16 encoded protein in capsid assembly or
maturation.
Length = 329
Score = 31.1 bits (71), Expect = 0.76
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 139 SLPDQVHDIIRRNLRILVEGDDVPPACCSFRLMKLPESLVRAL 181
++ D + D+I +G++VP ++L++L E L R +
Sbjct: 281 TITDDLSDVIGGVTA---DGEEVPVNSEGWQLVRLSELLSRLI 320
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 30.8 bits (70), Expect = 0.98
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 12/63 (19%)
Query: 45 DDEDNNKDSTDEENDESKVWGRMSNISLLDQHSELKKMAEAKKESAKEKQLKEEEKILRS 104
D++D+ KDS DEE DE K + + K A+AK + A + +++E+EK R
Sbjct: 28 DEDDDVKDSWDEEEDEEK------------EEEKAKVAAKAKAKKALKAKIEEKEKAKRE 75
Query: 105 VAE 107
E
Sbjct: 76 KEE 78
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 31.0 bits (71), Expect = 1.2
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 299 EYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHV 353
EYL G++ +H D ER + R G+ DV+V ++ +GLD E+ V
Sbjct: 464 EYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV 518
>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 = 30.9 bits (70), Expect = 1.2
Identities = 16/70 (22%), Positives = 33/70 (47%)
Query: 285 LIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKG 344
+I+ ++ + + L G+ A A H G + R F++ + V+VAT G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 345 LDFEEIKHVI 354
++ +++ VI
Sbjct: 290 INKPDVRFVI 299
>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 = 30.5 bits (69), Expect = 1.3
Identities = 35/137 (25%), Positives = 62/137 (45%), Gaps = 12/137 (8%)
Query: 219 LLFSATMPKKIQNFARSAL--VKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLEC 276
LL SAT+PK ++ +A + +++ + + P + E + V + + + LLE
Sbjct: 158 LLMSATLPKFLKEYAEKIGYVEENEPLDL-KPNERAP--FIKIESDKVGEISSLERLLEF 214
Query: 277 LQKTEPPVLIFAEKKQDVDAIHEYLLLKG--VEAVAIHGG---KDQEERT-RSVESFRKG 330
++K V I ++ L KG E + IH KD+ ++ + F+K
Sbjct: 215 IKK-GGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKS 273
Query: 331 QKDVMVATDVASKGLDF 347
+K V+VAT V LD
Sbjct: 274 EKFVIVATQVIEASLDI 290
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 30.8 bits (70), Expect = 1.3
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 11/91 (12%)
Query: 267 EAKIVY--LLECLQKTEPPVLIF-----AEKKQDVDAIHEYLLLKGVEA---VA-IHGGK 315
E IVY + E + K +++ +EK A Y LK V +HG
Sbjct: 433 EKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRM 492
Query: 316 DQEERTRSVESFRKGQKDVMVATDVASKGLD 346
+E+ +E FR+G+ D++VAT V G+D
Sbjct: 493 KSDEKEAVMEEFREGEVDILVATTVIEVGVD 523
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 30.1 bits (68), Expect = 1.4
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 32 QERHEEKKKLVLSDDEDNNKDSTDEENDESKVWGRMSNISLLDQHSELKKMAE---AKKE 88
E E K+K + D +++ D +D +D + D+ + L + E KKE
Sbjct: 100 DEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETAAL--LRELEKIKKE 157
Query: 89 SAKEKQLKEEEK 100
A+EK+ +EEEK
Sbjct: 158 RAEEKEREEEEK 169
>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 = 30.3 bits (69), Expect = 1.6
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 299 EYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHV 353
+YL G++ +H D ER + R G+ DV+V ++ +GLD E+ V
Sbjct: 460 DYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV 514
>gnl|CDD|99814 cd06218, DHOD_e_trans, FAD/NAD binding domain in the electron
transfer subunit of dihydroorotate dehydrogenase.
Dihydroorotate dehydrogenases (DHODs) catalyze the only
redox reaction in pyrimidine de novo biosynthesis. They
catalyze the oxidation of (S)-dihydroorotate to orotate
coupled with the reduction of NAD+. In L. lactis, DHOD B
(encoded by pyrDa) is co-expressed with pyrK and both
gene products are required for full activity, as well as
3 cofactors: FMN, FAD, and an [2Fe-2S] cluster.
Length = 246
Score = 29.4 bits (67), Expect = 2.8
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 282 PPVLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVA 341
P+L A++ L +G++ + G + + VE F +V VATD
Sbjct: 111 APLLFLAKQ----------LAERGIKVTVLLGFRS-ADDLFLVEEFEALGAEVYVATDDG 159
Query: 342 SKG 344
S G
Sbjct: 160 SAG 162
>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 = 28.7 bits (65), Expect = 2.8
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 273 LLECLQKTEPPVLIF----AEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFR 328
+LE L+ VL+ + +Q + + LL KG+E + + G + R + +E F+
Sbjct: 1 ILELLEAIPGGVLVLFPSYSLLEQVAELLASELLEKGIE-LLVQG---EGSREKLLERFK 56
Query: 329 KGQKDVMVATDVASKGLDF 347
KG+ ++ +G+DF
Sbjct: 57 KGKGAILFGVGSFWEGIDF 75
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 29.3 bits (66), Expect = 3.0
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 1/84 (1%)
Query: 17 KERKKQKLIQLGRLAQERHEEKKKLVLSDDEDNNKDSTDEENDESKVWGRMSNISLLDQH 76
+E + + LI+ E E++++ D ED+ +D+ + + +S S+L +
Sbjct: 187 EEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSPKSGSSSPAKPTSILKK- 245
Query: 77 SELKKMAEAKKESAKEKQLKEEEK 100
S K+ AK+ +
Sbjct: 246 SAAKRSEAPSSSKAKKNSRGIPKP 269
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 29.4 bits (66), Expect = 3.4
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 312 HGGKDQEERTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVI 354
H G + ER ++FR+G V+ AT S G++ + +I
Sbjct: 302 HAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVII 344
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesises the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyze the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 86
Score = 27.2 bits (61), Expect = 3.6
Identities = 17/56 (30%), Positives = 26/56 (46%)
Query: 284 VLIFAEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATD 339
LI E D A+ + + G VA G E + ++ KG K+V++ATD
Sbjct: 1 ELIIVEGPSDAIALEKAGGVLGGAVVATSGHALDLEHIKELKKALKGAKEVILATD 56
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 28.6 bits (64), Expect = 5.9
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 15/90 (16%)
Query: 15 SVKERKKQKLIQLGRLAQERHEEKKKLVLSDDEDNNKDSTDEENDESKVWGRMSNISLLD 74
+K+ KK KL Q + + KKKL + DD DN DS + SK + ISL+
Sbjct: 68 DLKDSKKTKLKQ-------KKKIKKKLHIDDDYDNFFDS----KNNSKQFAGPLAISLMR 116
Query: 75 ----QHSELKKMAEAKKESAKEKQLKEEEK 100
+ +LKK K + K+K+ K
Sbjct: 117 KPKPKTEKLKKKITVNKSTNKKKKKVLSSK 146
>gnl|CDD|99998 cd04949, GT1_gtfA_like, This family is most closely related to the
GT1 family of glycosyltransferases and is named after
gtfA in Streptococcus gordonii, where it plays a role in
the O-linked glycosylation of GspB, a cell surface
glycoprotein involved in platelet binding. In general
glycosyltransferases catalyze the transfer of sugar
moieties from activated donor molecules to specific
acceptor molecules, forming glycosidic bonds. The
acceptor molecule can be a lipid, a protein, a
heterocyclic compound, or another carbohydrate residue.
This group of glycosyltransferases is most closely
related to the previously defined glycosyltransferase
family 1 (GT1). The members of this family may transfer
UDP, ADP, GDP, or CMP linked sugars. The diverse
enzymatic activities among members of this family
reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed for
nucleotide-sugar-dependent glycosyltransferases. GTB
proteins have distinct N- and C- terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two domains
includes the catalytic center and permits a high degree
of flexibility. The members of this family are found in
bacteria.
Length = 372
Score = 28.3 bits (64), Expect = 6.4
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 5 SDDEHYVPYVSVKERKKQKLIQLGRLAQERH 35
D K+RK K+I + RLA E+
Sbjct: 190 IDPLKLP--AQFKQRKPHKIITVARLAPEKQ 218
>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 = 28.5 bits (64), Expect = 6.4
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 323 SVESFRKGQKDVMVATDVASKGLDFEEIKHV 353
+ F G+ D+++ T + +KG F + V
Sbjct: 304 LLNQFANGKADILIGTQMIAKGHHFPNVTLV 334
>gnl|CDD|183481 PRK12376, PRK12376, putative translaldolase; Provisional.
Length = 236
Score = 28.0 bits (63), Expect = 7.0
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 177 LVRALEAKGIK-KPTPI----QVQGIPAALSEDVRTIFSFFRG 214
L++ L A G+K T I QV+ + AL+ V I S F G
Sbjct: 104 LIKKLSADGVKLNVTAIFTIEQVKEVVDALTPGVPAIVSVFAG 146
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 28.3 bits (64), Expect = 7.6
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 292 QDVDAIHEYL--LLKGVEAVAIHGGKDQEERTRSVESFRKGQKDVMVATDVASKGLD 346
Q + ++E L L ++ +HG E+ +E+F++G+ D++VAT V G+D
Sbjct: 492 QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVD 548
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 28.4 bits (64), Expect = 8.0
Identities = 16/74 (21%), Positives = 26/74 (35%), Gaps = 11/74 (14%)
Query: 177 LVRALEAKGIKKPTPIQVQGIPAA--LSEDVRTIFSFFRGQRQTLL-----FSATMPKKI 229
L L A K P AA L+ + + + Q TL A +P ++
Sbjct: 579 LAARLRAAAAKSQDP----DAAAAGRLAASLDRLLAKAPAQAATLRALQGALLAGLPGEL 634
Query: 230 QNFARSALVKPITI 243
S +P+T+
Sbjct: 635 DRLRDSLQAEPVTL 648
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 28.1 bits (63), Expect = 9.0
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 67 MSNISLLDQHSELKKMAEAKKESAKEKQLKEEEKILRS 104
++ ++L EL +A + LK E LRS
Sbjct: 620 LTEVNLNSFAEELDALANNLPNGKLKVALKNEALDLRS 657
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 28.1 bits (63), Expect = 9.4
Identities = 24/107 (22%), Positives = 51/107 (47%), Gaps = 6/107 (5%)
Query: 265 KQEAKIVYLLECLQKTEP-PVLIF----AEKKQDVDAIHEYLLLKGVEAVAIHGGKDQEE 319
IV ++ + +L+F E ++ + + + L +E + ++G EE
Sbjct: 242 ILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEE 301
Query: 320 RTRSVESFRKGQKDVMVATDVASKGLDFEEIKHVINT-EAKIKKREH 365
+ R E G++ V++AT++A L I++VI++ AK K+ +
Sbjct: 302 QVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDP 348
>gnl|CDD|234020 TIGR02801, tolR, TolR protein. The model describes the inner
membrane protein TolR, part of the TolR/TolQ complex
that transduces energy from the proton-motive force,
through TolA, to an outer membrane complex made up of
TolB and Pal (peptidoglycan-associated lipoprotein). The
complex is required to maintain outer membrane
integrity, and defects may cause a defect in the import
of some organic compounds in addition to the resulting
morphologic. While several gene pairs homologous to talR
and tolQ may be found in a single genome, but the scope
of this model is set to favor finding only bone fide
TolR, supported by operon structure as well as by score
[Transport and binding proteins, Other, Cellular
processes, Pathogenesis].
Length = 129
Score = 26.8 bits (60), Expect = 9.6
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 226 PKKIQNFARSALVKPITINVGRAGKIMPSMNVVQEVEYVKQEAKIVYLLECL-QKTEPPV 284
PK +S KPIT++V GKI + N + + E + + + + L + PV
Sbjct: 37 PKSSAKPLQSKDKKPITVSVDADGKIYLNDNKIDKDEQLDADELLAEIAAALAANPDTPV 96
Query: 285 LIFAEKKQDVDAIHEYL-LLK--GVEAVA 310
LI A+K + + + LLK G+E V
Sbjct: 97 LIRADKTVPYGEVIKVMALLKQAGIEKVG 125
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
0.314 0.131 0.359
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,434,886
Number of extensions: 1801245
Number of successful extensions: 2306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2190
Number of HSP's successfully gapped: 173
Length of query: 367
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 269
Effective length of database: 6,590,910
Effective search space: 1772954790
Effective search space used: 1772954790
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (26.8 bits)