RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13287
(140 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 = 124 bits (313), Expect = 2e-34
Identities = 42/136 (30%), Positives = 70/136 (51%), Gaps = 4/136 (2%)
Query: 2 LDHVISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINL---MEELTLKGVTQYYAFV 58
++ ++ LP +RQ LL+SAT P ++ ++L DP EI + E TLK + Q+Y V
Sbjct: 195 IEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEV 254
Query: 59 -QERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNR 117
E +K+ L L + I+F + + VE LA+ + + G+ +H + Q R+R
Sbjct: 255 ESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDR 314
Query: 118 VFHDFRSGLCRNLVCS 133
F+ G R LV +
Sbjct: 315 ALEKFKDGELRVLVAT 330
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 91.0 bits (226), Expect = 1e-22
Identities = 47/129 (36%), Positives = 73/129 (56%), Gaps = 2/129 (1%)
Query: 5 VISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINL-MEELTLKGVTQYYAFVQ-ERQ 62
V LP + Q+ L+SAT P + K ++DP I + +ELTL+G+ Q+Y V+ E
Sbjct: 194 VFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEW 253
Query: 63 KVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDF 122
K L L+ L I Q+II+CN+ ++V+ L KK+ E + +H M Q R+ + +F
Sbjct: 254 KFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREF 313
Query: 123 RSGLCRNLV 131
RSG R L+
Sbjct: 314 RSGSTRVLI 322
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 69.1 bits (170), Expect = 1e-14
Identities = 33/130 (25%), Positives = 61/130 (46%)
Query: 2 LDHVISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINLMEELTLKGVTQYYAFVQER 61
+D +I P RQ LL+SAT+P + ++ +DP E+ + L + Q + V
Sbjct: 168 IDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPAIEQRFYEVSPD 227
Query: 62 QKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHD 121
+++ L L Q ++FCN+ + + +A + G+ +H + Q R++V
Sbjct: 228 ERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVR 287
Query: 122 FRSGLCRNLV 131
F + C LV
Sbjct: 288 FANRSCSVLV 297
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 68.3 bits (167), Expect = 2e-14
Identities = 47/140 (33%), Positives = 70/140 (50%), Gaps = 9/140 (6%)
Query: 1 MLD--------HVISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINLMEELTL-KGV 51
MLD V++ LP +RQ LL+SATF +K EK L +P EI + T + V
Sbjct: 161 MLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQV 220
Query: 52 TQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMA 111
TQ+ FV +++K L+ + K Q ++F + LA+++ + G IH +
Sbjct: 221 TQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKS 280
Query: 112 QAHRNRVFHDFRSGLCRNLV 131
Q R R DF+SG R LV
Sbjct: 281 QGARTRALADFKSGDIRVLV 300
>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 = 63.4 bits (155), Expect = 8e-14
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 51 VTQYYAFVQERQKVHCLNTLFSKLQIN--QSIIFCNSTQRVELLAKKITELGYCCYYIHA 108
+ QY V E +K+ L L + + +IFC S + ++ LA+ + + G +H
Sbjct: 2 IKQYVLPV-EDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 109 RMAQAHRNRVFHDFRSGLCRNLVCS 133
+Q R V DFR G LV +
Sbjct: 61 DGSQEEREEVLKDFREGEIVVLVAT 85
>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 = 57.5 bits (140), Expect = 5e-11
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 2 LDHVISILPHERQILLYSATFPLTVKNFMEKHLKDPYEIN 41
+ ++ +LP +RQ LL+SAT P V++ K L++P I
Sbjct: 164 IREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 53.2 bits (128), Expect = 4e-09
Identities = 34/127 (26%), Positives = 60/127 (47%), Gaps = 8/127 (6%)
Query: 5 VISILPHERQILLYSATFPLTVKNFMEKHLKD-PYEINLMEELTLKG---VTQYYAFVQE 60
V I P +RQ L++SAT+P V++ K+ P +N+ L L + Q V+E
Sbjct: 302 VSQIRP-DRQTLMWSATWPKEVQSLARDLCKEEPVHVNV-GSLDLTACHNIKQEVFVVEE 359
Query: 61 RQKVHCLNTLFSKLQINQS--IIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRV 118
+K L L ++ + +IF + + + L K++ G+ IH Q R V
Sbjct: 360 HEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWV 419
Query: 119 FHDFRSG 125
++F++G
Sbjct: 420 LNEFKTG 426
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 51.1 bits (122), Expect = 2e-08
Identities = 37/144 (25%), Positives = 59/144 (40%), Gaps = 11/144 (7%)
Query: 1 MLD--------HVISILPH--ERQILLYSATFPLTVKNFMEKHLKDPYEINL-MEELTLK 49
MLD +I P ERQ LL+SATF V N ++ DP + + E +
Sbjct: 249 MLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASD 308
Query: 50 GVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHAR 109
V Q+ V K L L ++ + ++F N V + +++ + G +
Sbjct: 309 TVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGD 368
Query: 110 MAQAHRNRVFHDFRSGLCRNLVCS 133
+ Q R + FR G R LV +
Sbjct: 369 VPQHKRIKTLEGFREGKIRVLVAT 392
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 47.6 bits (114), Expect = 3e-07
Identities = 42/141 (29%), Positives = 63/141 (44%), Gaps = 21/141 (14%)
Query: 1 MLD----HVISILPHE----RQILLYSATFPL---TVKNFMEKHLKDPYEIN----LMEE 45
MLD I + E +Q LL+SAT L V++F E+ L DP E+ E
Sbjct: 159 MLDMGFAQDIETIAAETRWRKQTLLFSAT--LEGDAVQDFAERLLNDPVEVEAEPSRRER 216
Query: 46 LTLKGVTQYYAFVQERQ-KVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCY 104
K + Q+Y + + K L L + ++ +SI+F + +RV LA + + G C
Sbjct: 217 ---KKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCC 273
Query: 105 YIHARMAQAHRNRVFHDFRSG 125
Y+ M QA RN G
Sbjct: 274 YLEGEMVQAKRNEAIKRLTDG 294
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 44.1 bits (105), Expect = 5e-07
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 90 ELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCS 133
E LA+ + ELG +H ++Q R + F +G + LV +
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVAT 44
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 47.3 bits (112), Expect = 5e-07
Identities = 32/122 (26%), Positives = 58/122 (47%), Gaps = 1/122 (0%)
Query: 13 RQILLYSATFPLTVKNFMEKHLKDPYEINL-MEELTLKGVTQYYAFVQERQKVHCLNTLF 71
RQ LL+SAT V +H+ +P ++ + E +T V Q F + +K L L
Sbjct: 193 RQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLL 252
Query: 72 SKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLV 131
S+ + ++++F N+ VE +A+ + GY + + Q R + + F+ G LV
Sbjct: 253 SRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILV 312
Query: 132 CS 133
+
Sbjct: 313 AT 314
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 44.1 bits (104), Expect = 5e-06
Identities = 30/128 (23%), Positives = 58/128 (45%), Gaps = 7/128 (5%)
Query: 2 LDHVISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINLMEELTLK-GVTQYYAFVQE 60
++ +++ +P Q L+SAT P ++ + +K+P E+ + +T + ++Q Y V
Sbjct: 170 VETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWG 229
Query: 61 RQKVHCLNTLFSKLQINQSIIFC---NSTQRVELLAKKITELGYCCYYIHARMAQAHRNR 117
+K L + +IIF N+T V A+ + GY ++ M QA R +
Sbjct: 230 MRKNEALVRFLEAEDFDAAIIFVRTKNATLEV---AEALERNGYNSAALNGDMNQALREQ 286
Query: 118 VFHDFRSG 125
+ G
Sbjct: 287 TLERLKDG 294
>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 = 41.4 bits (98), Expect = 7e-06
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 94 KKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVCS 133
K + + G +H ++Q R + DFR+G + LV +
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVAT 40
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 42.1 bits (99), Expect = 2e-05
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 2 LDHVISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINLMEELTLKGVTQY 54
L+ ++ +LP Q+LL SAT P ++N +E L DP I++ L+ + Q+
Sbjct: 150 LEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDV-GFTPLEPIEQF 201
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 37.8 bits (88), Expect = 7e-04
Identities = 37/128 (28%), Positives = 55/128 (42%), Gaps = 10/128 (7%)
Query: 14 QILLYSATFPLTVKNFMEKHLKDPYEINL-MEELTLKGVTQYYAFVQERQKVHCLNTLFS 72
Q+LL+SAT V+ F KD I++ K V Q +V+ +QK LF
Sbjct: 302 QVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQ---KLFD 358
Query: 73 KLQINQ-----SIIFCNSTQRVELLAKKITEL-GYCCYYIHARMAQAHRNRVFHDFRSGL 126
L+ Q +++F +S +LLA IT + G IH + R V F G
Sbjct: 359 ILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418
Query: 127 CRNLVCSG 134
+V +G
Sbjct: 419 VPVIVATG 426
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 37.5 bits (87), Expect = 0.001
Identities = 14/48 (29%), Positives = 20/48 (41%)
Query: 78 QSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSG 125
Q+I+F S +R LA +T G HA + R V F +
Sbjct: 442 QTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQ 489
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 36.1 bits (84), Expect = 0.003
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 79 SIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDFRSGLCRNLVC 132
II+C + ++VE LA+ + + G HA ++ R RV F + + +V
Sbjct: 233 GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVA 286
>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 = 35.4 bits (82), Expect = 0.005
Identities = 30/131 (22%), Positives = 49/131 (37%), Gaps = 21/131 (16%)
Query: 1 MLDHVISILPHERQILLYSATFPLTVKNFMEK-HLKDPYEI-------NLMEELTLKGVT 52
L + P +I L + T ++ E L D E NL
Sbjct: 152 RLGSLAERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNL---------- 201
Query: 53 QYYAFVQERQKVHCLNTLFSKLQINQS-IIFCNSTQRVELLAKKITELGYCCYYIHARMA 111
++ V++ K L + K QS II+ +S ++VE LA+++ G HA ++
Sbjct: 202 -RFSVVKKNNKQKFL-LDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLS 259
Query: 112 QAHRNRVFHDF 122
R DF
Sbjct: 260 NKVRAENQEDF 270
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 35.1 bits (81), Expect = 0.008
Identities = 22/110 (20%), Positives = 39/110 (35%), Gaps = 8/110 (7%)
Query: 15 ILLYSATFPLTVKNFMEKHLKDPYEINLMEELTLK----GVTQYYAFVQERQKVHCLNTL 70
+LL SAT P +K ++K L E+ + K G+ + V
Sbjct: 373 VLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKE-RVDVEDGPQEELIE 431
Query: 71 FSKLQINQSI---IFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNR 117
++ + + N+ R L +K+ E G +H+R R
Sbjct: 432 LISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREE 481
>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 = 34.2 bits (79), Expect = 0.009
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 2 LDHVISILPHERQILLYSATFPLTVKNF 29
L+ ++S LP +RQILL SAT P +++
Sbjct: 142 LEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 34.7 bits (80), Expect = 0.010
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 15/78 (19%)
Query: 41 NLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELG 100
L+E+ K + Q +VQE Q+ II+CNS +VE A ++ G
Sbjct: 216 TLVEKF--KPLDQLMRYVQE-QRGKS------------GIIYCNSRAKVEDTAARLQSRG 260
Query: 101 YCCYYIHARMAQAHRNRV 118
HA + R V
Sbjct: 261 ISAAAYHAGLDNDVRADV 278
>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 = 34.7 bits (80), Expect = 0.011
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 80 IIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHRNRVFHDF 122
II+C S ++ E + + LG HA + + R+ V H F
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKF 272
>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 = 31.6 bits (72), Expect = 0.096
Identities = 21/116 (18%), Positives = 37/116 (31%), Gaps = 24/116 (20%)
Query: 15 ILLYSATFPLTVKNFMEKHLKDPYEINLMEELTLKGVTQYYAFVQERQKVHCLN-TLFSK 73
ILL SAT P +K + EK E N + + + + +
Sbjct: 157 ILLMSATLPKFLKEYAEKI--GYVEENEPLD---------LKPNERAPFIKIESDKVGEI 205
Query: 74 LQIN----------QSIIFCNSTQRVELLAKKITELGYCCYY--IHARMAQAHRNR 117
+ I N+ R + +++ E G IH+R + R +
Sbjct: 206 SSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAK 261
>gnl|CDD|225625 COG3083, COG3083, Predicted hydrolase of alkaline phosphatase
superfamily [General function prediction only].
Length = 600
Score = 30.5 bits (69), Expect = 0.24
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 13 RQILLYSATFPL----TVKNFMEKH 33
R I + A FPL T ++F+EKH
Sbjct: 197 RPITMQRANFPLSYPMTARSFLEKH 221
>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 = 29.7 bits (67), Expect = 0.43
Identities = 25/110 (22%), Positives = 45/110 (40%), Gaps = 9/110 (8%)
Query: 15 ILLYSATFPLTVKNFMEKHLKDPYEINLMEELT-LKGVTQYYAFVQERQKVHCLNTLFSK 73
ILL SAT P +K + EK E N +L + ++ E KV +++L
Sbjct: 158 ILLMSATLPKFLKEYAEKI--GYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERL 215
Query: 74 LQI----NQSIIFCNSTQRVELLAKKITELG--YCCYYIHARMAQAHRNR 117
L+ + I N+ R + +++ E +H+R + R +
Sbjct: 216 LEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAK 265
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 28.8 bits (65), Expect = 1.1
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 79 SIIFCNSTQRVELLAKKITELGYCCYYIH-ARMAQAHRNRVFHDFRSGLCRNLVCS 133
++IF N+ E LA ++ +LG +H +++ R V + G + +V +
Sbjct: 256 TLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVAT 311
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.6 bits (64), Expect = 1.3
Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 1/70 (1%)
Query: 56 AFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLAKKITELGYCCYYIHARMAQAHR 115
A ER+ L + ++++IF + + +AK G I + R
Sbjct: 263 AIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGIVE-AITGETPKEER 321
Query: 116 NRVFHDFRSG 125
+ FR+G
Sbjct: 322 EAILERFRTG 331
>gnl|CDD|225042 COG2131, ComEB, Deoxycytidylate deaminase [Nucleotide transport and
metabolism].
Length = 164
Score = 27.7 bits (62), Expect = 1.8
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 83 CNSTQRVELLAKKITELGYCCYYIHARM---AQAHRNRV 118
C + +T G+CC +HA QA R+ V
Sbjct: 55 CIDRGCLRDKVVFVTTCGHCCRTLHAEQNAILQAARHGV 93
>gnl|CDD|217996 pfam04264, YceI, YceI-like domain. E. coli YceI is a base-induced
periplasmic protein. The recent structure of a member of
this family shows that it binds to polyisoprenoid. The
structure consists of an extended, eight-stranded,
antiparallel beta-barrel that resembles the lipocalin
fold.
Length = 161
Score = 26.5 bits (59), Expect = 3.9
Identities = 8/41 (19%), Positives = 13/41 (31%), Gaps = 5/41 (12%)
Query: 16 LLYSATFP---LTVKNFMEKHLKDPYEINLMEELTLKGVTQ 53
A +P ++ +LTL GVT+
Sbjct: 69 FFDVAKYPTATFKSTKVEATGGPGTVTVSG--DLTLHGVTK 107
>gnl|CDD|222996 PHA03131, PHA03131, dUTPase; Provisional.
Length = 286
Score = 26.5 bits (59), Expect = 4.6
Identities = 6/29 (20%), Positives = 8/29 (27%)
Query: 1 MLDHVISILPHERQILLYSATFPLTVKNF 29
L + I P S P +F
Sbjct: 138 SLPQDLVIFPTTTFTFTLSLCCPPISPHF 166
>gnl|CDD|224073 COG1151, COG1151, 6Fe-6S prismane cluster-containing protein
[Energy production and conversion].
Length = 576
Score = 26.2 bits (58), Expect = 7.2
Identities = 12/51 (23%), Positives = 14/51 (27%), Gaps = 8/51 (15%)
Query: 83 CNSTQRVELLAKKI--TELGYCCYYIHARMAQAHRNRVF-HDFRSGLCRNL 130
C T RV + G CY A R G+C L
Sbjct: 27 CGKTDRVADQQDLLIFGLKGLSCYLCSAG-----PCRYIDEKVPRGICGAL 72
>gnl|CDD|221295 pfam11893, DUF3413, Domain of unknown function (DUF3413). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is about 250
amino acids in length. This domain is found associated
with pfam00884.
Length = 253
Score = 25.7 bits (57), Expect = 8.1
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 4/25 (16%)
Query: 13 RQILLYSATFPL----TVKNFMEKH 33
R I + PL T ++FMEKH
Sbjct: 196 RPITMQDNNLPLSYPATARSFMEKH 220
>gnl|CDD|163405 TIGR03693, ocin_ThiF_like, putative thiazole-containing bacteriocin
maturation protein. Members of this protein family are
found in a three-gene operon in Bacillus anthracis and
related Bacillus species, where the other two genes are
clearly identified with maturation of a putative
thiazole-containing bacteriocin precursor. While there
is no detectable pairwise sequence similarity between
members of this family and the proposed
cyclodehydratases such as SagC of Streptococcus pyogenes
(see family TIGR03603), both families show similarity
through PSI-BLAST to ThiF, a protein involved in
biosynthesis of the thiazole moiety for thiamine
biosynthesis. This family, therefore, may contribute to
cyclodehydratase function in heterocycle-containing
bacteriocin biosyntheses. In Bacillus licheniformis ATCC
14580, the bacteriocin precursor gene is adjacent to the
gene for this protein [Cellular processes, Toxin
production and resistance].
Length = 637
Score = 26.1 bits (57), Expect = 8.3
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 5 VISILPHERQILLYSATFPLTVKNFMEKHLKDPYEINLMEE 45
++ L H + Y F L ++ F+++ L Y + + +E
Sbjct: 596 LLLALKHLEEHHFYPFVFDLAIEPFLKEKLAGIYCVLIAKE 636
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
0.328 0.137 0.415
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: 6,806,278
Number of extensions: 577583
Number of successful extensions: 721
Number of sequences better than 10.0: 1
Number of HSP's gapped: 706
Number of HSP's successfully gapped: 38
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.5 bits)