RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9627
(129 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 143 bits (363), Expect = 1e-41
Identities = 62/116 (53%), Positives = 80/116 (68%), Gaps = 2/116 (1%)
Query: 11 KPDRQVLMWSATWPREVQKLAEDFL-DSYIQINIGSLTLSANHNIQQVVEVCAEHEKENK 69
+PDRQ LMWSATWP+EVQ LA D + + +N+GSL L+A HNI+Q V V EHEK K
Sbjct: 306 RPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGK 365
Query: 70 LFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVL 125
L LL I +D +K +IF ETK+ D +TK ++ GW A+ IHGDK Q+ER +VL
Sbjct: 366 LKMLLQRIM-RDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVL 420
>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 = 103 bits (258), Expect = 6e-27
Identities = 40/117 (34%), Positives = 65/117 (55%), Gaps = 5/117 (4%)
Query: 12 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGS-LTLSANHNIQQVVEVC-AEHEKENK 69
PDRQ L++SAT P ++++LA +L+ ++I + I+Q +E EK
Sbjct: 204 PDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLEL 263
Query: 70 LFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLK 126
L LL D DE + I+F TKR V+++ +S++ G+ +HGD Q+ERD L+
Sbjct: 264 LLKLLKDE---DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALE 317
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 74.5 bits (184), Expect = 9e-17
Identities = 29/114 (25%), Positives = 59/114 (51%), Gaps = 5/114 (4%)
Query: 12 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 71
RQ L++SAT+P + +++ F +++ + S I+Q + E+ L
Sbjct: 177 ARRQTLLFSATYPEGIAAISQRFQRDPVEVKVEST--HDLPAIEQRFYEVSPDERLPALQ 234
Query: 72 GLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVL 125
LL + E+ ++F TK++ ++ ++ G++A+ +HGD Q++RD VL
Sbjct: 235 RLLLH--HQPES-CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVL 285
>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 = 57.2 bits (139), Expect = 1e-11
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 53 NIQQVVEVCAEHEKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGI 112
I+Q V E EK L LL + K K +IF +K+ +D++ + ++ G +
Sbjct: 1 PIKQYVLPV-EDEKLEALLELLKEHLKKGG-KVLIFCPSKKMLDELAELLRKPGIKVAAL 58
Query: 113 HGDKSQQERDYVLK 126
HGD SQ+ER+ VLK
Sbjct: 59 HGDGSQEEREEVLK 72
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 57.1 bits (138), Expect = 1e-10
Identities = 38/115 (33%), Positives = 59/115 (51%), Gaps = 7/115 (6%)
Query: 15 QVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLL 74
QVL++SAT EV+K A I I+IG+ N ++Q+ +K+ KLF +L
Sbjct: 302 QVLLFSATVSPEVEKFASSLAKDIILISIGNPN-RPNKAVKQLAIWVETKQKKQKLFDIL 360
Query: 75 NDISSKDENK--TIIFAETKRKVDKITKSIQ-NYGWAAVGIHGDKSQQERDYVLK 126
SK K ++F ++ D + +I G A+ IHG+KS +ER V+K
Sbjct: 361 ---KSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMK 412
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 55.2 bits (133), Expect = 6e-10
Identities = 37/116 (31%), Positives = 59/116 (50%), Gaps = 5/116 (4%)
Query: 12 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 71
PD QV ++SAT P E+ +L F+ +I + L+ Q V V EKE F
Sbjct: 200 PDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAV----EKEEWKF 255
Query: 72 GLLNDI-SSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLK 126
L D+ + + II+ T+RKVD +TK + + +HGD Q++RD +++
Sbjct: 256 DTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMR 311
>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 = 52.5 bits (127), Expect = 2e-09
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 12 PDRQVLMWSATWPREVQKLAEDFLDSYIQIN 42
DRQ L++SAT P+EV+ LA FL + ++I
Sbjct: 173 KDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 52.6 bits (126), Expect = 4e-09
Identities = 33/120 (27%), Positives = 69/120 (57%), Gaps = 4/120 (3%)
Query: 6 RAMTYKPDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHE 65
R M + RQ L++SAT V +LA + ++ ++ + + T++A ++Q + A+ E
Sbjct: 185 RRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAAR-VRQRIYFPADEE 243
Query: 66 KENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVL 125
K+ L GLL S + +T++F TK V+++ ++++ +G+ + GD Q++R+ +L
Sbjct: 244 KQTLLLGLL---SRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLL 300
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 50.7 bits (121), Expect = 2e-08
Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 4/116 (3%)
Query: 6 RAMTYKPDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHE 65
R K +RQ L++SAT+ +V LA+ + + I + A+ ++Q V A +
Sbjct: 263 RQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV-ASDTVEQHVYAVAGSD 321
Query: 66 KENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQER 121
K L+ L+ + ++FA K +V +I + + G A + GD Q +R
Sbjct: 322 KYKLLYNLVTQ---NPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKR 374
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 47.5 bits (113), Expect = 2e-07
Identities = 28/110 (25%), Positives = 53/110 (48%), Gaps = 4/110 (3%)
Query: 12 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 71
RQ L++SAT+ +++ LAE L + ++I + +A+ + Q V + K L
Sbjct: 179 AKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRN-TASEQVTQHVHFVDKKRKRELLS 237
Query: 72 GLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQER 121
+ I + + ++F TK + + + + G + IHG+KSQ R
Sbjct: 238 QM---IGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGAR 284
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 37.9 bits (88), Expect = 5e-04
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 11 KPDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQV 57
+ Q+L+ SAT P E++ L E FL+ + I++G I+Q
Sbjct: 158 PKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTP---LEPIEQF 201
>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 = 37.0 bits (86), Expect = 0.001
Identities = 15/57 (26%), Positives = 32/57 (56%)
Query: 65 EKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQER 121
+K NK LL+ + II+A +++KV+++ + +++ G +A+ H S + R
Sbjct: 207 KKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVR 263
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 35.0 bits (81), Expect = 0.006
Identities = 24/114 (21%), Positives = 47/114 (41%), Gaps = 10/114 (8%)
Query: 14 RQVLMW-SATWPREVQK--LAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKL 70
++ +AT V+ + L GS +VVE E ++L
Sbjct: 166 NPPVLALTATATPRVRDDIREQLGLQDANIF-RGSFDRPNLAL--KVVEK---GEPSDQL 219
Query: 71 FGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYV 124
L + ++ II+ T++KV+++ + ++ G +A H S +ER+ V
Sbjct: 220 AFLATVLPQLSKS-GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERV 272
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 34.1 bits (78), Expect = 0.012
Identities = 25/112 (22%), Positives = 54/112 (48%), Gaps = 4/112 (3%)
Query: 15 QVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLL 74
Q ++SAT P ++++ F+ ++ I S +++ +I Q K L L
Sbjct: 182 QTALFSATMPEAIRRITRRFMKEPQEVRIQS-SVTTRPDISQSYWTVWGMRKNEALVRFL 240
Query: 75 NDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLK 126
++D + IIF TK ++ ++++ G+ + ++GD +Q R+ L+
Sbjct: 241 ---EAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLE 289
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 33.2 bits (76), Expect = 0.024
Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 5/98 (5%)
Query: 25 REVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLLNDISSKDENK 84
+ ++ + ++ TL A + +++ A K + GLL + D K
Sbjct: 230 EDEEREYAKESARFRELLRARGTLRAENEARRIAI--ASERKIAAVRGLLLKHARGD--K 285
Query: 85 TIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERD 122
T+IFA +I K G I G+ ++ER+
Sbjct: 286 TLIFASDVEHAYEIAKLFLAPGIVEA-ITGETPKEERE 322
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 33.0 bits (76), Expect = 0.026
Identities = 34/137 (24%), Positives = 61/137 (44%), Gaps = 30/137 (21%)
Query: 3 WASRAMTYKPDRQVLMWSATWPREVQKLAEDFLDS--YIQINIGSLTLSANHNIQQVVEV 60
W R M R +++SAT V++LA + +++ Y+++ T H I++
Sbjct: 180 WLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKT---GHRIKE---- 232
Query: 61 CAEHE-----KENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIH-- 113
E E K+ L I + ++ IIFA TK + ++I +G A H
Sbjct: 233 ----ELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEI------WGHLAADGHRV 282
Query: 114 ----GDKSQQERDYVLK 126
GD +Q++R +L+
Sbjct: 283 GLLTGDVAQKKRLRILE 299
>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 = 30.7 bits (70), Expect = 0.14
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 12 PDRQVLMWSATWPREVQKL 30
PDRQ+L+ SAT PR ++ L
Sbjct: 151 PDRQILLLSATLPRNLEDL 169
>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 = 29.7 bits (67), Expect = 0.41
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 66 KENKLFGLLNDISSKDENKT-IIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYV 124
L LL I + + K+ II+ +++K +++T S+QN G AA H RD V
Sbjct: 209 TPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDV 268
>gnl|CDD|107383 cd06388, PBP1_iGluR_AMPA_GluR4, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR4 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR4 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 371
Score = 28.5 bits (63), Expect = 1.1
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 50 ANHNIQQVVEVCAEHEKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAA 109
A N QV +C E+ + LL D+ + E K +I E +R + I + I + G
Sbjct: 147 AGQNGWQVSAICVENFNDASYRRLLEDLDRRQEKKFVIDCEIER-LQNILEQIVSVGKHV 205
Query: 110 VGIH 113
G H
Sbjct: 206 KGYH 209
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 27.2 bits (61), Expect = 1.2
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 96 DKITKSIQNYGWAAVGIHGDKSQQERDYVLK 126
+++ + ++ G +HG SQ+ER+ +L
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILD 31
>gnl|CDD|171679 PRK12717, flgL, flagellar hook-associated protein FlgL;
Provisional.
Length = 523
Score = 28.2 bits (63), Expect = 1.4
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 65 EKENKLFGLLNDISSKDENKTIIFAETK 92
+ E +L GL+N SKD N +FA +K
Sbjct: 116 QIEAQLLGLMN---SKDANGQYLFAGSK 140
>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 = 26.7 bits (60), Expect = 1.4
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 100 KSIQNYGWAAVGIHGDKSQQERDYVLK 126
K ++ G +HG SQ+ER+ +L+
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILE 27
>gnl|CDD|132156 TIGR03112, 6_pyr_pter_rel, 6-pyruvoyl tetrahydropterin
synthase-related domain. Members of this family are
small proteins, or small domains of larger proteins,
that occur in certain Firmicutes in the same regions as
members of families TIGR03110 and TIGR03111. Members of
TIGR03110 resemble exosortase, a proposed protein
sorting transpeptidase (see TIGR02602). TIGR03111
represents a small clade among the group 2
glycosyltransferases. Members of the current protein
family resemble eukaryotic known and prokaryotic
predicted 6-pyruvoyl tetrahydropterin synthases.
Length = 113
Score = 26.9 bits (60), Expect = 1.6
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 79 SKDENKTIIFAETKRKVDKITKSIQN 104
K E+K I+F + ++KV+K K QN
Sbjct: 34 IKKEDKFILFNDVEKKVEKYLKPYQN 59
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 27.3 bits (61), Expect = 2.6
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 22/85 (25%)
Query: 25 REVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKL--FGLLNDISSKDE 82
+V KL + + INIGS T +VV + K++ + L + +
Sbjct: 382 TKVAKLKKG---ESLMINIGSTTTGG-----RVVGI-----KDDGIAKLELTTPVCTSVG 428
Query: 83 NKTIIFAETKRKVDKITKSIQNYGW 107
K + R+VDK + I GW
Sbjct: 429 EKIAL----SRRVDKHWRLI---GW 446
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 26.9 bits (60), Expect = 3.2
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 50 ANHNIQQVVEVCAEHEKENKLFGLLNDISSK-DENKTIIFAETKRKVDKITKSIQNYG 106
A + + E EH K KL +L + K +++ I+F E + ++I ++ G
Sbjct: 333 ALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIG 390
>gnl|CDD|132561 TIGR03522, GldA_ABC_ATP, gliding motility-associated ABC
transporter ATP-binding subunit GldA. Members of this
protein family are exclusive to the Bacteroidetes phylum
(previously Cytophaga-Flavobacteria-Bacteroides). GldA
is an ABC transporter ATP-binding protein (pfam00005)
linked to a type of rapid surface gliding motility found
in certain Bacteroidetes, such as Flavobacterium
johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA
abolish the gliding phenotype. Gliding motility appears
closely linked to chitin utilization in the model
species Flavobacterium johnsoniae. Bacteroidetes with
members of this protein family appear to have all of the
genes associated with gliding motility.
Length = 301
Score = 26.7 bits (59), Expect = 3.5
Identities = 27/106 (25%), Positives = 43/106 (40%), Gaps = 14/106 (13%)
Query: 25 REVQKLAEDFLDSYIQINIGSLTLS------ANHNIQQVVEVCAEHEKENKLFGLLNDIS 78
+EV+ + D I IN G + + N +QV+EV E + + +LF L +IS
Sbjct: 193 QEVEAIC----DRVIIINKGKIVADKKLDELSAANKKQVIEVEFEEQIDLQLFETLEEIS 248
Query: 79 S---KDENKTIIFAETKRKVDK-ITKSIQNYGWAAVGIHGDKSQQE 120
S N + ET I K Q G + + ++ E
Sbjct: 249 SVKNTGGNTWKLTFETPNDTRPEIFKLAQQKGLKLISLQQNEKNLE 294
>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is
present in several RNA-processing factors such as Pcf11
and Nrd1. Pcf11 is a conserved and essential subunit of
the yeast cleavage factor IA, which is required for
polyadenylation-dependent 3'-RNA processing and
transcription termination. Nrd1 is implicated in
polyadenylation-independent 3'-RNA processing. CID binds
tightly to the carboxy-terminal domain (CTD) of RNA
polymerase (Pol) II. During transcription, Pol II
synthesizes eukaryotic messenger RNA. Transcription is
coupled to RNA processing through the CTD, which
consists of up to 52 repeats of the sequence Tyr 1-Ser
2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight
alpha-helices in a right-handed superhelical
arrangement, which closely resembles that of the VHS
domains and ARM (Armadillo) repeat proteins, except for
its two amino-terminal helices.
Length = 114
Score = 26.0 bits (58), Expect = 3.7
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 18/80 (22%)
Query: 40 QINIGSLTLSANHNIQ---QVVEVCAEHEK----ENKLFGL--LNDIS--SKDENKTI-- 86
Q +I +LT A N + ++VE+ +H K E KL L L+ I + K
Sbjct: 18 QPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFS 77
Query: 87 -----IFAETKRKVDKITKS 101
+F + KVD+ T+
Sbjct: 78 EFLVPLFLDAYEKVDEKTRK 97
>gnl|CDD|223942 COG1010, CobJ, Precorrin-3B methylase [Coenzyme metabolism].
Length = 249
Score = 26.4 bits (59), Expect = 4.3
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 52 HNIQQVVEVCAEHEKENKLFGLLNDISSKDENKTII 87
+ + E+ EH + G++ + + E I
Sbjct: 171 EQLGRAFEILREHRSPDTPVGIVRNAGREGEEVRIT 206
>gnl|CDD|224816 COG1904, UxaC, Glucuronate isomerase [Carbohydrate transport and
metabolism].
Length = 463
Score = 26.5 bits (59), Expect = 4.8
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 9 TYKPDRQVLMWSATWPREVQKLAE 32
++PD V + A + V+KL E
Sbjct: 179 AWRPDAAVDIERAGFADYVEKLGE 202
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 26.2 bits (58), Expect = 5.6
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 86 IIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYV 124
II+ ++ KV+ +Q+ G +A H R V
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADV 278
>gnl|CDD|226059 COG3528, COG3528, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 330
Score = 26.0 bits (57), Expect = 7.2
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 89 AETKRKVDKITKSIQNYGWA 108
E + KI + + YGW
Sbjct: 147 QEVQNLAHKIIGAEKYYGWN 166
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 26.0 bits (58), Expect = 7.6
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 63 EHEKENKLFGLLNDI-SSKDENKTIIFAETKRKVDKITK 100
EH K KL ++ + +++ I+F + + +KI
Sbjct: 345 EHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVD 383
>gnl|CDD|236851 PRK11114, PRK11114, cellulose synthase regulator protein;
Provisional.
Length = 756
Score = 26.0 bits (58), Expect = 8.1
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 4 ASRAMT-----YKPDRQVLMWSATWPREVQKLAEDFLDSYIQINI-GSLTL 48
A A+ + R V+ A PR + L + D + I G + +
Sbjct: 640 AMAALIGFESPFNSQRSVVALLADSPRGLALLNDALNDPGKRAQIFGDVAV 690
>gnl|CDD|151328 pfam10879, DUF2674, Protein of unknown function (DUF2674). This
family of proteins with unknown function appears to be
conserved to Rickettsia spp.
Length = 67
Score = 24.2 bits (52), Expect = 9.4
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 84 KTIIFAETKRKVDKITKSIQNYGWAAV 110
K I F+E K +++I K+I+ GWA V
Sbjct: 7 KVISFSEHKADIERIKKAIEE-GWAIV 32
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 25.7 bits (57), Expect = 9.8
Identities = 23/109 (21%), Positives = 49/109 (44%), Gaps = 4/109 (3%)
Query: 14 RQVLMWSATWPRE-VQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFG 72
+Q L++SAT + VQ AE L+ +++ + I Q + E + L
Sbjct: 179 KQTLLFSATLEGDAVQDFAERLLNDPVEVEAEP-SRRERKKIHQWYYRADDLEHKTAL-- 235
Query: 73 LLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQER 121
L + + + ++I+F T+ +V ++ ++ G + G+ Q +R
Sbjct: 236 LCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKR 284
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
0.315 0.129 0.379
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: 6,224,999
Number of extensions: 513137
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 607
Number of HSP's successfully gapped: 50
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)