RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17746
(182 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 172 bits (438), Expect = 3e-50
Identities = 67/126 (53%), Positives = 85/126 (67%), Gaps = 4/126 (3%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGRE 60
++LATNIAETS+T+PGI+YVIDSGL K+K + P TGL L+ IS+A A QR GRAGR
Sbjct: 316 VVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRT 375
Query: 61 AEGFCYRMYSEEDFRRMNKNTVPEIQRTNLASTALTLLSLEI--NAATFDFMDKPPKE-- 116
G CYR+YSEEDF + T+PEI RT+L+ L L SL I + A F F+D PP+
Sbjct: 376 GPGICYRLYSEEDFLAFPEFTLPEILRTDLSGLVLQLKSLGIGQDIAPFPFLDPPPEAAI 435
Query: 117 IESRQL 122
+ L
Sbjct: 436 QAALTL 441
Score = 40.8 bits (96), Expect = 2e-04
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 12/71 (16%)
Query: 111 DKPPKEIESRQLVSIHPSS-SLAGSLPEYILFTELLQTSRCY-----------MKTLSVI 158
+P + V HPSS L L E+I + E L+T + Y ++TL +
Sbjct: 638 GRPYVTLSDNTPVFAHPSSVRLGLVLLEWIKYAEFLRTRKGYLREGRGERWPDVQTLIEL 697
Query: 159 DPAWITEMVPG 169
W+ E V G
Sbjct: 698 LKLWLKEQVKG 708
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 124 bits (312), Expect = 4e-33
Identities = 59/116 (50%), Positives = 76/116 (65%), Gaps = 1/116 (0%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGRE 60
I+LATN+AETS+TVPGIKYVID G + + T + L + ISQA A QR GR GR
Sbjct: 340 IVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV 399
Query: 61 AEGFCYRMYSEEDFRRMNKNTVPEIQRTNLASTALTLLSLEI-NAATFDFMDKPPK 115
+EG C R+YSE+DF + T PEI RTNLAS L + +L + + A F F++ P K
Sbjct: 400 SEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAFPFVEAPDK 455
Score = 35.8 bits (83), Expect = 0.009
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 124 SIHPSSSLAGSLPEYILFTELLQTSRCYMKTLSVIDPAWITEMVPGYAAQHRI 176
SI P S L P++++ EL++TSR + + + I+P WI + AQH I
Sbjct: 649 SIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPL-----AQHLI 696
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 123 bits (311), Expect = 4e-33
Identities = 61/119 (51%), Positives = 77/119 (64%), Gaps = 2/119 (1%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGRE 60
I+LATN+AETS+TVPGI YVID+G + + T + L + ISQA A QR GR GR
Sbjct: 333 IVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV 392
Query: 61 AEGFCYRMYSEEDFRRMNKNTVPEIQRTNLASTALTLLSLEINA-ATFDFMDKP-PKEI 117
A G C R+YSEEDF + T PEI RTNLAS L +L+L + A F F++ P P+ I
Sbjct: 393 APGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRAI 451
Score = 44.8 bits (106), Expect = 1e-05
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 124 SIHPSSSLAGSLPEYILFTELLQTSRCYMKTLSVIDPAWITEMVP 168
I P S L P++++ EL++TS+ Y + ++ I+P W+ +
Sbjct: 639 HIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAG 683
>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 = 113 bits (285), Expect = 1e-29
Identities = 55/125 (44%), Positives = 74/125 (59%), Gaps = 3/125 (2%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGRE 60
++LATNIAETS+T+ GI+ VIDSGL + P TG+ L+ ISQA A QR GRAGR
Sbjct: 265 VVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL 324
Query: 61 AEGFCYRMYSEEDFRRMNKNTVPEIQRTNLASTALTLLSLEINA-ATFDFMDKPP--KEI 117
G CYR++SEE +R+ PEI + +L+ AL L + ++D PP
Sbjct: 325 EPGVCYRLWSEEQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALA 384
Query: 118 ESRQL 122
+RQL
Sbjct: 385 AARQL 389
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 105 bits (263), Expect = 1e-26
Identities = 50/116 (43%), Positives = 67/116 (57%), Gaps = 1/116 (0%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGRE 60
++LATNIAETS+T+ GI+ V+DSGL + P TGL L ISQA QR GRAGR
Sbjct: 268 VVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL 327
Query: 61 AEGFCYRMYSEEDFRRMNKNTVPEIQRTNLASTALTLLSLEIN-AATFDFMDKPPK 115
G C +YS+E R + PEI ++L+ L LL + A ++D+PP
Sbjct: 328 EPGICLHLYSKEQAERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPA 383
>gnl|CDD|219532 pfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding
(OB)-fold. This family is found towards the C-terminus
of the DEAD-box helicases (pfam00270). In these
helicases it is apparently always found in association
with pfam04408. There do seem to be a couple of
instances where it occurs by itself - . The structure
PDB:3i4u adopts an OB-fold. helicases (pfam00270). In
these helicases it is apparently always found in
association with pfam04408. This C-terminal domain of
the yeast helicase contains an
oligonucleotide/oligosaccharide-binding (OB)-fold which
seems to be placed at the entrance of the putative
nucleic acid cavity. It also constitutes the binding
site for the G-patch-containing domain of Pfa1p. When
found on DEAH/RHA helicases, this domain is central to
the regulation of the helicase activity through its
binding of both RNA and G-patch domain proteins.
Length = 109
Score = 67.3 bits (165), Expect = 3e-15
Identities = 23/51 (45%), Positives = 36/51 (70%), Gaps = 1/51 (1%)
Query: 121 QLVSIHPSSSLAGSLP-EYILFTELLQTSRCYMKTLSVIDPAWITEMVPGY 170
Q V IHPSS L G P E++++ EL++T++ YM+ ++ IDP W+ E+ P Y
Sbjct: 59 QPVFIHPSSVLFGKKPPEWVVYHELVETTKEYMRDVTAIDPEWLLELAPHY 109
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 46.4 bits (111), Expect = 2e-07
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 18/59 (30%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGR 59
+++AT++AE + +PG+ VI L S A QR GRAGR
Sbjct: 40 VLVATDVAERGLDLPGVDLVIIYDL------------------PWSPASYIQRIGRAGR 80
>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 = 46.4 bits (111), Expect = 2e-07
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 18/59 (30%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGR 59
+++AT++A I +P + VI+ L + A QR GRAGR
Sbjct: 36 VLVATDVAGRGIDLPDVNLVINYDL------------------PWNPASYIQRIGRAGR 76
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 41.9 bits (99), Expect = 9e-05
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGRE 60
II++T E+S+T+ +V D+G V P G + IS++ QR GR GR
Sbjct: 449 IIISTPYLESSVTIRNATHVYDTGRVYVPE--PFGG----KEMFISKSMRTQRKGRVGRV 502
Query: 61 AEGFCYRMYS 70
+ G Y
Sbjct: 503 SPGTYVYFYD 512
>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 = 39.1 bits (92), Expect = 2e-04
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 19/69 (27%)
Query: 1 IILATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGR- 59
+++AT++ I +P + VI P S + QR GRAGR
Sbjct: 81 VLVATDVIARGIDLPNVSVVI-------NYDLP-----------WSPSSYLQRIGRAGRA 122
Query: 60 EAEGFCYRM 68
+G +
Sbjct: 123 GQKGTAILL 131
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 32.7 bits (75), Expect = 0.11
Identities = 20/73 (27%), Positives = 31/73 (42%)
Query: 77 MNKNTVPEIQRTNLASTALTLLSLEINAATFDFMDKPPKEIESRQLVSIHPSSSLAGSLP 136
N TV +I+ N L L + T D +D E SR L ++ +L S+P
Sbjct: 355 ENVKTVIDIKNRNEGEIVLEEGELVEKSFTPDHLDNEDLEEYSRTLAPLNHLQNLKNSIP 414
Query: 137 EYILFTELLQTSR 149
E + F E+ +
Sbjct: 415 ESVTFLEMYGVKK 427
>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 = 30.1 bits (68), Expect = 0.67
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 18/60 (30%)
Query: 4 ATNIAETSITVPGIKYVIDSGLVKQKTHHPGTGLDVLQVTSISQAQAWQRTGRAGREAEG 63
TN E + + G+ V+ +G PGT +A WQ+ GRAGR +G
Sbjct: 335 TTNALELGVDISGLDAVVIAG-------FPGT-----------RASLWQQAGRAGRRGQG 376
>gnl|CDD|233554 TIGR01739, tegu_FGAM_synt, herpesvirus tegument
protein/v-FGAM-synthase. This model describes a family
of large proteins of herpesvirues. The protein is
described variably as tegument protein or
phosphoribosylformylglycinamidine synthase
(FGAM-synthase). Most of the length of the protein shows
homology to eukaryotic FGAM-synthase. Functional
characterizations were not verified during construction
of this model.
Length = 1202
Score = 29.3 bits (66), Expect = 1.5
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 122 LVSIHPSSSLAGSLPEYIL---FTELLQTSRCYMKTL 155
+S+HPS +LAGS+ E IL F L S +K L
Sbjct: 721 WLSLHPSYTLAGSIFEQILGLSFIRLPALSPVSLKKL 757
>gnl|CDD|133389 cd04761, HTH_MerR-SF, Helix-Turn-Helix DNA binding domain of
transcription regulators from the MerR superfamily.
Helix-turn-helix (HTH) transcription regulator MerR
superfamily, N-terminal domain. The MerR family
transcription regulators have been shown to mediate
responses to stress including exposure to heavy metals,
drugs, or oxygen radicals in eubacterial and some
archaeal species. They regulate transcription of
multidrug/metal ion transporter genes and oxidative
stress regulons by reconfiguring the spacer between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of two distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 49
Score = 26.0 bits (58), Expect = 2.4
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 44 SISQAQAWQRTG--RAGREAEGFCYRMYSEEDFRRMN 78
S S + ++R G R G YR+YS+ D R+
Sbjct: 13 SPSTLRYYERIGLLSPARTEGG--YRLYSDADLERLR 47
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 28.4 bits (64), Expect = 2.6
Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 51 WQRTGRAGR---EAEGFCYRMYSEEDFR 75
+Q TGRAGR AE +YS ED R
Sbjct: 315 YQETGRAGRDGLPAE--AILLYSPEDIR 340
>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 = 27.7 bits (62), Expect = 3.4
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 51 WQRTGRAGREAE-GFCYRMYSEEDF---RRMNKNTVPEIQR 87
+Q GRAGR+ +YS D +R + + +
Sbjct: 309 YQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQSEADDDY 349
>gnl|CDD|180933 PRK07329, PRK07329, hypothetical protein; Provisional.
Length = 246
Score = 27.3 bits (61), Expect = 4.9
Identities = 8/29 (27%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 95 LTLLSLEINAATFDFMDKPPKEIESRQLV 123
L LLS+ N +D++D +++ ++L+
Sbjct: 96 LKLLSVHHNG-VYDYLDDEVADMDKKELL 123
>gnl|CDD|117932 pfam09390, DUF1999, Protein of unknown function (DUF1999). This
family contains a putative Fe-S binding reductase whose
structure adopts an alpha and beta fold.
Length = 161
Score = 26.5 bits (58), Expect = 7.1
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 66 YRMYSEEDFRRMNKNTVPEIQRTNLASTAL 95
YR ++E D R+ + E +RT L
Sbjct: 3 YRPFTEPDLERLQALDLAEQRRTAPEYDVL 32
>gnl|CDD|178354 PLN02753, PLN02753, triacylglycerol lipase.
Length = 531
Score = 27.0 bits (59), Expect = 7.4
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 52 QRTGRAGREAEGFCYRMYSEEDFRRMNKNTVPE 84
+R G EAEG + ED RR +K T E
Sbjct: 68 ERQGLLIDEAEGAGELWLTAEDIRRRDKKTEEE 100
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
0.317 0.131 0.376
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: 9,023,168
Number of extensions: 786400
Number of successful extensions: 585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 576
Number of HSP's successfully gapped: 32
Length of query: 182
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 91
Effective length of database: 6,901,388
Effective search space: 628026308
Effective search space used: 628026308
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 (21.7 bits)
S2: 56 (25.3 bits)