RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10449
(114 letters)
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 118 bits (297), Expect = 3e-32
Identities = 45/110 (40%), Positives = 64/110 (58%), Gaps = 2/110 (1%)
Query: 5 IVSGVYGFGCEDALTHLLNYVWPNIFETSPHLVQAFMDAVEGLRVALGPVRILQYVLQGL 64
+V G G EDA HLLN +WPNI E SPH++Q+F + +E LG +++YV QGL
Sbjct: 868 LVLNCPGTGDEDAAIHLLNLLWPNILEPSPHVIQSFDEGMESFATVLGSGAMMKYVQQGL 927
Query: 65 FHPARKVRDVYWKIYNSLYIGGQDALISAYPRIQNDMKNVYLRYELDYVL 114
FHP+ VR YW +YN +Y+ DA++ YP ++ N L L +
Sbjct: 928 FHPSSTVRKRYWTVYNIMYVFDSDAMVPCYPVEEDL--NPELARTLHICI 975
>gnl|CDD|217598 pfam03520, KCNQ_channel, KCNQ voltage-gated potassium channel.
This family matches to the C-terminal tail of KCNQ type
potassium channels.
Length = 201
Score = 28.2 bits (63), Expect = 0.68
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 31 ETSPHLVQAFMDAVEGLRVALGPVRILQY-VLQGLFHPARK---VRDV 74
E + D + A+ +R ++Y V + F A K V+DV
Sbjct: 58 EKELPCITTVEDLTPAHKTAIRAIRRMKYFVAKRKFKEALKPYDVKDV 105
>gnl|CDD|222041 pfam13312, DUF4081, Domain of unknown function (DUF4081). This
domain is often found N-terminal to the GNAT
acetyltransferase domain, pfam00583 and FR47,
pfam08445.
Length = 107
Score = 26.8 bits (60), Expect = 1.4
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 9 VYGFGCEDALTHLLNYVWPNI--FETSPHLVQAFMDAV--EGLRVA--LGP---VRILQY 59
V+G G + LT L + N+ P ++AF D G R + +GP V L
Sbjct: 4 VWGVGDDGRLTALC-WAGANLVPVAADPAALRAFADRARRRGRRCSSIVGPADAVLGLWE 62
Query: 60 VLQGLFHPARKVRD 73
L+ + PAR+VR
Sbjct: 63 RLEPTWGPAREVRA 76
>gnl|CDD|219580 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 27.6 bits (62), Expect = 1.6
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 34 PHLVQAFMDAVEGLRVALGPVRIL-----QYVLQGL 64
L QAF DA EGL + + IL +YVL L
Sbjct: 164 EALCQAFRDACEGLGLDIKVKLILLKLFERYVLAQL 199
>gnl|CDD|182990 PRK11139, PRK11139, DNA-binding transcriptional activator GcvA;
Provisional.
Length = 297
Score = 26.7 bits (60), Expect = 2.4
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 29 IFETSPHLVQAFMDAVEGLRVALGPVRIL 57
IF S +QA A+ G VALG R+L
Sbjct: 219 IFSHSSMALQA---AIHGQGVALGN-RVL 243
>gnl|CDD|183114 PRK11388, PRK11388, DNA-binding transcriptional regulator DhaR;
Provisional.
Length = 638
Score = 26.6 bits (59), Expect = 3.0
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 15 EDALTHLLNYVWP-NIFE 31
+DAL L++Y WP N FE
Sbjct: 525 DDALARLVSYRWPGNDFE 542
>gnl|CDD|219970 pfam08689, Med5, Mediator complex subunit Med5. The mediator
complex is required for the expression of nearly all
RNA pol II dependent genes in Saccharomyces cerevisiae.
Deletion of the MED5 gene leads to increased
transcription of nuclear genes encoding components of
the oxidative phosphorylation machinery, and decreased
transcription of mitochondrial genes encoding
components of the same machinery. There is no
orthologue from pombe, and this subunit appears to be
fungal specific.
Length = 977
Score = 26.7 bits (59), Expect = 3.3
Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 27 PNIFETSPHLVQAFMDAVEGLRVA----LGPVRILQYVLQGLFHPARKVRDVYWKIYNSL 82
+ E P +A D + R+A L P+ + Y++ LF ++ + L
Sbjct: 29 NELNEKYPISEEALADLLLRPRIANHISLDPLLLALYIVVLLFQGVNYNSELLKALLPKL 88
Query: 83 YIGGQDALI 91
G + L+
Sbjct: 89 PSVGNEKLL 97
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional.
Length = 1092
Score = 26.2 bits (58), Expect = 5.7
Identities = 13/37 (35%), Positives = 14/37 (37%), Gaps = 6/37 (16%)
Query: 16 DALTHLLNYVWPNIFETSPHLVQAFMDAVE-GLRVAL 51
DALTHL N FE L + R AL
Sbjct: 668 DALTHLANRAS---FEK--QLRRLLQTVNSTHQRHAL 699
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 25.8 bits (57), Expect = 6.1
Identities = 11/19 (57%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 14 CEDALTHLLNYVWP-NIFE 31
+DAL LL Y WP NI E
Sbjct: 510 DDDALARLLAYRWPGNIRE 528
>gnl|CDD|222959 PHA02999, PHA02999, Hypothetical protein; Provisional.
Length = 382
Score = 25.9 bits (57), Expect = 6.5
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 21 LLNYVWPNIFETSPHLVQAFMDAVEGLRV 49
L+NY++PN+FE + + ++G V
Sbjct: 182 LMNYMFPNLFEDDKRHIFYRCNPMKGYCV 210
>gnl|CDD|176123 cd08432, PBP2_GcdR_TrpI_HvrB_AmpR_like, The C-terminal substrate
domain of LysR-type GcdR, TrPI, HvR and beta-lactamase
regulators, and that of other closely related homologs;
contains the type 2 periplasmic binding fold. This CD
includes the C-terminal substrate domain of LysR-type
transcriptional regulators involved in controlling the
expression of glutaryl-CoA dehydrogenase (GcdH),
S-adenosyl-L-homocysteine hydrolase, cell division
protein FtsW, tryptophan synthase, and beta-lactamase.
The structural topology of this substrate-binding domain
is most similar to that of the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 194
Score = 25.2 bits (56), Expect = 7.2
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 30 FETSPHLVQAFMDAVEGLRVALGP 53
F+ S +QA AV GL VAL P
Sbjct: 126 FDDSSLALQA---AVAGLGVALAP 146
>gnl|CDD|164918 PHA02456, PHA02456, zinc metallopeptidase motif-containing
protein.
Length = 141
Score = 25.3 bits (55), Expect = 7.4
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 13 GCEDALTHLLNYVW 26
GC D L H LN+ W
Sbjct: 78 GCRDTLAHELNHAW 91
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 25.6 bits (56), Expect = 7.7
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 7 SGVYGFGCEDALTHLLNYVWPNIFETSP 34
SGV F E+ L +VW N+F + P
Sbjct: 141 SGVLEFTAEEGSVGLPPHVWSNLFPSDP 168
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 25.3 bits (56), Expect = 8.4
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 16 DALTHLLNYVWPNIFETSPHLVQAFMDAVEGL 47
D+L L FE +P L++ MD + L
Sbjct: 575 DSLRQLTKL---KTFEPAPRLIRVLMDIINAL 603
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 25.6 bits (56), Expect = 8.8
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 78 IYNSLYIGGQDALISAYP--RIQNDMKNV 104
I+ +L GQ L+ + P RIQND N+
Sbjct: 862 IWRTLERNGQVVLLGSAPDPRIQNDFVNL 890
>gnl|CDD|152582 pfam12147, Methyltransf_20, Putative methyltransferase. This
domain is found in bacteria and eukaryotes and is
approximately 110 amino acids in length. It is found in
association with pfam00561. The family shows homology to
methyltransferases.
Length = 311
Score = 25.3 bits (56), Expect = 8.8
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 26 WPNIFETSPHLVQAFMDAVEGLRVALGPVRIL-------QYVLQGLFHPARKVRDVYWKI 78
W I + HL + A+ LR + PVRIL +YVL L ++ + +
Sbjct: 109 WRGIRQRKLHLEELLRYAIARLRASGRPVRILDIAAGHGRYVLDALAKAPQRPDSILLRD 168
Query: 79 YNSLYIGGQDALISA 93
Y+ L + ALI+
Sbjct: 169 YSPLNVEQGRALIAE 183
>gnl|CDD|226233 COG3710, CadC, DNA-binding winged-HTH domains [Transcription].
Length = 148
Score = 25.0 bits (55), Expect = 10.0
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 4/38 (10%)
Query: 21 LLNYVWPNIFETSPHLVQAFMDAVEGLRVALGPVRILQ 58
LL+ VWP T L Q A+ LR AL +
Sbjct: 56 LLDAVWPGRIVTVNTLTQ----AISALRRALRDIGDGH 89
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 0.145 0.460
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,905,521
Number of extensions: 512959
Number of successful extensions: 577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 577
Number of HSP's successfully gapped: 29
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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 (21.7 bits)
S2: 53 (24.1 bits)