RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12287
(76 letters)
>gnl|CDD|205991 pfam13820, Nucleic_acid_bd, Putative nucleic acid-binding region.
This is a family of putative nucleic acid-binding
proteins. Several members are annotated as being
nuclear receptor coactivator 6 proteins but this could
not be confirmed.
Length = 149
Score = 72.5 bits (178), Expect = 4e-18
Identities = 34/50 (68%), Positives = 38/50 (76%)
Query: 20 RKVEPWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDELI 69
RKVEPW SVRVTF+IP+EAA RLR LA + L LGILSVQ+EGD I
Sbjct: 40 RKVEPWKSVRVTFSIPREAAARLRNLADHSDPRLRDLGILSVQIEGDNPI 89
>gnl|CDD|220992 pfam11130, TraC_F_IV, F pilus assembly Type-IV secretion system for
plasmid transfer. This family of TraC proteins is
conserved in Proteobacteria. TraC is a cytoplasmic,
peripheral membrane protein and is one of the proteins
encoded by the F transfer region of the conjugative
plasmid that is required for the assembly of F pilin
into the mature F pilus structure. F pili are
filamentous appendages that help establish the physical
contact between donor and recipient cells involved in
the conjugation process.
Length = 236
Score = 34.6 bits (80), Expect = 0.002
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 1 MKYLYK-VCFNLGGTEGINLRKVEPWNSVRVTFTIPK-EAAVRLRQLAQQGNATLLQLGI 58
+ + LG + LR SV+V ++P E L +L ++ A+L G+
Sbjct: 101 ADFHLRGASKPLGDEDVTQLRDFRLVISVKVPKSLPSEEPIEELNELRERLEASLASAGL 160
Query: 59 LSVQVEGDELI 69
+ +++ ++LI
Sbjct: 161 AARRLDPEDLI 171
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 32.2 bits (73), Expect = 0.012
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQV 63
R F+I A LR A++ TL L + + V
Sbjct: 272 RYEFSIDPALAEALRGTARRQGLTLFMLLLGAFNV 306
>gnl|CDD|224709 COG1796, POL4, DNA polymerase IV (family X) [DNA replication,
recombination, and repair].
Length = 326
Score = 29.2 bits (66), Expect = 0.15
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 19 LRKVEP--WNSVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDELI 69
R V P + + FT KE +++RQLA+ L + G+ E+I
Sbjct: 246 FRVVPPEAFGAALQHFTGSKEHNIKIRQLAKAKGEKLSEYGLFRD---SGEII 295
>gnl|CDD|237108 PRK12467, PRK12467, peptide synthase; Provisional.
Length = 3956
Score = 29.0 bits (65), Expect = 0.18
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQ 62
R+ F +P A LR LA++ TL L + S Q
Sbjct: 1337 RLAFELPPALAEGLRALARREGVTLFMLLLASFQ 1370
Score = 26.7 bits (59), Expect = 1.4
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQV 63
R+ +P+ + L+ LAQ+ TL + + S Q
Sbjct: 272 RLRVDLPQALSAGLKALAQREGVTLFMVLLASFQT 306
>gnl|CDD|237036 PRK12284, PRK12284, tryptophanyl-tRNA synthetase; Reviewed.
Length = 431
Score = 27.7 bits (62), Expect = 0.46
Identities = 12/43 (27%), Positives = 18/43 (41%)
Query: 32 FTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDELILTLHQ 74
F PK+A + +L Q G A LLQ+ + + L
Sbjct: 382 FASPKDAGQVIARLQQGGAADLLQVADSPQFADAAAVDAALEA 424
>gnl|CDD|179902 PRK04965, PRK04965, NADH:flavorubredoxin oxidoreductase;
Provisional.
Length = 377
Score = 26.0 bits (58), Expect = 1.6
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 34 IPKEAAVRL-RQLAQQGNATLLQLGILSVQVEGDELILTLH 73
+P E + RL +L + G LL+ + ++ + TL
Sbjct: 181 MPPEVSSRLQHRLTEMGVHLLLKSQLQGLEKTDSGIRATLD 221
>gnl|CDD|182645 PRK10682, PRK10682, putrescine transporter subunit:
periplasmic-binding component of ABC superfamily;
Provisional.
Length = 370
Score = 26.0 bits (57), Expect = 2.2
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 20 RKVEPWNSVRVTFTIPKEAAV 40
R E N V V+++IPKE A+
Sbjct: 254 RAKEAKNGVNVSYSIPKEGAL 274
>gnl|CDD|107325 cd06330, PBP1_Arsenic_SBP_like, Periplasmic solute-binding domain
of active transport proteins. Periplasmic
solute-binding domain of active transport proteins
found in bacteria and Archaea that is predicted to be
involved in the efflux of toxic compounds. Members of
this subgroup include proteins from Herminiimonas
arsenicoxydans, which is resistant to arsenic and
various heavy metals such as cadmium and zinc.
Moreover, they show significant sequence similarity to
the cluster of AmiC and active transport systems for
short-chain amides and urea (FmdDEF), and thus are
likely to exhibit a ligand-binding mode similar to that
of the amide sensor protein AmiC from Pseudomonas
aeruginosa.
Length = 346
Score = 25.7 bits (57), Expect = 2.6
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 16 GINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILS 60
GI RK+E VR P EA R+L + +L I S
Sbjct: 35 GIGGRKIEL--VVRDEAGKPDEAIREARELVENEGVDMLIGLISS 77
>gnl|CDD|224896 COG1985, RibD, Pyrimidine reductase, riboflavin biosynthesis
[Coenzyme metabolism].
Length = 218
Score = 25.3 bits (56), Expect = 2.9
Identities = 18/70 (25%), Positives = 26/70 (37%), Gaps = 18/70 (25%)
Query: 21 KVEPWNSVRVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEG--------------D 66
K+ V + + V L L ++ L + GI SV VEG D
Sbjct: 110 KLRELKEAGVEVILLPDGRVDLAALLEE----LAERGINSVLVEGGATLNGSFLEAGLVD 165
Query: 67 ELILTLHQAI 76
EL+L + I
Sbjct: 166 ELLLYIAPKI 175
>gnl|CDD|236827 PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase;
Provisional.
Length = 741
Score = 25.3 bits (56), Expect = 3.0
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 41 RLRQLAQQGNATLLQLGILSVQVEGD 66
LR A+Q + L LGI V + GD
Sbjct: 568 TLRADARQAISELKALGIKGVMLTGD 593
>gnl|CDD|199821 cd10496, MH2_I-SMAD, C-terminal Mad Homology 2 (MH2) domain in
Inhibitory SMADs. The MH2 domain is located at the
C-terminus of the SMAD (small mothers against
decapentaplegic) family of proteins, which are signal
transducers and transcriptional modulators that mediate
multiple signaling pathways. The MH2 domain is
responsible for type I receptor interaction,
phosphorylation-triggered homo- and
hetero-oligomerization, and transactivation. It is
negatively regulated by the N-terminal MH1 domain,
which prevents it from forming a complex with SMAD4.
SMAD6 and SMAD7 are inhibitory SMADs (I-SMADs) that
function as negative regulators of signaling mediated
by the TGF-beta superfamily. SMAD6 specifically
inhibits bone morphogenetic protein (BMP) type I
receptor mediated signaling, while SMAD7 enhances
muscle differentiation and is often associated with
cancer, tissue fibrosis and inflammatory diseases.
Length = 165
Score = 25.0 bits (55), Expect = 3.5
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 26 NSVRVTFTIPKEAAVRLRQLAQQGNAT 52
+V + +PK L L +QGNA+
Sbjct: 22 PAVNIFDDLPKGDGFCLGALNRQGNAS 48
>gnl|CDD|234903 PRK01115, PRK01115, DNA polymerase sliding clamp; Validated.
Length = 247
Score = 24.8 bits (55), Expect = 4.2
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 15 EGINLRKVEPWNSVRVTFTIPKEA 38
+GI LR ++P V +PKEA
Sbjct: 33 DGIRLRALDPAKVAMVDLELPKEA 56
>gnl|CDD|226200 COG3675, COG3675, Predicted lipase [Lipid metabolism].
Length = 332
Score = 24.9 bits (54), Expect = 4.4
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 10 NLGGTEGINL-RKVEPWNSVRVTFTIPKEAAVRLRQLAQQGNAT 52
+ G RK +++ VTF P R Q +G A
Sbjct: 187 AIICVRGTYFERKYPRVDNLVVTFGQPAITDWRFPQYVHEGFAH 230
>gnl|CDD|204996 pfam12651, RHH_3, Ribbon-helix-helix domain. This short
bacterial protein contains a ribbon-helix-helix domain
that is likely to be DNA-binding.
Length = 44
Score = 23.3 bits (51), Expect = 5.6
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 26 NSVRVTFTIPKEAAVRLRQLAQQ 48
N R + +I KE +L++L+++
Sbjct: 1 NRTRFSTSIDKELLEKLKELSEE 23
>gnl|CDD|234921 PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase II;
Provisional.
Length = 724
Score = 24.7 bits (55), Expect = 6.0
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 4/48 (8%)
Query: 29 RVTFTIPKEAAVRLRQLAQQGNATLLQLGILSVQVEGDELILTLHQAI 76
R ++P E LA+ ++G V GD L + +
Sbjct: 662 RYVVSVPPENEEAFEALAEAAGVPATRIG----VVGGDALKVKGNDTE 705
>gnl|CDD|234045 TIGR02876, spore_yqfD, sporulation protein YqfD. YqfD is part of
the sigma-E regulon in the sporulation program of
endospore-forming Gram-positive bacteria. Mutation
results in a sporulation defect in Bacillus subtilis.
Members are found in all currently known
endospore-forming bacteria, including the genera
Bacillus, Symbiobacterium, Carboxydothermus,
Clostridium, and Thermoanaerobacter [Cellular
processes, Sporulation and germination].
Length = 382
Score = 24.6 bits (54), Expect = 6.6
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 9 FNLGGTEGINLRKVEPWNSVRVTFTIPKEAAVRLRQLAQQGN 50
NL GI + V+ N+ +TF + + +L+ +A++
Sbjct: 22 LNLCWRNGILVWDVKKINAETLTFKVSLKDFKKLKPIARKTG 63
>gnl|CDD|236311 PRK08609, PRK08609, hypothetical protein; Provisional.
Length = 570
Score = 24.1 bits (53), Expect = 7.6
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 32 FTIPKEAAVRLRQLAQQ 48
FT K+ VR+RQLA++
Sbjct: 256 FTGSKDHNVRMRQLAKE 272
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
0.322 0.138 0.396
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,762,357
Number of extensions: 289389
Number of successful extensions: 338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 23
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.4 bits)