RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17120
(137 letters)
>gnl|CDD|238014 cd00057, FA58C, Coagulation factor 5/8 C-terminal domain, discoidin
domain; Cell surface-attached carbohydrate-binding
domain, present in eukaryotes and assumed to have
horizontally transferred to eubacterial genomes.
Length = 143
Score = 43.5 bits (103), Expect = 3e-06
Identities = 34/134 (25%), Positives = 53/134 (39%), Gaps = 34/134 (25%)
Query: 4 GALGLENGVIPDKDISASSAHDSSSVGPQFGSSYIFQISCIKRHNLIESLFLIHSRLRHD 63
LG+E+G + D I+ASS+ SS +RL
Sbjct: 1 EPLGMESG-LADDQITASSS-YSSGWEAS------------------------RARL--- 31
Query: 64 KNGGAWCPKHMVGNDGHEYIEVNLHDLHIVTGVQLQGRFGNGLGQEYAEEIVVDFWRPGF 123
+ AW P ND ++++V+L VTG+Q QGR G E+ V + G
Sbjct: 32 NSDNAWTPA---VNDPPQWLQVDLGKTRRVTGIQTQGRK-GGGSSEWVTSYKVQYSLDG- 86
Query: 124 TKWRRWKGRNGKEV 137
W +K + ++V
Sbjct: 87 ETWTTYKDKGEEKV 100
>gnl|CDD|214572 smart00231, FA58C, Coagulation factor 5/8 C-terminal domain,
discoidin domain. Cell surface-attached
carbohydrate-binding domain, present in eukaryotes and
assumed to have horizontally transferred to eubacterial
genomes.
Length = 139
Score = 40.2 bits (94), Expect = 5e-05
Identities = 27/80 (33%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 57 HSRLRHDKNGGAWCPKHMVGNDGHEYIEVNLHDLHIVTGVQLQGRFGNGLGQEYAEEIVV 116
+RL + + G WCP ND +I+V+L L VTGV R GNG Y E
Sbjct: 25 IARL-NGGSDGGWCPA---KNDLPPWIQVDLGRLRTVTGVITGRRHGNGDWVTYKLE-YS 79
Query: 117 DFWRPGFTKWRRWKGRNGKE 136
D W +K N K
Sbjct: 80 DDGVN----WTTYKDGNSKV 95
>gnl|CDD|216100 pfam00754, F5_F8_type_C, F5/8 type C domain. This domain is also
known as the discoidin (DS) domain family.
Length = 128
Score = 36.7 bits (85), Expect = 8e-04
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 58 SRLRHDKNGGAWCPKHMVGNDGHEYIEVNLHDLHIVTGVQLQGR--FGNGLGQEY 110
+ AW K D ++++V+L +TGV QGR GNG + Y
Sbjct: 17 AAAIDGNGSTAWSSKW---GDAPQWLQVDLGKPKKITGVVTQGRQDGGNGYVKSY 68
>gnl|CDD|205399 pfam13218, DUF4026, Protein of unknown function (DUF4026). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 450 amino acids in length.
The family is found in association with pfam10077.
Length = 323
Score = 28.6 bits (64), Expect = 1.1
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 8/47 (17%)
Query: 25 DSSSVGPQFGSSYI-FQISCIKRHNL---IESLFLIHSRLRHDKNGG 67
D S+ G F ++ FQ+ +L IESL++IH+ D+NG
Sbjct: 128 DISAAGKVFTREWLNFQLE----DDLMPDIESLYVIHAVYDTDENGE 170
>gnl|CDD|189017 cd09610, M3B_PepF_5, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 472
Score = 28.4 bits (64), Expect = 1.4
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 56 IHSRLRHDKNGGAWCPKHMVGNDGHEYIEVN 86
I + R K GGA+C H V H Y+ +N
Sbjct: 234 IDAPPRPGKRGGAFC--HPVTPSAHPYVLLN 262
>gnl|CDD|225959 COG3425, PksG, 3-hydroxy-3-methylglutaryl CoA synthase [Lipid
metabolism].
Length = 377
Score = 28.0 bits (63), Expect = 1.6
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 115 VVDFWRPGFTKWRRWKGR 132
DFWRP + GR
Sbjct: 184 TPDFWRPDGQPYPYVDGR 201
>gnl|CDD|226225 COG3702, VirB3, Type IV secretory pathway, VirB3 components
[Intracellular trafficking and secretion].
Length = 105
Score = 27.0 bits (60), Expect = 2.0
Identities = 7/32 (21%), Positives = 11/32 (34%)
Query: 38 IFQISCIKRHNLIESLFLIHSRLRHDKNGGAW 69
+ +I + N L S +NG W
Sbjct: 57 VARIIVKRDPNFFSLLLAWLSTTGRSRNGLFW 88
>gnl|CDD|222857 PHA02531, 20, portal vertex protein; Provisional.
Length = 514
Score = 27.7 bits (62), Expect = 2.2
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 15/60 (25%)
Query: 75 VGNDGHEYIEVNLHDLHIVTGVQLQGRFGNGLGQEYAEEI-----VVDFWRPGFTKWRRW 129
V + E + VNL + F + ++ EE ++DF R G+ +RRW
Sbjct: 98 VYEEDDEPVSVNLDNT----------EFSKSIKKKIREEFDYVLNLLDFDRKGYEIFRRW 147
>gnl|CDD|206005 pfam13834, DUF4193, Domain of unknown function (DUF4193). This
domain of unknown function contains four conserved
cysteines and a conserved histidine, including a CXXXXH
motif.
Length = 99
Score = 26.4 bits (59), Expect = 2.8
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 52 SLFLIH--SRLRHDKNGGAWC 70
S FL+H S+L +K+G C
Sbjct: 75 SCFLVHHRSQLAREKDGQPIC 95
>gnl|CDD|172853 PRK14377, PRK14377, hypothetical protein; Provisional.
Length = 104
Score = 26.7 bits (58), Expect = 2.8
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 7/40 (17%)
Query: 28 SVGPQFGSSYIFQISC-------IKRHNLIESLFLIHSRL 60
++ P G+ F +C +K+H L +SLFLI RL
Sbjct: 20 AISPFLGAPCRFFPTCSEYALVALKKHPLRKSLFLIAKRL 59
>gnl|CDD|180526 PRK06315, PRK06315, type III secretion system ATPase; Provisional.
Length = 442
Score = 27.2 bits (60), Expect = 2.8
Identities = 12/25 (48%), Positives = 13/25 (52%)
Query: 90 LHIVTGVQLQGRFGNGLGQEYAEEI 114
LHI G L GR NGLG+ E
Sbjct: 94 LHIRAGNGLLGRVLNGLGEPIDTET 118
>gnl|CDD|114907 pfam06215, ISAV_HA, Infectious salmon anaemia virus haemagglutinin.
This family consists of several infectious salmon
anaemia virus haemagglutinin proteins. Infectious salmon
anaemia virus (ISAV), an orthomyxovirus-like virus, is
an important fish pathogen in marine aquaculture.
Length = 391
Score = 26.9 bits (59), Expect = 3.6
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 75 VGNDGHEYIEVNLHDLHIVTGVQ--LQGRFGNGLGQEYAEEIVVDFWRPGFTKWR 127
+G+ + VN L +VT + LQ + GNGL ++ + D++ P TK+R
Sbjct: 29 IGDSRSDQSRVNPQSLDLVTEFKGVLQAKNGNGLLKQMSGRFPSDWYTPT-TKYR 82
>gnl|CDD|176219 cd08258, Zn_ADH4, Alcohol dehydrogenases of the MDR family. This
group shares the zinc coordination sites of the
zinc-dependent alcohol dehydrogenases. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of an
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 306
Score = 26.5 bits (59), Expect = 4.3
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 89 DLHIVTGVQLQGRFGNGLGQEYAEEIV-----VDFWRPG 122
DLHI G LG E++ IV V+ W+ G
Sbjct: 42 DLHIYKGDYDPVETPVVLGHEFSGTIVEVGPDVEGWKVG 80
>gnl|CDD|172861 PRK14385, PRK14385, hypothetical protein; Provisional.
Length = 96
Score = 25.6 bits (56), Expect = 4.8
Identities = 9/35 (25%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 33 FGSSYIFQ-------ISCIKRHNLIESLFLIHSRL 60
G I++ + C+K++N++ +L LI R+
Sbjct: 29 VGFQCIYKPSCSNYALECLKKYNILTALILITLRI 63
>gnl|CDD|176036 cd08390, C2A_Synaptotagmin-15-17, C2A domain first repeat present
in Synaptotagmins 15 and 17. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. It is thought to be involved in
the trafficking and exocytosis of secretory vesicles in
non-neuronal tissues and is Ca2+ independent. Human
synaptotagmin 15 has 2 alternatively spliced forms that
encode proteins with different C-termini. The larger,
SYT15a, contains a N-terminal TM region, a putative
fatty-acylation site, and 2 tandem C terminal C2
domains. The smaller, SYT15b, lacks the C-terminal
portion of the second C2 domain. Unlike most other
synaptotagmins it is nearly absent in the brain and
rather is found in the heart, lungs, skeletal muscle,
and testis. Synaptotagmin 17 is located in the brain,
kidney, and prostate and is thought to be a peripheral
membrane protein. Previously all synaptotagmins were
thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the first C2
repeat, C2A, and has a type-I topology.
Length = 123
Score = 25.7 bits (57), Expect = 5.6
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 31 PQFGSSYIFQIS--CIKRHNLIESLFLIHSRLRHDKNGGAWCP 71
P F +++FQ+S ++R L S++ + RH G P
Sbjct: 63 PNFDETFVFQVSFKELQRRTLRLSVYDVDRFSRHCIIGHVLFP 105
>gnl|CDD|236417 PRK09224, PRK09224, threonine dehydratase; Reviewed.
Length = 504
Score = 25.9 bits (58), Expect = 7.5
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 91 HIVTGVQLQGRFGNGLGQEYAEEIVVDFWRPGF 123
HI GVQL GQE EI+ G+
Sbjct: 368 HIFVGVQLSR------GQEERAEIIAQLRAHGY 394
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 25.8 bits (56), Expect = 8.6
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 37 YIFQISCIKRHNLIESLFLIHSRLRHDKNGGAW 69
Y+F I I R NL + + + HDK G W
Sbjct: 274 YVFIIDEINRANLSKVFGEVMMLMEHDKRGENW 306
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
0.320 0.140 0.457
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,104,806
Number of extensions: 609209
Number of successful extensions: 477
Number of sequences better than 10.0: 1
Number of HSP's gapped: 476
Number of HSP's successfully gapped: 23
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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 (21.8 bits)
S2: 54 (24.8 bits)