RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9603
(150 letters)
>gnl|CDD|220625 pfam10191, COG7, Golgi complex component 7 (COG7). COG7 is a
component of the conserved oligomeric Golgi complex
which is required for normal Golgi morphology and
localisation. Mutation in COG7 causes a congenital
disorder of glycosylation.
Length = 768
Score = 32.8 bits (75), Expect = 0.048
Identities = 9/47 (19%), Positives = 25/47 (53%)
Query: 16 IKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKEDI 62
+++ +++E +M + D+ +++ + +KE M +K+DI
Sbjct: 47 VQQVNYALEESSGQALQNMPRVLRDVEALRQEASFLKEQMILVKQDI 93
Score = 30.1 bits (68), Expect = 0.45
Identities = 10/52 (19%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 1 MIKEDMGSIKEDMASIKEDMVSIKED----MASIKVDMGSIKEDMGSIKDDM 48
++++ +KE M +K+D+ ++D M + + ++K+ M + K+ +
Sbjct: 74 ALRQEASFLKEQMILVKQDIKKFEQDTGQSMQVL-ERLDTVKQRMQAAKESL 124
>gnl|CDD|201451 pfam00804, Syntaxin, Syntaxin. Syntaxins are the prototype
family of SNARE proteins. They usually consist of three
main regions - a C-terminal transmembrane region, a
central SNARE domain which is characteristic of and
conserved in all syntaxins (pfam05739), and an
N-terminal domain that is featured in this entry. This
domain varies between syntaxin isoforms; in syntaxin 1A
it is found as three alpha-helices with a left-handed
twist. It may fold back on the SNARE domain to allow
the molecule to adopt a 'closed' configuration that
prevents formation of the core fusion complex - it thus
has an auto-inhibitory role. The function of syntaxins
is determined by their localisation. They are involved
in neuronal exocytosis, ER-Golgi transport and
Golgi-endosome transport, for example. They also
interact with other proteins as well as those involved
in SNARE complexes. These include vesicle coat
proteins, Rab GTPases, and tethering factors.
Length = 103
Score = 31.2 bits (71), Expect = 0.060
Identities = 14/75 (18%), Positives = 33/75 (44%)
Query: 2 IKEDMGSIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKED 61
I+E++ I++++ +++ I S K ++E IK +IK+ + S+++
Sbjct: 12 IREEIQKIRQNLEELQKLHKRILTAPDSDKELREELEELTQEIKQLARAIKKKLKSLQQL 71
Query: 62 IGGYGVDKRGYGVDK 76
VD+
Sbjct: 72 NKSEQGLGHSSAVDR 86
>gnl|CDD|217485 pfam03310, Cauli_DNA-bind, Caulimovirus DNA-binding protein.
Length = 121
Score = 31.5 bits (71), Expect = 0.074
Identities = 11/51 (21%), Positives = 25/51 (49%)
Query: 13 MASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKEDIG 63
+A+I ++ + + ++ +I E GS K + ++E A I +D+
Sbjct: 1 LAAILSEIRELIQSQKKTANEIKAILERNGSGKPESTGLEEVAAKIIKDLT 51
>gnl|CDD|218704 pfam05701, DUF827, Plant protein of unknown function (DUF827).
This family consists of several plant proteins of
unknown function. Several sequences in this family are
described as being "myosin heavy chain-like".
Length = 484
Score = 28.0 bits (62), Expect = 1.9
Identities = 10/62 (16%), Positives = 30/62 (48%)
Query: 2 IKEDMGSIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKED 61
I + S+ +++ K ++ E+ S++ + S+K+++ K ++ ++E +E
Sbjct: 250 IMASVASVLKELEEAKANLEKAAEEEKSLRNLVESLKQELEEEKKELEELREKEGEAEEA 309
Query: 62 IG 63
Sbjct: 310 AS 311
Score = 26.9 bits (59), Expect = 5.4
Identities = 10/58 (17%), Positives = 30/58 (51%)
Query: 3 KEDMGSIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKE 60
K ++ E+ S++ + S+K+++ K ++ ++E G ++ S++ ++ K
Sbjct: 265 KANLEKAAEEEKSLRNLVESLKQELEEEKKELEELREKEGEAEEAASSLEAELNRTKS 322
>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566). Family of
related proteins that is plant specific.
Length = 313
Score = 27.6 bits (61), Expect = 2.7
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 31 KVDMGSIKEDMGSIKDDMGSIKEDMAS 57
K DM S+KE + S D M + M S
Sbjct: 260 KADMQSLKEAVSSAVDVM----QAMGS 282
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.7 bits (62), Expect = 3.1
Identities = 7/61 (11%), Positives = 30/61 (49%)
Query: 2 IKEDMGSIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKED 61
+ E++ + +A I+ + ++E+ +++ + + + D+ ++++ +KE+
Sbjct: 418 LSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEE 477
Query: 62 I 62
Sbjct: 478 Y 478
Score = 27.3 bits (61), Expect = 3.5
Identities = 5/61 (8%), Positives = 28/61 (45%)
Query: 2 IKEDMGSIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKED 61
+ + I+ + ++E+ ++ + + + D+ + ++ +KE+ ++++
Sbjct: 425 LNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLAADLSKYEQELYDLKEEYDRVEKE 484
Query: 62 I 62
+
Sbjct: 485 L 485
>gnl|CDD|220664 pfam10267, Tmemb_cc2, Predicted transmembrane and coiled-coil 2
protein. This family of transmembrane coiled-coil
containing proteins is conserved from worms to humans.
Its function is unknown.
Length = 387
Score = 27.5 bits (61), Expect = 3.2
Identities = 6/26 (23%), Positives = 14/26 (53%)
Query: 37 IKEDMGSIKDDMGSIKEDMASIKEDI 62
+ E++ IK+ ++E +KE +
Sbjct: 210 LLEELREIKEGQSRLEESYERLKEQL 235
Score = 27.1 bits (60), Expect = 4.5
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 1 MIKEDMGSIKEDMASIKEDMVSIKED 26
+ E++ IKE + ++E +KE
Sbjct: 209 KLLEELREIKEGQSRLEESYERLKEQ 234
>gnl|CDD|206779 cd11386, MCP_signal, Methyl-accepting chemotaxis protein (MCP),
signaling domain. Methyl-accepting chemotaxis proteins
(MCPs or chemotaxis receptors) are an integral part of
the transmembrane protein complex that controls
bacterial chemotaxis, together with the histidine kinase
CheA, the receptor-coupling protein CheW,
receptor-modification enzymes, and localized
phosphatases. MCPs contain a four helix trans membrane
region, an N-terminal periplasmic ligand binding domain,
and a C-terminal HAMP domain followed by a cytoplasmic
signaling domain. This C-terminal signaling domain
dimerizes into a four-helix bundle and interacts with
CheA through the adaptor protein CheW.
Length = 200
Score = 27.2 bits (61), Expect = 3.4
Identities = 9/61 (14%), Positives = 19/61 (31%)
Query: 2 IKEDMGSIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKED 61
I+E + I+E E M E++ + I + + + + I
Sbjct: 122 IEELIEEIQEQTEEAVEAMEETSEEVEEGVELVEETGRAFEEIVASVEEVADGIQEISAA 181
Query: 62 I 62
Sbjct: 182 T 182
>gnl|CDD|131187 TIGR02132, phaR_Bmeg, polyhydroxyalkanoic acid synthase, PhaR
subunit. This model describes a protein, PhaR,
localized to polyhydroxyalkanoic acid (PHA) inclusion
granules in Bacillus cereus and related species. PhaR is
required for PHA biosynthesis along with PhaC and may be
a regulatory subunit.
Length = 189
Score = 26.7 bits (58), Expect = 4.2
Identities = 11/53 (20%), Positives = 33/53 (62%)
Query: 10 KEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKEDI 62
KED+A++ +++++E + I+ +++ + ++ ++K+D+ +K+DI
Sbjct: 71 KEDIANVASLVINLEEKVDLIEEFFDDKFDELEAQQEQAPALKKDVTKLKQDI 123
>gnl|CDD|213980 TIGR04367, HpnR_B12_rSAM, hopanoid C-3 methylase HpnR. Members of
this are family are a B12-binding domain/radical SAM
domain protein required for 3-methylhopanoid production.
Activity was confirmed by mutant phenotype by disrupting
this gene in Methylococcus capsulatus strain Bath. This
protein family should only occur in genomes that encode
a squalene-hopene cyclase (see TIGR01507) [Fatty acid
and phospholipid metabolism, Biosynthesis].
Length = 490
Score = 27.0 bits (60), Expect = 5.0
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 9 IKEDMASIKEDMVSIKEDMASIKVDMG 35
E++A I+E + I +D+A I + G
Sbjct: 220 AGEELARIREPGIFIVDDVAFIHAEHG 246
>gnl|CDD|216919 pfam02181, FH2, Formin Homology 2 Domain.
Length = 372
Score = 26.1 bits (58), Expect = 8.3
Identities = 6/44 (13%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 18 EDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKED 61
++ +++ A+ KVD+ +++D+ ++ + ++ ++ D
Sbjct: 265 SELSHVEK--AA-KVDLEQLEKDVKELEKGLKKLERELELSALD 305
>gnl|CDD|163494 TIGR03782, Bac_Flav_CT_J, Bacteroides conjugative transposon TraJ
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the
Bacteroides lineage. This family is related conjugation
system proteins in the Proteobacteria, including TrbL
of Agrobacterium Ti plasmids and VirB6 [Cellular
processes, DNA transformation].
Length = 322
Score = 26.2 bits (58), Expect = 8.4
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 33 DMGSIKEDMGSIKDDMGSIKEDMASIKEDIGGYG 66
D ++ E + S+ D+M + DM + + I G G
Sbjct: 1 DFDNLHEVLRSLYDEMMPLCSDMTGVAKGIAGLG 34
>gnl|CDD|203795 pfam07889, DUF1664, Protein of unknown function (DUF1664). The
members of this family are hypothetical plant proteins
of unknown function. The region featured in this family
is approximately 100 amino acids long.
Length = 125
Score = 25.4 bits (56), Expect = 8.5
Identities = 9/37 (24%), Positives = 22/37 (59%)
Query: 22 SIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASI 58
S ++++ I+ D+ +I ED+ S+ + ++ + SI
Sbjct: 85 STRDEVTEIREDLSNIGEDVKSVHQAVEGLEGKLDSI 121
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 26.0 bits (58), Expect = 8.9
Identities = 8/55 (14%), Positives = 28/55 (50%)
Query: 8 SIKEDMASIKEDMVSIKEDMASIKVDMGSIKEDMGSIKDDMGSIKEDMASIKEDI 62
+++ + S+++ I E +A ++ ++E++ I + I+++ + E +
Sbjct: 352 QLEKQLESLEKQYDEITERIAEQEIAYSELQEELEEILKQLEEIEKEQEKLSEML 406
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
0.313 0.140 0.395
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,944,704
Number of extensions: 789100
Number of successful extensions: 547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 537
Number of HSP's successfully gapped: 47
Length of query: 150
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 62
Effective length of database: 7,034,450
Effective search space: 436135900
Effective search space used: 436135900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.6 bits)