RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17939
(81 letters)
>gnl|CDD|227427 COG5096, COG5096, Vesicle coat complex, various subunits
[Intracellular trafficking and secretion].
Length = 757
Score = 48.6 bits (116), Expect = 2e-08
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 9 IEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTT 68
+E + KI+A+KK+I ++ GE + + +I+ V +D +K+LL ++ E K
Sbjct: 28 LESSNDYKKIDAMKKIIAQMSLGEDMSSLFPDVIKNVA-TRDVELKRLLYLYLERYAKLK 86
Query: 69 PDGKLL 74
P+ LL
Sbjct: 87 PELALL 92
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha,
beta and gamma subunits of the AP-1, AP-2 and AP-3
adaptor protein complexes. The adaptor protein (AP)
complexes are involved in the formation of
clathrin-coated pits and vesicles. The N-terminal
region of the various adaptor proteins (APs) is
constant by comparison to the C-terminal which is
variable within members of the AP-2 family; and it has
been proposed that this constant region interacts with
another uniform component of the coated vesicles.
Length = 522
Score = 47.6 bits (114), Expect = 5e-08
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 11 KGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPD 70
+ D + K EA+KK+I +I GE + + +++ V D +K+L ++ +++ + +PD
Sbjct: 16 RDDPRKKKEAVKKLIYLIMLGEDISFLFFEVVKLVA-SNDFTLKRLGYLYLKLLAEESPD 74
>gnl|CDD|237282 PRK13055, PRK13055, putative lipid kinase; Reviewed.
Length = 334
Score = 25.7 bits (57), Expect = 2.9
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 12 GDTKIKIEALKKVIQMIANGERLP 35
GD + E LK+ I+ AN + +
Sbjct: 282 GDAPMTFENLKQHIEFFANTDEIS 305
>gnl|CDD|181146 PRK07851, PRK07851, acetyl-CoA acetyltransferase; Provisional.
Length = 406
Score = 25.7 bits (57), Expect = 3.0
Identities = 8/14 (57%), Positives = 9/14 (64%), Gaps = 2/14 (14%)
Query: 60 FW--EIVPKTTPDG 71
F+ EI P T PDG
Sbjct: 210 FFEREITPVTLPDG 223
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 24.9 bits (54), Expect = 5.9
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 1 MAPCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIR--FVLPMQDHM 52
+ P + H + + KIK EA + + G P I+ ++ F+ P+ D +
Sbjct: 370 LIPPLIHLLSSAEYKIKKEACWAISNATSGGLNRPDIIRYLVSQGFIKPLCDLL 423
>gnl|CDD|220778 pfam10487, Nup188, Nucleoporin subcomplex protein binding to Pom34.
This is one of the many peptides that make up the
nucleoporin complex (NPC), and is found across
eukaryotes. The Nup188 subcomplex
(Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six
that make up the NPC, and as such is symmetrically
localised on both faces of the NPC at the nuclear end,
being integrally bound to the C-terminus of Pom34p.
Length = 931
Score = 24.8 bits (54), Expect = 5.9
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 40 IIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDG 71
+ +QD+ +K L F+ + ++ DG
Sbjct: 887 FLTDLQSKIQDYRLKVSLYEFFTTLVESKQDG 918
>gnl|CDD|197395 cd10160, CsoR-like_DUF156_3, Uncharacterized family 3; belongs to
a superfamily containing the transcriptional regulators
CsoR (copper-sensitive operon repressor), RcnR, and
FrmR, and related domains; this family was previously
known as part of DUF156. Uncharacterized family 3,
belonging to a larger superfamily that contains various
transcriptional regulators that respond to different
stressors such as Cu(I), Ni(I), sulfite, and
formaldehyde, and includes CsoRs (copper-sensitive
operon repressors). CsoRs form homotetramers (dimer of
dimers). In Mycobacterium tuberculosis CsoR, within
each dimer, two Cys residues on opposite subunits,
along with a His residue, bind the Cu(I) ion (forming a
triagonal S2N coordination complex, C-H-C). These
residues are conserved in the majority of members of
this superfamily, including this family; however, a
conserved Tyr and a Glu residue that facilitate
allosteric regulation of DNA binding for CsoRs are not
conserved.
Length = 85
Score = 24.3 bits (53), Expect = 6.1
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 4 CVSHHIEKGDTKIKIEALKKVIQMIAN 30
CV IE GD IE K I+ +
Sbjct: 58 CVRDGIEHGDADETIEDFSKAIEYFSR 84
>gnl|CDD|216595 pfam01595, DUF21, Domain of unknown function DUF21. This
transmembrane region has no known function. Many of the
sequences in this family are annotated as hemolysins,
however this is due to a similarity to Treponema
hyodysenteriae hemolysin C that does not contain this
domain. This domain is found in the N-terminus of the
proteins adjacent to two intracellular CBS domains
pfam00571.
Length = 182
Score = 24.4 bits (54), Expect = 6.2
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 56 LLLIFWEIVPKT 67
L+L+F EI+PKT
Sbjct: 98 LILVFGEILPKT 109
>gnl|CDD|236760 PRK10792, PRK10792, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 24.5 bits (54), Expect = 6.7
Identities = 8/28 (28%), Positives = 18/28 (64%)
Query: 15 KIKIEALKKVIQMIANGERLPGILMIII 42
+++ E +KV +A G R PG+ ++++
Sbjct: 14 QVRSEVAQKVQARVAAGLRAPGLAVVLV 41
>gnl|CDD|224376 COG1459, PulF, Type II secretory pathway, component PulF [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 397
Score = 24.5 bits (54), Expect = 7.5
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 22 KKVIQMIANGE---RLPGILMIIIRFVLPMQDHMIKKLL 57
++QMIA GE +L +L + F + I KL
Sbjct: 325 PLLLQMIAVGEESGKLDEMLEKVADFYEEEVERKIDKLT 363
>gnl|CDD|197394 cd10159, CsoR-like_DUF156_2, Uncharacterized family 2; belongs to
a superfamily containing transcriptional regulators
CsoR (copper-sensitive operon repressor), RcnR, and
FrmR, and related domains; this family was previously
known as part of DUF156. Uncharacterized family 2,
belonging to a larger superfamily that contains various
transcriptional regulators that respond to different
stressors such as Cu(I), Ni(I), sulfite, and
formaldehyde, and includes CsoRs (copper-sensitive
operon repressors). CsoRs form homotetramers (dimer of
dimers). In Mycobacterium tuberculosis CsoR, within
each dimer, two Cys residues on opposite subunits,
along with a His residue, bind the Cu(I) ion (forming a
triagonal S2N coordination complex, C-H-C). These
residues are conserved in the majority of members of
this superfamily, including this family, and a
conserved Tyr and a Glu residue that facilitate
allosteric regulation of DNA binding for CsoRs are also
conserved.
Length = 82
Score = 23.7 bits (52), Expect = 8.3
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 1 MAPCVSHHIEKGDTKIKIEALKKVI 25
M CV +E D + KIE + +++
Sbjct: 55 MKHCVKEAVESEDAEEKIEEIIELL 79
>gnl|CDD|151672 pfam11230, DUF3029, Protein of unknown function (DUF3029). Some
members in this family of proteins are annotated as
ykkI. Currently no function is known.
Length = 487
Score = 24.2 bits (53), Expect = 10.0
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 40 IIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDG 71
++ FV + + I + L F + +T PD
Sbjct: 105 LLEPFVGGLDEEEIYRKLKRFLIHLDRTLPDA 136
>gnl|CDD|234741 PRK00380, panC, pantoate--beta-alanine ligase; Reviewed.
Length = 281
Score = 23.9 bits (53), Expect = 10.0
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 20 ALKKVIQMIANGERLPGILMIIIRFVL 46
AL+ + IA GER P L+ R L
Sbjct: 205 ALRAAAEAIAAGERDPAALLAAARATL 231
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
0.327 0.143 0.431
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,215,170
Number of extensions: 349242
Number of successful extensions: 487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 485
Number of HSP's successfully gapped: 19
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (24.2 bits)