RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15717
(72 letters)
>gnl|CDD|202045 pfam01920, Prefoldin_2, Prefoldin subunit. This family includes
prefoldin subunits that are not detected by pfam02996.
Length = 106
Score = 29.9 bits (68), Expect = 0.044
Identities = 14/54 (25%), Positives = 31/54 (57%)
Query: 10 GEIFVDLIKRNSEKSLEESRQNIKSDIASIEQTMSSIKTVMSDLKTHLYAKFGN 63
G++ V K ++ LEE ++ ++ +I ++E+ + ++ + +LK LY FG
Sbjct: 52 GDVLVKQDKEEVKEELEERKETLEKEIKTLEKQLEKLEKELEELKEELYKLFGQ 105
>gnl|CDD|224300 COG1382, GimC, Prefoldin, chaperonin cofactor [Posttranslational
modification, protein turnover, chaperones].
Length = 119
Score = 26.1 bits (58), Expect = 1.3
Identities = 10/60 (16%), Positives = 28/60 (46%)
Query: 10 GEIFVDLIKRNSEKSLEESRQNIKSDIASIEQTMSSIKTVMSDLKTHLYAKFGNHIKLEA 69
G + V + K + LEE ++ ++ I ++E+ ++ + +L++ + G+
Sbjct: 60 GNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGDAANGGG 119
>gnl|CDD|234348 TIGR03761, ICE_PFL4669, integrating conjugative element protein,
PFL_4669 family. Members of this protein family, such
as PFL4669, are found in integrating conjugative
elements (ICE) of the PFGI-1 class as in Pseudomonas
fluorescens.
Length = 216
Score = 26.1 bits (58), Expect = 1.4
Identities = 4/30 (13%), Positives = 16/30 (53%)
Query: 22 EKSLEESRQNIKSDIASIEQTMSSIKTVMS 51
E+ L +RQ +++ + ++ ++ + +
Sbjct: 66 EEKLLSARQEMQALLQRLDDLLAQLPPALD 95
>gnl|CDD|177069 CHL00149, odpA, pyruvate dehydrogenase E1 component alpha subunit;
Reviewed.
Length = 341
Score = 26.4 bits (58), Expect = 1.4
Identities = 13/40 (32%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 21 SEKSLEESRQNIKSDIA-SIEQTMSSIKTVMSDLKTHLYA 59
S+K L + ++ +K +I +++ +SS + +SDLK +L+A
Sbjct: 301 SQKELNKIQREVKIEIEQAVQFAISSPEPNISDLKKYLFA 340
>gnl|CDD|211364 cd09253, AP-4_Mu4_Cterm, C-terminal domain of medium Mu4 subunit
in adaptor protein (AP) complex AP-4. AP complexes
participate in the formation of intracellular coated
transport vesicles and select cargo molecules for
incorporation into the coated vesicles in the late
secretory and endocytic pathways. There are four AP
complexes, AP-1, AP-2, AP-3, and AP-4, described in
various eukaryotic organisms. Each AP complex consists
of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the
different AP complexes exhibits similarity with each
other. This family corresponds to the C-terminal domain
of heterotetrameric adaptor protein complex 4 (AP-4)
medium mu4 subunit. AP-4 plays a role in
signal-mediated trafficking of integral membrane
proteins in mammalian cells. Unlike other AP complexes,
AP-4 is found only in mammals and plants. It is
believed to be part of a nonclathrin coat, since it
might function independently of clathrin, a scaffolding
protein participating in the formation of coated
vesicles. Recruitment of AP-4 to the trans-Golgi
network (TGN) membrane is regulated by a small GTPase,
ADP-ribosylation factor 1 (ARF1) or a related protein.
Membrane-anchored cargo molecules interact with
adaptors through short sorting signals in their
cytosolic segments. One of the most important sorting
signals binding to mu subunits of AP complexes are
tyrosine-based endocytotic signals, which are of the
form Y-X-X-Phi, where Y is tyrosine, X is any amino
acid and Phi is a bulky hydrophobic residue that can be
Leu, Ile, Met, Phe, or Val. However, AP-4 does not bind
most canonical tyrosine-based signals except for two
naturally occurring ones from the lysosomal membrane
proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E
motif, where X can be any residue, from the cytosolic
tails of amyloid precursor protein (APP) family members
in a distinct way.
Length = 271
Score = 25.6 bits (57), Expect = 2.0
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 2 SRVERNGAGEIFVDLIKR 19
R ++ EIFVD+++R
Sbjct: 3 PRSSQDKKNEIFVDVLER 20
>gnl|CDD|227444 COG5113, UFD2, Ubiquitin fusion degradation protein 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 929
Score = 25.3 bits (55), Expect = 3.2
Identities = 8/36 (22%), Positives = 15/36 (41%)
Query: 15 DLIKRNSEKSLEESRQNIKSDIASIEQTMSSIKTVM 50
D+ R + SRQ ++ S+ T+S +
Sbjct: 226 DVAARALDYLGIRSRQVVEKSRRSLRLTLSDHSDKL 261
>gnl|CDD|150280 pfam09551, Spore_II_R, Stage II sporulation protein R
(spore_II_R). SpoIIR is designated stage II
sporulation protein R. A comparative genome analysis of
all sequenced genomes of Firmicutes shows that the
proteins are strictly conserved among the sub-set of
endospore-forming species. SpoIIR is a signalling
protein that links the activation of sigma E to the
transcriptional activity of sigma F during sporulation.
Length = 132
Score = 24.8 bits (55), Expect = 4.0
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 23 KSLEESRQNIKSDIASIEQT 42
KS+EE+R+ IK ++ IE+
Sbjct: 42 KSIEEARRVIKENLPEIEEI 61
>gnl|CDD|216231 pfam00995, Sec1, Sec1 family.
Length = 554
Score = 24.9 bits (55), Expect = 4.3
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 25 LEESRQNIKSD--IASIEQTMSSIKTVMSDLKTHLYAKFGNHI 65
+E R+ + I I T ++ ++ DLK Y + HI
Sbjct: 34 IENKREPLPDLPAIYFIRPTEENVDRIIDDLKNPKYKSY--HI 74
>gnl|CDD|151965 pfam11528, DUF3224, Protein of unknown function (DUF3224). This
bacterial family of proteins has no known function.
Length = 133
Score = 24.6 bits (54), Expect = 4.3
Identities = 6/28 (21%), Positives = 12/28 (42%)
Query: 17 IKRNSEKSLEESRQNIKSDIASIEQTMS 44
+ + E + E+ K A + +T S
Sbjct: 12 VTKWDESTYAETDGGFKLGRAEVTKTYS 39
>gnl|CDD|236418 PRK09225, PRK09225, threonine synthase; Validated.
Length = 462
Score = 24.7 bits (55), Expect = 4.7
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 1 MSRVERNGAGEIFVDLIKRNSEKSLEESRQNIKSDIASIEQTMSSIKTV 49
M +E G ++ S++ L R++ + S E+T+++I+ V
Sbjct: 334 MEDLEEKGEYDL--------SDEELAALREDFSAGSVSDEETLATIREV 374
>gnl|CDD|169387 PRK08335, PRK08335, translation initiation factor IF-2B subunit
alpha; Validated.
Length = 275
Score = 24.7 bits (54), Expect = 5.3
Identities = 11/45 (24%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 2 SRVERNGAGEIFVDLIKRNSEKSLEESRQNIKSDIASIEQTMSSI 46
S + + GA E ++ L + + LE + + ++ +I + TM+S+
Sbjct: 22 SWLAKKGA-EAYLLLAEELDGEELENALKELREEIPEVNPTMASL 65
>gnl|CDD|131884 TIGR02837, spore_II_R, stage II sporulation protein R. A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is designated stage II
sporulation protein R [Cellular processes, Sporulation
and germination].
Length = 168
Score = 24.3 bits (53), Expect = 5.7
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 23 KSLEESRQNIKSDIASIEQTMSSI 46
KSLEE+R+ I+ ++ IE+ S+
Sbjct: 76 KSLEEARRVIRENLPEIERIAESV 99
>gnl|CDD|182736 PRK10793, PRK10793, D-alanyl-D-alanine carboxypeptidase fraction
A; Provisional.
Length = 403
Score = 24.4 bits (53), Expect = 5.8
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 16 LIKRNSEKSLEESRQNIKSDIASIEQTMSS 45
LI NS K L E +++ D AS+ + M+S
Sbjct: 51 LIDYNSGKVLAEQNADVRRDPASLTKMMTS 80
>gnl|CDD|225531 COG2984, COG2984, ABC-type uncharacterized transport system,
periplasmic component [General function prediction
only].
Length = 322
Score = 24.2 bits (53), Expect = 6.6
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 23 KSLEESRQNIK--SDIASIEQTMSSIKTVMSDLKT 55
KSLE+ N+ SD+ + Q + IK ++ + K+
Sbjct: 127 KSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAKS 161
>gnl|CDD|233228 TIGR00998, 8a0101, efflux pump membrane protein (multidrug
resistance protein A). [Transport and binding proteins,
Other].
Length = 334
Score = 24.4 bits (53), Expect = 7.0
Identities = 8/39 (20%), Positives = 21/39 (53%)
Query: 9 AGEIFVDLIKRNSEKSLEESRQNIKSDIASIEQTMSSIK 47
G++ V L N+E +L ++ N+ + + +Q +++
Sbjct: 66 QGDVLVRLDPTNAELALAKAEANLAALVRQTKQLEITVQ 104
>gnl|CDD|218536 pfam05282, AAR2, AAR2 protein. This family consists of several
eukaryotic AAR2-like proteins. The yeast protein AAR2 is
involved in splicing pre-mRNA of the a1 cistron and
other genes that are important for cell growth.
Length = 339
Score = 24.2 bits (53), Expect = 7.7
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 11 EIFVDLIKRNSEKSLEESRQNIKSDIASIEQTMSSIKTVMSDLKTHLYAKFGNHI 65
+ F D + L +N+ E ++K+ + LK L KFG +
Sbjct: 284 DFFFDTLLSEDN-FLLSLLKNLFEIEVDDELVRGTLKSKLEKLKASLKKKFGWDL 337
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
0.310 0.127 0.324
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,316,318
Number of extensions: 232321
Number of successful extensions: 351
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 39
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
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: 53 (24.2 bits)