RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10374
(65 letters)
>gnl|CDD|185656 PTZ00478, PTZ00478, Sec superfamily; Provisional.
Length = 81
Score = 79.0 bits (195), Expect = 1e-21
Identities = 30/50 (60%), Positives = 41/50 (82%)
Query: 9 NSIRLVKRCTKPDRREFQKIAIATAIGFSIMGFIGFFVKLIHIPINNIIV 58
+S RL+++CTKPD +E+ IA A ++GF IMGFIG+ +KL+ IPINNIIV
Sbjct: 29 DSRRLIRKCTKPDAKEYTNIAYACSVGFFIMGFIGYSIKLVFIPINNIIV 78
>gnl|CDD|225292 COG2443, Sss1, Preprotein translocase subunit Sss1 [Intracellular
trafficking and secretion].
Length = 65
Score = 55.4 bits (134), Expect = 2e-12
Identities = 23/46 (50%), Positives = 30/46 (65%)
Query: 12 RLVKRCTKPDRREFQKIAIATAIGFSIMGFIGFFVKLIHIPINNII 57
R++K KPD E+ KIA T +G ++G IGF + LI IPIN II
Sbjct: 20 RVLKVARKPDWEEYSKIAKITGLGILLIGIIGFIIYLIMIPINGII 65
>gnl|CDD|232921 TIGR00327, secE_euk_arch, protein translocase SEC61 complex gamma
subunit, archaeal and eukaryotic. This model describes
archaeal SEC61-like and eukaryotic SEC61 but not
bacterial secE proteins, for which a Pfam pfam00584
(SecE) has been created [Protein fate, Protein and
peptide secretion and trafficking].
Length = 61
Score = 50.5 bits (121), Expect = 1e-10
Identities = 20/47 (42%), Positives = 30/47 (63%)
Query: 12 RLVKRCTKPDRREFQKIAIATAIGFSIMGFIGFFVKLIHIPINNIIV 58
R++ C KPD E+ K+A T IG I+G IG+ +K+I IPI ++
Sbjct: 15 RVLAVCKKPDLEEYLKVAKVTGIGIIIVGIIGYIIKIIAIPIRGVLK 61
>gnl|CDD|201325 pfam00584, SecE, SecE/Sec61-gamma subunits of protein
translocation complex. SecE is part of the SecYEG
complex in bacteria which translocates proteins from
the cytoplasm. In eukaryotes the complex, made from
Sec61-gamma and Sec61-alpha translocates protein from
the cytoplasm to the ER. Archaea have a similar
complex.
Length = 56
Score = 44.8 bits (107), Expect = 2e-08
Identities = 10/49 (20%), Positives = 20/49 (40%)
Query: 9 NSIRLVKRCTKPDRREFQKIAIATAIGFSIMGFIGFFVKLIHIPINNII 57
+K+ P R+E K + + +M + V L+ + N+I
Sbjct: 8 EVKAELKKVVWPTRKETLKTTVVVLVFVLVMALFLWLVDLVFGWLVNLI 56
>gnl|CDD|236497 PRK09400, secE, preprotein translocase subunit SecE; Reviewed.
Length = 61
Score = 36.8 bits (86), Expect = 4e-05
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 10 SIRLVKRCTKPDRREFQKIAIATAIGFSIMGFIGFFVKLI 49
R++K KP R EF +A T +G ++G IGF + LI
Sbjct: 17 YKRVLKVARKPTREEFLLVAKVTGLGILLIGLIGFIIYLI 56
>gnl|CDD|165141 PHA02776, PHA02776, E7 protein; Provisional.
Length = 101
Score = 31.2 bits (70), Expect = 0.012
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 8 SNSIRLVKRCTKPDRREFQKIAIAT 32
N++RLV CT+PD +E + + +
Sbjct: 65 DNNVRLVVECTEPDIQELHNLLLGS 89
>gnl|CDD|132261 TIGR03217, 4OH_2_O_val_ald, 4-hydroxy-2-oxovalerate aldolase.
Members of this protein family are
4-hydroxy-2-oxovalerate aldolase, also called
4-hydroxy-2-ketovalerate aldolase and
2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of
the pathway for the meta-cleavage of catechol, produces
pyruvate and acetaldehyde. Acetaldehyde is then
converted by acetaldehyde dehydrogenase (acylating)
(DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are
tightly associated [Energy metabolism, Other].
Length = 333
Score = 28.1 bits (63), Expect = 0.21
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 3 AAHKGSNSIRLVKRCTKPDRREFQKIAIATAIGFSIMGFI 42
A G+ ++R+ CT+ D E Q I +A +G +GF+
Sbjct: 96 AYDAGARTVRVATHCTEADVSE-QHIGMARELGMDTVGFL 134
>gnl|CDD|153352 cd07668, BAR_SNX9, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexin 9. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs
also contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
SNX9, also known as SH3PX1, is a cytosolic protein that
interacts with proteins associated with clathrin-coated
pits such as Cdc-42-associated tyrosine kinase 2
(ACK2). It binds class I polyproline sequences found in
dynamin 1/2 and the WASP/N-WASP actin regulators. SNX9
is localized to plasma membrane endocytic sites and
acts primarily in clathrin-mediated endocytosis. Its
array of interacting partners suggests that SNX9
functions at the interface between endocytosis and
actin cytoskeletal organization. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 210
Score = 27.7 bits (61), Expect = 0.35
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 15 KRCTKPDRREFQKIAIA---TAIGFSIMGFIG 43
KRCT P +E+QKI A A FS G+ G
Sbjct: 40 KRCTGPLPKEYQKIGKALQSLATVFSTSGYQG 71
>gnl|CDD|227397 COG5065, PHO88, Protein involved in inorganic phosphate transport
[Inorganic ion transport and metabolism].
Length = 185
Score = 27.5 bits (61), Expect = 0.40
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 21 DRREFQKIAIATAIGFSIMGFIGFFVKLIH-IPINNIIVLRNSFT 64
D E K + + IGF+IM F+ ++K + + +I LR+ F
Sbjct: 89 DLSELTKASRSAVIGFAIMSFMHLYMKYAQPLFVQSISPLRSLFL 133
>gnl|CDD|215395 PLN02742, PLN02742, Probable galacturonosyltransferase.
Length = 534
Score = 26.3 bits (58), Expect = 0.96
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 19 KPDRREFQKIAIATAIGFSIMGFIGFFVKLIHIPINNIIVLRNS 62
+P RR + GFS++G + F K I + RN
Sbjct: 10 RPVRRRLSQWIWWLLGGFSVLGLVLFVHKHSEIEPRPPLSERNY 53
>gnl|CDD|151029 pfam10456, BAR_3_WASP_bdg, WASP-binding domain of Sorting nexin
protein. The C-terminal region of the Sorting nexin
group of proteins appears to carry a BAR-like
(Bin/amphiphysin/Rvs) domain. This domain is very
diverse and the similarities with other BAR domains are
few. In the Sorting nexins it is associated with family
PX, pfam00787.13, and in combination with PX appears to
be necessary to bind WASP along with p85 to form a
multimeric signalling complex.
Length = 237
Score = 25.1 bits (55), Expect = 2.8
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 13 LVKRCTKPDRREFQKIAIA 31
K+C P ++E+QKI A
Sbjct: 67 FWKKCAGPFKKEYQKIGKA 85
>gnl|CDD|234087 TIGR03013, EpsB_2, sugar transferase, PEP-CTERM system
associated. Members of this protein family belong to
the family of bacterial sugar transferases (pfam02397).
Nearly all are found in species that encode the
PEP-CTERM/exosortase system predicted to act in protein
sorting in a number of Gram-negative bacteria (notable
exceptions appear to include Magnetococcus sp. MC-1 and
Myxococcus xanthus DK 1622 ). These genes are generally
found near one or more of the PrsK, PrsR or PrsT genes
that have been related to the PEP-CTERM system by
phylogenetic profiling methods. The nature of the sugar
transferase reaction catalyzed by members of this clade
is unknown and may conceivably be variable with respect
to substrate by species. These proteins are homologs of
the EpsB protein found in Methylobacillus sp. strain
12S , which is also associated with a PEP-CTERM system,
but of a distinct type. A name which appears attached
to a number of genes (by transitive annotation) in this
family is "undecaprenyl-phosphate galactose
phosphotransferase", which comes from relatively
distant characterized enterobacterial homologs, and is
considerably more specific than warranted from the
currently available evidence.
Length = 442
Score = 25.0 bits (55), Expect = 3.1
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 25 FQKIAIATAIGFSIMGFIGFFVKLIHIPI 53
++AI+ + F + FI +F ++
Sbjct: 65 IARLAISLLVSFLALSFIFYFYPEFYLGR 93
>gnl|CDD|226453 COG3944, COG3944, Capsular polysaccharide biosynthesis protein
[Cell envelope biogenesis, outer membrane].
Length = 226
Score = 23.9 bits (52), Expect = 6.3
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 22 RREFQKIAIATAIGFSIMGFIGFFV 46
+ + I I T + +I + FFV
Sbjct: 15 MKRKKLILIVTILFVAISAIVSFFV 39
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins
encompasses the E. coli WcaJ protein involved in
colanic acid biosynthesis , the Methylobacillus EpsB
protein involved in methanolan biosynthesis , as well
as the GumD protein involved in the biosynthesis of
xanthan. All of these are closely related to the
well-characterized WbaP (formerly RfbP) protein which
is the first enzyme in O-antigen biosynthesis in
Salmonella typhimurium. The enzyme transfers galactose
from UDP-galactose (NOTE: not glucose) to a polyprenyl
carrier (utilizing the highly conserved C-terminal
sugar transferase domain, pfam02397) a reaction which
takes place at the cytoplasmic face of the inner
membrane. The N-terminal hydrophobic domain is then
believed to facilitate the "flippase" function of
transferring the liposaccharide unit from the
cytoplasmic face to the periplasmic face of the inner
membrane. Most of these genes are found within large
operons dedicated to the production of complex
exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 23.7 bits (52), Expect = 9.1
Identities = 8/35 (22%), Positives = 14/35 (40%)
Query: 16 RCTKPDRREFQKIAIATAIGFSIMGFIGFFVKLIH 50
R R +I +A + F I+ + F +K
Sbjct: 55 RRRSRLREMLLRILLAWTLTFLILALLAFLLKYGT 89
>gnl|CDD|218111 pfam04493, Endonuclease_5, Endonuclease V. Endonuclease V is
specific for single-stranded DNA or for duplex DNA that
contains uracil or that is damaged by a variety of
agents.
Length = 205
Score = 23.4 bits (51), Expect = 9.7
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 9 NSIRLVKRCTKPDRREFQKIAIA 31
++++L K+ +K R + A
Sbjct: 179 SALKLAKKLSKGYIRLPEPTRQA 201
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
0.333 0.145 0.428
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,339,058
Number of extensions: 249751
Number of successful extensions: 828
Number of sequences better than 10.0: 1
Number of HSP's gapped: 823
Number of HSP's successfully gapped: 51
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 53 (24.1 bits)