RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4516
(115 letters)
>gnl|CDD|219341 pfam07225, NDUF_B4, NADH-ubiquinone oxidoreductase B15 subunit
(NDUFB4). This family consists of several
NADH-ubiquinone oxidoreductase B15 subunit proteins
(EC:1.6.5.3).
Length = 125
Score = 52.5 bits (126), Expect = 6e-10
Identities = 30/83 (36%), Positives = 47/83 (56%), Gaps = 7/83 (8%)
Query: 14 EKKTKMRMALREEFIKQVYNPHRHATGEGGVLFDPAMQRYM-TMSTNRYRYFKPTPKTSW 72
++ +R L+ E++ Q+ +PHR G++ DPA+ R+ + N Y F+PTPKTS
Sbjct: 30 AERLAIRARLKREYLLQLNDPHRK-----GLIEDPALFRWAYARTMNIYPNFRPTPKTSL 84
Query: 73 LGLGLILGPIVATMLYIQKTKDD 95
LGL GP++ Y+ KT D
Sbjct: 85 LGLLFGFGPLI-FWYYVFKTDRD 106
>gnl|CDD|151338 pfam10890, DUF2741, Protein of unknown function (DUF2741). Members
in this family of proteins are annotated as
ubiquinol-cytochrome C reductase however this cannot be
confirmed.
Length = 72
Score = 28.7 bits (64), Expect = 0.20
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 69 KTSWLGLGLILGPIVATMLYIQKTKDDDEHQLR 101
+W+ L+L P+V T Y K++++ + R
Sbjct: 39 SENWISATLLLAPLVGTYWYALNYKENEKLEHR 71
>gnl|CDD|215436 PLN02815, PLN02815, L-aspartate oxidase.
Length = 594
Score = 29.3 bits (66), Expect = 0.40
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 40 GEGGVLFDPAMQRYMTMSTNR 60
G+GG+L++ A +R+M + R
Sbjct: 287 GDGGILYNLAGERFMPLYDER 307
>gnl|CDD|218306 pfam04878, Baculo_p48, Baculovirus P48 protein.
Length = 375
Score = 28.8 bits (65), Expect = 0.55
Identities = 19/65 (29%), Positives = 25/65 (38%), Gaps = 27/65 (41%)
Query: 13 FEKKTK--------MRMALREEFIKQVYNPHRHATGEGGVLFDPAMQRYMTMSTNRYRYF 64
FE K + LR+EFI QV P+ F MQ Y+ +Y+
Sbjct: 71 FESKQDNDHEVKQIFSLFLRDEFIGQV--PN----------FQTIMQ-YLQ------KYY 111
Query: 65 KPTPK 69
KP P
Sbjct: 112 KPIPS 116
>gnl|CDD|188230 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha
chain. This model represents a small clade of
ribonucleoside-diphosphate reductase, alpha chains which
are sufficiently divergent from the usual Class I RNR
alpha chains (NrdE or NrdA, TIGR02506) as to warrant
their own model. The genes from Thermus thermophilus,
Dichelobacter and Salinibacter are adjacent to the usual
RNR beta chain [Purines, pyrimidines, nucleosides, and
nucleotides, 2'-Deoxyribonucleotide metabolism].
Length = 548
Score = 28.7 bits (64), Expect = 0.67
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 72 WLGLGLILGPIVATMLYIQKTKDDDEHQLRTGQVAYRDRWNKFL 115
WLG+ L P + + + DD ++ G R RW K +
Sbjct: 168 WLGIQL-ENPASQHVGWGVEVGDDWYEKMIAGDPEKRARWAKLM 210
>gnl|CDD|218236 pfam04735, Baculo_helicase, Baculovirus DNA helicase.
Length = 1173
Score = 27.6 bits (62), Expect = 1.8
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 81 PIVATMLYIQKTKDDDEHQLRTGQVAYRDRWNKF 114
P V TML+ K +EH L ++ ++ K+
Sbjct: 1114 PYVETMLHYSLRKRVNEHTL---CAEFKRKFKKY 1144
>gnl|CDD|212054 cd11485, SLC-NCS1sbd_YbbW-like, uncharacterized
nucleobase-cation-symport-1 (NCS1) transporter
subfamily, YbbW-like; solute-binding domain. NCS1s are
essential components of salvage pathways for nucleobases
and related metabolites; their known substrates include
allantoin, uracil, thiamine, and nicotinamide riboside.
This subfamily includes the putative allantoin
transporter Escherichia coli YbbW (also known as GlxB2).
NCS1s belong to a superfamily which also contains the
solute carrier 5 family sodium/glucose transporters
(SLC5s), and solute carrier 6 family neurotransmitter
transporters (SLC6s).
Length = 459
Score = 27.1 bits (61), Expect = 2.0
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 71 SWL-GLGLILGPIVATML--Y--IQKTK-DDDEHQLRTGQVAYRDRWN 112
+WL G G +LGPI M+ Y +++T+ D D+ R G+ Y + WN
Sbjct: 363 TWLGGYGALLGPIAGIMIADYWLVRRTRLDLDDLYRRGGRYWYSNGWN 410
>gnl|CDD|233123 TIGR00770, Dcu, anaerobic c4-dicarboxylate membrane transporter
family protein. These proteins are members of th
C4-Dicarboxylate Uptake (Dcu) Family (TC 2.A.13). Most
proteins in this family have 12 GES predicted
transmembrane regions; however one member has 10
experimentally determined transmembrane regions with
both the N- and C-termini localized to the periplasm.
The two Escherichia coli proteins, DcuA and DcuB,
transport aspartate, malate, fumarate and succinate, and
function as antiporters with any two of these
substrates. Since DcuA is encoded in an operon with the
gene for aspartase, and DcuB is encoded in an operon
with the gene for fumarase, their physiological
functions may be to catalyze aspartate:fumarate and
fumarate:malate exchange during the anaerobic
utilization of aspartate and fumarate, respectively
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 430
Score = 27.0 bits (60), Expect = 2.5
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 47 DPAMQRYMT---MSTNRYRYFKPTPKTSWLGLGLILGPIVATMLY 88
DP Q + + R + K T K++ L + + LG +VA +LY
Sbjct: 193 DPEYQERLKAGKIVPTRGKKEKETSKSAKLSVWIFLGGVVAVVLY 237
>gnl|CDD|185011 PRK15051, PRK15051, 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol
flippase subunit ArnE; Provisional.
Length = 111
Score = 26.3 bits (58), Expect = 3.0
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 63 YFKPTPKTSWLGLGLILGPIV 83
+ +P W G+ I+G IV
Sbjct: 85 WHEPVSPRHWCGVAFIIGGIV 105
>gnl|CDD|216247 pfam01019, G_glu_transpept, Gamma-glutamyltranspeptidase.
Length = 495
Score = 26.4 bits (59), Expect = 4.1
Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 14/66 (21%)
Query: 54 MTMSTNRYRYFKPTPKTSWLGLGLILG-------PIVATMLYIQKTKDDDEHQLRTGQVA 106
++ Y ++P P + L IL + Y+ + ++A
Sbjct: 213 LSGDYGGYTVYEPPPSSGGAVLLQILNILEGFDLSGPNSAEYVH-------LLVEAMKLA 265
Query: 107 YRDRWN 112
Y DR
Sbjct: 266 YADRSR 271
>gnl|CDD|233744 TIGR02138, phosphate_pstC, phosphate ABC transporter, permease
protein PstC. The typical operon for the high affinity
inorganic phosphate ABC transporter encodes an
ATP-binding protein, a phosphate-binding protein, and
two permease proteins. This family consists of one of
the two permease proteins, PstC, which is homologous to
PstA (TIGR00974). In the model bacterium Escherichia
coli, this transport system is induced when the
concentration of extrallular inorganic phosphate is low.
A constitutive, lower affinity transporter operates
otherwise [Transport and binding proteins, Anions].
Length = 295
Score = 26.1 bits (58), Expect = 4.6
Identities = 8/49 (16%), Positives = 17/49 (34%), Gaps = 4/49 (8%)
Query: 42 GGVLFDPAMQRYMTMSTNRYRYFKPTPKTSWLGLGLILG----PIVATM 86
G + P ++ + P L G++L P +A++
Sbjct: 121 GLFVLVPFLKPHFQPFLGSNLGLIPLFGGPILTAGIVLAIMILPTIASI 169
>gnl|CDD|235385 PRK05277, PRK05277, chloride channel protein; Provisional.
Length = 438
Score = 26.0 bits (58), Expect = 5.6
Identities = 8/48 (16%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 43 GVLFDPAMQRYMTMSTNRYRYFKPTPKTSWLGLGLILGPIVATMLYIQ 90
GVLF+ + + + + + K W+ +G +G + + +
Sbjct: 231 GVLFN----KLLLRTQDLFDRLHGGNKKRWVLMGGAVGGLCGLLGLLA 274
>gnl|CDD|149105 pfam07851, TMPIT, TMPIT-like protein. A number of members of this
family are annotated as being transmembrane proteins
induced by tumour necrosis factor alpha, but no
literature was found to support this.
Length = 330
Score = 25.9 bits (57), Expect = 5.9
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 12/48 (25%)
Query: 67 TPKTSWLGLGLILGPIVATMLYIQKTKDDDEHQLRTGQVAYRDRWNKF 114
PK + L L L+LG + T+L +K + AY+D + KF
Sbjct: 91 LPKKNGLYLRLVLGNVNVTLL----SKQA--------KFAYKDEYEKF 126
>gnl|CDD|216222 pfam00972, Flavi_NS5, Flavivirus RNA-directed RNA polymerase.
Flaviviruses produce a polyprotein from the ssRNA
genome. This protein is also known as NS5. This
RNA-directed RNA polymerase possesses a number of short
regions and motifs homologous to other RNA-directed RNA
polymerases.
Length = 649
Score = 25.9 bits (57), Expect = 6.6
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 11 ELFEKKTKMRMALREEFIKQVYN 33
L +K + R+ +EEFI +V +
Sbjct: 133 RLLGRKKRPRLCTKEEFIAKVRS 155
>gnl|CDD|235047 PRK02509, PRK02509, hypothetical protein; Provisional.
Length = 973
Score = 25.7 bits (57), Expect = 6.7
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 44 VLFDPAMQRYMTMSTNRYRYFKPTPKTSWLGLGLI--LGPIVATMLYIQ 90
L A+ + +R F P P +LG+ LI L P V L +Q
Sbjct: 343 WLLWRAIFGSLKQRKSRRFPFLPYPLILYLGILLIGWLLPEVVQSLIVQ 391
>gnl|CDD|218299 pfam04869, Uso1_p115_head, Uso1 / p115 like vesicle tethering
protein, head region. Also known as General vesicular
transport factor, Transcytosis associated protein (TAP)
and Vesicle docking protein, this myosin-shaped molecule
consists of an N-terminal globular head region, a
coiled-coil tail which mediates dimerisation, and a
short C-terminal acidic region. p115 tethers COP1
vesicles to the Golgi by binding the coiled coil
proteins giantin (on the vesicles) and GM130 (on the
Golgi), via its C-terminal acidic region. It is required
for intercisternal transport in the golgi stack. This
family consists of part of the head region. The head
region is highly conserved, but its function is unknown.
It does not seem to be essential for vesicle tethering.
The N-terminal part of the head region, not within this
family, contains context-detected
Armadillo/beta-catenin-like repeats (pfam00514).
Length = 308
Score = 25.7 bits (57), Expect = 7.2
Identities = 5/44 (11%), Positives = 15/44 (34%)
Query: 21 MALREEFIKQVYNPHRHATGEGGVLFDPAMQRYMTMSTNRYRYF 64
+ F+K + +T + + +S + Y+ +
Sbjct: 70 EEGQLHFLKTQIPSYASSTDPSANILTGLLDYDADLSLDPYKNW 113
>gnl|CDD|193129 pfam12652, CotJB, CotJB protein. CotJ is a sigma E-controlled
operon involved in the spore coat of Bacillus subtilis.
This protein has been identified as a spore coat
protein.
Length = 78
Score = 24.4 bits (54), Expect = 8.0
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 11 ELFEKKTKMRMALREEFIKQVYNP 34
E + + + R L++E+ KQ Y P
Sbjct: 33 EYYNEYSAKRKQLKKEYEKQ-YGP 55
>gnl|CDD|212719 cd11785, SH3_SH3RF_C, C-terminal (Fourth) Src Homology 3 domain
of SH3 domain containing ring finger 1 (SH3RF1),
SH3RF3, and similar domains. SH3RF1 (or POSH) and
SH3RF3 (or POSH2) are scaffold proteins that function
as E3 ubiquitin-protein ligases. They contain an
N-terminal RING finger domain and four SH3 domains.
This model represents the fourth SH3 domain, located at
the C-terminus of SH3RF1 and SH3RF3, and similar
domains. SH3RF1 plays a role in calcium homeostasis
through the control of the ubiquitin domain protein
Herp. It may also have a role in regulating death
receptor mediated and JNK mediated apoptosis. SH3RF3
interacts with p21-activated kinase 2 (PAK2) and
GTP-loaded Rac1. It may play a role in regulating JNK
mediated apoptosis in certain conditions. SH3 domains
are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 24.0 bits (52), Expect = 9.4
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 60 RYRYFKPTPKTSWLGLGLILGPIVATMLYIQKTKDD 95
RYR P P S L L G IV ++ K ++D
Sbjct: 1 RYRVIVPYPPQSEAELELKEGDIV----FVHKKRED 32
>gnl|CDD|220546 pfam10060, DUF2298, Uncharacterized membrane protein (DUF2298).
This domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 413
Score = 25.1 bits (55), Expect = 9.9
Identities = 8/28 (28%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 61 YRYFKPT---PKTSWLGLGLILGPIVAT 85
Y + L LGL LG + A+
Sbjct: 206 AIYRRKEEKRRILLLLLLGLSLGLLFAS 233
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
0.323 0.136 0.420
Gapped
Lambda K H
0.267 0.0821 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,107,406
Number of extensions: 522815
Number of successful extensions: 547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 546
Number of HSP's successfully gapped: 29
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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 (22.0 bits)
S2: 53 (24.0 bits)