RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12747
(84 letters)
>gnl|CDD|148593 pfam07074, TRAP-gamma, Translocon-associated protein, gamma subunit
(TRAP-gamma). This family consists of several
eukaryotic translocon-associated protein, gamma subunit
(TRAP-gamma) sequences. The translocation site
(translocon), at which nascent polypeptides pass through
the endoplasmic reticulum membrane, contains a component
previously called 'signal sequence receptor' that is now
renamed as 'translocon-associated protein' (TRAP). The
TRAP complex is comprised of four membrane proteins
alpha, beta, gamma and delta which are present in a
stoichiometric relation, and are genuine neighbors in
intact microsomes. The gamma subunit is predicted to
span the membrane four times.
Length = 170
Score = 132 bits (335), Expect = 2e-41
Identities = 63/82 (76%), Positives = 73/82 (89%)
Query: 1 MAKKLSDDKKMSKKEKDERILWKKNEVADFEATTFSIFYNNALFLAIVIFLSFYILKSFT 60
+ +KL+DDKKMS+KEKDERILWKKNEVAD+EATTFSIFYNNALFL +VIF SF+IL+SFT
Sbjct: 89 VNRKLADDKKMSRKEKDERILWKKNEVADYEATTFSIFYNNALFLTLVIFASFFILRSFT 148
Query: 61 PTFNYIFSLWISAGFLALLSTG 82
PT NYI S ++G LALLSTG
Sbjct: 149 PTVNYILSTGGASGLLALLSTG 170
>gnl|CDD|227333 COG5000, NtrY, Signal transduction histidine kinase involved in
nitrogen fixation and metabolism regulation [Signal
transduction mechanisms].
Length = 712
Score = 29.4 bits (66), Expect = 0.18
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 42 ALFLAIVIFLSFYILKSFTPTFNYIF-SLWISAGFLALLST 81
A+ LAIV+ +P F+YI + ++ L +LS
Sbjct: 15 AIVLAIVLCGLLAGTTPISPAFDYILALVAVNLALLLILSA 55
>gnl|CDD|223054 PHA03359, PHA03359, UL17 tegument protein; Provisional.
Length = 686
Score = 28.4 bits (64), Expect = 0.32
Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 30 FEATTFSIFYNNALFLAIVIFLSFYI----LKSFTPTFNYIFSLW 70
+ + F N+AL A++ L+ + + P +
Sbjct: 529 IQNESAEEFSNSALMSAVLAHLAARSTRGRGRGYVPYHRASLARL 573
>gnl|CDD|188151 TIGR01517, ATPase-IIB_Ca, plasma-membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
plasma membrane of eukaryotes , out of the cell. In some
organisms, this type of pump may also be found in
vacuolar membranes. In humans and mice, at least, there
are multiple isoforms of the PMCA pump with overlapping
but not redundant functions. Accordingly, there are no
human diseases linked to PMCA defects, although
alterations of PMCA function do elicit physiological
effects. The calcium P-type ATPases have been
characterized as Type IIB based on a phylogenetic
analysis which distinguishes this group from the Type
IIA SERCA calcium pump. A separate analysis divides Type
IIA into sub-types (SERCA and PMR1) which are modelled
by TIGR01116 and TIGR01522. This model is well separated
from those.
Length = 944
Score = 27.0 bits (60), Expect = 1.1
Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 31 EATTFSIFYNNALFLAIVIF------LSFYILKSFTPTFNYIFSLWISAGFLALLS 80
E F + N +F+ I+ F + SF T + WI L +LS
Sbjct: 876 ERNVFEGLFKNRIFVTIMGFTFGFQVIIVEFGGSFFSTVSLSIEQWIGCVLLGMLS 931
>gnl|CDD|237462 PRK13665, PRK13665, hypothetical protein; Provisional.
Length = 316
Score = 26.8 bits (60), Expect = 1.2
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 43 LFLAIVIFLSFYILKSFTPTFNYIFSLWISA 73
+ +A++I + + SF P LWISA
Sbjct: 8 IIIAVLIIIFLIVFFSFVP-----VGLWISA 33
>gnl|CDD|144140 pfam00434, VP7, Glycoprotein VP7.
Length = 326
Score = 26.7 bits (59), Expect = 1.4
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 35 FSIFYNNALFLAIVIFLSFYILKSFTPTFNYIFSLWI 71
+ I Y L I I L YILK+ T +YI ++
Sbjct: 2 YGIEYTTILTFLISIILLNYILKTITRIMDYIIYRFL 38
>gnl|CDD|222477 pfam13965, SID-1_RNA_chan, dsRNA-gated channel SID-1. This is a
family of proteins that are transmembrane dsRNA-gated
channels. They passively transport dsRNA into cells and
do not act as ATP-dependent pumps. They are required for
systemic RNA interference.
Length = 567
Score = 26.6 bits (59), Expect = 1.6
Identities = 10/58 (17%), Positives = 17/58 (29%), Gaps = 2/58 (3%)
Query: 14 KEKDERILWKKNEVADFEAT-TFSIFYNNALFLAIVIFLSFYILKSFTPTFNYIFSLW 70
R + + + F T SI Y + LSF +L + +
Sbjct: 89 SGNTSRKINNRTKSITFNVTILESISYFVPTLAMVFFLLSFCLLFIVF-VIHIFRNRR 145
>gnl|CDD|180941 PRK07352, PRK07352, F0F1 ATP synthase subunit B; Validated.
Length = 174
Score = 26.1 bits (58), Expect = 2.2
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 35 FSIFYNNALFLAIVIFLSFYILKSF 59
++ N + LAIVI L +Y + F
Sbjct: 19 LNLLETNLINLAIVIGLLYYFGRGF 43
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 25.7 bits (56), Expect = 3.7
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 57 KSFTPTFNYIFSLWISAGFLALLSTG 82
K PT N + S+W A FL++++T
Sbjct: 844 KFIIPTLNNLASIWFLALFLSIIATS 869
>gnl|CDD|227201 COG4864, COG4864, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 328
Score = 25.3 bits (55), Expect = 3.9
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 10/42 (23%)
Query: 43 LFLAIVIFLSFYILKSFTPTFNYIFSLWISAGFLALLSTGTK 84
+ +A+VI ++ + +F P LWISA L+ G K
Sbjct: 7 IIIAVVIIIALAVFFTFVPV-----GLWISA-----LAAGVK 38
>gnl|CDD|236302 PRK08578, PRK08578, preprotein translocase subunit SecF; Reviewed.
Length = 292
Score = 25.3 bits (56), Expect = 4.3
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 11/49 (22%)
Query: 43 LFLAIVIFLSFYILKSFTPTFNYIFSLW----ISAGFLAL----LSTGT 83
+ +A+V+FL F ++ P+ I S + I+ + L LS T
Sbjct: 145 IGMAVVVFLIF---RTPVPSLAVILSAFSDIIIALALMNLFGIELSLAT 190
>gnl|CDD|214413 MTH00062, ND4, NADH dehydrogenase subunit 4; Provisional.
Length = 417
Score = 24.9 bits (55), Expect = 5.3
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 38 FYNNALFLAIVIFLSFYILKSFTPT---FNYIFSLWISAGFLALL 79
N +L L +++ SF L SF PT F +F + S G L L
Sbjct: 317 GINGSLVLRVIVVFSFLSLCSFPPTIQFFCEVFLVSSSFGVLVYL 361
>gnl|CDD|130728 TIGR01667, YCCS_YHJK, integral membrane protein, YccS/YhfK family.
This model represents two clades of putative
transmembrane proteins including the E. coli YccS and
YhfK proteins. The YccS hypothetical equivalog
(TIGR01666) is found in beta and gamma proteobacteria,
while the smaller YhfK group is only found in E. coli,
Salmonella and Yersinia. TMHMM on the 19 hits to this
model shows a consensus of 11 transmembrane helices
separated into two clusters, an N-terminal cluster of 6
and a central cluster of 5. This would indicate two
non-membrane domains one on each side of the membrane.
Length = 701
Score = 25.2 bits (55), Expect = 5.8
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 36 SIFYNNALFLAIVIFLSFYILKSFTPTFNYIFSLWI 71
S + +A+ L++V+ L + IL Y WI
Sbjct: 380 SPLFRHAVRLSLVVMLGYAILMGTALHLGY----WI 411
>gnl|CDD|129794 TIGR00711, efflux_EmrB, drug resistance transporter, EmrB/QacA
subfamily. This subfamily of drug efflux proteins, a
part of the major faciliator family, is predicted to
have 14 potential membrane-spanning regions. Members
with known activities include EmrB (multiple drug
resistance efflux pump) in E. coli, FarB (antibacterial
fatty acid resistance) in Neisseria gonorrhoeae, TcmA
(tetracenomycin C resistance) in Streptomyces
glaucescens, etc. In most cases, the efflux pump is
described as having a second component encoded in the
same operon, such as EmrA of E. coli [Cellular
processes, Toxin production and resistance, Transport
and binding proteins, Other].
Length = 485
Score = 25.0 bits (55), Expect = 5.9
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 37 IFYNNALFLAIVIFLSFYILKSFTPT----FNYIFSLWISAGFLALL 79
IF N IV+ ++F+IL P F+++ L +S G +LL
Sbjct: 158 IFLINVPIGIIVVVVAFFILPRDKPAASENFDFLGLLLLSVGLGSLL 204
>gnl|CDD|216029 pfam00622, SPRY, SPRY domain. SPRY Domain is named from SPla and
the RYanodine Receptor. Domain of unknown function.
Distant homologues are domains in
butyrophilin/marenostrin/pyrin homologues.
Length = 125
Score = 24.6 bits (54), Expect = 6.3
Identities = 8/35 (22%), Positives = 9/35 (25%), Gaps = 1/35 (2%)
Query: 29 DFEATTFSIFYNNALFLAIVIFLSFYILKSFTPTF 63
D E S F N L F + P
Sbjct: 75 DLEEGEIS-FTKNGKDLGGYTFRNVEFGGPLYPAV 108
>gnl|CDD|216390 pfam01252, Peptidase_A8, Signal peptidase (SPase) II.
Length = 143
Score = 24.3 bits (54), Expect = 8.2
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 35 FSIFYNNALFL-----AIVIFLSFYILKSFTPTFNYIFSL 69
FS+F FL ++ L +Y+L+ + +L
Sbjct: 46 FSLFSGQRWFLSLIALLAILALLYYLLRLKKRSRLAAIAL 85
>gnl|CDD|216063 pfam00689, Cation_ATPase_C, Cation transporting ATPase, C-terminus.
Members of this families are involved in Na+/K+, H+/K+,
Ca++ and Mg++ transport. This family represents 5
transmembrane helices.
Length = 175
Score = 24.5 bits (54), Expect = 8.2
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 34 TFSIFYNNALFLAIVIFLSFYILKSFTPTFNYIFSL-------WISAGFLALLST 81
+F N L LA+++ L +L + P +F W+ LAL+
Sbjct: 112 KIGLFSNKLLLLAVLLSLLLQLLIIYVPGLQAVFGTTPLSLEQWLIVLGLALVVL 166
>gnl|CDD|204557 pfam10843, DUF2578, Protein of unknown function (DUF2578). This is
a Saccharomycete family of proteins with unknown
function. The protein in S. cerevisiae is strongly
induced in response to many stress conditions and is
repressed in drug resistant yeast strains.
Length = 159
Score = 24.3 bits (53), Expect = 9.3
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 9 KKMSKKEKDERILWKKNEVADFEATTFSI 37
KK SK+E E+I WK + D F I
Sbjct: 110 KKKSKEETFEKITWKYGDETDHYDRHFKI 138
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
0.325 0.136 0.397
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,377,183
Number of extensions: 367065
Number of successful extensions: 1148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1132
Number of HSP's successfully gapped: 159
Length of query: 84
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 32
Effective length of database: 8,631,194
Effective search space: 276198208
Effective search space used: 276198208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)