RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6814
(171 letters)
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 41.4 bits (98), Expect = 8e-06
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 66 VITLSILFIFIPAYVFSSIEPNWSYLDSLYFCFISITTIGLGDYIPGESPQQEFKSLYKI 125
++ L +L Y W +LD+LYF F+++TTIG GD +P ++
Sbjct: 1 ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLT-------DAGRL 53
Query: 126 IVSVYLILSLLFTMFVLKTF 145
+Y+++ + + L
Sbjct: 54 FTIIYILIGIPLFLLFLAVL 73
Score = 41.0 bits (97), Expect = 1e-05
Identities = 19/73 (26%), Positives = 33/73 (45%)
Query: 12 VITLSILFIFIPAYVFSSIEPNWSYLDSLYFCFISITTIGLGDYIPGLSYLGSLVITLSI 71
++ L +L Y W +LD+LYF F+++TTIG GD +P I +
Sbjct: 1 ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYIL 60
Query: 72 LFIFIPAYVFSSI 84
+ I + + +
Sbjct: 61 IGIPLFLLFLAVL 73
>gnl|CDD|224397 COG1480, COG1480, Predicted membrane-associated HD superfamily
hydrolase [General function prediction only].
Length = 700
Score = 30.4 bits (69), Expect = 0.41
Identities = 20/116 (17%), Positives = 39/116 (33%), Gaps = 22/116 (18%)
Query: 6 SYLGSLVITLSILFIFIPAYVFSSIEPNWSYLDSLYFCFISITTIGLG------------ 53
L LVI L +LF A + +SL ++S+ + L
Sbjct: 278 LGLLILVIFLILLF----ALYERRTKSPLKLRNSLLLLYLSLAILTLSLLRIVGYFNYSA 333
Query: 54 -DYIPGLSYLGSLVITL--SILFIFIPAYVFSSIEP--NWSYLDSLYFCFISITTI 104
+ + L+I L + IF + + ++ SY +S +++
Sbjct: 334 SGLLVPPALGPMLLILLVFLRIAIFSSSMIAIALLYLFGGSY-NSEIALIALLSSF 388
Score = 29.7 bits (67), Expect = 0.73
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 6/83 (7%)
Query: 58 GLSYLGSLVITLSILFIFIPAYVFSSIEPNWSYLDSLYFCFISITTIGLGDYIPGESPQQ 117
L L LVI L +LF A + +SL ++S+ + L
Sbjct: 276 PLLGLLILVIFLILLF----ALYERRTKSPLKLRNSLLLLYLSLAILTLSLLRIV--GYF 329
Query: 118 EFKSLYKIIVSVYLILSLLFTMF 140
+ + ++ + L+ +F
Sbjct: 330 NYSASGLLVPPALGPMLLILLVF 352
>gnl|CDD|220520 pfam10011, DUF2254, Predicted membrane protein (DUF2254). Members
of this family of bacterial proteins comprises various
hypothetical and putative membrane proteins. Their exact
function, has not, as yet, been defined.
Length = 369
Score = 29.1 bits (66), Expect = 1.3
Identities = 9/37 (24%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 42 FCFISITTIGLGDY--IPGLSYLGSLVITLSILFIFI 76
+ + + TI G Y +P LS L ++++ + + I
Sbjct: 106 YSLLVLITIRGGAYGFVPRLSVLVTILLAVLSVAALI 142
>gnl|CDD|183259 PRK11652, emrD, multidrug resistance protein D; Provisional.
Length = 394
Score = 28.3 bits (64), Expect = 1.9
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 14/82 (17%)
Query: 6 SYLGSLVITLSILFIF-IPAYVFSS-----IEPNWSYLDSLYFCFISITTIGLGDYIPGL 59
+ LG +T+SILFI IPA F + +S L ++ I GL +IPG
Sbjct: 236 AVLGLSSMTVSILFILPIPAAFFGAWFAGRPNKRFSTL--MWQSVICCLLAGLLMWIPGW 293
Query: 60 SYLGSLVITLSILFIFIPAYVF 81
++ ++L +PA +F
Sbjct: 294 F---GVMNVWTLL---VPAALF 309
>gnl|CDD|225892 COG3356, COG3356, Predicted membrane protein [Function unknown].
Length = 578
Score = 28.2 bits (63), Expect = 2.3
Identities = 16/111 (14%), Positives = 33/111 (29%), Gaps = 9/111 (8%)
Query: 1 LKIKFSYLGSLVITLSILFIFIPAYVFSSIEPNWSYLDS---------LYFCFISITTIG 51
K+K S + V + + V +I P L +S
Sbjct: 73 FKLKRSSFLAFVSLVIWSTFLVLLLVLLAIRPVDVSLILAVALVLSFRFLIVLVSYKNSV 132
Query: 52 LGDYIPGLSYLGSLVITLSILFIFIPAYVFSSIEPNWSYLDSLYFCFISIT 102
+P ++Y+ S +I F+ + + I + L + +
Sbjct: 133 PSSVLPSMNYVYSPLIVYLKGFVAQYSLIVPFIISSLLILLLASLLYGRVL 183
>gnl|CDD|217401 pfam03169, OPT, OPT oligopeptide transporter protein. The OPT
family of oligopeptide transporters is distinct from the
ABC pfam00005 and PTR pfam00854 transporter families.
OPT transporters were first recognised in fungi (Candida
albicans and Schizosaccharomyces pombe), but this
alignment also includes orthologues from Arabidopsis
thaliana. OPT transporters are thought to have 12-14
transmembrane domains and contain the following motif:
SPYxEVRxxVxxxDDP.
Length = 619
Score = 27.7 bits (62), Expect = 3.7
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 7 YLGSLVITLSILFIFIPAYVFSSIEPNWSYLDSLYFCFISITTIGLGDYIPGLSYLGSLV 66
YL LV++L + + A + + P W L +L F+ YI GL+ S V
Sbjct: 354 YLAGLVLSLVLGIALVAALFPTQL-PVWGLLLALLLAFVFAIPSA---YIAGLTGS-SPV 408
Query: 67 ITLSILFIFIPAYVF 81
L IL I YV
Sbjct: 409 SGLGILTELIAGYVL 423
>gnl|CDD|161732 TIGR00147, TIGR00147, lipid kinase, YegS/Rv2252/BmrU family. The
E. coli member of this family, YegS has been purified
and shown to have phosphatidylglycerol kinase activity.
The member from M. tuberculosis, Rv2252, has
diacylglycerol kinase activity. BmrU from B. subtilis is
in an operon with multidrug efflux transporter Bmr, but
is uncharacterized [Unknown function, Enzymes of unknown
specificity].
Length = 293
Score = 27.1 bits (60), Expect = 5.3
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 96 FCFISITTIGLGDYIPGESPQQEFKSLYKIIVSVYLILSLLFTMFVLKTF 145
+CFI++ G G I E+P++ +L + Y ILS L M L+ F
Sbjct: 131 YCFINMAGGGFGTEITTETPEKLKAALGSL---SY-ILSGLMRMDTLQPF 176
>gnl|CDD|219145 pfam06703, SPC25, Microsomal signal peptidase 25 kDa subunit
(SPC25). This family consists of several microsomal
signal peptidase 25 kDa subunit proteins. Translocation
of polypeptide chains across the endoplasmic reticulum
(ER) membrane is triggered by signal sequences.
Subsequently, signal recognition particle interacts with
its membrane receptor and the ribosome-bound nascent
chain is targeted to the ER where it is transferred into
a protein-conducting channel. At some point, a second
signal sequence recognition event takes place in the
membrane and translocation of the nascent chain through
the membrane occurs. The signal sequence of most
secretory and membrane proteins is cleaved off at this
stage. Cleavage occurs by the signal peptidase complex
(SPC) as soon as the lumenal domain of the translocating
polypeptide is large enough to expose its cleavage site
to the enzyme. The signal peptidase complex is possibly
also involved in proteolytic events in the ER membrane
other than the processing of the signal sequence, for
example the further digestion of the cleaved signal
peptide or the degradation of membrane proteins.
Mammalian signal peptidase is as a complex of five
different polypeptide chains. This family represents the
25 kDa subunit (SPC25).
Length = 161
Score = 26.1 bits (58), Expect = 8.9
Identities = 10/47 (21%), Positives = 21/47 (44%)
Query: 94 LYFCFISITTIGLGDYIPGESPQQEFKSLYKIIVSVYLILSLLFTMF 140
L + ++ Y + P E K + V++Y +LS + T++
Sbjct: 30 LALGYSAVAIAAAAFYYDYKYPFPESKPVLIACVALYFVLSGILTLW 76
>gnl|CDD|233564 TIGR01768, GGGP-family, geranylgeranylglyceryl phosphate synthase
family protein. This model represents a family of
sequences including geranylgeranylglyceryl phosphate
synthase which catalyzes the first committed step in the
synthesis of ether-linked membrane lipids in archaea.
The clade of bacterial sequences may have the same
function or a closely related function. This model
supercedes TIGR00265, which has been retired.
Length = 223
Score = 26.3 bits (58), Expect = 9.4
Identities = 12/59 (20%), Positives = 18/59 (30%), Gaps = 1/59 (1%)
Query: 22 IPAYVFSSIEPNWSYLDSLYFCFISITTIGLGDYIPGLSYLGSLVITLSILFIFIPAYV 80
+P +F S N S F F S+ +I G + I Y+
Sbjct: 56 LPIILFPSNPTNVSRDADALF-FPSVLNSDDPYWIIGAQIEAAPKFKKIGEEIIPEGYI 113
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
0.330 0.147 0.446
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,936,922
Number of extensions: 858643
Number of successful extensions: 2134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1982
Number of HSP's successfully gapped: 306
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
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 (21.8 bits)
S2: 55 (24.9 bits)