RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16921
(235 letters)
>gnl|CDD|216528 pfam01490, Aa_trans, Transmembrane amino acid transporter protein.
This transmembrane region is found in many amino acid
transporters including UNC-47 and MTR. UNC-47 encodes a
vesicular amino butyric acid (GABA) transporter, (VGAT).
UNC-47 is predicted to have 10 transmembrane domains.
MTR is a N system amino acid transporter system protein
involved in methyltryptophan resistance. Other members
of this family include proline transporters and amino
acid permeases.
Length = 406
Score = 77.7 bits (192), Expect = 1e-16
Identities = 49/228 (21%), Positives = 92/228 (40%), Gaps = 43/228 (18%)
Query: 7 IIVDFFIFWNHLGICCVYINFIADNFDQACHHFSPDTSLAKIHWELIITVVMIVLNQVKN 66
+++ F I N G+C Y+ F DN F ++ +++ +I ++ I L+ + N
Sbjct: 86 LLILFAILVNLFGVCISYLIFAGDNLPAIFDSFFDTCHISLVYFIIIFGLIFIPLSFIPN 145
Query: 67 LHFLSPFSSIESLINQRSKAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIG 126
L LS S + ++ ++ + I
Sbjct: 146 LSALSILSLVAAV---------------------------------------SSLYIVIL 166
Query: 127 LGMVCYYIFRDGLDQPILRPGDVELFGKLYEVPLFMGTFLFASLGIGVLIALEDEMKTPS 186
+ V L + KL + L +G +FA G VL+ +++ MK+PS
Sbjct: 167 VLSVAELGVLTAQGVGSL---GAKTNIKLARLFLAIGIIVFAFEGHAVLLPIQNTMKSPS 223
Query: 187 SYRKNPFGIFNMGFTTIIIIYLFVGVIGYYKYGQLVEGSITLNIPKDD 234
+ K + + ++Y+ VG++GY +G V+G+I LN+PK D
Sbjct: 224 KF-KAMTKVLLTAIIIVTVLYILVGLVGYLAFGNNVKGNILLNLPKSD 270
>gnl|CDD|225364 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
PilT [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 353
Score = 31.9 bits (73), Expect = 0.29
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 61 LNQVKNLHFLS---P----FSSIESLINQRSKAGTKVHSFSNLIKG 99
+N+ K H L+ P S +SLINQR + G SF+N ++
Sbjct: 149 INKHKAKHILTIEDPIEYVHESKKSLINQR-EVGRDTLSFANALRA 193
>gnl|CDD|237531 PRK13850, PRK13850, type IV secretion system protein VirD4;
Provisional.
Length = 670
Score = 30.6 bits (69), Expect = 0.74
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 123 LTIGL-GMVCYYIFRDGLD-QPILRPGDVELFGKLYEVPLFMG---TFLFASLGIGVLIA 177
L G Y FR G + + ++ ++F YE PL++G + L I V +
Sbjct: 19 LAAGFCAASLYVTFRHGFNGEAMMT---FDVFAFWYETPLYLGYATPVFYRGLAIVVSTS 75
Query: 178 L 178
+
Sbjct: 76 V 76
>gnl|CDD|223884 COG0814, SdaC, Amino acid permeases [Amino acid transport and
metabolism].
Length = 415
Score = 30.3 bits (69), Expect = 0.76
Identities = 35/228 (15%), Positives = 65/228 (28%), Gaps = 52/228 (22%)
Query: 7 IIVDFFIFWNHLGICCVYINFIADNFDQACHHFSPDTSLAKIHWELIITVVMIVLNQVKN 66
I++ F+ G+ YI I + + L + LI +V+ L
Sbjct: 88 ILIGLSYFFALYGLLVAYIVGIGNLLASFLGNQFGLNPLPRKLGSLIFALVLAFL----- 142
Query: 67 LHFLSPFSSIESLINQRSKAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIG 126
S + +LK LL G
Sbjct: 143 ------------------------------------------SWLGTLAVLKITSLLVFG 160
Query: 127 LGMVC--YYIFRDGLDQP-ILRPGDVELFGKLYEVPLFMGTFLFASLGIGVLIALEDEMK 183
+ ++ P L + L + F+F+ G + +L + M+
Sbjct: 161 KVIYLVLLVVYLIPHWNPANLFALPSASQSFWKYLLLAIPVFVFSFGFHGNIPSLVNYMR 220
Query: 184 TPSSYRKNPFGIFNMGFTTIIIIYLFVGVIGYYKYGQLVEGSITLNIP 231
S + I +++ Y+ VG + +G LV G+I
Sbjct: 221 KNSK-KAVRKAILIGSLIALVL-YILVGFFVFGCFGSLVFGNILAAKE 266
>gnl|CDD|90317 pfam07239, OpcA, Outer membrane protein OpcA. This family consists
of several Neisseria species specific OpcA outer
membrane proteins. Opc (formerly called 5C) is one of
the major outer membrane proteins and has been shown to
play an important role in meningococcal adhesion and
invasion of both epithelial and endothelial cells.
Length = 244
Score = 29.4 bits (65), Expect = 1.4
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 11/63 (17%)
Query: 38 HFSPDTSLAKIHWELIITVVMIVLNQVKNLHFLSPFSSIESLINQRSKAGTKVHSFSNLI 97
H S + LAK+H +L L+Q+ N +++P+S ++ +N R K T V +NL
Sbjct: 130 HSSRQSWLAKVHADL--------LSQLGNGWYINPWSEVKFDLNSRYKLNTGV---TNLK 178
Query: 98 KGV 100
K +
Sbjct: 179 KDI 181
>gnl|CDD|217300 pfam02950, Conotoxin, Conotoxin. Conotoxins are small snail
toxins that block ion channels.
Length = 73
Score = 27.4 bits (61), Expect = 2.0
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 55 TVVMIVLNQVKNLHFLSPFSSIESLINQRSKAGTKVHSFSN 95
T V+IV L L+ ++ + +Q +K K S +
Sbjct: 4 TCVLIVA-----LLLLTTLATADLDGDQPAKRDAKALSDRD 39
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 27.9 bits (63), Expect = 4.4
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 137 DGLDQPILRPGDVELFGKLYEVPL 160
D LD ILRPG F ++ EVPL
Sbjct: 281 DILDPAILRPGR---FDRIIEVPL 301
>gnl|CDD|184756 PRK14584, hmsS, hemin storage system protein; Provisional.
Length = 153
Score = 27.1 bits (60), Expect = 5.7
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 6/49 (12%)
Query: 178 LEDEMKTPSSYRKNPFGIFNMGFTTIIIIYLFVGV------IGYYKYGQ 220
L + + P I+ + T I +YL + I + KY Q
Sbjct: 37 LLEMISRAPHMGPIPLRIYILSGLTTIALYLAIAAFNAVLLIIWAKYNQ 85
>gnl|CDD|193205 pfam12729, 4HB_MCP_1, Four helix bundle sensory module for signal
transduction. This family is a four helix bundle that
operates as a ubiquitous sensory module in prokaryotic
signal-transduction. The 4HB_MCP is always found between
two predicted transmembrane helices indicating that it
detects only extracellular signals. In many cases the
domain is associated with a cytoplasmic HAMP domain
suggesting that most proteins carrying the bundle might
share the mechanism of transmembrane signalling which is
well-characterized in E coli chemoreceptors.
Length = 181
Score = 26.8 bits (60), Expect = 8.8
Identities = 7/33 (21%), Positives = 18/33 (54%)
Query: 196 FNMGFTTIIIIYLFVGVIGYYKYGQLVEGSITL 228
+ F + ++ + VG++G Y ++ + S T+
Sbjct: 8 LILLFLLLALLLIIVGIVGLYSLKKINKNSETM 40
>gnl|CDD|224812 COG1900, COG1900, Uncharacterized conserved protein [Function
unknown].
Length = 365
Score = 27.0 bits (60), Expect = 9.9
Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 15/89 (16%)
Query: 151 LFGKLYEV-PLFMGTFLFAS------LGIGVLIALEDEMKTPSSYRKN---PFGIFNMGF 200
L G L E+ P +MG S GIGV I + +E S + + +
Sbjct: 237 LKGDLKEMDPEYMGGAYRTSYGPELYNGIGVPIPVLNEKVAESLAVLDSDIVLPVVDYSI 296
Query: 201 TTIIIIYLFVGVIGYYKYGQLVEGSITLN 229
I Y Y +L G I +
Sbjct: 297 RRRDR-----PEITYVDYWELRSGRIEIE 320
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as
twitching motility.
Length = 198
Score = 26.5 bits (59), Expect = 9.9
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 61 LNQVKNLHFLS---P----FSSIESLINQRSKAGTKVHSFSNLIK 98
+N+ K H L+ P S SLINQR + G SF N +K
Sbjct: 25 INKNKTHHILTIEDPIEFVHESKRSLINQR-EVGLDTLSFENALK 68
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
0.328 0.146 0.451
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,464,839
Number of extensions: 1231945
Number of successful extensions: 1708
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1698
Number of HSP's successfully gapped: 76
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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 (21.7 bits)
S2: 57 (25.6 bits)