RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9216
(125 letters)
>gnl|CDD|233179 TIGR00911, 2A0308, L-type amino acid transporter. [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 501
Score = 100 bits (250), Expect = 7e-26
Identities = 44/100 (44%), Positives = 60/100 (60%), Gaps = 4/100 (4%)
Query: 3 KKKADSAAGREPKLVSALEDPTSQDNLVPGSNVPDNKIRLQKELGLMDGVAMIVGVIVGS 62
+ + + S+ + + V G + L+KE+ L+ GV +IVG I+GS
Sbjct: 5 RVFRSQSNATNYQFSSSGRKKSVSASTVDG----GEAVALKKEITLLSGVGIIVGTIIGS 60
Query: 63 GIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAEL 102
GIFVSP GVLKNAGS GLALI+W + G S++GAL YAEL
Sbjct: 61 GIFVSPKGVLKNAGSVGLALIMWAVCGIFSIVGALVYAEL 100
>gnl|CDD|183096 PRK11357, frlA, putative fructoselysine transporter; Provisional.
Length = 445
Score = 49.5 bits (118), Expect = 5e-08
Identities = 27/61 (44%), Positives = 38/61 (62%)
Query: 42 LQKELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAE 101
LQ++LG +A+ VG VGSGIFVS V K AG+P L ++ +V+ G + + YAE
Sbjct: 6 LQRKLGFWAVLAIAVGTTVGSGIFVSVGEVAKAAGTPWLTVLAFVIGGLIVIPQMCVYAE 65
Query: 102 L 102
L
Sbjct: 66 L 66
>gnl|CDD|222193 pfam13520, AA_permease_2, Amino acid permease.
Length = 425
Score = 43.8 bits (104), Expect = 5e-06
Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 7/59 (11%)
Query: 46 LGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVM--SGALSMIGALCYAEL 102
L L+ A+++G I+GSGIFV+P+ S G A I+W + S+ AL YAEL
Sbjct: 1 LSLLSAFALVIGSIIGSGIFVTPL-----IASAGAAAILWGWIAALIFSLAVALVYAEL 54
>gnl|CDD|223605 COG0531, PotE, Amino acid transporters [Amino acid transport and
metabolism].
Length = 466
Score = 42.8 bits (101), Expect = 1e-05
Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 42 LQKELGLMDGVAMI-VGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYA 100
L+K+LGL D + + VG ++GSGIF P AG A++ W+++G + + AL YA
Sbjct: 10 LKKKLGLFDLLTALGVGSMIGSGIFALP---GSAAGLAPAAILAWLIAGIIILFLALSYA 66
Query: 101 ELVEKICHLSGA 112
EL I GA
Sbjct: 67 ELSSAIPSAGGA 78
>gnl|CDD|129984 TIGR00906, 2A0303, cationic amino acid transport permease.
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 557
Score = 41.0 bits (96), Expect = 5e-05
Identities = 17/61 (27%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 41 RLQKELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYA 100
++++ L D +A+ +G +G+GI+V V +N P + ++ +++SG +++ CYA
Sbjct: 25 KMKRCLTTWDLMALGIGSTIGAGIYVLTGEVARNDSGPAI-VLSFLISGLAAVLSGFCYA 83
Query: 101 E 101
E
Sbjct: 84 E 84
>gnl|CDD|129987 TIGR00909, 2A0306, amino acid transporter. [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 429
Score = 40.1 bits (94), Expect = 9e-05
Identities = 26/63 (41%), Positives = 40/63 (63%), Gaps = 6/63 (9%)
Query: 42 LQKELGLMDGVAMIVGVIVGSGIF-VSPIGVLKNAGSPGLALIV-WVMSGALSMIGALCY 99
L +ELGL D + +G ++G+GIF V+ I AG G A+I+ +V++G ++ AL Y
Sbjct: 1 LSRELGLFDLTMLGIGAMIGTGIFVVTGIA----AGKAGPAVILSFVLAGLTALFIALVY 56
Query: 100 AEL 102
AEL
Sbjct: 57 AEL 59
>gnl|CDD|129983 TIGR00905, 2A0302, transporter, basic amino acid/polyamine
antiporter (APA) family. This family includes several
families of antiporters that, rather commonly, are
encoded next to decarboxylases that convert one of the
antiporter substrates into the other. This arrangement
allows a cycle that can remove proteins from the
cytoplasm and thereby protect against acidic conditions
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 473
Score = 40.0 bits (94), Expect = 1e-04
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 44 KELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAELV 103
K+LGL A+++G ++GSGIF P L + PG +I W+++G + A +A L
Sbjct: 7 KKLGLFALTALVIGSMIGSGIFSLPQN-LASVAGPGAVIIGWIITGVGMLALAFVFAILA 65
Query: 104 EKICHLSG 111
K L G
Sbjct: 66 TKKPELDG 73
>gnl|CDD|163522 TIGR03810, arg_ornith_anti, arginine-ornithine antiporter. Members
of this protein family are the arginine/ornithine
antiporter, ArcD. This exchanger of ornithine for
arginine occurs in a system with arginine deiminase,
ornithine carbamoyltransferase, and carbamate kinase,
with together turn arginine to ornithine with the
generation of ATP and release of CO2 [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 468
Score = 33.5 bits (77), Expect = 0.018
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 44 KELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAELV 103
K+LGL A++VG ++GSGIF P + A G LI WV++G + A + L
Sbjct: 1 KKLGLGALTALVVGSMIGSGIFSLPSDMAAGAA-AGAVLIGWVITGVGMLALAFSFQNLA 59
Query: 104 EKICHLSG 111
K L G
Sbjct: 60 NKKPELDG 67
>gnl|CDD|223884 COG0814, SdaC, Amino acid permeases [Amino acid transport and
metabolism].
Length = 415
Score = 32.2 bits (74), Expect = 0.049
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 51 GVAMIVGVIVGSGIFVSPIGVLKNAG-SPGLALIVWVMSGALSMIGALCYAELV 103
GV ++ G +G+G+ P+ G PGL L+ +++ L+ + L E +
Sbjct: 14 GVLILAGTAIGAGVLFLPVA-FGGGGFWPGLLLL--IIAWPLTYLSLLLLLEAL 64
>gnl|CDD|215858 pfam00324, AA_permease, Amino acid permease.
Length = 473
Score = 30.4 bits (69), Expect = 0.20
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 51 GVAMI-VGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAELV 103
V MI +G ++G+G+FV VL AG P AL+ ++++G + + L E+
Sbjct: 1 HVLMIALGGVIGTGLFVGSGSVLGQAG-PAGALLGYLIAGVVIFLTMLSLGEMS 53
>gnl|CDD|182613 PRK10644, PRK10644, arginine:agmatin antiporter; Provisional.
Length = 445
Score = 29.0 bits (65), Expect = 0.55
Identities = 19/61 (31%), Positives = 38/61 (62%), Gaps = 7/61 (11%)
Query: 44 KELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMS--GALSMIGALCYAE 101
++GL+ M+ G I+GSG+F+ P + A + G+A+ W+++ GAL + ++ YA+
Sbjct: 8 HKVGLIPVTLMVAGNIMGSGVFLLPANL---ASTGGIAIYGWLVTIIGALGL--SMVYAK 62
Query: 102 L 102
+
Sbjct: 63 M 63
>gnl|CDD|162039 TIGR00790, fnt, formate/nitrite transporter. The Formate-Nitrite
Transporter (FNT) Family (TC 2.A.44)The prokaryotic
proteins of the FNT family probably function in the
transport of the structurally related compounds, formate
and nitrite. The homologous yeast protein may function
as a short chain aliphatic carboxylate H+
symporter,transporting formate, acetate and propionate,
and functioning primarily as an acetate uptake permease.
The putative formate efflux transporters (FocA) of
bacteria associated with pyruvate-formate lyase (pfl)
comprise cluster I; the putative formate uptake
permeases (FdhC) of bacteria and archaea associated with
formate dehydrogenase comprise cluster II; the putative
nitrite uptake permeases (NirC) of bacteria comprise
cluster III, and the single yeast protein, the putative
acetate:H+ symporter alone comprises cluster IV. The
energy coupling mechanisms for proteins of the FNT
family have not been extensively characterized. HCO2 -,
CH3CO2 - and NO2 - uptakes are probably coupled to
H+symport. HCO2 - efflux may be driven by the membrane
potential by a uniport mechanism or by H+ antiport
[Transport and binding proteins, Anions].
Length = 239
Score = 28.8 bits (65), Expect = 0.66
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 47 GLMDGVAMIVGVIVGSGIFVS-----PIGVLKNAGSPGLALIVWVMSGALSMIGALCYAE 101
G + +I+ VI GS +F + +L+ S G LI WV+S +++GAL A
Sbjct: 47 GATFPIGLILVVIAGSDLFTGNTLFVTMALLRGKISWGDLLINWVVSWLGNLVGALFVAY 106
Query: 102 LVEKICHLSGA 112
L +L G
Sbjct: 107 L---FSYLGGI 114
>gnl|CDD|185174 PRK15267, PRK15267, subtilase cytotoxin subunit B-like protein;
Provisional.
Length = 141
Score = 28.2 bits (62), Expect = 0.75
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 86 VMSGALSMIGALCYAELVEKICHLSGAAVNALDFG---SGG 123
V++ AL+ I ++CYA + + ++S +N L +G SGG
Sbjct: 7 VLTLALASISSVCYAAMADYDTYVSNVQINNLSYGVYTSGG 47
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 27.8 bits (62), Expect = 1.2
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 4/50 (8%)
Query: 51 GVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYA 100
G+ +I I +F + +G L L I + G + + L
Sbjct: 15 GLLLIASGIALLVLFGAGLGAL----ISTLLGIALLALGLVLLALGLLCL 60
>gnl|CDD|112053 pfam03222, Trp_Tyr_perm, Tryptophan/tyrosine permease family.
Length = 393
Score = 26.9 bits (60), Expect = 2.9
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 44 KELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAEL 102
K L+ GV +I G +G+G+ P+ AG +L++ ++S L + L E+
Sbjct: 1 KTPSLLGGVLIIAGTAIGAGMLALPV-ATAGAGFIP-SLLLLILSWFLMLASGLLLLEV 57
>gnl|CDD|240605 cd12922, VKOR_5, Vitamin K epoxide reductase family in bacteria.
This family includes vitamin K epoxide reductase (VKOR)
mostly present in actinobacteria. VKOR (also named
VKORC1) is an integral membrane protein that catalyzes
the reduction of vitamin K 2,3-epoxide and vitamin K to
vitamin K hydroquinone, an essential co-factor
subsequently used in the gamma-carboxylation of glutamic
acid residues in blood coagulation enzymes. All homologs
of VKOR contain an active site CXXC motif, which is
switched between reduced and disulfide-bonded states
during the reaction cycle. In some bacterial homologs,
the VKOR domain is fused with domains of the thioredoxin
family of oxidoreductases which may function as redox
partners in initiating the reduction cascade.
Length = 133
Score = 26.4 bits (59), Expect = 3.0
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 46 LGLMDGVAMI-VGVIVGSGI-FVSPIGVLKNAG-SPGLALIVWVMSGALSMIGALC 98
+GL +I VGV + +G V AG + GL + W++ +L +IGALC
Sbjct: 61 IGLAAFAVVITVGVALLAGARLPRWFWVGLQAGLAAGLVFVHWLIYQSLFVIGALC 116
>gnl|CDD|217759 pfam03845, Spore_permease, Spore germination protein.
Length = 320
Score = 26.8 bits (60), Expect = 3.0
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 54 MIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGALCYAEL 102
+IV +GSGI P + K AG I ++ G + ++ L Y +L
Sbjct: 10 LIVSFQLGSGILTLPRSLAKQAGD---GWIAVLLGGLIGLLLVLLYYKL 55
>gnl|CDD|237275 PRK13022, secF, preprotein translocase subunit SecF; Reviewed.
Length = 289
Score = 26.6 bits (60), Expect = 3.8
Identities = 11/21 (52%), Positives = 17/21 (80%), Gaps = 3/21 (14%)
Query: 52 VAMIVGVIVG--SGIFV-SPI 69
+A+++G+IVG S IFV SP+
Sbjct: 258 LALLIGIIVGTYSSIFVASPL 278
>gnl|CDD|227409 COG5077, COG5077, Ubiquitin carboxyl-terminal hydrolase
[Posttranslational modification, protein turnover,
chaperones].
Length = 1089
Score = 26.8 bits (59), Expect = 3.9
Identities = 7/23 (30%), Positives = 9/23 (39%)
Query: 28 NLVPGSNVPDNKIRLQKELGLMD 50
+VP D K+RL G
Sbjct: 1004 VIVPFETFLDTKVRLVARFGYKY 1026
>gnl|CDD|153376 cd07364, PCA_45_Dioxygenase_B, Subunit B of the Class III extradiol
dioxygenase, Protocatechuate 4,5-dioxygenase, which
catalyzes the oxidization and subsequent ring-opening of
protocatechuate. Protocatechuate 4,5-dioxygenase
(LigAB) catalyzes the oxidization and subsequent
ring-opening of protocatechuate (or 3,4-dihydroxybenzoic
acid, PCA), an intermediate in the breakdown of lignin
and other compounds. Protocatechuate 4,5-dioxygenase is
an aromatic ring opening dioxygenase belonging to the
class III extradiol enzyme family, a group of enyzmes
that cleaves aromatic rings between a hydroxylated
carbon and an adjacent non-hydroxylated carbon using a
non-heme Fe(II). LigAB is composed of two subunits,
designated A and B, which form a tetramer composed of
two copies of each subunit. The B subunit (LigB) is the
catalytic subunit of LigAB.
Length = 277
Score = 26.6 bits (59), Expect = 4.1
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 72 LKNAGSPGLALIVW-VMSGALS 92
L+ AGS G+ L++W +M GAL
Sbjct: 231 LREAGSEGIELVMWLIMRGALD 252
>gnl|CDD|224753 COG1840, AfuA, ABC-type Fe3+ transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 299
Score = 26.2 bits (58), Expect = 4.7
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 56 VGVIV---GSGIFVSPIGVLKNAGSPGLA--LIVWVMS 88
V V+ G+G+ S + +LK A +P A I +++S
Sbjct: 198 VEVVYPEEGTGVNPSGVALLKKAKNPEAAKLFIDFLLS 235
>gnl|CDD|234809 PRK00654, glgA, glycogen synthase; Provisional.
Length = 466
Score = 26.2 bits (59), Expect = 5.4
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 38 NKIRLQKELGLMDGVAMIVGVI 59
NK LQ+ GL D A + ++
Sbjct: 267 NKRALQERFGLPDDDAPLFAMV 288
>gnl|CDD|200510 cd11249, Sema_3A, The Sema domain, a protein interacting module, of
semaphorin 3A (Sema3A). Sema3A has been reported to
inhibit the growth of certain experimental tumors and to
regulate endothelial cell migration and apoptosis in
vitro, as well as arteriogenesis in the muscle, skin
vessel permeability, and tumor angiogenesis in vivo. The
function of Sema3A is mediated through receptors
neuropilin-1 (NP1) and plexins, although little is known
about the requirement of specific plexins in its
receptor complex. It is known however that Plexin-A4 is
the receptor for Sema3A in the Toll-like receptor- and
sepsis-induced cytokine storm during immune response.
Sema3A is a member of the Class 3 semaphorin family of
secreted proteins. Semaphorins are regulatory molecules
in the development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 493
Score = 26.1 bits (57), Expect = 5.5
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 12 REPKLVSALEDPTSQDNLVPGSNVPDNKIRLQK 44
REP +SA+E T Q L GS + +++ L +
Sbjct: 459 REPTAISAMELSTKQQQLYIGSAIGVSQLPLHR 491
>gnl|CDD|224216 COG1297, COG1297, Predicted membrane protein [Function unknown].
Length = 624
Score = 26.2 bits (58), Expect = 5.6
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 46 LGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPG-----LALIVWVMSGALSMIGA 96
+GL G+AM++G+ + G+ V P+ L G A VW IGA
Sbjct: 216 VGLPAGIAMLIGIFIAWGVAV-PLLTLIVPGPSDQEAGVQAWKVWSSKVR--FIGA 268
>gnl|CDD|182881 PRK10983, PRK10983, putative inner membrane protein; Provisional.
Length = 368
Score = 25.7 bits (57), Expect = 7.4
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 40 IRLQKELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLA-LIVWVMSGALSM 93
++LQK L +A++V ++ +FV PI +L N+ LI W SG +++
Sbjct: 53 LKLQKILWGRRSLAVLVMTLLLVLLFVIPIALLVNSLVDNSGPLIKWASSGDMTL 107
>gnl|CDD|237276 PRK13024, PRK13024, bifunctional preprotein translocase subunit
SecD/SecF; Reviewed.
Length = 755
Score = 25.6 bits (57), Expect = 8.2
Identities = 10/21 (47%), Positives = 17/21 (80%), Gaps = 3/21 (14%)
Query: 52 VAMIVGVIVG--SGIFV-SPI 69
+A++VG+IVG S IF+ +P+
Sbjct: 708 LALLVGLIVGTYSSIFIAAPL 728
>gnl|CDD|225721 COG3180, AbrB, Putative ammonia monooxygenase [General function
prediction only].
Length = 352
Score = 25.3 bits (56), Expect = 9.2
Identities = 12/46 (26%), Positives = 20/46 (43%)
Query: 52 VAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMSGALSMIGAL 97
++G ++GS S + K L I+ +M+ A M G L
Sbjct: 242 AQALIGALIGSRFDRSILREAKRLLPAILVSIIALMAIAAGMAGLL 287
>gnl|CDD|182458 PRK10435, cadB, lysine/cadaverine antiporter; Provisional.
Length = 435
Score = 25.5 bits (56), Expect = 9.4
Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 7/64 (10%)
Query: 44 KELGLMDGVAMIVGVIVGSGIFVSPIGVLKNAGSPGLALIVWVMS--GALSMIGALCYAE 101
K++GL ++ G ++GSGI + P L + GS +A+ W++S GA+S+ A YA
Sbjct: 5 KKIGLFACTGVVAGNMMGSGIALLP-ANLASIGS--IAIWGWIISIIGAMSL--AYVYAR 59
Query: 102 LVEK 105
L K
Sbjct: 60 LATK 63
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
0.317 0.136 0.407
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,412,511
Number of extensions: 594969
Number of successful extensions: 704
Number of sequences better than 10.0: 1
Number of HSP's gapped: 696
Number of HSP's successfully gapped: 101
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.2 bits)