RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4781
(83 letters)
>gnl|CDD|129984 TIGR00906, 2A0303, cationic amino acid transport permease.
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 557
Score = 77.9 bits (192), Expect = 1e-18
Identities = 33/71 (46%), Positives = 47/71 (66%), Gaps = 4/71 (5%)
Query: 1 MGVKGSAFINSFLTLANLMVMGIVIVVGFYYGRLDNW----INEGGGFLPYGISGVVAGA 56
GVK SA++N T N++V+ VI+ GF + NW GGF+PYG +GV++GA
Sbjct: 178 FGVKESAWVNKIFTAINILVLLFVIIAGFTKADVANWSITEEKGAGGFMPYGFTGVLSGA 237
Query: 57 ATCFYAYVGFD 67
ATCF+A++GFD
Sbjct: 238 ATCFFAFIGFD 248
>gnl|CDD|129987 TIGR00909, 2A0306, amino acid transporter. [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 429
Score = 44.4 bits (105), Expect = 9e-07
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 2 GVKGSAFINSFLTLANLMVMGIVIVVGFYYGRLDNWINEGGGFLPYGISGVVAGAATCFY 61
G K S +N L + + + + +G + +N+ F+P G GV A A F+
Sbjct: 151 GAKESGKVNDILVVLKVAALLLFAALGAIHFASNNYTP----FMPMGFGGVGAATALVFF 206
Query: 62 AYVGFD 67
A++GF+
Sbjct: 207 AFIGFE 212
>gnl|CDD|224038 COG1113, AnsP, Gamma-aminobutyrate permease and related permeases
[Amino acid transport and metabolism].
Length = 462
Score = 33.4 bits (77), Expect = 0.005
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 13 LTLANLMVMGIVIVVGFYYGR-----LDNWINEGGGFLPYGISGVVAGAATCFYAYVG 65
+ +V+GIV++ G + G N + GGF P G G ++ +A+ G
Sbjct: 162 AAIIAFIVVGIVLLFGGFGGGGGAAGFSNLWD-HGGFFPNGFLGFLSALQIVMFAFGG 218
>gnl|CDD|223605 COG0531, PotE, Amino acid transporters [Amino acid transport and
metabolism].
Length = 466
Score = 31.3 bits (71), Expect = 0.032
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 1 MGVKGSAFINSFLTLANLMVMGIVIVVGFYYGRLDNW-INEGGGFLPYGISGVVAGAATC 59
G+K SA INS +T+ ++++ I I++G + N + G++A
Sbjct: 151 RGIKASAKINSIITILKIIILLIFIILGLFAFGFSNGNLFAPFNPGGGSFGGILAAILLA 210
Query: 60 FYAYVGFD 67
F+A+ GF+
Sbjct: 211 FFAFTGFE 218
>gnl|CDD|222193 pfam13520, AA_permease_2, Amino acid permease.
Length = 425
Score = 28.4 bits (64), Expect = 0.29
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 1 MGVKGSAFINSFLTLAN-LMVMGIVIVVGFYYGRLD---NWINEGGGFLPYGISGVVAGA 56
G+K SA I + L + L+ + ++I++G N F P G GV G
Sbjct: 135 RGIKESAKIQNILGIVKLLLPLILIILLGLVLALGGGFNLLPNSWTTFFPSGWPGVFLGL 194
Query: 57 ATCFYAYVGFDKC 69
+++ GF+
Sbjct: 195 LIVLWSFGGFESA 207
>gnl|CDD|233567 TIGR01773, GABAperm, gamma-aminobutyrate permease. GABA permease
(gabP) catalyzes the translocation of 4-aminobutyrate
(GABA) across the plasma membrane, with homologues
expressed in Gram-negative and Gram-positive organisms.
This permease is a highly hydrophobic transmembrane
protein consisting of 12 transmembrane domains with
hydrophilic N- and C-terminal ends. Induced by
nitrogen-limited culture conditions in both Escherichia
coli and Bacillus subtilis, gabP is an energy dependent
transport system stimulated by membrane potential and
has been observed adjacent and distant from other GABA
degradation proteins. GabP is highly homologous to amino
acid permeases from B. subtilis, E. coli, as well as to
other members of the amino acid permease family
(pfam00324). A member of the APC
(amine-polyamine-choline) transporter superfamily, GABA
permease possesses a "consensus amphiphatic region"
(CAR) found to be evolutionarily conserved within this
transport family. This amphiphatic region is located
between helix 8 and cytoplasmic loop 8-9, forming a
potential channel domain and suggested to play a
significant role in ligand recognition and
translocation. Unique to GABA permeases, a conserved
cysteine residue (CYS-300, E.coli) located at the
beginning of the amphiphatic domain, has been determined
to be critical for catalytic specificity [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 452
Score = 28.7 bits (64), Expect = 0.32
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 13 LTLANLMVMGIVIVVGFYYGRLDNWIN---EGGGFLPYGISGVVAGAATCFYAYVG 65
+ + +++G V + GF G + + GGF P GI V+ ++++G
Sbjct: 161 IAIIAFIILGAVAIFGFAPGSEVSGFSNLTGKGGFFPNGIGAVLLAILVTMFSFMG 216
>gnl|CDD|234371 TIGR03839, termin_org_P1, adhesin P1. Members of this protein
family are the major adhesin of the Mycoplasma terminal
organelle. The protein is called adhesin P1, cytadhesin
P1, P140, attachment protein, and MgPa, with locus names
MG191 in Mycoplasma genitalium and MPN141 in M.
pneumoniae. A conserved C-terminal region is shared by
additional paralogs in M. pneumoniae and M.
gallisepticum, as well as by the member of this family
[Cell envelope, Surface structures, Cellular processes,
Pathogenesis].
Length = 1425
Score = 27.4 bits (60), Expect = 0.92
Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 12/62 (19%)
Query: 1 MGVKGSAFINSFLTLANLMVMG-IVIVVGFYYGRLD---NWINEGGGFL--------PYG 48
M V G + L LA + MG V Y L+ N + +G G L PYG
Sbjct: 537 MAVGGVKGVGGNLVLAGTITMGDTATVPRLLYDELESNLNLVAQGQGLLREDLQWFTPYG 596
Query: 49 IS 50
+
Sbjct: 597 WA 598
>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 = 26.9 bits (60), Expect = 1.2
Identities = 14/34 (41%), Positives = 24/34 (70%)
Query: 2 GVKGSAFINSFLTLANLMVMGIVIVVGFYYGRLD 35
GV+G+AFIN+ T+A L+ + + IV+G + + D
Sbjct: 141 GVEGAAFINTITTIAKLVPLFVFIVIGIFAFKGD 174
>gnl|CDD|226494 COG4006, COG4006, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 278
Score = 26.8 bits (59), Expect = 1.3
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 37 WINEGGGFLPYG----ISGVVAGAATCFYAYVGFDK 68
+IN GGF P ++G +AGA+ +Y + F+
Sbjct: 155 YINATGGFKPESGFLTLAGSLAGASAVYYIHEAFND 190
>gnl|CDD|216195 pfam00923, Transaldolase, Transaldolase.
Length = 244
Score = 26.4 bits (59), Expect = 1.5
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 26 VVGFYYGRLDNWINEGGGFLPYGISGV 52
V+ + GR+D+W ++ G G GV
Sbjct: 151 VISPFVGRIDDWGDKRLGAALRGDDGV 177
>gnl|CDD|236830 PRK11049, PRK11049, D-alanine/D-serine/glycine permease;
Provisional.
Length = 469
Score = 26.2 bits (58), Expect = 1.8
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 18 LMVMGIVIV-VGF-----YYGRLDNWINEGGGFLPYGISGVVAGAATCFYAYVG 65
L+V+G+V+V + F + N+GG F P G+SG AG +A+VG
Sbjct: 174 LIVVGLVMVAMHFQSPTGVEASFAHLWNDGGMF-PKGLSGFFAGFQIAVFAFVG 226
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 26.1 bits (58), Expect = 2.2
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 42 GGFLPYGISGV--VA-GAATCFYAYVGFDKCWKCLIRIGVRTT 81
GG L +GV +A G AT Y+ +K ++ IR GVRT+
Sbjct: 35 GGTLDPAATGVLPIALGKATRLLPYLPGEKTYRGTIRFGVRTS 77
>gnl|CDD|224515 COG1599, RFA1, Single-stranded DNA-binding replication protein A
(RPA), large (70 kD) subunit and related ssDNA-binding
proteins [DNA replication, recombination, and repair].
Length = 407
Score = 25.9 bits (57), Expect = 2.4
Identities = 8/37 (21%), Positives = 10/37 (27%), Gaps = 7/37 (18%)
Query: 20 VMGIVIVVGFYYGRLDNW-------INEGGGFLPYGI 49
I + R+ W INE GI
Sbjct: 300 GKDIGLDDLTGKIRVTLWGDATEVLINEESVEALKGI 336
>gnl|CDD|224099 COG1178, ThiP, ABC-type Fe3+ transport system, permease component
[Inorganic ion transport and metabolism].
Length = 540
Score = 26.1 bits (58), Expect = 2.6
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 6 SAFINSFL--TLANLMVMGIVIVVGF----YYGRLDNWINEGGGFLPYGISGVVAGAA 57
A +NS L A L+ + + +++ + RL + E LP + GVV
Sbjct: 333 QALLNSLLLALAAALLAVVLALLLAYAVRRLRSRLSRLL-ERLSMLPLAVPGVVLALG 389
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 25.8 bits (57), Expect = 3.1
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 15 LANL--MVMGI---VIVVGFYYGRL 34
L NL + M I V+VVG YYG L
Sbjct: 1 LGNLVSLCMKIINSVVVVGLYYGFL 25
>gnl|CDD|182324 PRK10238, PRK10238, aromatic amino acid transporter; Provisional.
Length = 456
Score = 25.7 bits (56), Expect = 3.7
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 40 EGGGFLPYGISGVVAGAATCFYAYVGFD 67
+ GGFLP+G +G+V A +++ G +
Sbjct: 190 DQGGFLPHGFTGLVMMMAIIMFSFGGLE 217
>gnl|CDD|214398 MTH00004, ND5, NADH dehydrogenase subunit 5; Validated.
Length = 602
Score = 25.5 bits (57), Expect = 3.8
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 11 SFLTLANLMVMGIVIVVGFY 30
S LT+ NL +MG + GFY
Sbjct: 370 SCLTIGNLALMGTPFLSGFY 389
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is
unknown, it is known to be an essential gene.
Length = 832
Score = 25.3 bits (56), Expect = 4.3
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 24 VIVVGFYYGRL 34
V+VVG YYG L
Sbjct: 2 VVVVGLYYGFL 12
>gnl|CDD|130585 TIGR01522, ATPase-IIA2_Ca, golgi membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
golgi membrane of fungi and animals , and is of
particular importance in the sarcoplasmic reticulum of
skeletal and cardiac muscle in vertebrates. The calcium
P-type ATPases have been characterized as Type IIA based
on a phylogenetic analysis which distinguishes this
group from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the former of which is
modelled by TIGR01116.
Length = 884
Score = 25.2 bits (55), Expect = 5.1
Identities = 8/26 (30%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 13 LTLANLMVMGIVIVVGFYYGRLDNWI 38
L+L + V+G++ +VG++ G+ +W+
Sbjct: 249 LSLVSFGVIGVICLVGWFQGK--DWL 272
>gnl|CDD|235105 PRK03124, PRK03124, S-adenosylmethionine decarboxylase proenzyme;
Provisional.
Length = 127
Score = 24.5 bits (54), Expect = 7.1
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 44 FLPYGISGVV 53
F P G+SGVV
Sbjct: 49 FSPQGVSGVV 58
>gnl|CDD|177874 PLN02229, PLN02229, alpha-galactosidase.
Length = 427
Score = 24.5 bits (53), Expect = 8.2
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 52 VVAGAATCFYAYVGFDKCWKCLIR 75
V G A Y +V D CW L R
Sbjct: 90 VSTGLADLGYIHVNIDDCWSNLKR 113
>gnl|CDD|153238 cd03144, GATase1_ScBLP_like, Type 1 glutamine amidotransferase
(GATase1)-like domain found in proteins similar to
Saccharomyces cerevisiae biotin-apoprotein ligase
(ScBLP). Type 1 glutamine amidotransferase
(GATase1)-like domain found in proteins similar to
Saccharomyces cerevisiae biotin-apoprotein ligase
(ScBLP). Biotin-apoprotein ligase modifies proteins by
covalently attaching biotin. ScBLP is known to
biotinylate acety-CoA carboxylase and pyruvate
carboxylase. The catalytic triad typical of GATase1
domains is not conserved in this GATase1-like domain.
However, the Cys residue found in the sharp turn
between a beta strand and an alpha helix termed the
nucleophile elbow in a typical GATase1 domain is
conserved.
Length = 114
Score = 23.7 bits (52), Expect = 9.5
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 8/31 (25%)
Query: 33 RLDNWINEGGGFLPYGISGVVAGAATCFYAY 63
R+ N++ GG +L G+ AGA + AY
Sbjct: 69 RIRNFVRNGGNYL-----GICAGA---YLAY 91
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 0.148 0.487
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,391,365
Number of extensions: 373536
Number of successful extensions: 712
Number of sequences better than 10.0: 1
Number of HSP's gapped: 704
Number of HSP's successfully gapped: 81
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
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: 53 (24.1 bits)