RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12819
(675 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 = 118 bits (298), Expect = 1e-28
Identities = 49/215 (22%), Positives = 94/215 (43%), Gaps = 16/215 (7%)
Query: 26 HLLKASLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYILVQCGHVLYRRTKVTSM 85
+L+KA +G G+LS+PYAF+ G G+ L V+V +I + ++LVQC + +
Sbjct: 11 NLIKAIIGAGVLSLPYAFKQLGWIPGLILLVIVGLISLYTLHLLVQCSKYVDKVKGKRRK 70
Query: 86 SFADIGEVAFAKGPAWGRRYARFARICILLGLFLAYFGTCSVYTVIIAKNFSKVI-NHYT 144
S+ D+G F ++ IL + + FG C Y + N + + +
Sbjct: 71 SYGDLGYRLFGP----------KGKLLILFAILVNLFGVCISYLIFAGDNLPAIFDSFFD 120
Query: 145 GTELDIRVYISAFLIPLILLSWVPNLKSLAPVSMVANLLMGTGLGITFYYIV-----WDL 199
+ + +I F + I LS++PNL +L+ +S+VA + + +
Sbjct: 121 TCHISLVYFIIIFGLIFIPLSFIPNLSALSILSLVAAVSSLYIVILVLSVAELGVLTAQG 180
Query: 200 HKPMEMPQIADISTMPTFFSIVIFAIEAIGVVISF 234
+ ++ + I++FA E V++
Sbjct: 181 VGSLGAKTNIKLARLFLAIGIIVFAFEGHAVLLPI 215
Score = 64.6 bits (158), Expect = 6e-11
Identities = 41/184 (22%), Positives = 83/184 (45%), Gaps = 24/184 (13%)
Query: 431 HPVTDGETLTHLLKASLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYILGWRNTD 490
++ + + +L+KA +G G+LS+PYAF+ G G+ L V+V +I + ++L +
Sbjct: 1 GTISAWQAVFNLIKAIIGAGVLSLPYAFKQLGWIPGLILLVIVGLISLYTLHLLVQ-CSK 59
Query: 491 PLAESFTRYRNSIHALCVRFDLYSRFELS--------SKISIRISQVI-----------N 531
+ + + R S L R L+ + + IS +I +
Sbjct: 60 YVDKVKGKRRKSYGDLGYR--LFGPKGKLLILFAILVNLFGVCISYLIFAGDNLPAIFDS 117
Query: 532 HYTGTELDIRVYISAFLIPLILLSWVPNLKSLAPVSMVANLLMGTGLGITFYYIVYKVAV 591
+ + + +I F + I LS++PNL +L+ +S+VA + + V ++ V
Sbjct: 118 FFDTCHISLVYFIIIFGLIFIPLSFIPNLSALSILSLVAAVSSLY--IVILVLSVAELGV 175
Query: 592 VPAK 595
+ A+
Sbjct: 176 LTAQ 179
Score = 56.1 bits (136), Expect = 3e-08
Identities = 29/146 (19%), Positives = 56/146 (38%), Gaps = 21/146 (14%)
Query: 259 VQCGHVLYRRTKVTSMSFADIGEVAFAKGPAWGRRYARFARICILLGLFLAYFGTCSVYT 318
VQC + + S+ D+G F ++ IL + + FG C Y
Sbjct: 55 VQCSKYVDKVKGKRRKSYGDLGYRLFGP----------KGKLLILFAILVNLFGVCISYL 104
Query: 319 VIIAKNFSKSSKISIRISQVINHYTGTELDIRVYISAFLIPLILLSWVPNLKSLAPVSMV 378
+ N + + + + +I F + I LS++PNL +L+ +S+V
Sbjct: 105 IFAGDNLPAIFD---------SFFDTCHISLVYFIIIFGLIFIPLSFIPNLSALSILSLV 155
Query: 379 ANLLMGTGLGITFYYIVYKVAVVPAK 404
A + + V ++ V+ A+
Sbjct: 156 AAVSSLY--IVILVLSVAELGVLTAQ 179
Score = 51.1 bits (123), Expect = 1e-06
Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 622 HPVTDGETLTHLLKASLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYIL 675
++ + + +L+KA +G G+LS+PYAF+ G G+ L V+V +I + ++L
Sbjct: 1 GTISAWQAVFNLIKAIIGAGVLSLPYAFKQLGWIPGLILLVIVGLISLYTLHLL 54
>gnl|CDD|223884 COG0814, SdaC, Amino acid permeases [Amino acid transport and
metabolism].
Length = 415
Score = 82.3 bits (204), Expect = 1e-16
Identities = 39/215 (18%), Positives = 72/215 (33%), Gaps = 18/215 (8%)
Query: 27 LLKASLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYILVQCGHVLYRRTKVTSMS 86
L ++G G+L +P AF G G+ L ++ + +L++ + S
Sbjct: 18 LAGTAIGAGVLFLPVAFGGGGFWPGLLLLIIAWPLTYLSLLLLLEA----LLSSPNGKAS 73
Query: 87 FADIGEVAFAKGPAWGRRYARFARICILLGLFLAYFGTCSVYTVIIAKNFSKVINHYTGT 146
+ E G G I I L F A +G Y V I + + + G
Sbjct: 74 ITSLVEDYL--GKKGG--------ILIGLSYFFALYGLLVAYIVGIGNLLASFLGNQFGL 123
Query: 147 E-LDIRVYISAFLIPLILLSWVPNLKSLAPVSMVANLLMGTGLGITFYYIV---WDLHKP 202
L ++ F + L LSW+ L L S++ + + + Y I
Sbjct: 124 NPLPRKLGSLIFALVLAFLSWLGTLAVLKITSLLVFGKVIYLVLLVVYLIPHWNPANLFA 183
Query: 203 MEMPQIADISTMPTFFSIVIFAIEAIGVVISFRTA 237
+ + + + +F+ G + S
Sbjct: 184 LPSASQSFWKYLLLAIPVFVFSFGFHGNIPSLVNY 218
Score = 47.3 bits (113), Expect = 2e-05
Identities = 29/166 (17%), Positives = 55/166 (33%), Gaps = 28/166 (16%)
Query: 442 LLKASLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYILGWRNTDPLAESFTRYRN 501
L ++G G+L +P AF G G+ L ++ + + L E+ N
Sbjct: 18 LAGTAIGAGVLFLPVAFGGGGFWPGLLLLIIAWPLTYLSLLL--------LLEALLSSPN 69
Query: 502 SIHALC------------------VRFDLYS-RFELSSKISIRISQVINHYTGTE-LDIR 541
++ F LY I ++ + + G L +
Sbjct: 70 GKASITSLVEDYLGKKGGILIGLSYFFALYGLLVAYIVGIGNLLASFLGNQFGLNPLPRK 129
Query: 542 VYISAFLIPLILLSWVPNLKSLAPVSMVANLLMGTGLGITFYYIVY 587
+ F + L LSW+ L L S++ + + + Y I +
Sbjct: 130 LGSLIFALVLAFLSWLGTLAVLKITSLLVFGKVIYLVLLVVYLIPH 175
Score = 42.3 bits (100), Expect = 7e-04
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 633 LLKASLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYIL 675
L ++G G+L +P AF G G+ L ++ + +L
Sbjct: 18 LAGTAIGAGVLFLPVAFGGGGFWPGLLLLIIAWPLTYLSLLLL 60
Score = 37.2 bits (87), Expect = 0.027
Identities = 26/129 (20%), Positives = 42/129 (32%), Gaps = 19/129 (14%)
Query: 268 RTKVTSMSFADIGEVAFAKGPAWGRRYARFARICILLGLFLAYFGTCSVYTVIIAKNFSK 327
+ S + E G G I I L F A +G Y V I +
Sbjct: 66 SSPNGKASITSLVEDYL--GKKGG--------ILIGLSYFFALYGLLVAYIVGIGNLLA- 114
Query: 328 SSKISIRISQVINHYTGTELDIRVYISAFLIPLILLSWVPNLKSLAPVSMVANLLMGTGL 387
S + N + L ++ F + L LSW+ L L S++ + +
Sbjct: 115 --------SFLGNQFGLNPLPRKLGSLIFALVLAFLSWLGTLAVLKITSLLVFGKVIYLV 166
Query: 388 GITFYYIVY 396
+ Y I +
Sbjct: 167 LLVVYLIPH 175
>gnl|CDD|234293 TIGR03648, Na_symport_lg, probable sodium:solute symporter, VC_2705
subfamily. This family belongs to a larger family of
transporters of the sodium:solute symporter superfamily,
TC 2.A.21. Members of this strictly bacterial protein
subfamily are found almost invariably immediately
downstream from a member of family TIGR03647.
Occasionally, the two genes are fused.
Length = 552
Score = 39.5 bits (93), Expect = 0.005
Identities = 18/59 (30%), Positives = 25/59 (42%)
Query: 184 MGTGLGITFYYIVWDLHKPMEMPQIADISTMPTFFSIVIFAIEAIGVVISFRTATLLSR 242
M TGLG TF YIV+ +F I I IG+ ++F A ++S
Sbjct: 475 MLTGLGFTFSYIVYFKPWGFIGTNPGANVPENWWFGISPEGIGLIGMPVNFAVAIVVSL 533
>gnl|CDD|233139 TIGR00814, stp, serine transporter. The Hydroxy/Aromatic Amino
Acid Permease (HAAAP) Family- serine/threonine subfamily
(TC 2.A.42.2) The HAAAP family includes well
characterized aromatic amino acid:H+ symport permeases
and hydroxy amino acid permeases. This subfamily is
specific for hydroxy amino acid transporters and
includes the serine permease, SdaC, of E. coli, and the
threonine permease, TdcC, of E. coli.//added GO terms,
none avaialbelf or ser/thr specifically [SS 2/6/05]
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 397
Score = 38.5 bits (90), Expect = 0.010
Identities = 59/226 (26%), Positives = 99/226 (43%), Gaps = 38/226 (16%)
Query: 31 SLGTGILSMPYAFRNAGLTGGIFLTVLVAVICTHCSYILVQCGHVLYRRTKVTSMSFA-D 89
++G G+L +P AGL GG+++ VL+A+I +Y L GH R ++S + D
Sbjct: 16 AIGAGVLFLPI---QAGL-GGLWVLVLMAII----AYPLTYFGHRALARFLLSSKNPCED 67
Query: 90 IGEVA---FAKGPAWGRRYARFARICILLGL--FLAYFGTCSVYTVIIAKNFSKVINHYT 144
I EV F K WG IL+ L F A + +Y+V I + + + +
Sbjct: 68 ITEVVEEHFGKN--WG----------ILITLLYFFAIYPILLIYSVAITNDSASFLVNQL 115
Query: 145 GTELDIRVYISAFLIPLILLSWVPNLKSLAPVS--MVANLLMGTGLGITFYYIVWDLHKP 202
GT +R +S LI +++ K L + +V L+ + ++ Y I
Sbjct: 116 GTAPPLRGLLSLALILILVAIMSFGEKLLFKIMGPLVFPLV-LILVLLSLYLI------- 167
Query: 203 MEMPQIADISTMPTFFSIVIFAIEAIGV-VISFRTATLLSRPVISR 247
A+++T P+F + I V V SF + ++S IS
Sbjct: 168 -PHWNGANLTTFPSFNGFLKTLWLTIPVMVFSFNHSPIISSFAISY 212
>gnl|CDD|223174 COG0096, RpsH, Ribosomal protein S8 [Translation, ribosomal
structure and biogenesis].
Length = 132
Score = 29.0 bits (66), Expect = 3.6
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 489 TDPLAESFTRYRNSIHALCVRFDLYSRFELSSKISIRISQVINHY 533
TDPLA+ TR RN A + ++ S +SK+ I +V+
Sbjct: 4 TDPLADMLTRIRN---AERAKKEVVSMP--ASKLKGAILKVLKKE 43
>gnl|CDD|212048 cd11478, SLC5sbd_u2, Uncharacterized bacterial solute carrier 5
subfamily; putative solute-binding domain. SLC5 (also
called the sodium/glucose cotransporter family or solute
sodium symporter family) is a family of proteins that
co-transports Na+ with sugars, amino acids, inorganic
ions or vitamins. Prokaryotic members of this family
include Vibrio parahaemolyticus glucose/galactose
(vSGLT), and Escherichia coli proline (PutP) and
pantothenate (PutF) cotransporters. One member of the
SLC5 family, human SGLT3, has been characterized as a
glucose sensor and not a transporter. This subfamily
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 495
Score = 30.3 bits (69), Expect = 4.1
Identities = 33/142 (23%), Positives = 55/142 (38%), Gaps = 32/142 (22%)
Query: 103 RRYARFARICILLGLFLAYFGTCSVYTVIIAKNFSKVINHYTGTELDIRVYISAFLIPLI 162
+ Y + RI ++G+ + S+ T IA +F+ ++++ ++ S F PL
Sbjct: 367 KHYLKVGRIATVVGVLI------SIGTAYIAMSFNNIMDY-------LQTLFSFFNAPLF 413
Query: 163 ---LLS--WVPNLKSLAPVSMVANLLMGTGLGITFYYIVWDLHKPMEMPQIADISTMPTF 217
LL W K P LL GT I Y + E+ + S M
Sbjct: 414 ATFLLGMFW----KRATPWGGFWGLLAGTASAIVLYGLY-------ELGMLPYFSDMAPN 462
Query: 218 FSIVIFAIEA---IGVVISFRT 236
F I+A + V++S T
Sbjct: 463 FYGAIWAFVVCFVVTVLVSLLT 484
>gnl|CDD|176127 cd08436, PBP2_LTTR_like_3, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 194
Score = 29.5 bits (67), Expect = 4.6
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 427 RKLAHPVTDGETLTHLLKASLGTGILSMPYAFRNAGLT 464
R++A V+D + L L+ LG +L A R GL
Sbjct: 125 RRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLA 162
Score = 29.5 bits (67), Expect = 4.6
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 618 RKLAHPVTDGETLTHLLKASLGTGILSMPYAFRNAGLT 655
R++A V+D + L L+ LG +L A R GL
Sbjct: 125 RRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLA 162
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
0.327 0.141 0.430
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: 35,102,040
Number of extensions: 3563870
Number of successful extensions: 4976
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4955
Number of HSP's successfully gapped: 115
Length of query: 675
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 572
Effective length of database: 6,369,140
Effective search space: 3643148080
Effective search space used: 3643148080
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: 62 (27.6 bits)