RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11010
(256 letters)
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 53.0 bits (128), Expect = 2e-08
Identities = 29/122 (23%), Positives = 51/122 (41%), Gaps = 5/122 (4%)
Query: 106 AFVQLLANPLVGILTHRVGYSLPMFTGFVIMFLSTLIFAFGRTYGVLFLARSLQGIGSSC 165
QL P+ + RVG + G I L+TL+ + VL A ++QG+G+
Sbjct: 49 GVSQLFYGPI----SDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTGV 104
Query: 166 SSVSGMGMLAERYPDDRERGNAMGIALGGLALGVLIGPPFGGIMYQFVGKTAPFLILSAL 225
V + + Y + + +A + G+ + L+ P GG++ A +L L L
Sbjct: 105 GGVMARTLPRDLY-ERTQLRHANSLLNMGILVSPLLAPLIGGLLDTMWNWRACYLFLLVL 163
Query: 226 AL 227
Sbjct: 164 CA 165
>2cfq_A Lactose permease; transport, transport mechanism, lactose/H+
symport, sugar transport, transmembrane, formylation;
2.95A {Escherichia coli} SCOP: f.38.1.2 PDB: 1pv7_A*
1pv6_A 2cfp_A 2v8n_A 2y5y_A*
Length = 417
Score = 51.5 bits (123), Expect = 8e-08
Identities = 20/135 (14%), Positives = 47/135 (34%), Gaps = 2/135 (1%)
Query: 95 TKAVGVMFGSKAFVQLLANPLVGILTHRVGYSLPMFTGFVIMFLSTLIFAFGRTYGVLFL 154
T+ G + + ++ +R+G + IM + + +F + + +
Sbjct: 258 TRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVI 317
Query: 155 ARSLQGIGSSCSSVSGMGMLAERYPDDRERGNAMGIALG-GLALGVLIGPPFGGIMYQFV 213
++L V + ++ R + L ++ G MY+ +
Sbjct: 318 LKTLHMFEVPFLLVGCFKYITSQFEV-RFSATIYLVCFCFFKQLAMIFMSVLAGNMYESI 376
Query: 214 GKTAPFLILSALALG 228
G +L+L +ALG
Sbjct: 377 GFQGAYLVLGLVALG 391
Score = 43.8 bits (103), Expect = 3e-05
Identities = 31/135 (22%), Positives = 52/135 (38%), Gaps = 5/135 (3%)
Query: 98 VGVMFGSKAFVQLLANPLVGILTHRVGYS---LPMFTGFVIMFLSTLIFAFGRTYGVLFL 154
G++F + + LL PL G+L+ ++G L + TG ++MF IF FG L
Sbjct: 45 TGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNIL 104
Query: 155 ARSLQGIGSSCSSVSGMGMLAERYPDD--RERGNAMGIALGGLALGVLIGPPFGGIMYQF 212
S+ G + E + + R G A +G +G GIM+
Sbjct: 105 VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALGASIVGIMFTI 164
Query: 213 VGKTAPFLILSALAL 227
+ +L +
Sbjct: 165 NNQFVFWLGSGCALI 179
>1pw4_A Glycerol-3-phosphate transporter; transmembrane, inner membrane,
major facilitator superfamily, secondary active membrane
transporter; 3.30A {Escherichia coli} SCOP: f.38.1.1
Length = 451
Score = 47.3 bits (113), Expect = 2e-06
Identities = 20/122 (16%), Positives = 41/122 (33%), Gaps = 6/122 (4%)
Query: 111 LANPLVGILTHRVGYSLPMFTGFVIMFLSTLIFAFGR----TYGVLFLARSLQGIGSSCS 166
+ ++G ++ R + + G ++ L F + V+F+ L G
Sbjct: 77 FSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMG 136
Query: 167 SVSGMGMLAERYPDDRERGNAMGIALGGLALGVLIGPP-FGGIMYQFVGKTAPFLILSAL 225
+ + +ERG + + +G I P F M F A + +
Sbjct: 137 WPPCGRTMVHWWSQ-KERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFC 195
Query: 226 AL 227
A+
Sbjct: 196 AI 197
Score = 27.7 bits (62), Expect = 4.2
Identities = 16/104 (15%), Positives = 28/104 (26%), Gaps = 10/104 (9%)
Query: 129 MFTGFVIMFLSTLIFAFGRTYGVLFLARSLQGIGSSCSSVSGMGMLAERYPDDRERGNAM 188
F V + V + + + G ML + + A
Sbjct: 326 FFMTLVTIATIVYWMNPAGNPTVDMIC-----MIVIGFLIYGPVMLIGLHALELAPKKAA 380
Query: 189 GIALG-----GLALGVLIGPPFGGIMYQFVGKTAPFLILSALAL 227
G A G G G + G F G F+++ ++
Sbjct: 381 GTAAGFTGLFGYLGGSVAASAIVGYTVDFFGWDGGFMVMIGGSI 424
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 43.3 bits (101), Expect = 5e-05
Identities = 42/292 (14%), Positives = 81/292 (27%), Gaps = 83/292 (28%)
Query: 4 FQV--VSYGRHTREELVVRLVAEMSRVKTSGAGHRGHSSGSGQHVAHHCRKKSRE---SR 58
F++ ++ E V+ ++ ++ R S + + H + + R S+
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 59 RLV--LVIVAIALVLDN---------------MLLTT----VEDVARENRHKYLMGETKA 97
L LVL N +LLTT V D ++ + +
Sbjct: 242 PYENCL------LVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHS 295
Query: 98 VGVMFGSKAFVQLLANPLVGILTHRVGYSLP--MFTG--FVIMFLSTLIFAFGR------ 147
+ LL L R LP + T + ++I R
Sbjct: 296 MT--LTPDEVKSLLLK----YLDCRPQ-DLPREVLTTNPRRL----SIIAESIRDGLATW 344
Query: 148 -TYGVLFLARSLQGIGSSCSSVSGMGMLAERYPDD-RERGNAMGIALGGLALGVLIGPP- 204
+ + + I SS L P + R+ + + + I P
Sbjct: 345 DNWKHVNCDKLTTIIESS---------LNVLEPAEYRKMFDRLSV----FPPSAHI-PTI 390
Query: 205 -----FGGIMYQFVGKTAPFLILSALALGDGCKCNYTIVQKSSSHDRNINLD 251
+ ++ V L +L + +I I L+
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI------PS--IYLE 434
>3o7q_A L-fucose-proton symporter; transporter, multi-PASS membrane protei
transport protein; HET: BNG; 3.14A {Escherichia coli}
PDB: 3o7p_A*
Length = 438
Score = 33.8 bits (77), Expect = 0.049
Identities = 17/104 (16%), Positives = 34/104 (32%), Gaps = 4/104 (3%)
Query: 110 LLANPLVGILTHRVGYSLPMFTGFVIMFLSTLIF---AFGRTYGVLFLARSLQGIGSSCS 166
+ GIL ++ Y + TG + L +F A Y + + + G C
Sbjct: 75 FIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCL 134
Query: 167 SVSGMGMLAERYPDDRERGNAMGIALGGLALGVLIGPPFGGIMY 210
+ + + + +A + G +I FG +
Sbjct: 135 ETAANPFVTV-LGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLI 177
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 32.7 bits (74), Expect = 0.12
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 22/63 (34%)
Query: 159 QGIGSSCSSVSGMGM-LAERYP------D--DRERGNAMGIALGGLALGVLIGPP----- 204
QG S GMGM L + + D + G ++ + V+ P
Sbjct: 1624 QG-----SQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDI---VINNPVNLTIH 1675
Query: 205 FGG 207
FGG
Sbjct: 1676 FGG 1678
Score = 32.7 bits (74), Expect = 0.12
Identities = 42/243 (17%), Positives = 81/243 (33%), Gaps = 58/243 (23%)
Query: 41 GSGQHV--AHHCRKKSRESRRL----------VLVIVAIALVLDNMLLTTVE---DVARE 85
GS Q K S+ ++ + + +V++N + T+ + +
Sbjct: 1625 GS-QEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR 1683
Query: 86 NRHKY--LMGETKAVGVMFGSKAFVQLLANPLVGILTHRVGY-SLPMFTGFVIMFLSTLI 142
R Y ++ ET G + K F ++ + G S FT + +
Sbjct: 1684 IRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAA 1743
Query: 143 FAFGRTYGVL----FLA-RSLQGIG--SSCSSVSG-MGMLAERYPDD-----RERGNAMG 189
F ++ G++ A SL G ++ +S++ M + + RG M
Sbjct: 1744 FEDLKSKGLIPADATFAGHSL---GEYAALASLADVMSI------ESLVEVVFYRGMTMQ 1794
Query: 190 IA-----LGGLALGVL-IGPPFGGIMYQFVGKTAPFLILSALALGDGCKC---NY----- 235
+A LG G++ I P G + + A ++ + G NY
Sbjct: 1795 VAVPRDELGRSNYGMIAINP---GRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQ 1851
Query: 236 TIV 238
V
Sbjct: 1852 QYV 1854
Score = 28.9 bits (64), Expect = 2.2
Identities = 39/209 (18%), Positives = 63/209 (30%), Gaps = 75/209 (35%)
Query: 6 VVSYGRHTREELVVRLVAEMSRVKTSGAGHRGHSSGSGQHVAHHCRKKSRESRRLVLVIV 65
VVS G + L L + + K SG Q +K + S R L +
Sbjct: 378 VVS-G--PPQSLY-GLNLTLRKAKAP--------SGLDQSRIPFSERKLKFSNRF-LPVA 424
Query: 66 ----------AIALVLDNMLLTTVEDVARENRHKYLMGETKAVGVMFGSKAFVQLLANPL 115
A L+ +D+ + N V F +K + P+
Sbjct: 425 SPFHSHLLVPASDLIN--------KDLVKNN-------------VSFNAKD----IQIPV 459
Query: 116 VGILTHRVGYSLPMFTGFVIMFLSTLIF----------AFGRTYGVLFLARSLQGIGSSC 165
G L + +G + + I F T+ + F G G
Sbjct: 460 YDTFD---GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDF------GPG--- 507
Query: 166 SSVSGMGMLAERYPDDRERGNAMGIALGG 194
SG+G+L R D G + + + G
Sbjct: 508 -GASGLGVLTHRNKD----GTGVRVIVAG 531
>4aps_A DI-OR tripeptide H+ symporter; transport protein, peptide
transport, major facilitator SUPE transporter, MFS;
3.30A {Streptococcus thermophilus}
Length = 491
Score = 31.6 bits (72), Expect = 0.22
Identities = 30/143 (20%), Positives = 51/143 (35%), Gaps = 5/143 (3%)
Query: 82 VARENRHKYLMGETKAVGVMFGSKAFVQLLANPLVG-ILTHRV-GYSLPMFTGFVIMFLS 139
+ + A +M + V L +G + R+ G +F G V++ L
Sbjct: 41 WFLISTGDLHITRATAASIMAIYASMVYLS--GTIGGFVADRIIGARPAVFWGGVLIMLG 98
Query: 140 TLIFAFGRTYGVLFLARSLQGIGSSCSSVSGMGMLAERYP-DDRERGNAMGIALGGLALG 198
++ A LF + L IG+ + ++ Y DR R I + G+ LG
Sbjct: 99 HIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAGFSIFVFGINLG 158
Query: 199 VLIGPPFGGIMYQFVGKTAPFLI 221
I P G + G F +
Sbjct: 159 AFIAPLIVGAAQEAAGYHVAFSL 181
>2xut_A Proton/peptide symporter family protein; transport protein,
membrane protein, major facilitator super transporter;
3.62A {Shewanella oneidensis}
Length = 524
Score = 28.5 bits (64), Expect = 2.7
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 110 LLANPLVGILTHRVGYSLPMFTGFVI----MFLSTLIFAFGR 147
A+ + +L G ++ F I MF++T+ F GR
Sbjct: 162 FFASLSMPLLLKNFGAAV----AFGIPGVLMFVATVFFWLGR 199
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 27.5 bits (61), Expect = 5.2
Identities = 10/59 (16%), Positives = 25/59 (42%)
Query: 5 QVVSYGRHTREELVVRLVAEMSRVKTSGAGHRGHSSGSGQHVAHHCRKKSRESRRLVLV 63
+ RH+R+ V ++ E++ V RG++ G+ + ++ R + +
Sbjct: 437 LLEQGLRHSRDLAFVGMLNEIAAVSPVAMPFRGYAVLGGEAGSQEVQQVPGSKRPVWFI 495
>2qko_A Possible transcriptional regulator, TETR family P; TETR family
protein, structural genomics, P protein structure
initiative; 2.35A {Rhodococcus SP}
Length = 215
Score = 27.1 bits (60), Expect = 5.8
Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 35 HRGHSSGSGQHVAHHCRKKSRESRRLVLVIVAIALVLDNMLL-TTVEDVARE 85
H HSSG +++ RR LV AI ++ T V E
Sbjct: 7 HHHHSSG-RENLYFQGHMAQNPERRAALVNAAIEVLAREGARGLTFRAVDVE 57
>3v2d_P 50S ribosomal protein L15; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 1vsp_J 2hgj_O 2hgq_O 2hgu_O 1vsa_J 2j03_P 2jl6_P
2jl8_P 2v47_P 2v49_P 2wdi_P 2wdj_P 2wdl_P 2wdn_P 2wh2_P
2wh4_P 2wrj_P 2wrl_P 2wro_P 2wrr_P ...
Length = 150
Score = 26.3 bits (59), Expect = 6.2
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 29 KTSGAGHRGHSSGSGQHVA 47
KT+ GH+G S SG
Sbjct: 29 KTATRGHKGQKSRSGGLKD 47
>3am6_A Rhodopsin-2, AR2; seven trans-membrane, transport protein; HET: RET
CLR; 3.20A {Acetabularia acetabulum}
Length = 229
Score = 26.5 bits (58), Expect = 9.7
Identities = 5/30 (16%), Positives = 10/30 (33%), Gaps = 2/30 (6%)
Query: 118 ILTHRVGYSLPMFTGFVIMFLSTLIFAFGR 147
+ T + + F IM + + F
Sbjct: 4 VETETGMIAQ--WIVFAIMAAAAIAFGVAV 31
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.139 0.413
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,931,455
Number of extensions: 240825
Number of successful extensions: 579
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 38
Length of query: 256
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 165
Effective length of database: 4,160,982
Effective search space: 686562030
Effective search space used: 686562030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.5 bits)