RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5252
(285 letters)
>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 = 38.9 bits (91), Expect = 0.001
Identities = 14/131 (10%), Positives = 38/131 (29%), Gaps = 16/131 (12%)
Query: 1 MVGIGEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIPIGSGLGYIVGSTAFSVMGAWPW 60
+ G + + + + R +++ + A +G G+ ++ + W
Sbjct: 128 LCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHA 187
Query: 61 SLRVTPVLGACAVLLILFFMEDP---------------ERGEAEGRVTEERTSFGEDIRA 105
+L + L M D + + +E T+ ++
Sbjct: 188 ALYMPAFCAILVALFAFAMMRDTPQSCGLPPIEEYKNDYPDDYNEKAEQELTAKQIFMQY 247
Query: 106 LCKNHRETWIF 116
+ N + W
Sbjct: 248 VLPN-KLLWYI 257
>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 = 34.1 bits (77), Expect = 0.060
Identities = 30/168 (17%), Positives = 51/168 (30%), Gaps = 46/168 (27%)
Query: 103 IRALCKNHRETWIFLNLNWSIVADMTLYVVLPLRRSTAEAFQILISHAFGDAGSPYLI-- 160
I ++ TW NW + + +I + + P
Sbjct: 333 IAESIRDGLATWD----NW--------------KHVNCDKLTTIIE-SSLNVLEPAEYRK 373
Query: 161 --GLLSEMFRHSLQLGASTL--------------VANAMLPSSLAPSLPFSSSNSTSLPL 204
LS +F S + L V N + SL P S + S+P
Sbjct: 374 MFDRLS-VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES--TISIPS 430
Query: 205 VSSLDETAHRSDEFLAHKS--DEFLAHK---SDEFLALQYALFITSFI 247
+ L+ +E+ H+S D + K SD+ + + S I
Sbjct: 431 I-YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477
Score = 30.6 bits (68), Expect = 0.68
Identities = 19/111 (17%), Positives = 37/111 (33%), Gaps = 33/111 (29%)
Query: 74 LLILFFMEDPERGEAEGRVTEERTSFGEDIRALCK---NHRETWIFLNLNWSIVADMTLY 130
LL+L +++ + A F ++ CK R + L+ A T +
Sbjct: 247 LLVLLNVQNAKAWNA----------F--NLS--CKILLTTRFKQVTDFLS----AATTTH 288
Query: 131 VVLPLRRST---AEAFQIL---ISHAFGD------AGSPYLIGLLSEMFRH 169
+ L T E +L + D +P + +++E R
Sbjct: 289 ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339
Score = 28.7 bits (63), Expect = 3.1
Identities = 32/269 (11%), Positives = 76/269 (28%), Gaps = 57/269 (21%)
Query: 2 VGIGEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIPIGSGLGYIVGSTAFSVMGAWPWS 61
G + Y I FV + + + +I + +I+ S
Sbjct: 11 TGEHQYQYKDILSVFEDA-FVDNFDCKDVQDMPKSILSKEEIDHIIMSK----------- 58
Query: 62 LRVTPVLGACAVLLILFFMEDPERGEAEGRVTEERTSFG---EDIRALCKN-HRETWIFL 117
V G + L + E + R ++ I+ + T +++
Sbjct: 59 ---DAVSGT--LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI 113
Query: 118 NLNWSIVADMTLYVVLPLRRSTAEAFQILISHAFGDAGSPYLI--GLLSEMFRHSLQLGA 175
+ D ++ + R + + L + ++ G + LG+
Sbjct: 114 EQRDRLYNDNQVFAKYNVSR--LQPYLKLRQALLELRPAKNVLIDG----V------LGS 161
Query: 176 --STLVANAMLPSSLAPSLPF-------SSSNSTSLPLVSSLDETAHRSDEFLAHKSD-- 224
+ + + L + + F + NS ++ L + ++ D +SD
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPET-VLEMLQKLLYQIDPNWTSRSDHS 220
Query: 225 -------EFLAHKSDEFLAL-QY--ALFI 243
+ + L Y L +
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLV 249
>4aps_A DI-OR tripeptide H+ symporter; transport protein, peptide
transport, major facilitator SUPE transporter, MFS;
3.30A {Streptococcus thermophilus}
Length = 491
Score = 33.6 bits (77), Expect = 0.068
Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 1 MVGIGEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIPIGSGLGYIVGSTAFSVMGAWPW 60
+V +GE S + ++ + L K SQM++ ++ + +GS L + + ++ +
Sbjct: 395 LVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGSALNAQLVT-LYNAKSEVAY 453
Query: 61 SLRVTPVLGACAVLLILF 78
++L+
Sbjct: 454 FSYFGLGSVVLGIVLVFL 471
>2xut_A Proton/peptide symporter family protein; transport protein,
membrane protein, major facilitator super transporter;
3.62A {Shewanella oneidensis}
Length = 524
Score = 32.3 bits (74), Expect = 0.15
Identities = 8/89 (8%), Positives = 26/89 (29%), Gaps = 9/89 (10%)
Query: 1 MVGIGEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIPIGSGLGYIVGS--TAFSVMGAW 58
++ GE S K ++ +++F+ ++ +G+ + + +V
Sbjct: 414 LLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGNLWVLLANVSVKSPTVTEQI 473
Query: 59 PWSLRVTPVLG-------ACAVLLILFFM 80
+ A ++
Sbjct: 474 VQTGMSVTAFQMFFFAGFAILAAIVFALY 502
>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 = 32.3 bits (73), Expect = 0.20
Identities = 58/358 (16%), Positives = 100/358 (27%), Gaps = 117/358 (32%)
Query: 5 GEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIP------------------IGSGLGYI 46
G + + PT + F+ SQ+ F +P +G LGY+
Sbjct: 14 GSLEHVLLVPT--ASFFIA---SQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV 68
Query: 47 VGSTAFSVMGAWPWSLRVTPVLGACAVLLILF---FMEDPERGE-----AEGRVTEERTS 98
S +G + VL + L F ++ G A + E T+
Sbjct: 69 SSLVEPSKVGQF------DQVL---NLCLTEFENCYL----EGNDIHALAAKLLQENDTT 115
Query: 99 FGEDIRALCKNHRETWIFLNLNWSIVADMTLYVVLPLRRSTAEAFQI-LISHAFG----- 152
+ + L KN+ I + ++ L R Q+ I FG
Sbjct: 116 LVK-TKELIKNYITARIMAKRPFDKKSNSAL-----FRAVGEGNAQLVAI---FGGQGNT 166
Query: 153 -----------DAGSPYLIGLLSEMFRHSLQLGASTLVANAMLPSSL-----------AP 190
+ L+ +L +TL A + L P
Sbjct: 167 DDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTP 226
Query: 191 SLPFSSSNSTSLPLVSSLDETAH----------RSDEFLAHKSDEFLAHKSDEFLALQYA 240
+ S S PL+ + + AH E ++ H A+ A
Sbjct: 227 DKDYLLSIPISCPLI-GVIQLAHYVVTAKLLGFTPGELRSYLKG-ATGHSQGLVTAVAIA 284
Query: 241 L------FITSFIEVLGGIFFLLG------------SLYIVQDRARANREIAGEDNPA 280
F S + + + F +G I++D + N E P+
Sbjct: 285 ETDSWESFFVSVRKAI-TVLFFIGVRCYEAYPNTSLPPSILED-SLEN----NEGVPS 336
Score = 31.9 bits (72), Expect = 0.24
Identities = 26/155 (16%), Positives = 40/155 (25%), Gaps = 52/155 (33%)
Query: 46 IVGSTAFSVMGAWPWSLRVT-----PVLGACAVLLILFFMEDPERGEAEGRVTEER---- 96
+ S F L V +L A LI +D + + +
Sbjct: 414 LKFSNRF---------LPVASPFHSHLL-VPASDLIN---KDLVKNNVSFNAKDIQIPVY 460
Query: 97 -TSFGEDIRALCKNHRET---WIF-LNLNWSIVADMTLYVVLPLRRSTAEAFQILISHA- 150
T G D+R L + E I L + W +H
Sbjct: 461 DTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFK------------------ATHIL 502
Query: 151 -FGDAGSPYLIGLLSEMFRHSLQ-LGASTLVANAM 183
FG P L + + G +VA +
Sbjct: 503 DFG----PGGASGLGVLTHRNKDGTGVRVIVAGTL 533
Score = 30.8 bits (69), Expect = 0.68
Identities = 30/203 (14%), Positives = 58/203 (28%), Gaps = 59/203 (29%)
Query: 100 GEDIRALCKNHRETW------IFLNLNWSIVA-------DMTLYVVLPLRRSTAEAFQIL 146
G D+ K ++ W +SI+ ++T++ + E + +
Sbjct: 1632 GMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAM 1691
Query: 147 ISHAFGDAG--SPYLIGLLSE-----MFRHSLQLGASTLVAN---AMLPSSLAPSLPFSS 196
I D + + ++E FR L ++T A+ A
Sbjct: 1692 IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT--QFTQPALTLMEKA------- 1742
Query: 197 SNSTSLPLVSSLDETAHRSDEFLAHKSDEFLA-HKS-DEFLALQYALFITSFIEVLGGIF 254
L + L +D A H S E+ AL +L +
Sbjct: 1743 -------AFEDLKS------KGLI-PADATFAGH-SLGEYAAL-ASL---------ADVM 1777
Query: 255 FLLGSLYIVQDRARANREIAGED 277
+ + +V R + D
Sbjct: 1778 SIESLVEVVFYRGMTMQVAVPRD 1800
>2hv2_A Hypothetical protein; PSI, protein structure initiative, midwest
center for struct genomics, MCSG, structural genomics,
unknown function; HET: EPE PG4; 2.40A {Enterococcus
faecalis} SCOP: d.106.1.4 d.108.1.10
Length = 400
Score = 31.6 bits (71), Expect = 0.27
Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 3/61 (4%)
Query: 127 MTLYVVLPLRRSTAEAFQILISHAFGDAGSPYLIGLLSEMFRHSLQLGA---STLVANAM 183
MT V + + + L+ +AF + ++ H+ G L + M
Sbjct: 4 MTTKRVKKMGKEEMKEMFDLVIYAFNQEPTAERQERFEKLLSHTQSYGFLIDEQLTSQVM 63
Query: 184 L 184
Sbjct: 64 A 64
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 30.4 bits (68), Expect = 0.48
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 15/45 (33%)
Query: 79 FMEDPERGE---AE-GRVTEERTSFGEDIRALCKNHRETW-IFLN 118
+E G+ A G V ++ D R+ E W F N
Sbjct: 34 IVERFSEGDVVCALCGLVLSDKL---VDTRS------E-WRTFSN 68
>2any_A Kininogenin, plasma kallikrein, light chain, fletcher factor;
mutagenically deglycosyalted human plasma kallikrein
protease domain; HET: BAM; 1.40A {Homo sapiens} PDB:
2anw_A*
Length = 241
Score = 27.6 bits (62), Expect = 4.3
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 46 IVGSTAFSVMGAWPW--SLRVTPVLG 69
IVG T S G WPW SL+V
Sbjct: 1 IVGGTE-SSWGEWPWQVSLQVKLTAQ 25
>1fiw_A Beta-acrosin heavy chain; anti-parallel beta-barrel, hydrolase;
HET: NAG FUL BMA MAN PBZ; 2.10A {Ovis aries} SCOP:
b.47.1.2 PDB: 1fiz_A*
Length = 290
Score = 27.3 bits (61), Expect = 5.7
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 46 IVGSTAFSVMGAWPW--SLRVTPVLG 69
I+G + GAWPW SL++
Sbjct: 1 IIGGQD-AAHGAWPWMVSLQIFTYHN 25
>2eab_A Alpha-fucosidase; glycoside hydrolase; 1.12A {Bifidobacterium
bifidum} PDB: 2eac_A* 2ead_A* 2eae_A*
Length = 899
Score = 27.6 bits (60), Expect = 6.3
Identities = 19/125 (15%), Positives = 43/125 (34%), Gaps = 23/125 (18%)
Query: 80 MEDPERGEAEGRVTEERTSFGEDIRALCKNHRETWIFLNLNWSIVADMTLYVVLPLRRST 139
+++ E +A R G +++ N W+I + + +T
Sbjct: 694 IDNSEYMDAAKTSLRYRCFKGNVLQS------------NTGWAIGQRINSWARTGDGNTT 741
Query: 140 AEAFQILISHAFG----DAGSPYLI-------GLLSEMFRHSLQLGASTLVANAMLPSSL 188
+ ++ + +A D +P+ I + EM S T + +++
Sbjct: 742 YQLVELQLKNAMYANLFDYHAPFQIDGNFGNTSGVDEMLLQSNSTFTDTAGKKYVNYTNI 801
Query: 189 APSLP 193
P+LP
Sbjct: 802 LPALP 806
>3rj1_B Mediator of RNA polymerase II transcription subun; RNA polymeras
II, POL II, head module, head, regulator, helical
bundle; 4.30A {Saccharomyces cerevisiae}
Length = 583
Score = 27.2 bits (59), Expect = 6.7
Identities = 19/122 (15%), Positives = 39/122 (31%), Gaps = 15/122 (12%)
Query: 131 VVLPLRRSTAEAFQILISHAFGDAGSPYLIGLLSEMFRHSLQLGASTLVANAMLPSSLAP 190
V+ +R T+ + I + + D+GS Y R++++ L+ P S +
Sbjct: 224 VIFKIRDRTSGQKLLAIKYGYEDSGSTYKHDRGIANIRNNIESQNLDLI-----PHSSSV 278
Query: 191 SLPFSSSNSTSLPL-VSSLDETAHRSDEFL---------AHKSDEFLAHKSDEFLALQYA 240
+S L V + D L + + + L+
Sbjct: 279 FKGTDFVHSVKKFLRVRIFTKIESEDDYILSGESVMDRDSESEEAETKDIRKQIQLLKKI 338
Query: 241 LF 242
+F
Sbjct: 339 IF 340
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 27.2 bits (61), Expect = 7.3
Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 3/99 (3%)
Query: 3 GIGEASYSTIAPTIISDLFVKDLRSQMLAFFYFAIPIGSGLGYIVGSTAFSVMGAWPWSL 62
G+G +A T+ DL+ + + I + L ++G ++ W
Sbjct: 99 GMGTGVGGVMARTLPRDLYERTQLRHANSLLNMGILVSPLLAPLIGGLLDTMWN-WRACY 157
Query: 63 RVTPVLGACAVLLILFFMEDPERGEAEGRVTEERTSFGE 101
VL A + +M PE + T TS+
Sbjct: 158 LFLLVLCAGVTFSMARWM--PETRPVDAPRTRLLTSYKT 194
>1t8o_A Chymotrypsin A; chymotrypsin, serine proteinase, BPTI,
protein-protein interaction, non-cognate binding, S1
pocket, primary specificity; 1.70A {Bos taurus} SCOP:
b.47.1.2 PDB: 1cgi_E 1cgj_E 1chg_A 1ex3_A 1acb_E 1gl0_E
1gl1_A 1gcd_A* 1oxg_A 1k2i_1 1p2n_A 1p2o_A 1p2q_A
1t7c_A 1t8l_A 1t8m_A 1t8n_A 1p2m_A 2cga_A 2y6t_A ...
Length = 245
Score = 26.8 bits (60), Expect = 8.6
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 38 PIGSGLGYIVGSTAFSVMGAWPW--SLRV 64
P+ SGL IV +V G+WPW SL+
Sbjct: 8 PVLSGLSRIVNGEE-AVPGSWPWQVSLQD 35
>4dgj_A Enteropeptidase catalytic light chain; serine protease,
hydrolase; 1.90A {Homo sapiens} PDB: 1ekb_B
Length = 235
Score = 26.4 bits (59), Expect = 9.0
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 46 IVGSTAFSVMGAWPW--SLRV 64
IVG + + GAWPW L
Sbjct: 1 IVGGSD-AKEGAWPWVVGLYY 20
>1z8g_A Serine protease hepsin; serine protease hepsin, protease,
hydrolase-hydrolase inhibi complex; HET: AR7; 1.55A
{Homo sapiens} SCOP: b.47.1.2 d.170.1.2 PDB: 3t2n_A
1o5e_H* 1o5f_H* 1p57_B* 1o5e_L* 1o5f_L* 1p57_A*
Length = 372
Score = 26.6 bits (59), Expect = 9.3
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 3/21 (14%)
Query: 46 IVGSTAFSVMGAWPW--SLRV 64
IVG + +G WPW SLR
Sbjct: 118 IVGGRD-TSLGRWPWQVSLRY 137
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
0.322 0.137 0.400
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,244,606
Number of extensions: 251799
Number of successful extensions: 515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 512
Number of HSP's successfully gapped: 26
Length of query: 285
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 192
Effective length of database: 4,105,140
Effective search space: 788186880
Effective search space used: 788186880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.6 bits)