RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2997
(415 letters)
>2y69_D Cytochrome C oxidase subunit 4 isoform 1; electron transport,
complex IV, proton pumps, membrane prote; HET: TPO HEA
CHD PEK PGV DMU; 1.95A {Bos taurus}
Length = 169
Score = 158 bits (402), Expect = 3e-47
Identities = 46/168 (27%), Positives = 82/168 (48%), Gaps = 8/168 (4%)
Query: 25 AIVQQKSVSTLTRLFPFTGNREVVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLRE 83
+++ ++++ST + + VV + +Y D P P + + K + L+E
Sbjct: 8 SLIGRRAISTSVCV---RAHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKE 64
Query: 84 KEKGHWNALSKEEKKMLYRASFRQTFAEFTRHGAYPDTEYLGSVGLSMVVIAVSLFYYAF 143
KEK W++LS +EK LYR F+++FAE R E+ VG +M I + +
Sbjct: 65 KEKASWSSLSIDEKVELYRLKFKESFAEMNR----STNEWKTVVGAAMFFIGFTALLLIW 120
Query: 144 LKAFFLPPLPATMTPEGWENTVTKMIQLQWNPITGMASKWDYENDRWR 191
K + P+P T E +M+ ++ PI G ++KWDY+ + W+
Sbjct: 121 EKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 168
Score = 151 bits (382), Expect = 2e-44
Identities = 45/172 (26%), Positives = 74/172 (43%), Gaps = 20/172 (11%)
Query: 219 SGRLGEHGNREVVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLREKEKGHWNALSK 277
S + + VV + +Y D P P + + K + L+EKEK W++LS
Sbjct: 16 STSVCVRAHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSI 75
Query: 278 EEKKMLYRASFRQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSLF 337
+EK LYR F+++FAE R E+ VG +M I +
Sbjct: 76 DEKVELYRLKFKESFAEMNR----STNEWKTVVGAAMFFIG---------------FTAL 116
Query: 338 YYAFLKAFFLPPLPTTMTPEGWENTVTKMIQLQWNPITGMASKWDYENDRWR 389
+ K + P+P T E +M+ ++ PI G ++KWDY+ + W+
Sbjct: 117 LLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 168
>1v54_D Cytochrome C oxidase subunit IV isoform 1; oxidoreductase; HET: FME
TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: f.23.1.1 PDB: 1oco_D* 1occ_D* 1ocz_D* 1ocr_D*
1v55_D* 2dyr_D* 2dys_D* 2eij_D* 2eik_D* 2eil_D* 2eim_D*
2ein_D* 2occ_D* 2ybb_O* 2zxw_D* 3abk_D* 3abl_D* 3abm_D*
3ag1_D* 3ag2_D* ...
Length = 147
Score = 144 bits (365), Expect = 3e-42
Identities = 44/150 (29%), Positives = 72/150 (48%), Gaps = 5/150 (3%)
Query: 43 GNREVVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLREKEKGHWNALSKEEKKMLY 101
+ VV + +Y D P P + + K + L+EKEK W++LS +EK LY
Sbjct: 1 AHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELY 60
Query: 102 RASFRQTFAEFTRHGAYPDTEYLGSVGLSMVVIAVSLFYYAFLKAFFLPPLPATMTPEGW 161
R F+++FAE R E+ VG +M I + + K + P+P T E
Sbjct: 61 RLKFKESFAEMNR----STNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWV 116
Query: 162 ENTVTKMIQLQWNPITGMASKWDYENDRWR 191
+M+ ++ PI G ++KWDY+ + W+
Sbjct: 117 AKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 146
Score = 134 bits (339), Expect = 2e-38
Identities = 44/165 (26%), Positives = 72/165 (43%), Gaps = 20/165 (12%)
Query: 226 GNREVVGHGRNGIAAYGDNVLCPFPAIRY-KVFDSDLLLLREKEKGHWNALSKEEKKMLY 284
+ VV + +Y D P P + + K + L+EKEK W++LS +EK LY
Sbjct: 1 AHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELY 60
Query: 285 RASFRQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSHSTVSLFYYAFLKA 344
R F+++FAE R E+ VG +M I + + K
Sbjct: 61 RLKFKESFAEMNR----STNEWKTVVGAAMFFIG---------------FTALLLIWEKH 101
Query: 345 FFLPPLPTTMTPEGWENTVTKMIQLQWNPITGMASKWDYENDRWR 389
+ P+P T E +M+ ++ PI G ++KWDY+ + W+
Sbjct: 102 YVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWK 146
>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 = 42.7 bits (100), Expect = 2e-04
Identities = 70/442 (15%), Positives = 121/442 (27%), Gaps = 171/442 (38%)
Query: 2 VLR--FSHDEPTPSY-------PRNP--------GWINRHAIVQQKSVSTLTRL------ 38
L+ F+ P P+ P P G+++ V+ V ++
Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSL--VEPSKVGQFDQVLNLCLT 89
Query: 39 -F--PFTGNREVVGHGRNGIAA--YGDN---VLCPFPAIR-YKVFDSDLLLLREKEKGHW 89
F + ++ H +AA +N ++ I+ Y + ++ R +K
Sbjct: 90 EFENCYLEGNDI--HA---LAAKLLQENDTTLVKTKELIKNY--ITARIMAKRPFDKKSN 142
Query: 90 NALSK-----------------------EEKKMLYR----------ASFRQTFAEFTR-- 114
+AL + EE + LY+ +T +E R
Sbjct: 143 SALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTT 202
Query: 115 --------HG-----------AYPDTEYLGSVGLSMVVIAVSLF--YYAFLKAFFLPP-- 151
G PD +YL S+ +S +I V Y K P
Sbjct: 203 LDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE 262
Query: 152 --------------------LPATMTPEGWENTVTKMIQ-LQWNPITGMASKWDYENDRW 190
+ T + E + +V K I L + G+ Y
Sbjct: 263 LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF---IGVRCYEAY----- 314
Query: 191 RPGFKPCV---PVLLRLS--QGILPPSP-------PHHHDSGRLGEHGNREVVGHGRNGI 238
P P +L S PSP + N + + I
Sbjct: 315 -----PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV-NKTNSHLPAGKQVEI 368
Query: 239 AAY-GDN--VLCPFPAIRYKVFDSDL----LLLREKEKGHWNALSK---EEKKMLYRASF 288
+ G V+ P L L LR+ + S+ E+K+ + F
Sbjct: 369 SLVNGAKNLVVSGPPQ--------SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF 420
Query: 289 RQTFAEFTRHGAYPDTEYLGGV 310
+ F H + L
Sbjct: 421 LPVASPF--H-----SHLLVPA 435
Score = 38.5 bits (89), Expect = 0.005
Identities = 47/278 (16%), Positives = 84/278 (30%), Gaps = 84/278 (30%)
Query: 125 GSVGLSMVVIAVSLFYYAFLKAFFLPPLPA-TMTPEGWENT-------------VTKMIQ 170
GS+ ++V S F + L+ F LP T + V+ +++
Sbjct: 14 GSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVE 73
Query: 171 ----------------------LQWNPITGMASKWDYENDRWRPGFKPCVPVLLR---LS 205
L+ N I +A+K END L++ +
Sbjct: 74 PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEND----TTLVKTKELIKNYITA 129
Query: 206 QGILPPSPPHHHDSGRLGEHGNREVVGHGRNGIAA-YG--DNVLCPFPAIR-----YKVF 257
+ + +S L G + A +G N F +R Y V
Sbjct: 130 RIMAKRPFDKKSNS-ALFRAVGE-----GNAQLVAIFGGQGNTDDYFEELRDLYQTYHVL 183
Query: 258 DSDLL-----LLREKEKGHWNALSKEEKKMLYRASFRQTFAEFTRH-GAYPDTEYLGGVG 311
DL+ L E + + + + ++ E+ + PD +YL +
Sbjct: 184 VGDLIKFSAETLSELIR------TTLDAEKVFTQGLN--ILEWLENPSNTPDKDYLLSIP 235
Query: 312 LSMVVIAEITIFLITNFLSHSTVSLFYYAFLKAFFLPP 349
+S + I +I L+H Y K P
Sbjct: 236 ISCPL-----IGVIQ--LAH------YVVTAKLLGFTP 260
>2blf_B SORB, sulfite\:cytochrome C oxidoreductase subunit B; sulfite
oxidase, molybdopterin, C-type cytochrome, heme,
electron transport; HET: MSS HEC; 1.8A {Starkeya
novella} PDB: 2bpb_B* 2c9x_B* 2ca3_B* 2ca4_B*
Length = 81
Score = 29.6 bits (66), Expect = 0.36
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 153 PATMTPEGWENTVTKMIQLQWNPIT 177
P W+ V KMI++ P+
Sbjct: 42 PPGKGQAFWDAEVQKMIKVYHAPVD 66
Score = 28.9 bits (64), Expect = 0.63
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 351 PTTMTPEGWENTVTKMIQLQWNPIT 375
P W+ V KMI++ P+
Sbjct: 42 PPGKGQAFWDAEVQKMIKVYHAPVD 66
>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 = 31.4 bits (70), Expect = 0.64
Identities = 32/211 (15%), Positives = 59/211 (27%), Gaps = 73/211 (34%)
Query: 215 HHHDSGRLGE--HGNREVVGHGRNGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHW 272
HHH GE + ++++ + V + D +++ K
Sbjct: 4 HHHMDFETGEHQYQYKDILSVFEDAF-----------------VDNFDCKDVQDMPK--- 43
Query: 273 NALSKEEKKMLYRASFRQTFAEFTRHGAYPDTEYLGGVGLSMVVIAEITIFLITNFLSH- 331
+ LSKEE + + D T+ L LS
Sbjct: 44 SILSKEEIDHIIMS---------------KDAV-------------SGTLRLFWTLLSKQ 75
Query: 332 -STVSLFYYAFLKAFFLPPLPTTMTPEGWENTVTKMIQLQWNPITGMASKWDYENDR-WR 389
V F L+ + + + I+ + + M + + DR +
Sbjct: 76 EEMVQKFVEEVLRINY-----------KF---LMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 390 --PGFKPWFLDYLPKNSPLR----ELTPEEG 414
F + + L LR EL P +
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKN 152
>2kmw_A Uncharacterized protein AT3G03773; protein structure initiative,
center for eukaryotic structural genomics, CESG,
structural genomics; NMR {Arabidopsis thaliana}
Length = 150
Score = 29.2 bits (65), Expect = 1.6
Identities = 8/35 (22%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 67 PAIRYKVFDSDL-LLLREKEKGHWNALSKEEKKML 100
R V ++ ++++E+ W L K E+K
Sbjct: 62 TEYRKNVGLRNIIFSIQKEERSWWTRLLKSEEKPA 96
Score = 29.2 bits (65), Expect = 1.6
Identities = 8/35 (22%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 250 PAIRYKVFDSDL-LLLREKEKGHWNALSKEEKKML 283
R V ++ ++++E+ W L K E+K
Sbjct: 62 TEYRKNVGLRNIIFSIQKEERSWWTRLLKSEEKPA 96
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 29.6 bits (66), Expect = 2.3
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 366 MIQLQWNPITGMASKWDYEND-RWRPGFKPWFLDYLPKNSPLRELT 410
MI + + M YE+ R LD +P + +LT
Sbjct: 346 MISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLT 391
>1jmx_A Amine dehydrogenase; oxidoreductase; HET: TRQ HEC; 1.90A
{Pseudomonas putida} SCOP: a.3.1.7 a.3.1.7 b.1.18.14
b.1.18.14 b.61.4.1 PDB: 1jmz_A*
Length = 494
Score = 29.3 bits (65), Expect = 2.3
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 156 MTPEGWENTVTKMIQLQWNPIT 177
TPEGW ++ +M + I+
Sbjct: 32 KTPEGWLMSIARMQVMHGLQIS 53
Score = 29.3 bits (65), Expect = 2.3
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 354 MTPEGWENTVTKMIQLQWNPIT 375
TPEGW ++ +M + I+
Sbjct: 32 KTPEGWLMSIARMQVMHGLQIS 53
>1pby_A Quinohemoprotein amine dehydrogenase 60 kDa subunit;
oxidoreductase; HET: TRW HEM; 1.70A {Paracoccus
denitrificans} SCOP: a.3.1.7 a.3.1.7 b.1.18.14 b.1.18.14
b.61.4.1 PDB: 1jju_A*
Length = 489
Score = 29.3 bits (65), Expect = 2.3
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 156 MTPEGWENTVTKMIQLQWNPIT 177
TPEGW+ TVT+M++ +
Sbjct: 31 KTPEGWDMTVTRMMRNHGVALE 52
Score = 29.3 bits (65), Expect = 2.3
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 354 MTPEGWENTVTKMIQLQWNPIT 375
TPEGW+ TVT+M++ +
Sbjct: 31 KTPEGWDMTVTRMMRNHGVALE 52
>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 665
Score = 28.8 bits (64), Expect = 3.5
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 366 MIQLQWNPITGMASKWDYEND-RWRPGFKPWFLDYLPKNSPLRELT 410
MI + + M YE+ R LD +P + +LT
Sbjct: 346 MISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLT 391
>2bcg_G Secretory pathway GDP dissociation inhibitor; RABGTPase,
geranylgeranylation, vesicular transport, protein
transport; HET: GDP GER; 1.48A {Saccharomyces
cerevisiae} SCOP: c.3.1.3 c.3.1.3 d.16.1.6 PDB: 1ukv_G*
3cpi_G 3cph_G 3cpj_G*
Length = 453
Score = 28.7 bits (63), Expect = 3.7
Identities = 9/69 (13%), Positives = 19/69 (27%), Gaps = 6/69 (8%)
Query: 53 NGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHW------NALSKEEKKMLYRASFR 106
+G + + PA + S L+ + EK + + + +
Sbjct: 116 SGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDK 175
Query: 107 QTFAEFTRH 115
T E
Sbjct: 176 NTMDEVYYK 184
Score = 28.7 bits (63), Expect = 3.7
Identities = 9/69 (13%), Positives = 19/69 (27%), Gaps = 6/69 (8%)
Query: 236 NGIAAYGDNVLCPFPAIRYKVFDSDLLLLREKEKGHW------NALSKEEKKMLYRASFR 289
+G + + PA + S L+ + EK + + + +
Sbjct: 116 SGSYVFKQGKIYKVPANEIEAISSPLMGIFEKRRMKKFLEWISSYKEDDLSTHQGLDLDK 175
Query: 290 QTFAEFTRH 298
T E
Sbjct: 176 NTMDEVYYK 184
>1ti6_B Pyrogallol hydroxytransferase small subunit; molybdenum binding
enzyme, MGD-cofactors, DMSO-reductase family,
4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter
acidigallici} SCOP: b.3.5.1 d.58.1.5 PDB: 1ti2_B*
1ti4_B* 1vld_N* 1vle_N* 1vlf_N*
Length = 274
Score = 28.3 bits (63), Expect = 4.2
Identities = 6/32 (18%), Positives = 7/32 (21%), Gaps = 5/32 (15%)
Query: 172 QWNPITGMASKWDYENDR----WRPGFKP-CV 198
WN +A K P C
Sbjct: 115 YWNEEENVAQKCTMCAHLLDDESWAPKMPRCA 146
>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 648
Score = 28.8 bits (64), Expect = 4.3
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 366 MIQLQWNPITGMASKWDYEND-RWRPGFKPWFLDYLPKNSPLRELT 410
MI + + M YE+ R LD +P + +LT
Sbjct: 346 MISGNFADVREMVYPQFYEHKLNDRNVASMVKLDKVPVMDEIYDLT 391
>3g3e_A D-amino-acid oxidase; FAD, flavoprotein, oxidoreductase, PER; HET:
FAD G3E; 2.20A {Homo sapiens} PDB: 3cuk_A* 2e48_A*
2e49_A* 2e4a_A* 2e82_A* 2du8_A* 1ve9_A* 1dao_A* 1ddo_A*
1kif_A* 1an9_A* 1evi_A*
Length = 351
Score = 27.7 bits (61), Expect = 7.9
Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 5/75 (6%)
Query: 173 WNPITGMASKWDYENDRWRPGFKPCVPVLLRLSQGILPPSPPHHHDSGRLGEHGNREVV- 231
W+ + + R ++ G P P + +L + V
Sbjct: 247 WSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGPSNTEVI 306
Query: 232 ---GHGRNGI-AAYG 242
GHG G+ +G
Sbjct: 307 HNYGHGGYGLTIHWG 321
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
0.321 0.139 0.448
Gapped
Lambda K H
0.267 0.0496 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,948,332
Number of extensions: 423472
Number of successful extensions: 822
Number of sequences better than 10.0: 1
Number of HSP's gapped: 810
Number of HSP's successfully gapped: 31
Length of query: 415
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 319
Effective length of database: 4,021,377
Effective search space: 1282819263
Effective search space used: 1282819263
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: 58 (26.7 bits)