RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6250
(778 letters)
>3rrk_A V-type ATPase 116 kDa subunit; alpha beta fold, proton pump,
subunit I/A, V-ATPase, proton; HET: NHE; 2.64A
{Meiothermus ruber}
Length = 357
Score = 139 bits (352), Expect = 2e-36
Identities = 38/303 (12%), Positives = 67/303 (22%), Gaps = 45/303 (14%)
Query: 1 NHLERTESEILELSQNAINLKSNYLELTELKHVLEKTQTFFHEIWNIFFGGRYIILLMGL 60
L S L + L+ + EK H + + I L+
Sbjct: 99 AVLRPVASRAEVLGKERAALEEEIQTIELFGKAAEKLAALAHGL-DESPRLGVIPFLVA- 156
Query: 61 FSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMENRDLILDPATSDYDQIPYPFVKFDY 120
+ A + +
Sbjct: 157 --------KPEELEAVRKALQEALADRF-------------------------------- 176
Query: 121 SLLFQGNEIYKTVFVAFFQGEQLKSRVKKVCSGFHASFYPCPSAHQERTDMVQGVKTRLE 180
L + E V + E +R G +P +K R
Sbjct: 177 VLEAEPLENQLAALVVVKRSELEAARSSLSRLGLAELRFPGAYGAMPLGKAAARMKERAR 236
Query: 181 DLNMVLNQTRDHRQRVLVSVAKELHAWSVMVRKMKAIYHTLNSFNMDVTKKCLIGECWVP 240
L R+ R+ + L A + A Y + +M K WVP
Sbjct: 237 LAPEELVGIREEVARLSRESGEALIALWTRAKDEVARYKAVA--DMAAGKYGAALMGWVP 294
Query: 241 VKHLTFVRLTLAEGSKAVGSSIPSFLNVIETNEMPPTFNQTNRFTQGFQNLIDSYGIATY 300
K V L + + ++ + P + + + F+ L Y
Sbjct: 295 QKAKGKVEEALGRLRDQIVYTFEP-VDEHHESHQVPVTLENPAWAKPFELLHGFLNTPAY 353
Query: 301 REL 303
Sbjct: 354 GSH 356
>2nvj_A 25MER peptide from vacuolar ATP synthase subunit A, vacuolar
isoform; ALFA helix, 3,10 helix, PI helix, hydrolase;
NMR {Synthetic}
Length = 26
Score = 50.1 bits (119), Expect = 1e-08
Identities = 20/25 (80%), Positives = 23/25 (92%)
Query: 691 EYVLSTISHTASYLRLWALSLAHAQ 715
E+ L+ +SHTASYLRLWALSLAHAQ
Sbjct: 1 EFCLNCVSHTASYLRLWALSLAHAQ 25
>2jtw_A Transmembrane helix 7 of yeast vATPase; peptide, micelle-bound,
membrane protein; NMR {Synthetic} PDB: 2rpw_X
Length = 26
Score = 44.9 bits (105), Expect = 8e-07
Identities = 20/20 (100%), Positives = 20/20 (100%)
Query: 698 SHTASYLRLWALSLAHAQLS 717
SHTASYLRLWALSLAHAQLS
Sbjct: 3 SHTASYLRLWALSLAHAQLS 22
>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 = 51.6 bits (123), Expect = 9e-07
Identities = 103/629 (16%), Positives = 183/629 (29%), Gaps = 227/629 (36%)
Query: 247 VR-LTLAEGSKAVGSSIPS------------FLNVIETNEMPPT--FNQTN--------- 282
R LTL+ GS +P+ F ++ PT F +
Sbjct: 6 TRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPE----PTEGFAADDEPTTPAELV 61
Query: 283 -RFTQGF-QNLIDSYGIATYRELNPGLYTIVTFPFLFGIMFGDAGHGIILTL-------- 332
+F G+ +L++ + + ++ L +T F + G+ H + L
Sbjct: 62 GKFL-GYVSSLVEPSKVGQFDQV---LNLCLTE-FENCYLEGNDIHALAAKLLQENDTTL 116
Query: 333 ----------FGAFMVIWEQ-------KLMKKKTTNEIWNIF--FGG-----RYIILLMG 368
A ++ L + + FGG Y L
Sbjct: 117 VKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNA-QLVAIFGGQGNTDDYFEELRD 175
Query: 369 LFSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMENRDLILDPATSDYDQIPYPFGLDP 428
L+ Y L+ D S L T D +++ + GL+
Sbjct: 176 LYQTYHVLV-GDLIKFSAETLSE------------------LIRTTLDAEKV-FTQGLNI 215
Query: 429 V-W-QVAENK--IIFLNSYKMKLSIIFGVVHMIFGVTLSVINHVHFRKPVNILLEFLPQL 484
+ W + N +L S P++ P L
Sbjct: 216 LEWLENPSNTPDKDYLLSI-----------------------------PIS-----CP-L 240
Query: 485 IFLVLLFGYMVTLMFMKWIMYAPQNPLLTSPR----CAPSVLI-LFINMMLFKHSIPFPG 539
I ++ L Y+VT K + + P L + + + ++ + I
Sbjct: 241 IGVIQLAHYVVTA---KLLGFTPGE-LRSYLKGATGHSQGLVTAVAIAE---------TD 287
Query: 540 CEEYMYESQHQVQTVLVLISLAC---IPVMLL-------------GKPIYLIFFASKNKH 583
E + S + TVL I + C P L G P + + N
Sbjct: 288 SWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPM--LSISNLT 345
Query: 584 KHQQVSNNGDLQGGIEL---HSNDEHQVQTVLVLISLACIP--VMLLGKPIYLIFFASKN 638
+ Q +Q + H QV+ ISL +++ G P L N
Sbjct: 346 QEQ-------VQDYVNKTNSHLPAGKQVE-----ISLVNGAKNLVVSGPPQSLYGL---N 390
Query: 639 KHKHQQVSNNGDLQGGIELHS------NDEVLP-SSPEGPEEEHE---EPAEILIHQSI- 687
+ + +G Q I S ++ LP +SP H PA LI++ +
Sbjct: 391 LTLRKAKAPSGLDQSRIP-FSERKLKFSNRFLPVASP-----FHSHLLVPASDLINKDLV 444
Query: 688 -HTIEY--------VLSTISHTASYLRLWALSLAHA---QLSE--VLWNMVLKLGLQSES 733
+ + + V T S LR+ + S++ + V W + +
Sbjct: 445 KNNVSFNAKDIQIPVYDT--FDGSDLRVLSGSISERIVDCIIRLPVKWETTTQF---KAT 499
Query: 734 HAGAIMLYISFALWAMFTLAILV--MMEG 760
H + F L +L +G
Sbjct: 500 HI------LDFGPGGASGLGVLTHRNKDG 522
Score = 41.6 bits (97), Expect = 0.001
Identities = 37/247 (14%), Positives = 68/247 (27%), Gaps = 87/247 (35%)
Query: 49 FGG-----RYIILLMGLFSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMEN----RDL 99
FGG Y L L+ Y L+ D S + + + +
Sbjct: 160 FGGQGNTDDYFEELRDLYQTYHVLV-GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW 218
Query: 100 ILDPAT---SDY-DQIPY--PFVKFDYSLLFQ-GNEIYKTV----------FVAFFQG-- 140
+ +P+ DY IP P + + Q + Y ++ +G
Sbjct: 219 LENPSNTPDKDYLLSIPISCPLI-----GVIQLAH--YVVTAKLLGFTPGELRSYLKGAT 271
Query: 141 ------------------EQLKSRVKKVCS-----GFHA-SFYPC----PSAHQERTD-- 170
E V+K + G YP PS ++ +
Sbjct: 272 GHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENN 331
Query: 171 ------M--VQG-----VKTRLEDLNMVLNQTRD--------HRQRVLVSVAKELHAWSV 209
M + V+ + N L + + V+ + L+ ++
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 210 MVRKMKA 216
+RK KA
Sbjct: 392 TLRKAKA 398
>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 = 49.5 bits (117), Expect = 4e-06
Identities = 86/618 (13%), Positives = 173/618 (27%), Gaps = 201/618 (32%)
Query: 1 NHLERTESEILELSQNAI--NLKSNYLELTELKHVLEKTQTFF--HEIWNIFFGG---RY 53
+H++ E+ + I + +++ + K V + ++ EI +I
Sbjct: 5 HHMD-FETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG 63
Query: 54 IILLMGLFSIYTGLIYNDFFSKSISVFGSAWKNNYN-LSTIMENRDLILDPATSDYDQ-- 110
+ L + F + NY L + ++ T Y +
Sbjct: 64 TLRLFWTLLSKQEEMVQKFV-------EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR 116
Query: 111 -----IPYPFVKFDYS-----------LLFQGNEIY----------KTVFVAFFQGEQLK 144
F K++ S LL KT +
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL----DVCL 172
Query: 145 SRVKKVCSGFHA---SFYPCPSA-----------------HQERTDMVQGVKTRLEDLNM 184
S + F + C S R+D +K R+ +
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232
Query: 185 VLN---QTRDHRQRVLVSVAKEL-HAWSVMVRKMKAIYHTLNSFNMDVTKKC--LI---- 234
L +++ + +LV L + + N+FN+ C L+
Sbjct: 233 ELRRLLKSKPYENCLLV-----LLNVQNAKA---------WNAFNL----SCKILLTTRF 274
Query: 235 ----------GECWVPVKHLTFVRLTLAEG----SKAVGSSI-----------PSFLNVI 269
+ + H + LT E K + P L++I
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMT-LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333
Query: 270 --ETNEMPPTFNQTNR-FTQGFQNLIDSYGIATYRELNPGLYTIVTFPFLFGIMFGDAGH 326
+ T++ +I+S + L P Y MF
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIES----SLNVLEPAEYRK---------MFDR--- 377
Query: 327 GIILTLF--------GAFMVIWE-----------QKLMKKKTTNEIWNIFFGGRYIILLM 367
L++F +IW KL K + I +
Sbjct: 378 ---LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK-----ESTISIP 429
Query: 368 GLFSIYTGLIYNDF-FSKSISVFGSAWKNNYNLSTIMENRDLILDPATSD---YDQIPY- 422
++ + N++ +SI ++YN+ ++ DLI D Y I +
Sbjct: 430 SIYLELKVKLENEYALHRSIV-------DHYNIPKTFDSDDLIPPYL--DQYFYSHIGHH 480
Query: 423 PFGLDPVWQVAENKIIFLN----SYKMKLSIIFGVVHMIFGVTLSVI------------N 466
++ ++ +++FL+ K++ G L+ + N
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHD---STAWNASGSILNTLQQLKFYKPYICDN 537
Query: 467 HVHFRKPVNILLEFLPQL 484
+ + VN +L+FLP++
Sbjct: 538 DPKYERLVNAILDFLPKI 555
Score = 41.8 bits (97), Expect = 0.001
Identities = 101/632 (15%), Positives = 195/632 (30%), Gaps = 196/632 (31%)
Query: 69 YNDFFSKSISVFGSAWKNNYNLSTIMENRDLILDPATSDYDQI---PYPFVKFDY---SL 122
Y D +SVF A+ +N++ + + IL + + D I +L
Sbjct: 18 YKDI----LSVFEDAFVDNFDCKDVQDMPKSIL--SKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 123 LFQGNEIYKTVFVAFFQG------EQLKSRVKKVCSGFHASFYPCPSAHQERTDMVQGVK 176
L + E+ + F + + L S +K PS T M +
Sbjct: 72 LSKQEEMVQ----KFVEEVLRINYKFLMSPIKTEQRQ--------PSM---MTRMYIEQR 116
Query: 177 TRLEDLNMVL---NQTRDHRQRVLVSVAKEL-HAWSVMVRKMKAIYHTLNSFNMDVTKKC 232
RL + N V N +R L EL A +V++ + K
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS-----------GKTW 165
Query: 233 LIGE-C--------------WVPVKHLTFVRLTLAEGSKAVGSSIPSFLNVIETNEMPP- 276
+ + C W+ +K+ L K + P++ + + +
Sbjct: 166 VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 277 TFNQT----NRF--TQGFQN--LI--DSYGIATYRELNPGLYTIVTFPFLFGIMFGDAGH 326
+ R ++ ++N L+ + + N ++T F F A
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285
Query: 327 GIILTLFGAFMVIWEQKLMKKKTTNEIWNIFFGGRYIILLMGLFSIYTGLIYND------ 380
++L T +E + L Y D
Sbjct: 286 TTHISL---------DHHSMTLTPDE-------------VKSLLLKYLDCRPQDLPREVL 323
Query: 381 --------FFSKSISVFGSAWKN--NYN---LSTIMENRDLILDPAT--SDYDQ------ 419
++SI + W N + N L+TI+E+ +L+PA +D+
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP 383
Query: 420 ---IPYPFGLDPVWQ--VAENKIIFLNSYKMKLSIIFG-------VVHMIFGVTLSVINH 467
IP L +W + + ++ +N K S++ + I+ + +
Sbjct: 384 SAHIPTIL-LSLIWFDVIKSDVMVVVNKL-HKYSLVEKQPKESTISIPSIYLELKVKLEN 441
Query: 468 ---VHFRKPV---NILLEFLPQLIFLVLLFGY-------------------MVTLMFM-- 500
+H R V NI F + L Y + ++F+
Sbjct: 442 EYALH-RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF 500
Query: 501 KWIMYAPQNPL--LTSPRCAP-SVLILFINMMLFKHSI----P-----------F-PGCE 541
+++ + + ++ A S+L + +K I P F P E
Sbjct: 501 RFL----EQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556
Query: 542 EYMYESQHQVQTVLVLISLACIPVMLLGKPIY 573
E + S++ T L+ I+L M + I+
Sbjct: 557 ENLICSKY---TDLLRIAL-----MAEDEAIF 580
>3gff_A IROE-like serine hydrolase; NP_718593.1, structural genomics center
for structural genomics, JCSG, protein structure INI
PSI-2; 2.12A {Shewanella oneidensis}
Length = 331
Score = 32.3 bits (73), Expect = 0.53
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 57 LMGLFSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMENR 97
GL ++ FS +++ S W ++ + T++E R
Sbjct: 146 FGGLVAMEALRTDRPLFSAYLALDTSLWFDSPHYLTLLEER 186
Score = 32.3 bits (73), Expect = 0.53
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 366 LMGLFSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMENR 406
GL ++ FS +++ S W ++ + T++E R
Sbjct: 146 FGGLVAMEALRTDRPLFSAYLALDTSLWFDSPHYLTLLEER 186
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 1.0
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 23/50 (46%)
Query: 643 QQVSNNGDLQGGIELHSNDEVLPSSPEGPEEEHEEPAEILIHQSIH-TIE 691
Q + LQ ++L++ S PA L +I T+E
Sbjct: 20 QALKK---LQASLKLYA-----DDSA---------PA--L---AIKATME 47
Score = 30.3 bits (67), Expect = 1.3
Identities = 7/28 (25%), Positives = 11/28 (39%), Gaps = 13/28 (46%)
Query: 500 MKWIMYAPQNPLLTSPRCAPSVLILFIN 527
+K +YA + AP+ L I
Sbjct: 29 LK--LYADDS--------APA---LAIK 43
>2qm0_A BES; alpha-beta structure, structural genomics, PSI-2, protein ST
initiative, midwest center for structural genomics,
MCSG; HET: SVY; 1.84A {Bacillus cereus atcc 14579}
Length = 275
Score = 30.7 bits (69), Expect = 1.9
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 57 LMGLFSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMENRDLILDPA 104
L GLF+++ + F S W NN ++ EN + L+ A
Sbjct: 161 LGGLFALHILFTNLNAFQNYFISSPSIWWNNKSVLEKEENLIIELNNA 208
Score = 30.7 bits (69), Expect = 1.9
Identities = 13/48 (27%), Positives = 21/48 (43%)
Query: 366 LMGLFSIYTGLIYNDFFSKSISVFGSAWKNNYNLSTIMENRDLILDPA 413
L GLF+++ + F S W NN ++ EN + L+ A
Sbjct: 161 LGGLFALHILFTNLNAFQNYFISSPSIWWNNKSVLEKEENLIIELNNA 208
>2ww8_A RRGA, cell WALL surface anchor family protein; IGG, pilus, CNA_B,
adhesin, integrin, cell adhesion; HET: EPE; 1.90A
{Streptococcus pneumoniae}
Length = 893
Score = 30.5 bits (66), Expect = 2.5
Identities = 11/63 (17%), Positives = 22/63 (34%)
Query: 293 DSYGIATYRELNPGLYTIVTFPFLFGIMFGDAGHGIILTLFGAFMVIWEQKLMKKKTTNE 352
G A + + PG YT+ G + + G V EQ +++ ++
Sbjct: 84 AQTGEAIFSNIKPGTYTLTEAQPPVGYKPSTKQWTVEVEKNGRTTVQGEQVENREEALSD 143
Query: 353 IWN 355
+
Sbjct: 144 QYP 146
>3nkh_A Integrase; alpha-fold, MRSA protein, structural genomics, PSI-2,
protei structure initiative; 2.50A {Staphylococcus
aureus subsp}
Length = 244
Score = 29.6 bits (67), Expect = 3.6
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 15/72 (20%)
Query: 21 KSNYLELTELKHVLEKTQTFFHEIWNIFFGGRYI-ILLMGLFSIYTGL------------ 67
+ YLEL E++ +++ T ++ + Y+ + LM F G+
Sbjct: 22 SNAYLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNED 81
Query: 68 IYNDFFSKSISV 79
I DF +KS+++
Sbjct: 82 I--DFDNKSLNI 91
>3c8d_A Enterochelin esterase; alpha-beta-alpha sandwich, IROD, iron
aquisition, structural genomics, PSI-2, protein
structure initiative; HET: CIT; 1.80A {Shigella flexneri
2a str} SCOP: b.1.18.20 c.69.1.2 PDB: 2b20_A 3c87_A*
3c8h_A 3mga_A*
Length = 403
Score = 28.8 bits (64), Expect = 6.8
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 59 GLFSIYTGLIYNDFFSKSISVFGSAWKNN 87
GL ++Y GL + + F +S GS W +
Sbjct: 287 GLSALYAGLHWPERFGCVLSQSGSYWWPH 315
Score = 28.8 bits (64), Expect = 6.8
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 368 GLFSIYTGLIYNDFFSKSISVFGSAWKNN 396
GL ++Y GL + + F +S GS W +
Sbjct: 287 GLSALYAGLHWPERFGCVLSQSGSYWWPH 315
>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F
1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H
Length = 191
Score = 28.1 bits (63), Expect = 8.9
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 456 MIFGVTLS-----VINHVHFRKPVNILLEFLPQLIFLVLLFGY 493
MI GVT + HF VNI+ + + I + G
Sbjct: 78 MITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD 120
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 0.425
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 11,658,897
Number of extensions: 695752
Number of successful extensions: 1834
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1820
Number of HSP's successfully gapped: 27
Length of query: 778
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 677
Effective length of database: 3,881,772
Effective search space: 2627959644
Effective search space used: 2627959644
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: 61 (27.4 bits)