RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 017722
(367 letters)
>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 = 47.5 bits (112), Expect = 5e-06
Identities = 81/499 (16%), Positives = 138/499 (27%), Gaps = 163/499 (32%)
Query: 1 MVEPFVKDFLGGD-KVLGTEIEVNPRTKR--------------------ATGFVKRP--- 36
MV+ FV++ L + K L + I+ R A V R
Sbjct: 78 MVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPY 137
Query: 37 --------------GVLV------GKWKKLA--VLKEFG-EDAPDLGI-----GDRQTDH 68
VL+ GK +A V + + D I + +
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGSGKTW-VALDVCLSYKVQCKMDFKIFWLNLKNCNSPE 196
Query: 69 DFMSICKEGYMVL-PSKSAKPLPRDRLKSRIIFHDG-----RLVQRPDPLNALI------ 116
+ + ++ + P+ +++ +K RI H RL++ N L+
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI--HSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 117 -TYIWLPFGF---ILSIIR-----------VYFNLPLPERIVRYTY-EMLGIHLVIRGNP 160
W F IL R ++ L + T E+ + L
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 161 PPA-PSSGSPGNLYVCNHRTPLDPIVIAI--ALGRKVSCV-----TYSVSKLSR------ 206
P P N P ++I R + KL+
Sbjct: 315 PQDLPREVLTTN-----------PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363
Query: 207 -FLSP------------------IPAIALTR----DRAADAARISELLQKGDLVVC-PEG 242
L P IP I L+ +D + L K LV P+
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Query: 243 TTCR-ENFLLRFSALF---AEMSDRIVPVAVNCKQNMFYGTTVRGVKFWDPYFFF----- 293
+T + L + IV N + + + + D YF+
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVD-HYNIPKT--FDSDDLIPPYLDQYFYSHIGHH 480
Query: 294 -MNPRPTYEVT-----FLD-RLPEEMTCKAGGKSAIEVANYVQKVLGDVLGFECTGLTRK 346
N +T FLD R E+ +A + + L + ++
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDS--TAWNASGSILNTLQQLKFYK------- 531
Query: 347 DKYMLLGGNDGKVESMYNS 365
Y+ ND K E + N+
Sbjct: 532 -PYICD--NDPKYERLVNA 547
Score = 44.8 bits (105), Expect = 4e-05
Identities = 57/381 (14%), Positives = 107/381 (28%), Gaps = 105/381 (27%)
Query: 2 VEPFVKDFLGGD------KVLGTEIEVNPRTKRATGFVKRPGVLVGKWKKLAVLKEFGED 55
+ FV +F D +L E E++ + + G + L E+
Sbjct: 26 EDAFVDNFDCKDVQDMPKSILSKE-EIDH-------IIMSKDAVSGTLRLFWTLLSKQEE 77
Query: 56 APDLGIGDR-QTDHDFM--SICKEGYMVLPSKSAKPL--PRDRLKSRIIFHDGRL----- 105
+ + + ++ F+ I E PS + RDRL ++D ++
Sbjct: 78 MVQKFVEEVLRINYKFLMSPIKTE--QRQPSMMTRMYIEQRDRL-----YNDNQVFAKYN 130
Query: 106 VQRPDPLNALITYIWLPFGFILSIIRVYFNLPLPERIVRYTYEMLGI---HLVIRGNPPP 162
V R P L L +R P + V +LG + +
Sbjct: 131 VSRLQPYLKLRQ--------ALLELR-------PAKNV-LIDGVLGSGKTWVALDVCLSY 174
Query: 163 APSSGSPGNLY---VCNHRTPLDPIVIAIALGRKVSCVTYSVS---------------KL 204
++ + N +P + + L ++ S S +L
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 205 SRFLSPIP-AIAL------------------------TRDRAADAARISELLQKGDLVVC 239
R L P L TR + + L
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294
Query: 240 PEGTTCRENFLLRFSALFAEMSDRIVPVAVNCKQN-----MFYGTTVR-GVKFWDPYFFF 293
T E + + + + +P V N + ++R G+ WD +
Sbjct: 295 SMTLTPDE--VKSLLLKYLDCRPQDLPREV-LTTNPRRLSII-AESIRDGLATWDNWKHV 350
Query: 294 MNPRPTYEV-TFLDRL-PEEM 312
+ T + + L+ L P E
Sbjct: 351 NCDKLTTIIESSLNVLEPAEY 371
Score = 44.5 bits (104), Expect = 5e-05
Identities = 43/244 (17%), Positives = 76/244 (31%), Gaps = 88/244 (36%)
Query: 44 KKLAVLKEFGEDA--PD--LGI--GDRQTDHDFMSICKEGYMVLPSKSAKPLPRDRLKSR 97
+L+V F A P L + D D M + + L S + + +S
Sbjct: 376 DRLSV---FPPSAHIPTILLSLIWFDVIKS-DVMVVVNK----LHKYSL--VEKQPKEST 425
Query: 98 IIFHDGRLVQRPDPLN------ALIT-YIWLPFGFILSIIRVY-FNLPLPERIVRYTYEM 149
I L + N +++ Y +I + + + +P + +Y Y
Sbjct: 426 ISIPSIYLELKVKLENEYALHRSIVDHY---------NIPKTFDSDDLIPPYLDQYFYSH 476
Query: 150 LGIHLV------------------------IRGNPPPAPSSGSPGNL---------YVCN 176
+G HL IR + +SGS N Y+C+
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD 536
Query: 177 HRTPLDPIVIAIALGRKVSCVTYS--VSKLSRFLSPIPAIALTRDRAADAARISELLQKG 234
+ DP Y V+ + FL P L + D RI+ L+ +
Sbjct: 537 N----DP--------------KYERLVNAILDFL-PKIEENLICSKYTDLLRIA-LMAED 576
Query: 235 DLVV 238
+ +
Sbjct: 577 EAIF 580
Score = 31.4 bits (70), Expect = 0.64
Identities = 56/364 (15%), Positives = 100/364 (27%), Gaps = 87/364 (23%)
Query: 6 VKDFLGGDKVLGTEIEVNPRTKRATGFVKRPGVLVGKWKKLAVLKEFGEDAPDLGIGDRQ 65
F K+L + R K+ T F+ A D + + +
Sbjct: 259 WNAFNLSCKIL-----LTTRFKQVTDFLS-----------AATTTHISLDHHSMTLTPDE 302
Query: 66 TDHDFMSICKEGYMVLPSKSAKPLPRDRLKSRIIFHDGRLVQRPDPLNALITYIWLPFGF 125
+ LP + P + II + R A W
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNP---RRLSII---AESI-RDGL--ATWDN-WKHVNC 352
Query: 126 --ILSIIRVYFNLPLPERIVRYTYEMLGI---HLVIRGNPPPAPSSGSPGNLYVC--NHR 178
+ +II N+ L R ++ L + I P L
Sbjct: 353 DKLTTIIESSLNV-LEPAEYRKMFDRLSVFPPSAHI------------PTILLSLIWFDV 399
Query: 179 TPLDPIVIAIALGRKVSCV-------TYSVSKLS-RFLSPIPAIALTRDRAADAARISEL 230
D +V+ L + S V T S+ + + D I +
Sbjct: 400 IKSDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458
Query: 231 LQKGDLVVCPE--------G---TTCR--ENFLLRFSALFAE---MSDRIVPVAVNCKQN 274
DL+ G E L F +F + + +I + +
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL-FRMVFLDFRFLEQKIRHDSTAWNAS 517
Query: 275 MFYGTTVRGVKFWDPYFFFMNPRPTYE------VTFLDRLPEEMTCKAGGKSAIEVANYV 328
T++ +KF+ PY + P YE + FL ++ E + C + + +
Sbjct: 518 GSILNTLQQLKFYKPYIC--DNDPKYERLVNAILDFLPKIEENLICS-------KYTDLL 568
Query: 329 QKVL 332
+ L
Sbjct: 569 RIAL 572
>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 = 34.5 bits (78), Expect = 0.020
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 44 KKL-AVLKEFGED-APDLGI 61
KKL A LK + +D AP L I
Sbjct: 23 KKLQASLKLYADDSAPALAI 42
Score = 27.6 bits (60), Expect = 4.2
Identities = 5/22 (22%), Positives = 11/22 (50%), Gaps = 5/22 (22%)
Query: 200 SVSKLS---RFLSP--IPAIAL 216
++ KL + + PA+A+
Sbjct: 21 ALKKLQASLKLYADDSAPALAI 42
>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 = 33.9 bits (77), Expect = 0.11
Identities = 27/190 (14%), Positives = 52/190 (27%), Gaps = 54/190 (28%)
Query: 181 LDPIVIAIALGRKVSCVTY--SVSKLSRFLSPIPAIALTRDRAADAARISELL--QKGDL 236
L + K Y + R AL R A++ + Q
Sbjct: 108 LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ---- 163
Query: 237 VVCPEGTTCRENFL--LR---------FSALFAEMSDRIVP-VAVNCKQNMFYGTTVRGV 284
G T +++ LR L ++ + + + +G+
Sbjct: 164 -----GNT--DDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT---QGL 213
Query: 285 KF--W--DPYFFFMNPRPTYEVTFLDRLPEEM-------------TCKAGGKSAIEVANY 327
W +P + P + +L +P T K G + E+ +Y
Sbjct: 214 NILEWLENP-----SNTP--DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSY 266
Query: 328 VQKVLGDVLG 337
++ G G
Sbjct: 267 LKGATGHSQG 276
>3i96_A Ethanolamine utilization protein EUTS; structural protein; HET:
NHE; 1.65A {Escherichia coli} PDB: 3ia0_A
Length = 119
Score = 30.6 bits (69), Expect = 0.25
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 301 EVTFLDRLPEEMTCKAGGKSAIEVA-NYVQKVLGDVLGFECTGLTR 345
+ FLDR + G A+E A + LG +L + +T+
Sbjct: 66 HIGFLDRFSGALVI-YGSVGAVEEALSQTVSGLGRLLNYTLCEMTK 110
>3cgi_A Propanediol utilization protein PDUU; circular permutation, beta
barrel, bacterial microcompartmen propanediol, signaling
protein; 1.80A {Salmonella typhimurium}
Length = 124
Score = 29.9 bits (67), Expect = 0.49
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 301 EVTFLDRLPEEMTCKAGGKSAIEVA-NYVQKVLGDVLGFECTGLTRKDKY 349
E+ FLDR + G SA+E A V + LG+++ F +TR ++
Sbjct: 71 EIGFLDRFTGAVVL-TGDVSAVEYALKQVTRTLGEMMQFTTCSITRTLEH 119
>4axi_A EUTS, ethanolamine carboxysome structural protein; bacterial
microcompartment; HET: GOL; 1.51A {Clostridium
difficile}
Length = 125
Score = 29.8 bits (67), Expect = 0.52
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 301 EVTFLDRLPEEMTCKAGGKSAIEVA-NYVQKVLGDVLGFECTGLTR 345
+ F+DR + +G S++E A N V +VLG++L F T +TR
Sbjct: 72 SLGFIDRFSGSVVI-SGDVSSVESALNDVLEVLGNMLNFSSTKITR 116
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
ribosome; NMR {Homo sapiens} SCOP: d.52.3.1
Length = 92
Score = 27.9 bits (62), Expect = 1.8
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 1 MVEPFVKDFLGGDKVLGTEIEVNPRTKRATGFVKRPGVLVGKW----KKLAVL--KEFGE 54
+ F+ L D G E+ V P R ++G+ ++L + K FG
Sbjct: 11 ELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGF 70
Query: 55 DAPDLGI 61
+ +
Sbjct: 71 PEGSVEL 77
>3acz_A Methionine gamma-lyase; L-methionine; HET: LLP; 1.97A {Entamoeba
histolytica} PDB: 3aej_A* 3ael_A* 3aem_A* 3aen_A*
3aeo_A* 3aep_A*
Length = 389
Score = 28.6 bits (65), Expect = 3.6
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 221 AADAARISELLQKGDLVVCPE---GTTCR--ENFLLRF--SALFAEMSD 262
A ++ LQKGD ++ + G T ++L RF + SD
Sbjct: 85 GAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSD 133
>1qgn_A Protein (cystathionine gamma-synthase); methionine biosynthesis,
pyridoxal 5'-phosphate, gamma-famil; HET: PLP; 2.90A
{Nicotiana tabacum} SCOP: c.67.1.3 PDB: 1i41_A* 1i48_A*
1i43_A*
Length = 445
Score = 28.4 bits (64), Expect = 3.9
Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 7/49 (14%)
Query: 221 AADAARISELLQKGDLVVCPE---GTTCR--ENFLLRF--SALFAEMSD 262
A + L+ G +V T E L + +A + +D
Sbjct: 140 CASTVMLLALVPAGGHIVTTTDCYRKTRIFIETILPKMGITATVIDPAD 188
>1pff_A Methionine gamma-lyase; homocysteine; 2.50A {Trichomonas vaginalis}
SCOP: c.67.1.3
Length = 331
Score = 28.2 bits (64), Expect = 4.5
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 221 AADAARISELLQKGDLVVCPE---GTTCR--ENFLLRF--SALFAEMSD 262
A AA + L+ GD ++ + G T E+ L +F F +M+
Sbjct: 24 GAIAASVWTFLKAGDHLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAV 72
>1a9x_A Carbamoyl phosphate synthetase (large chain); amidotransferase,
thioester; HET: CYG ADP; 1.80A {Escherichia coli} SCOP:
a.92.1.1 c.24.1.1 c.30.1.1 c.30.1.1 d.142.1.2 d.142.1.2
PDB: 1ce8_A* 1m6v_A* 1c30_A* 1bxr_A* 1c3o_A* 1cs0_A*
1jdb_B* 1kee_A* 1t36_A*
Length = 1073
Score = 28.2 bits (64), Expect = 4.8
Identities = 10/20 (50%), Positives = 11/20 (55%), Gaps = 7/20 (35%)
Query: 20 IEVNPRTKR-------ATGF 32
IE+NPR R ATGF
Sbjct: 298 IEMNPRVSRSSALASKATGF 317
>3dwb_A ECE-1, endothelin-converting enzyme 1; protein, disease mutation,
glycoprotein, hirschsprung diseas hydrolase, membrane,
metal-binding; HET: 5HD RDF; 2.38A {Homo sapiens}
Length = 670
Score = 28.1 bits (63), Expect = 5.7
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 9/58 (15%)
Query: 3 EPFVK---DFLGGDKVLGTEIEVNPRTKRATGFVKRP-GVLVGKWKKLAVLKEFGEDA 56
+ F F+ + GT+ PR K + G +G + V F ED+
Sbjct: 308 QRFQDADEKFME--VMYGTKKTSLPRWKFCVSDTENNLGFALG---PMFVKATFAEDS 360
>3qhx_A Cystathionine gamma-synthase METB (CGS); structural genomics,
seattle structural genomics center for infectious
disease, ssgcid, CGS_LIKE; HET: LLP EPE; 1.65A
{Mycobacterium ulcerans} PDB: 3qi6_A*
Length = 392
Score = 27.5 bits (62), Expect = 7.4
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 221 AADAARISELLQKGDLVVCPE---GTTCR--ENFLLRF--SALFAEMSD 262
AA + +L+ GD VV P+ G T R + + ++D
Sbjct: 92 AAADCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTGWNVEYTPVALAD 140
>3fvv_A Uncharacterized protein; unknown function, structural genomics,
PSI,MCSG, protein STR initiative, midwest center for
structural genomics; 2.10A {Bordetella pertussis}
Length = 232
Score = 27.3 bits (61), Expect = 7.7
Identities = 16/89 (17%), Positives = 26/89 (29%), Gaps = 11/89 (12%)
Query: 1 MVEPFVKDFLGGDKVLGTEIEVNPRTKRATGFVKRPGVLVGKWKKLAV---LKEFGEDAP 57
+ P + G ++ T+ E R R TG ++ + K + V L G
Sbjct: 121 VTAP-IARAFGVQHLIATDPEY--RDGRYTGRIEGT-PSFREGKVVRVNQWLAGMGLALG 176
Query: 58 DL----GIGDRQTDHDFMSICKEGYMVLP 82
D D D + P
Sbjct: 177 DFAESYFYSDSVNDVPLLEAVTRPIAANP 205
>1u02_A Trehalose-6-phosphate phosphatase related protein; structural
genomics, PSI; 1.92A {Thermoplasma acidophilum} SCOP:
c.108.1.15
Length = 239
Score = 26.9 bits (60), Expect = 8.5
Identities = 7/44 (15%), Positives = 15/44 (34%)
Query: 38 VLVGKWKKLAVLKEFGEDAPDLGIGDRQTDHDFMSICKEGYMVL 81
+ V K + ++ + P + GD TD + +
Sbjct: 154 LRVPGVNKGSAIRSVRGERPAIIAGDDATDEAAFEANDDALTIK 197
>1gc0_A Methionine gamma-lyase; pyridoxal-5'-phosphate; HET: LLP; 1.70A
{Pseudomonas putida} SCOP: c.67.1.3 PDB: 1gc2_A* 1pg8_A*
1ukj_A* 2o7c_A*
Length = 398
Score = 27.1 bits (61), Expect = 9.1
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 221 AADAARISELLQKGDLVVCPE---GTTCR--ENFLLRF--SALFAEMSD 262
A + + LL+ GD V+ G T + + F +M+D
Sbjct: 91 GAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMAD 139
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
0.323 0.142 0.435
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,952,408
Number of extensions: 371399
Number of successful extensions: 795
Number of sequences better than 10.0: 1
Number of HSP's gapped: 792
Number of HSP's successfully gapped: 25
Length of query: 367
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 272
Effective length of database: 4,049,298
Effective search space: 1101409056
Effective search space used: 1101409056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.4 bits)