RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17539
(443 letters)
>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo sapiens}
Length = 530
Score = 190 bits (484), Expect = 4e-55
Identities = 113/297 (38%), Positives = 161/297 (54%), Gaps = 45/297 (15%)
Query: 2 FLDLFNRVEVTFCDKTILNDQGFTLELSLKMTYEQLVALVAQHLNTDKKLIQMFKVQAYK 61
F DL++RV+V FCDKTI ND GF + LS +M Y Q+ VAQ LNTD L+Q FK Q Y+
Sbjct: 233 FRDLYHRVDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTDPMLLQFFKSQGYR 292
Query: 62 DTPGNPLPHNFEGTLKDILAPINKPKMPKKMHYQKLSIPVVELINKRPFKVQAYKDTPGN 121
D PGNPL HN+EGTL+D+L P+ PKK++YQ+L + + + N+R FK
Sbjct: 293 DGPGNPLRHNYEGTLRDLLQFFK-PRQPKKLYYQQLKMKITDFENRRSFKCI-------- 343
Query: 122 PLPHNFEGTLKDILAPINKPKMPKKMHYQKLSIPVVELINKRPFKVRTQFLDEAKKDAAI 181
+ + +++++ + R L+E KK
Sbjct: 344 --------------------WLNSQFREEEITLYPDKHGCVR------DLLEECKK---- 373
Query: 182 QPELLGPDNGGSGLLRLLEISNQKITAELDHSVSMDQLFGMNATTKIYRLEEIPQDEVSL 241
+ SG LRLLEI + KI ++ L AT++ +R+EEIP D+V +
Sbjct: 374 ---AVELGEKASGKLRLLEIVSYKIIGVHQEDELLECL--SPATSRTFRIEEIPLDQVDI 428
Query: 242 DP-DELLIPVAHFQKDIHNIFGYPFLLRIKDNERFSKVKERLAKKLNIQEKEFEKVR 297
D +E+L+ VAHF K++ FG PFLLRI E F +V +R+ L+IQEKEFEK +
Sbjct: 429 DKENEMLVTVAHFHKEVFGTFGIPFLLRIHQGEHFREVMKRIQSLLDIQEKEFEKFK 485
Score = 109 bits (273), Expect = 5e-26
Identities = 55/178 (30%), Positives = 82/178 (46%), Gaps = 16/178 (8%)
Query: 264 PFLLRIKDNERFSKVKERLAKKLNIQEKEFEKVRVQD-------KIHPGRES----NPWP 312
L + + E K + + EK K+R+ + +H E +P
Sbjct: 353 EITLYPDKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPAT 412
Query: 313 SA--YMANAPPSKSN---PDELLIPVAHFQKDIHNIFGYPFLLRIKDNERFSKVKERLAK 367
S + P + + +E+L+ VAHF K++ FG PFLLRI E F +V +R+
Sbjct: 413 SRTFRIEEIPLDQVDIDKENEMLVTVAHFHKEVFGTFGIPFLLRIHQGEHFREVMKRIQS 472
Query: 368 KLNIQEKEFEKYKFGVINNNRITYIEEDSDCPVSINQFRSNISHQDYKVWLGLDHINK 425
L+IQEKEFEK+KF ++ R YI ED + + + WLGLDH NK
Sbjct: 473 LLDIQEKEFEKFKFAIVMMGRHQYINEDEYEVNLKDFEPQPGNMSHPRPWLGLDHFNK 530
>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 = 56.0 bits (134), Expect = 2e-08
Identities = 64/438 (14%), Positives = 132/438 (30%), Gaps = 119/438 (27%)
Query: 1 MFLDLFNRVEVTFCDKTILNDQGFTLELSLKMTYEQLVALVAQHLNT----------DKK 50
M L +++ + +D ++L + +L L+ + K
Sbjct: 201 MLQKLLYQIDPNWTS---RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 51 LIQMFKVQ-------------------AYKDTPGNPLPHNF-EGTLKDILA---PINKPK 87
F + + +K +L
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317
Query: 88 MP---KKMHYQKLSIPVVELINKRPFKVQAYKDTPGNPLPHNFEGTLKDILAPINKPKMP 144
+P + ++LSI + E I +K + L E +L ++L P
Sbjct: 318 LPREVLTTNPRRLSI-IAESIRDGLATWDNWKHVNCDKLTTIIESSL-NVLEPAE----- 370
Query: 145 KKMHYQKLSIPVVELINKRPFKVRTQFLDEAKKDAAIQPELLG----------PDNGGSG 194
+ + +LS+ F A I LL +
Sbjct: 371 YRKMFDRLSV----------------FPPSAH----IPTILLSLIWFDVIKSDVMVVVNK 410
Query: 195 LLR--LLEISNQKITAELDHSVSMDQLFGMNATTKIYR--LE--EIPQDEVSLDPDELLI 248
L + L+E ++ T + S+ ++ + ++R ++ IP+ + D D+L+
Sbjct: 411 LHKYSLVEKQPKESTISI-PSIYLELKVKLENEYALHRSIVDHYNIPK---TFDSDDLIP 466
Query: 249 PVAHFQKD--IHNIFGYPFLLRIKDNERFSKVKERLAKKLNIQEKEFEKVRVQDKI-HPG 305
P D ++ G+ L I+ ER + + L+ F ++ KI H
Sbjct: 467 P----YLDQYFYSHIGH-HLKNIEHPERMTLFRMVF---LDF---RF----LEQKIRHDS 511
Query: 306 RESNPWPSA---------YMANAPPSKSNPDELLIPVAHFQKDI-HNIFGYPF--LLRI- 352
N S Y + + L+ + F I N+ + LLRI
Sbjct: 512 TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIA 571
Query: 353 --KDNERFSKVKERLAKK 368
++E + + ++
Sbjct: 572 LMAEDEAIFEEAHKQVQR 589
Score = 34.1 bits (77), Expect = 0.097
Identities = 20/117 (17%), Positives = 45/117 (38%), Gaps = 19/117 (16%)
Query: 335 HFQKDIHNIFGYPFL--LRIKDNERFSK---VKERLAKKLNIQEKEFEKYK-FGVINNNR 388
+ KDI ++F F+ KD + K KE + + ++ + F + + +
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQ 75
Query: 389 ITYIEEDSDCPVSINQFRSNISHQDYKVWL--GLDHINKAPKRSRLNYLEKAIKIYN 443
++ +F + +YK +L + + P Y+E+ ++YN
Sbjct: 76 EEMVQ----------KFVEEVLRINYK-FLMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
>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 = 52.4 bits (125), Expect = 2e-07
Identities = 74/452 (16%), Positives = 133/452 (29%), Gaps = 159/452 (35%)
Query: 5 LFNRVE---VTFCDKTILNDQG-----FTLEL-SLKMTYEQLVA------------LVAQ 43
LF V I QG F EL L TY LV L+
Sbjct: 145 LFRAVGEGNAQLV--AIFGGQGNTDDYFE-ELRDLYQTYHVLVGDLIKFSAETLSELIRT 201
Query: 44 HLNTDKKLIQMFKVQAYKDTPGNPLPHNFEGTLKDILAPINKPKMPKKMHYQKLSIPVVE 103
L+ +K Q + + + P N ++ L + PI S P++
Sbjct: 202 TLDAEKVFTQGLNILEWLENPSNTPDKDY---L--LSIPI--------------SCPLIG 242
Query: 104 LINKRPFKV--QAYKDTPGNPLPHNFEGTL---KDILAPINKPKMPKKMHYQKLSIPVVE 158
+I + V + TPG L +G + ++ + + + +
Sbjct: 243 VIQLAHYVVTAKLLGFTPGE-LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301
Query: 159 LINKRPFK--VRTQFLDEAKKDAAIQPELLG--PDNG-G--SGLLRLLEISNQKITAELD 211
++ F VR EA + ++ P +L +N G S +L + ++ +++ ++
Sbjct: 302 VL----FFIGVRCY---EAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVN 354
Query: 212 HSVSMDQLFGMNATTKIYRLEEIPQDEVSL--DPDELLIPVAHFQKDIHNIFGYPFLLRI 269
N+ L Q E+SL + + G P L
Sbjct: 355 K---------TNS-----HLPAGKQVEISLVNGAK-------NL-----VVSGPPQSLY- 387
Query: 270 KDNERFSKVKERLAKKLNIQEKEFEKVRV-----QDKIHPGRE------------SNPWP 312
LN+ K + Q +I P E ++P+
Sbjct: 388 ---------------GLNLT---LRKAKAPSGLDQSRI-PFSERKLKFSNRFLPVASPFH 428
Query: 313 SAYMANAPPS----------KSNPDELLIPVAHFQ--KDIHNIFGYPFLLRIKDNERFSK 360
S + A N ++ IPV D LR+
Sbjct: 429 SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD----------LRVLSGS---- 474
Query: 361 VKERLAKKLNIQEKEFEKYKFGVINNNRITYI 392
+ ER+ + ++E + T+I
Sbjct: 475 ISERIVDCIIRLPVKWET-----TTQFKATHI 501
Score = 31.6 bits (71), Expect = 0.65
Identities = 31/144 (21%), Positives = 51/144 (35%), Gaps = 44/144 (30%)
Query: 97 LSIP-VVELINKRPFKVQAYKDTPGNPLPHNFEGTLKDILAPINKPKMPKKMHYQKLSIP 155
+SI +VE++ R +Q +P + G + IN ++ + L
Sbjct: 1777 MSIESLVEVVFYRGMTMQ-------VAVPRDELGRSNYGMIAINPGRVAASFSQEALQY- 1828
Query: 156 VVELINKRPFKVRTQFLDEAKKDAAIQPELLGP--DN--GG----SGLLRLLE------- 200
VVE + KR L+ N +G LR L+
Sbjct: 1829 VVERVGKR------------------TGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLN 1870
Query: 201 -ISNQKI-TAELDHSVSMDQLFGM 222
I QKI EL S+S++++ G
Sbjct: 1871 FIKLQKIDIIELQKSLSLEEVEGH 1894
Score = 28.1 bits (62), Expect = 7.5
Identities = 25/142 (17%), Positives = 46/142 (32%), Gaps = 48/142 (33%)
Query: 32 MTYEQLVALVAQHLNTDK--KLIQMFKVQAYKDTPGNPLPHNFEGTLKDILAPINKPKMP 89
M+ E LV +V +Q +P + G + IN ++
Sbjct: 1777 MSIESLVEVVFY------RGMTMQ------------VAVPRDELGRSNYGMIAINPGRVA 1818
Query: 90 KKMHYQKLSIPVVELINKR-PFKVQAYKDTPGNPLPHNFEG-------------TLKDIL 135
+ L VVE + KR + V+ N +N E T+ ++L
Sbjct: 1819 ASFSQEALQY-VVERVGKRTGWLVE-----IVN---YNVENQQYVAAGDLRALDTVTNVL 1869
Query: 136 APINKPK-----MPKKMHYQKL 152
I K + K + +++
Sbjct: 1870 NFIKLQKIDIIELQKSLSLEEV 1891
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.5 bits (68), Expect = 0.84
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 17/74 (22%)
Query: 230 RLEEIPQDEVSLDPDELLIPVAHFQKDIHNIFGYPFLLRIKDNERFSKVKERLAKKLN-I 288
RL+E D S ++ A +KD+ + R +E+ K K N I
Sbjct: 97 RLQE--LDAASKVMEQEWREKA--KKDLEE-----WNQRQ--SEQVEKNKIN-----NRI 140
Query: 289 QEKEFEKVRVQDKI 302
+K F + D I
Sbjct: 141 ADKAFYQQPDADII 154
>3hrq_A PKS, aflatoxin biosynthesis polyketide synthase; hot-DOG fold,
iterative type I PKS, norsolorinic acid, product
template domain; HET: PLM; 1.80A {Aspergillus
parasiticus} PDB: 3hrr_A*
Length = 357
Score = 29.7 bits (66), Expect = 1.9
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 392 IEEDSDCPVSINQFRSNISHQDYKVWLGLDH-INKAP 427
+EE + + ++IS +D H ++ P
Sbjct: 13 VEETTKPLGATLVVETDISRKDVNGLAR-GHLVDGIP 48
>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold,
coiled coil, riken structural genomics/proteomics
initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus}
SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A*
1iyw_A
Length = 862
Score = 28.3 bits (64), Expect = 6.4
Identities = 7/47 (14%), Positives = 16/47 (34%), Gaps = 10/47 (21%)
Query: 275 FSKVKERLAKKLNIQEKEFEKVRVQDKIHPGRESNPWPSAYMANAPP 321
+ + R K+L E+ + + ++P + AP
Sbjct: 798 VEEWRRRQEKRLKELLALAERSQ-------RKLASP---GFREKAPK 834
>3ott_A Two-component system sensor histidine kinase; beta-propeller,
beta-sandwich, transcription; HET: TBR; 2.30A
{Bacteroides thetaiotaomicron}
Length = 758
Score = 28.1 bits (63), Expect = 6.9
Identities = 6/30 (20%), Positives = 15/30 (50%)
Query: 368 KLNIQEKEFEKYKFGVINNNRITYIEEDSD 397
++N +++ + FG +NN I + +
Sbjct: 540 RINPKDESQQSISFGSFSNNEILSMTCVKN 569
Score = 27.7 bits (62), Expect = 9.6
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 368 KLNIQEKEFEKYKF-GVINNNRITYIEEDSD 397
K+N + +E K + Y+ D D
Sbjct: 497 KINPRTREVTKLFADELTGEKSPNYLLCDED 527
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
0.318 0.137 0.400
Gapped
Lambda K H
0.267 0.0456 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,830,120
Number of extensions: 421159
Number of successful extensions: 1112
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1101
Number of HSP's successfully gapped: 31
Length of query: 443
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 346
Effective length of database: 3,993,456
Effective search space: 1381735776
Effective search space used: 1381735776
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.2 bits)