RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13300
(346 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 = 52.2 bits (124), Expect = 1e-07
Identities = 62/421 (14%), Positives = 109/421 (25%), Gaps = 159/421 (37%)
Query: 6 KNVLKMIKKNIGNENAPW-MTRIAAYTQQ------IIINSSEELLKDP------FLPLAE 52
+ +++ + + N + M+ I +Q + I + L D + +
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135
Query: 53 RVKKRTDNLFHKEESLR-----------GFLKSSVDDTSQIESQIQEDWQLLVRDIYAFY 101
K L LR G K+ + D+ Y
Sbjct: 136 PYLKLRQAL----LELRPAKNVLIDGVLGSGKTW-----------------VALDVCLSY 174
Query: 102 PLLIKYVDLQKTHWL---RNNIPEAELI--------------------YNYVSEIFNIWS 138
+ K K WL N PE L N I +I +
Sbjct: 175 KVQCKMDF--KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232
Query: 139 KSQYFLREEQ---------NFISANEIDNM-----ILIMPTATRRSAVVSDSSVAGGVGG 184
+ + L+ + N +A + IL+ T TR V +
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILL--T-TR------FKQVTDFLSA 283
Query: 185 KMKKMPEYEIMEFVKTQLT------------------LP---DKIDP------ADEMS-- 215
+ ++ LT LP +P A+ +
Sbjct: 284 ATTT---HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG 340
Query: 216 ------WQHYLYSKLGNK-KDSTEVVPHAGQTP-----------VKPPTVDDVVERIVAM 257
W+H KL + S V P V P I
Sbjct: 341 LATWDNWKHVNCDKLTTIIESSLNV-----LEPAEYRKMFDRLSVFP---PSA--HI--P 388
Query: 258 AKVLFGLHMKMPEYEIMEFVKT--QLTLPDKIDPADEMSWQHYLYSKLGNKKDSTEVVPH 315
+L + + + ++M V + +L +K P + +Y +L K E H
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEK-QPKESTISIPSIYLEL-KVKLENEYALH 446
Query: 316 A 316
Sbjct: 447 R 447
Score = 38.7 bits (89), Expect = 0.003
Identities = 54/369 (14%), Positives = 100/369 (27%), Gaps = 127/369 (34%)
Query: 44 KDPFLPLAERVKKRTDNLFHKEESLRGFLKSS-VDDTSQIESQIQED----WQLL----- 93
KD + D ++ + L +D + + W LL
Sbjct: 19 KDILSVFEDAFVDNFD-CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEE 77
Query: 94 -----VRDI----YAFYPLLIKYVDLQKTHWLRNNIPEAELIYNYVSEIFNIWSKSQYFL 144
V ++ Y F IK Q + R I + + +YN +++F ++Y +
Sbjct: 78 MVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN-DNQVF-----AKYNV 131
Query: 145 -REEQNFISANEIDNMILIMPTATRRSAVVSDSSVAG----GVGGKMKKMPEYEIMEFVK 199
R + P R A++ GV G K ++ K
Sbjct: 132 SRLQ----------------PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 200 TQLTLPDKI---------DPADEMSWQHYLYSKLGNKKDSTEVVPHAGQTPVKPPTVDDV 250
Q + KI P + L ++ + T H+ ++ ++
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI--DPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 251 VERI---------------VAMAKVL--FGLHMKM-----------------PEYEIMEF 276
+ R+ V AK F L K+ + ++
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293
Query: 277 VKTQLT------------------LP---DKIDP------ADEMS--------WQHYLYS 301
LT LP +P A+ + W+H
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 302 KLGNKKDST 310
KL +S+
Sbjct: 354 KLTTIIESS 362
Score = 30.6 bits (68), Expect = 0.88
Identities = 18/122 (14%), Positives = 36/122 (29%), Gaps = 21/122 (17%)
Query: 213 EMSWQHYLYSKL------GNKKD-STEVVPHAGQTPVKPPTVDDVVER--IVAMAKVLFG 263
E Y Y + + + V ++ + +D ++ V+ LF
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 264 LHMKMPEYEIMEFVKTQLT-----LPDKI-----DPADEMSWQHYLYSKLGNKKDSTEVV 313
+ E + +FV+ L L I P+ +L N D+
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN--DNQVFA 127
Query: 314 PH 315
+
Sbjct: 128 KY 129
>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 = 43.1 bits (101), Expect = 1e-04
Identities = 64/441 (14%), Positives = 134/441 (30%), Gaps = 174/441 (39%)
Query: 1 MNQLLKNVLKMIKKNI--GNENAPWMTRIAAYTQQIIINSSEELLKDPFLPL----AERV 54
+Q+L L + GN+ I A +++ + L+K L A +
Sbjct: 80 FDQVLNLCLTEFENCYLEGND-------IHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 55 KKRTDNLFHKEESLRGFLKSSVDDTSQIESQI--Q---EDW--QLLVRDIYAFYPLLI-- 105
KR + S ++ + +Q+ + Q +D+ +L RD+Y Y +L+
Sbjct: 133 AKRPFDKKS--NSA--LFRAVGEGNAQLVAIFGGQGNTDDYFEEL--RDLYQTYHVLVGD 186
Query: 106 ------------------------KYVDLQKTHWLRN--NIPEAE-LIYNYVS--EIFNI 136
+ +++ + WL N N P+ + L+ +S I +
Sbjct: 187 LIKFSAETLSELIRTTLDAEKVFTQGLNILE--WLENPSNTPDKDYLLSIPISCPLIG-V 243
Query: 137 WSKSQYF------------LREE--------QNFISA-------------NEIDNMILIM 163
+ Y LR Q ++A + I ++
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL 303
Query: 164 -----------PTATRRSAVVSDSSVAGGVGGK--M---KKMPEYEIMEFV-KTQLTLP- 205
P + +++ D S+ G M + + ++ ++V KT LP
Sbjct: 304 FFIGVRCYEAYPNTSLPPSILED-SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPA 362
Query: 206 -DKI---------------DPADEMSWQHYLYS--------KLGNKKDSTEVVPHAGQTP 241
++ P LY K + D + +P + +
Sbjct: 363 GKQVEISLVNGAKNLVVSGPPQS-------LYGLNLTLRKAKAPSGLDQSR-IPFSERKL 414
Query: 242 V---------KP-------PTVDDVVERIVAMAKVLF-GLHMKMPEYEI-----MEFVKT 279
P P D + + + V F +++P Y+ + +
Sbjct: 415 KFSNRFLPVASPFHSHLLVPASDLINKD-LVKNNVSFNAKDIQIPVYDTFDGSDLRVLSG 473
Query: 280 QLT--LPDKI--DPADEMSWQ 296
++ + D I P W+
Sbjct: 474 SISERIVDCIIRLPVK---WE 491
>3mvn_A UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamayl-M diaminopimelate
ligase; structural genomics, MCSG, PSI-2; 1.90A
{Haemophilus ducreyi}
Length = 163
Score = 29.2 bits (66), Expect = 1.1
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 204 LPDKIDPADEMSWQHYLYSKLGNKKDSTEVVPHAGQTPVKPPTVDDVVERIVAMAK 259
L + AD + ++Y + +EV+ + Q + VD++V RIV AK
Sbjct: 86 LATSLQDADSV----FIYQPPTIEWQVSEVLANLAQPAISADDVDELVMRIVQQAK 137
Score = 29.2 bits (66), Expect = 1.1
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 283 LPDKIDPADEMSWQHYLYSKLGNKKDSTEVVPHAGQTPVKPPTVDDVVERIVAMAK 338
L + AD + ++Y + +EV+ + Q + VD++V RIV AK
Sbjct: 86 LATSLQDADSV----FIYQPPTIEWQVSEVLANLAQPAISADDVDELVMRIVQQAK 137
>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation,
transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A*
2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A*
Length = 394
Score = 28.2 bits (62), Expect = 4.6
Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 5/87 (5%)
Query: 247 VDDVVERIVAMAKVLFGLH-MKMPEYEIMEFVKTQLTLPDKIDPADEMSWQHYLYSKLGN 305
V +VV+ MAK+L + M P+ EI E P + H L+ N
Sbjct: 184 VSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHM-VYVPSHLYHMLFELFKN 242
Query: 306 KKDSTEVVPHAGQTPVKPPTVDDVVER 332
+ + ++ + P + +V
Sbjct: 243 ---AMRATVESHESSLILPPIKVMVAL 266
>3tdu_A DCN1-like protein 1; E2:E3, ligase-protein binding complex; 1.50A
{Homo sapiens} PDB: 3tdz_A
Length = 200
Score = 27.7 bits (61), Expect = 5.3
Identities = 31/143 (21%), Positives = 55/143 (38%), Gaps = 17/143 (11%)
Query: 32 QQIIINSSEELLKD--------PFLPLAERVKKRTDNLFHKEESLRGFLKSSVDDTSQIE 83
+I I+ ++ D L +A + + T F K+E + G + D +++
Sbjct: 20 NKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLK 79
Query: 84 SQIQEDWQLLV-----RDIYAFYPLLIKYVDLQKTHWLRNNIPEAELIYNYVSEIFNIWS 138
+QI + Q L +D Y F K QK L I L+ N + ++W+
Sbjct: 80 AQIPKMEQELKEPGRFKDFYQFTFNFAKNPG-QKGLDLEMAIAYWNLVLNGRFKFLDLWN 138
Query: 139 KSQYFLREEQNFISANEIDNMIL 161
FL E + N++L
Sbjct: 139 ---KFLLEHHKRSIPKDTWNLLL 158
>4ah2_B HLA class II histocompatibility antigen gamma CHA class II
histocompatibility antigen\,DRB1-1...; MHC II, immune
system, SELF antigen; 2.36A {Homo sapiens}
Length = 229
Score = 27.5 bits (61), Expect = 6.5
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 80 SQIESQIQEDWQLLVRDIYAFYPLLIKYVDLQKTHWLRNNIPEAE 124
++Q + LLV + FYP I + W RN E
Sbjct: 133 YPSKTQPLQHHNLLVCSVSGFYPGSI------EVRWFRNGQEEKA 171
>1fne_B Protein (MHC class II I-EK, beta chain); histocompatibility
antigen, immune system; HET: NAG; 1.90A {Mus musculus}
SCOP: b.1.1.2 d.19.1.1 PDB: 1iea_B* 1i3r_B* 1fng_B*
1ktd_B* 1ieb_B* 1kt2_B* 3o6f_B 3t0e_B
Length = 224
Score = 27.0 bits (60), Expect = 7.2
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 80 SQIESQIQEDWQLLVRDIYAFYPLLIKYVDLQKTHWLRNNIPEAE 124
++Q E LLV + FYP I + W RN E
Sbjct: 128 YPTKTQPLEHHNLLVCSVSDFYPGNI------EVRWFRNGKEEKT 166
>2p24_B H-2 class II histocompatibility antigen, A-U beta; MHC, I-AU,
immunoglobulin fold, MBP, immune system; 2.15A {Mus
musculus} PDB: 3cup_B* 1es0_B 3rdt_D 1lnu_B* 3c5z_D
3c60_D 3c6l_D
Length = 259
Score = 27.2 bits (60), Expect = 7.8
Identities = 11/34 (32%), Positives = 12/34 (35%), Gaps = 6/34 (17%)
Query: 91 QLLVRDIYAFYPLLIKYVDLQKTHWLRNNIPEAE 124
LV + FYP I K W RN E
Sbjct: 164 NTLVCSVTDFYPAKI------KVRWFRNGQEETV 191
>1iao_B MHC class II I-AD; MHC II, class II MHC, ovalbumin peptide; HET:
NAG; 2.60A {Mus musculus} SCOP: b.1.1.2 d.19.1.1
Length = 222
Score = 27.1 bits (60), Expect = 8.3
Identities = 12/45 (26%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 80 SQIESQIQEDWQLLVRDIYAFYPLLIKYVDLQKTHWLRNNIPEAE 124
S ++ LV + FYP I K W RN E
Sbjct: 128 SLSRTEALNHHNTLVCSVTDFYPAKI------KVRWFRNGQEETV 166
>3c5j_B MHC class II antigen; HLA, MHC class II, glycoprotein, immune
response, membrane, transmembrane, GTP-binding,
methylation; HET: NAG; 1.80A {Homo sapiens} PDB: 2q6w_B
1a6a_B* 1d5m_B* 1j8h_B* 1d5z_B* 1d5x_B* 1d6e_B* 2seb_B*
2wbj_B* 1ymm_B* 3l6f_B* 3s4s_B 3s5l_B 1fyt_B* 1seb_B
1bx2_B* 1zgl_B 1fv1_B 1h15_B* 1hqr_B ...
Length = 190
Score = 26.9 bits (60), Expect = 8.7
Identities = 11/34 (32%), Positives = 13/34 (38%), Gaps = 6/34 (17%)
Query: 91 QLLVRDIYAFYPLLIKYVDLQKTHWLRNNIPEAE 124
LLV + FYP I + W RN E
Sbjct: 113 NLLVCSVSGFYPGSI------EVRWFRNGQEEKT 140
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
0.317 0.133 0.388
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,353,008
Number of extensions: 318982
Number of successful extensions: 728
Number of sequences better than 10.0: 1
Number of HSP's gapped: 723
Number of HSP's successfully gapped: 20
Length of query: 346
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 252
Effective length of database: 4,077,219
Effective search space: 1027459188
Effective search space used: 1027459188
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: 58 (26.3 bits)