RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7983
(184 letters)
>3ei3_A DNA damage-binding protein 1; UV-damage, DDB, nucleotide excision
repair, xeroderma pigmentosum, cytoplasm, DNA repair;
HET: DNA PG4; 2.30A {Homo sapiens} PDB: 3ei1_A* 3ei2_A*
3ei4_A* 4a0l_A* 3e0c_A* 3i7k_A* 3i7h_A* 3i7l_A* 3i7n_A*
3i7o_A* 3i7p_A* 3i89_A* 3i8c_A* 3i8e_A* 2b5l_A 2b5m_A
2hye_A* 4a11_A* 4a0k_C* 4a0a_A* ...
Length = 1158
Score = 106 bits (264), Expect = 5e-27
Identities = 59/106 (55%), Positives = 77/106 (72%), Gaps = 1/106 (0%)
Query: 79 STGLVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIE 138
GLVT +S Y+ L D+Q RL + I+SVG+IEHSFWRSF+T+ K++ GFIDGDLIE
Sbjct: 1054 MIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIE 1113
Query: 139 SFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRIH 184
SFLD++ M+ + LQ GS KR+AT DD+IK+VE+LTRIH
Sbjct: 1114 SFLDISRPKMQEVVANLQYD-DGSGMKREATADDLIKVVEELTRIH 1158
Score = 54.2 bits (129), Expect = 4e-09
Identities = 41/106 (38%), Positives = 56/106 (52%)
Query: 15 HLALATDSTFTFGTIDEIQKLHIRTVPLGEAPRRIAYQESSQTFGVITTRIDIQEADASL 74
LALA +ST T GTIDEIQKLHIRTVPL E+PR+I YQE SQ FGV+++RI++Q+
Sbjct: 708 SLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGT 767
Query: 75 NSFVSTGLVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFN 120
+ + +S + S +E +
Sbjct: 768 TALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIID 813
>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 = 50.4 bits (120), Expect = 9e-08
Identities = 37/211 (17%), Positives = 71/211 (33%), Gaps = 64/211 (30%)
Query: 6 AVKKVTLAFHLALATDSTFTFGTI------DEIQK--------LHIRTVPLGEAPRRIAY 51
K +T+ F + + + ++ D ++ L I + + +
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNK 355
Query: 52 -----QESSQTFGVITTRIDIQEADASL-NS---FVSTGLVTQISPE-LYSFLFDLQERL 101
Q ++I SL N V +G P+ LY L++
Sbjct: 356 TNSHLPAGKQ--------VEI-----SLVNGAKNLVVSG-----PPQSLYGLNLTLRKAK 397
Query: 102 AQTIRSVGRIEHS-----FWRSF-------NTDVKSDACEGFIDGDLIESFLDLNIKDMK 149
A + RI S F F ++ + A + I+ DL+++ + N KD++
Sbjct: 398 APSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASD-LINKDLVKNNVSFNAKDIQ 456
Query: 150 ----SIATG--LQITPPGSTTKRDATVDDII 174
G L++ S + + VD II
Sbjct: 457 IPVYDTFDGSDLRVL---SGSISERIVDCII 484
Score = 30.0 bits (67), Expect = 0.49
Identities = 17/131 (12%), Positives = 33/131 (25%), Gaps = 37/131 (28%)
Query: 72 ASLNSFV-STGLVTQ---ISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDA 127
S S G + + + LQE+ + + F D +
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTE---GFAAD---DEPTTP 57
Query: 128 CE------GFID-----------GDLIESFLD------LNIKDMKSIATGLQITPPGSTT 164
E G++ ++ L L D+ ++A L
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL----LQEND 113
Query: 165 KRDATVDDIIK 175
++IK
Sbjct: 114 TTLVKTKELIK 124
>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 = 42.5 bits (99), Expect = 4e-05
Identities = 17/153 (11%), Positives = 43/153 (28%), Gaps = 30/153 (19%)
Query: 54 SSQTFGVITTRIDIQEADASLNSFVSTGLVTQISPELYSFLFDLQERLAQTIRSVGR--- 110
+ +I + + +N LV + E + + L + +
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR 447
Query: 111 --IEH-SFWRSF-NTDVKSDACEGFI------------DGDLIESF----LDLNIKDMKS 150
++H + ++F + D+ + + + + F LD + K
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507
Query: 151 IATGLQITPPGSTTKRDATVDDIIK----IVED 179
GS T+ + I ++
Sbjct: 508 RHDSTAWNASGSIL---NTLQQLKFYKPYICDN 537
Score = 41.4 bits (96), Expect = 7e-05
Identities = 32/213 (15%), Positives = 60/213 (28%), Gaps = 77/213 (36%)
Query: 30 DEIQKLHIRTVPLGEAPRRI----AYQES------------SQTFGV-----ITTRIDIQ 68
D + +R + RR+ Y+ F + +TTR
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR---- 273
Query: 69 EADASLNSFVSTGLVTQISPELYSFLFDLQERLAQTIRSVG------------------- 109
+ F+S T IS + +S E + ++ +
Sbjct: 274 --FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331
Query: 110 -----------RIEHSFWRSFNTDVKSDACEGFIDGDLIESFLD-LNIKDMKSIATGLQI 157
+ W+ N D + IES L+ L + + + L +
Sbjct: 332 IIAESIRDGLATWD--NWKHVNCDKLTTI---------IESSLNVLEPAEYRKMFDRLSV 380
Query: 158 TPPGS--TTK------RDATVDDIIKIVEDLTR 182
PP + T D D++ +V L +
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413
Score = 30.2 bits (67), Expect = 0.46
Identities = 8/52 (15%), Positives = 20/52 (38%), Gaps = 8/52 (15%)
Query: 134 GDLIESFLDLNIKDM--KSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183
D++ F D + + K + + +K + +D II + ++
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPK----SILSKEE--IDHIIMSKDAVSGT 64
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 33.8 bits (77), Expect = 0.025
Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 4/74 (5%)
Query: 85 QISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLD-- 142
EL L D E + G I F + ++ + D E + D
Sbjct: 256 HDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDY--RSDRREDYYDIQ 313
Query: 143 LNIKDMKSIATGLQ 156
L+IK K+I
Sbjct: 314 LSIKGKKNIFESFV 327
>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination,
hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9
PDB: 1nbf_A
Length = 353
Score = 32.9 bits (75), Expect = 0.040
Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 4/74 (5%)
Query: 85 QISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLD-- 142
EL L D E + G I F + ++ + D E + D
Sbjct: 87 HDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDY--RSDRREDYYDIQ 144
Query: 143 LNIKDMKSIATGLQ 156
L+IK K+I
Sbjct: 145 LSIKGKKNIFESFV 158
>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 = 28.8 bits (63), Expect = 0.69
Identities = 5/28 (17%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 146 KDMKSIATGLQITPPGSTTKR--DATVD 171
+ +K + L++ S AT++
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATME 47
>2eih_A Alcohol dehydrogenase; zinc ION binding protein, structural
genomics, NPPSFA, natio project on protein structural
and functional analyses; 2.30A {Thermus thermophilus}
Length = 343
Score = 27.5 bits (62), Expect = 2.7
Identities = 7/27 (25%), Positives = 11/27 (40%), Gaps = 2/27 (7%)
Query: 38 RTVPLGEAPRRIAYQESSQTFG--VIT 62
+ +PL A E + FG V+
Sbjct: 315 QVLPLEAAAEGHRLLEERRVFGKVVLQ 341
>1mgp_A Hypothetical protein TM841; two domain structure with mixed
alpha/beta structures in BOTH domains, structural
genomics; HET: PLM; 2.00A {Thermotoga maritima} SCOP:
c.119.1.1 PDB: 1vpv_A*
Length = 313
Score = 27.2 bits (61), Expect = 3.1
Identities = 13/80 (16%), Positives = 24/80 (30%), Gaps = 7/80 (8%)
Query: 17 ALATDSTFTFGTIDEIQKLHIRTVPLGEAPRRIAYQESSQTFGVITTRIDIQEADASLNS 76
+ DST ++K I ++PL S ++ + S
Sbjct: 29 KILVDSTADV-PFSWMEKYDIDSIPL---YVVWEDGRSEPDEREPEEIMNFYKRIREAGS 84
Query: 77 FVSTGLVTQISPELYSFLFD 96
T +Q S E + +
Sbjct: 85 VPKT---SQPSVEDFKKRYL 101
>3odm_A Pepcase, PEPC, phosphoenolpyruvate carboxylase; beta-barrel, lyase;
2.95A {Clostridium perfringens}
Length = 560
Score = 26.6 bits (58), Expect = 5.5
Identities = 15/96 (15%), Positives = 30/96 (31%), Gaps = 7/96 (7%)
Query: 88 PELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLDLNI-- 145
PEL L E + + + D+ A F +G + + +D
Sbjct: 428 PELMGMGRALNEIKTKYGQEGIDKLLEIYPILRKDLAFAA--RFANGGVSKKIIDEEARQ 485
Query: 146 ---KDMKSIATGLQITPPGSTTKRDATVDDIIKIVE 178
+DMK + L + + ++K +
Sbjct: 486 EYKEDMKYVNEILNLGLDYDFLNENEFYHTLLKTTK 521
>3lup_A DEGV family protein; PSI-2, MCSG, structural genomics, fatty acid
binding, protei structure initiative; HET: ELA; 2.65A
{Streptococcus agalactiae}
Length = 285
Score = 26.0 bits (58), Expect = 8.1
Identities = 4/26 (15%), Positives = 9/26 (34%), Gaps = 1/26 (3%)
Query: 17 ALATDSTFTFGTIDEIQKLHIRTVPL 42
AL TD++ + + +
Sbjct: 7 ALITDTSAYL-PEAIENHEDVYVLDI 31
>3pl5_A SMU_165, putative uncharacterized protein; fatty acid binding
protein, lipid binding protein; HET: PLM; 2.04A
{Streptococcus mutans}
Length = 320
Score = 26.1 bits (58), Expect = 8.2
Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 18/85 (21%)
Query: 17 ALATDSTFTFGTIDEIQKLHIRTVPL-----GEAPRRIAYQESSQTFGVITTRIDIQEAD 71
+ TDST Q+ ++ + L G Y+ T + E
Sbjct: 38 KILTDSTADL-PESWTQENDVQVLGLTVQLDGI-----TYETV---GPDRLTSRVLLEKI 88
Query: 72 ASLNSFVSTGLVTQISPELYSFLFD 96
A+ S +T +Q++ + F
Sbjct: 89 AA-GSKPTT---SQVNVGQFESYFR 109
>3fys_A Protein DEGV; fatty acid-binding, EDD fold, fatty acid-binding
protein; HET: PLM; 2.50A {Bacillus subtilis}
Length = 315
Score = 25.7 bits (57), Expect = 9.4
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 17 ALATDSTFTFGTIDEIQKLHIRTVPL 42
A+ TDST + ++ I +PL
Sbjct: 38 AVVTDSTAYI-PKEMREQHQIHMIPL 62
>2g7z_A Conserved hypothetical protein SPY1493; long-fatty acid binding
protein, lipid binding protein, PSI, structural
genomics; HET: MSE HXA; 2.05A {Streptococcus pyogenes}
Length = 282
Score = 25.6 bits (57), Expect = 9.6
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 17 ALATDSTFTFGTIDEIQKLHIRTVPL 42
+ TDS+ T + I+ L I VPL
Sbjct: 8 KIVTDSSITI-EPELIKALDITVVPL 32
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
0.320 0.135 0.375
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,735,042
Number of extensions: 155091
Number of successful extensions: 407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 400
Number of HSP's successfully gapped: 25
Length of query: 184
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 96
Effective length of database: 4,244,745
Effective search space: 407495520
Effective search space used: 407495520
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 (21.8 bits)
S2: 54 (24.7 bits)