RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3486
(222 letters)
>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha
solenoid, regulatory PART LID, hydrolase, protein
binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A
Length = 394
Score = 77.6 bits (190), Expect = 7e-17
Identities = 16/100 (16%), Positives = 36/100 (36%), Gaps = 4/100 (4%)
Query: 124 YKEMMSRYKQLLLYIK---SAVTRNYSEKSINSILDYIST-SKNMELLQDFYETTLEALK 179
+ L+ + S++++ + K + S++D + + +E K
Sbjct: 31 QEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAK 90
Query: 180 DAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQ 219
K L +L LYFD + + + QL + +
Sbjct: 91 QEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELK 130
Score = 54.9 bits (131), Expect = 4e-09
Identities = 12/54 (22%), Positives = 28/54 (51%)
Query: 1 MDDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIK 54
+D ++ H+ L + Q L ++I+PY+R+ + ++ + + V KL +
Sbjct: 286 AEDVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQ 339
Score = 51.4 bits (122), Expect = 5e-08
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 55 PYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNT 114
+ H+ + + + L ++I+PY+R+ + ++ + + VE L +ILD
Sbjct: 289 VIVQAHLGTLYDTMLEQ---NLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKK 345
Query: 115 VRGRIDQSN 123
G +DQ
Sbjct: 346 FSGILDQGE 354
>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 = 48.7 bits (115), Expect = 5e-07
Identities = 29/228 (12%), Positives = 73/228 (32%), Gaps = 38/228 (16%)
Query: 1 MDDPFIREHIEDLLRNIRTQVLI--------KLIKPYTRIHIPFISRQLNIETSDVLIKL 52
+ + + N+ ++L+ + T HI + + +V L
Sbjct: 250 LLNVQNAKAWNAF--NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307
Query: 53 IKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFIS--RQLNIETSDVESLLVSLI 110
+K Y + R++ + T+ + +I R + + +N +
Sbjct: 308 LK-YLDCRPQDLPREV-LTTNPRRLSIIAESIRDGLATWDNWKHVNCDK----------- 354
Query: 111 LDNTVRGRIDQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDF 170
L + ++ E + +L ++ SA + ++ I + S M ++
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSA---HIPTILLSLIWFDVIKSDVMVVVNKL 411
Query: 171 YETTLEALKDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSC 218
++ +L K K + + +Y + LH+S
Sbjct: 412 HKYSL-VEKQPKESTI------SIPSIYL---ELKVKLENEYALHRSI 449
Score = 42.9 bits (100), Expect = 5e-05
Identities = 33/187 (17%), Positives = 67/187 (35%), Gaps = 38/187 (20%)
Query: 44 ETSDVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVE 103
VL L K +I + SR + + I I+ R S+
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL--LKSKPYE------N 245
Query: 104 SLLVSLILDNTVRGR--IDQSNY--KEMM-SRYKQLLLYIKSAVTRNYSEKSINSILDYI 158
LL +L N V+ + N K ++ +R+KQ+ ++ +A T + S++ +
Sbjct: 246 CLL---VLLN-VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT---THISLDHHSMTL 298
Query: 159 STSKNMELLQDFYETTLEALKD-------------AKNDRLWFKTNTKLGKLYFDREDFN 205
+ + LL + + + L A++ R T + + +
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD-----NWKHVNCD 353
Query: 206 KLSRILK 212
KL+ I++
Sbjct: 354 KLTTIIE 360
Score = 41.4 bits (96), Expect = 1e-04
Identities = 39/257 (15%), Positives = 84/257 (32%), Gaps = 62/257 (24%)
Query: 3 DPFIRE----HIEDLLRNIRTQVLIK--LIKPYT-----RIHIPFISRQLNIETSDVLIK 51
D F+ ++D+ ++I ++ I ++ R+ +S+Q + V
Sbjct: 27 DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV 86
Query: 52 LIKPY----TRIHI----PFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVE 103
L Y + I P + ++ IE D L + + + ++ + L + + +E
Sbjct: 87 LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146
Query: 104 -----------------SLLVSLIL-DNTVRGR-------IDQSNYKEMMSRYKQL--LL 136
+ + + V+ + ++ N + + L LL
Sbjct: 147 LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL 206
Query: 137 YI--KSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALKDAKNDRLWFKTNTKL 194
Y + +R+ +I + I L YE L L + +N + W
Sbjct: 207 YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW------- 259
Query: 195 GKLYFDREDFNKLSRIL 211
FN +IL
Sbjct: 260 -------NAFNLSCKIL 269
Score = 31.4 bits (70), Expect = 0.27
Identities = 25/136 (18%), Positives = 41/136 (30%), Gaps = 48/136 (35%)
Query: 126 EMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTS------------------------ 161
E +YK +L + A N+ K + + I +
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLL 72
Query: 162 -KNMELLQDFYETTL--------EALKDAKN-------------DRLWFKTNTKLGKLYF 199
K E++Q F E L +K + DRL+ N K
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY-NDNQVFAKYNV 131
Query: 200 DR-EDFNKLSRILKQL 214
R + + KL + L +L
Sbjct: 132 SRLQPYLKLRQALLEL 147
>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export,
transcription; 2.12A {Homo sapiens}
Length = 203
Score = 46.1 bits (109), Expect = 2e-06
Identities = 18/128 (14%), Positives = 38/128 (29%), Gaps = 42/128 (32%)
Query: 3 DPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIP 62
FIR I +L ++ L K L+ ++ +
Sbjct: 107 AFFIRCGIFLILEKLKIITYRNLFKKVY---------------------LLLKTHQLSLD 145
Query: 63 FISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQS 122
L + +++ +V+ +L +LI V+G I
Sbjct: 146 AFLVALKFMQVE---------------------DVDIDEVQCILANLIYMGHVKGYISHQ 184
Query: 123 NYKEMMSR 130
+ K ++S+
Sbjct: 185 HQKLVVSK 192
>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
signaling protein; NMR {Mus musculus} SCOP: a.4.5.47
Length = 84
Score = 42.9 bits (101), Expect = 4e-06
Identities = 12/46 (26%), Positives = 19/46 (41%)
Query: 76 LIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQ 121
L+ K Y I + L I + E + +I + + G IDQ
Sbjct: 21 LLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQ 66
Score = 25.9 bits (57), Expect = 4.3
Identities = 8/41 (19%), Positives = 12/41 (29%)
Query: 8 EHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETSDV 48
L R + L+ K Y I + L I +
Sbjct: 7 GGSSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKA 47
>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 = 39.3 bits (91), Expect = 7e-04
Identities = 37/197 (18%), Positives = 71/197 (36%), Gaps = 46/197 (23%)
Query: 1 MDDPFIREHIEDLLRNIRTQVLIKLIKPYTRIHIPFISRQLNIETS-DVLIKLIKPYTRI 59
PF ++ L R + ++ F Q N + + L L + Y +
Sbjct: 133 AKRPFDKKSNSALFRAVGEGN--------AQLVAIF-GGQGNTDDYFEELRDLYQTYHVL 183
Query: 60 HIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIE--------TSDVESLL---VS 108
I +++ L +LI+ ++ LNI T D + LL +S
Sbjct: 184 VGDLIKF-----SAETLSELIRTTLDAE-KVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237
Query: 109 --LILDNTVRGRIDQSNY----KEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSK 162
LI G I ++Y K + +L Y+K A S+ + ++ I+ +
Sbjct: 238 CPLI------GVIQLAHYVVTAKLLGFTPGELRSYLKGATGH--SQGLVTAVA--IAETD 287
Query: 163 NMELLQDFYETTLEALK 179
+ E F+ + +A+
Sbjct: 288 SWE---SFFVSVRKAIT 301
Score = 36.6 bits (84), Expect = 0.005
Identities = 22/139 (15%), Positives = 42/139 (30%), Gaps = 39/139 (28%)
Query: 8 EHIEDLLRNIRTQV--------LIKLIKPYTRIH---------IPFISRQLNIETSDVLI 50
+ +E L N + L L + IPF R+L
Sbjct: 364 KQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR---- 419
Query: 51 KLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNI---ETSD------ 101
+ + PF S L + K + ++ F ++ + I +T D
Sbjct: 420 -----FLPVASPFHSHLL----VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRV 470
Query: 102 VESLLVSLILDNTVRGRID 120
+ + I+D +R +
Sbjct: 471 LSGSISERIVDCIIRLPVK 489
>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein
structure initiative, PSI, center for eukaryotic
structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}
Length = 307
Score = 34.1 bits (78), Expect = 0.025
Identities = 9/100 (9%), Positives = 35/100 (35%), Gaps = 1/100 (1%)
Query: 120 DQSNYKEMMSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEALK 179
D E + ++ + T + + +++ + + + Y+ +
Sbjct: 88 DLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEPLDLSKAVH-LYQQAAAVFE 146
Query: 180 DAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQ 219
+ + R + K +L ++ F++ + L++ +
Sbjct: 147 NEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYK 186
>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like
repeat, protein transport; 2.90A {Saccharomyces
cerevisiae} SCOP: a.118.8.1
Length = 292
Score = 32.3 bits (73), Expect = 0.11
Identities = 14/102 (13%), Positives = 28/102 (27%), Gaps = 1/102 (0%)
Query: 120 DQSNYKEMMSRYKQLL-LYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEAL 178
N + + + ++ R + + + D YE E
Sbjct: 89 SGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWY 148
Query: 179 KDAKNDRLWFKTNTKLGKLYFDREDFNKLSRILKQLHQSCQM 220
++ L K K L + + S I +L +S
Sbjct: 149 AQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMG 190
>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA,
nuclear, transcription; 2.90A {Saccharomyces cerevisiae}
Length = 455
Score = 27.8 bits (61), Expect = 3.3
Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 6/75 (8%)
Query: 49 LIKLIKPYTRIHIPFISRQLNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVS 108
++ I R L + I+ S + +VE++LV+
Sbjct: 353 SWTTEWGQNKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPK------NVENVLVT 406
Query: 109 LILDNTVRGRIDQSN 123
LI +R
Sbjct: 407 LINLGLLRANCFPQL 421
>3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; 1.90A {Rhodobacter sphaeroides}
Length = 249
Score = 27.2 bits (61), Expect = 3.6
Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 6/87 (6%)
Query: 133 QLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDFYETTLEA---LKDAKNDRLWFK 189
LL Y + I+ ++ +E L D +E LEA + K
Sbjct: 152 LLLAYEWRRQHDETPPEVIDMARVDFASGLEVEKLGDHFEEKLEAAGFFFPPEK-APGMK 210
Query: 190 TNTK--LGKLYFDREDFNKLSRILKQL 214
N + +L R D L +L+Q+
Sbjct: 211 LNLRNMWARLPLTRADVQTLHGMLRQI 237
>3u0j_B Type III effector HOPU1; ADP-ribosyltransferase, GRP7, transferase;
2.70A {Pseudomonas syringae PV}
Length = 270
Score = 27.6 bits (60), Expect = 3.7
Identities = 15/103 (14%), Positives = 39/103 (37%)
Query: 68 LNIETSDVLIKLIKPYTRIHIPFISRQLNIETSDVESLLVSLILDNTVRGRIDQSNYKEM 127
+ E L + + Y R+ R+ I+ D + +L + + +D + ++
Sbjct: 108 VRGEIGTPLYREVNNYLRLQHENSGREAEIDNHDEKLSPHIKMLSSALNRLMDVAAFRGT 167
Query: 128 MSRYKQLLLYIKSAVTRNYSEKSINSILDYISTSKNMELLQDF 170
+ R + L + + + ++ST++ + Q F
Sbjct: 168 VYRGIRGDLDTIARLYHLFDTGGRYVEPAFMSTTRIKDSAQVF 210
>2pgf_A Adenosine deaminase; metallo-dependent hydrolase, structural
genomics, medical ST genomics of pathogenic protozoa
consortium, MSGPP; HET: MSE ADN; 1.89A {Plasmodium
vivax} PDB: 2pgr_A* 2qvn_A* 3ewc_A* 3ewd_A* 2amx_A
Length = 371
Score = 26.8 bits (60), Expect = 6.6
Identities = 4/48 (8%), Positives = 14/48 (29%), Gaps = 1/48 (2%)
Query: 138 IKSAVTRNYSEKSINSILD-YISTSKNMELLQDFYETTLEALKDAKND 184
+ KS+ ++ I + + + A+ + +
Sbjct: 80 VLDYYLFAKGGKSLGEFVEKAIKVADIFHDYEVIEDLAKHAVFNKYKE 127
>2zrr_A Mundticin KS immunity protein; antiparallel four-helix bundle,
antimicrobial protein; 1.80A {Enterococcus mundtii}
Length = 118
Score = 25.7 bits (56), Expect = 9.0
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 6 IREHIEDLLRNIRTQVLIKLIKPY------TRIHIPFISRQLNIETSDVLIK 51
I E ++DL ++ + L K++ Y +P + ++NIE S+ + K
Sbjct: 41 ITELLDDLEIDLGNESLRKVLGSYLKKLKNEGTSVPLVLSRMNIEISNAIKK 92
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 0.138 0.384
Gapped
Lambda K H
0.267 0.0524 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,217,601
Number of extensions: 184506
Number of successful extensions: 525
Number of sequences better than 10.0: 1
Number of HSP's gapped: 509
Number of HSP's successfully gapped: 37
Length of query: 222
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,188,903
Effective search space: 552935196
Effective search space used: 552935196
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 (21.9 bits)
S2: 55 (25.4 bits)