RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8611
(280 letters)
>4akv_A Sorting nexin-33; transport protein, organelle biogenesis; 2.65A
{Homo sapiens}
Length = 386
Score = 55.2 bits (132), Expect = 5e-09
Identities = 19/143 (13%), Positives = 49/143 (34%), Gaps = 9/143 (6%)
Query: 21 LDSLESQLSHLHSSVEALALAR--------RDLSVYSAHLAKSLALVSNTEEHASVSRVV 72
++ + L + L + L ++ S + +++ +
Sbjct: 197 SKKMDDSVLQLSTVASELVRKHVGGFRKEFQKLGSAFQAISHSFQM-DPPFCSEALNSAI 255
Query: 73 STLGELYERTEGVYAAEAGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIIL 132
S G YE ++A + DL + + Y L++ D H + + + Q +
Sbjct: 256 SHTGRTYEAIGEMFAEQPKNDLFQMLDTLSLYQGLLSNFPDIIHLQKGAFAKVKESQRMS 315
Query: 133 NKKREAKVKLELAGRSDKSIQAA 155
++ R + + + R + + A
Sbjct: 316 DEGRMVQDEADGIRRRCRVVGFA 338
Score = 43.6 bits (102), Expect = 3e-05
Identities = 11/65 (16%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 205 KWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGYQQQEFKDTMVK 264
+ + + + + ++ E F R +FK M YL + + + Q+ + +
Sbjct: 320 MVQDEADGIRRRCRVVGFALQAEMNHFHQRRELDFKHMMQNYLRQQILFYQR-----VGQ 374
Query: 265 YLEEL 269
LE+
Sbjct: 375 QLEKT 379
>3dyt_A Sorting nexin-9; 3-helix bundle, BAR domain, PX domain,
phosphoprotein, protein transport, SH3 domain,
transport, transport protein; 2.08A {Homo sapiens} PDB:
3dyu_A 2raj_A 2rai_A 2rak_A*
Length = 366
Score = 46.3 bits (109), Expect = 5e-06
Identities = 17/114 (14%), Positives = 36/114 (31%), Gaps = 4/114 (3%)
Query: 30 HLHSSVEALALARRDLSVYSAHLAKSLALVSNTEEHASVSRVVSTLGELYERTEGVYAAE 89
H L + + LA + S + ++ ++ G+ YE + A +
Sbjct: 194 HWKRCTGPLPKEYQKIGKALQSLATVFSS-SGYQGETDLNDAITEAGKTYEEIASLVAEQ 252
Query: 90 AGADLNILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILNKKREAKVKLE 143
DL+ L E +Y + D + + +K+ L+
Sbjct: 253 PKKDLHFLMECNHEYKGFLGCFPDIIGTHKG---AIEKVKESDKLVATSKITLQ 303
Score = 43.6 bits (102), Expect = 4e-05
Identities = 8/63 (12%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 207 EHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGYQQQEFKDTMVKYL 266
+ + + +S ++ E F ++R+ ++ + YLE+ + + + + + L
Sbjct: 302 LQDKQNMVKRVSIMSYALQAEMNHFHSNRIYDYNSVIRLYLEQQVQFYET-----IAEKL 356
Query: 267 EEL 269
+
Sbjct: 357 RQA 359
>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 = 44.1 bits (103), Expect = 3e-05
Identities = 33/298 (11%), Positives = 82/298 (27%), Gaps = 76/298 (25%)
Query: 2 KSILKQLGGWPVLEDKGLLLDSLESQLSHLHSSVEALAL-AR-----RDLSVYSAHLAKS 55
++ L++L E+ L+L ++++ + A L + R V +
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNA-----KAWNAFNLSCKILLTTRFKQV-------T 278
Query: 56 LALVSNTEEHASVSRVVSTLGELYERTEGVYAAEAGADLNILAELFRD----YVCLIAAV 111
L + T H S+ TL + + + L + +IA
Sbjct: 279 DFLSAATTTHISLDHHSMTLTP--DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES 336
Query: 112 KDTFHARGKIYQTWQSWQIILNKKREAKVKLELAGRSDKSIQAAHEVTEVRIKYLLKTLF 171
A W +W+ + K ++ L E E R + ++F
Sbjct: 337 IRDGLAT------WDNWKHVNCDKLTTIIESSL---------NVLEPAEYRKMFDRLSVF 381
Query: 172 NCCPSDSILIVGTQGRTVSGGFRSDICDEQVRVKWEHKVERCQEDFA---AISAMIKREY 228
P + I + + W ++ ++++++
Sbjct: 382 ---PPS-----------------AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP 421
Query: 229 AGF-------------EASRVQEFKDTMVKYLEELMGYQQQEF-KDTMVKYLEELMGY 272
+ ++V + + + + +Y +G+
Sbjct: 422 KESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
>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 = 41.2 bits (96), Expect = 3e-04
Identities = 44/299 (14%), Positives = 76/299 (25%), Gaps = 118/299 (39%)
Query: 12 PVLEDKGLLLDSLESQ-LSH--LHSSVEAL------ALARRDLSVYSAHLAKSLALVSNT 62
VL L L E+ L +H+ L L + + + A+ +A
Sbjct: 82 QVLN---LCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFD 138
Query: 63 EEHASVSRVVSTLGELYERTEGVYAAEAG-ADL--------NI------LAELFRDYVCL 107
++ S L+ A G A L N L +L++ Y L
Sbjct: 139 KKSNS---------ALFR------AVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVL 183
Query: 108 IAAVKDTFHAR-----------GKIYQT---WQSWQIILNKK---------REAKVKLEL 144
+ + K++ W L + L
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW---LENPSNTPDKDYLLSIPISCPL 240
Query: 145 AGRSDKSIQAAHEVTEVRIKYL--LKTLFNCCPSDSILIVGTQGRTVSGGFRSDICDEQV 202
G IQ AH Y+ K L P + L +G T + +
Sbjct: 241 IG----VIQLAH--------YVVTAKLL-GFTPGE--LRSYLKGATG--------HSQGL 277
Query: 203 RVKWEHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEEL--MGYQ-QQEF 258
A A + F ++ K + L +G + + +
Sbjct: 278 VT-------------AVAIAE---------TDSWESFFVSVRKAITVLFFIGVRCYEAY 314
Score = 37.3 bits (86), Expect = 0.005
Identities = 45/255 (17%), Positives = 72/255 (28%), Gaps = 83/255 (32%)
Query: 39 ALARRDLSVYSAHLAKSLALVSNTEEHASVSRV----VSTLGELYERTEGVYAAEAGADL 94
A + R L++ L L LV T S++ L E TEG A +
Sbjct: 3 AYSTRPLTLSHGSLEHVL-LVP-TASFFIASQLQEQFNKILPE---PTEGFAADDEPTTP 57
Query: 95 NILAELFRDYVCLIAAVKDTFHARGKIYQTWQSWQIILNKKREAKVKLE---LAGRSD-- 149
AEL ++ ++++ + K+ Q Q + L + E L G D
Sbjct: 58 ---AELVGKFLGYVSSLVE----PSKVGQFDQVLNLCLTE-------FENCYLEGN-DIH 102
Query: 150 ---KSIQAAHEVTEVRIKYLLKTLFNCCPSDSILIVGTQGRTVSGGFRSDICDEQVRVKW 206
+ ++ T V+ K L+K R S +
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITAR--------IMAKRPFDKKSNSAL--------- 145
Query: 207 EHKVERCQEDFAAISAMIKREYAGF------EASRVQEFKDTMVKYLEELMG----YQQ- 255
F A+ + A F + Y EEL Y
Sbjct: 146 ----------FRAVGEGNAQLVAIFGGQGNTDD------------YFEELRDLYQTYHVL 183
Query: 256 -QEFKDTMVKYLEEL 269
+ + L EL
Sbjct: 184 VGDLIKFSAETLSEL 198
Score = 28.5 bits (63), Expect = 3.5
Identities = 21/107 (19%), Positives = 32/107 (29%), Gaps = 26/107 (24%)
Query: 21 LDSLESQL-----------SHLHSSVEALALARRDLSVY----SAHLAKSLALVSNTEEH 65
L L L S + S L + R L V S L + L++
Sbjct: 386 LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVK 445
Query: 66 ASVSRVVSTLGELYERTEGVYAAEAGADL-----NILAELFRDYVCL 107
+VS + VY G+DL +I + + L
Sbjct: 446 NNVSFNAKDIQI------PVYDTFDGSDLRVLSGSISERIVDCIIRL 486
>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 = 34.2 bits (77), Expect = 0.017
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 11/40 (27%)
Query: 25 ESQ-LSHLHSSVEALALARRDLSVYSAHLAKSLALVSNTE 63
E Q L L +S L +Y+ A +LA+ + E
Sbjct: 18 EKQALKKLQAS----------LKLYADDSAPALAIKATME 47
Score = 29.5 bits (65), Expect = 0.81
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 15/36 (41%)
Query: 129 QIILNKKREAKVKL-------ELAGRSDKSIQAAHE 157
Q + KK +A +KL LA I+A E
Sbjct: 20 QAL--KKLQASLKLYADDSAPALA------IKATME 47
Score = 29.1 bits (64), Expect = 0.86
Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 8/37 (21%)
Query: 64 EHASVSRVVSTLGELYERTEGVYAAEAGADLNILAEL 100
E ++ ++ ++L +LY A ++ L I A +
Sbjct: 18 EKQALKKLQASL-KLY-------ADDSAPALAIKATM 46
>3dpu_A RAB family protein; roccor, G-domain, COR, GTP-binding,
nucleotide-binding, SIGN protein; 2.90A {Chlorobaculum
tepidum}
Length = 535
Score = 30.0 bits (67), Expect = 0.89
Identities = 14/125 (11%), Positives = 32/125 (25%), Gaps = 21/125 (16%)
Query: 159 TEVRIKYLLKTLFNCCPSDSILIVGTQGRTVSGGFRSDICDEQVRVKWEHKVERCQE--- 215
T+ Y L+ + +++V + D + + ER
Sbjct: 133 TDSNKHYWLRHIEKYGGKSPVIVVMN---------KIDENPSYNIEQKKIN-ERFPAIEN 182
Query: 216 DFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGYQQQEFKDTMVKYLEELMGYQQQ 275
F IS V+ ++ + + +K E+L+
Sbjct: 183 RFHRISCK--------NGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTA 234
Query: 276 VSRIE 280
+
Sbjct: 235 QRYLN 239
>1nu7_D Staphylocoagulase; thrombin non-proteolytic activator,
hydrolase-hydrolase INHI complex, protein binding; HET:
0ZJ; 2.20A {Staphylococcus aureus} SCOP: a.8.6.1 a.8.6.1
PDB: 1nu9_C*
Length = 282
Score = 28.2 bits (62), Expect = 2.8
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 245 KYLEELMGYQQQEFKDTMVKYLEELMGYQQ 274
+ E Y ++E+KD K + ++G Q
Sbjct: 43 LGILETYHYGEKEYKDAKDKLMTRILGEDQ 72
>2a1d_D Staphylocoagulase; prothrombin activator, hydrolase-hydrolase
inhibitor complex; HET: 0G6 NDG; 3.50A {Staphylococcus
aureus}
Length = 329
Score = 27.9 bits (61), Expect = 4.1
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 238 EFKDTMVKYLEELMGYQQQEFKDTMVKYLEELMGYQQ 274
E + + E Y ++E+KD K + ++G Q
Sbjct: 36 ESQFINALDILETYHYGEKEYKDAKDKLMTRILGEDQ 72
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol
protease, UBL conjugation pathway, metal-binding,
zinc-finger,structural genomics; 2.80A {Homo sapiens}
Length = 854
Score = 27.9 bits (61), Expect = 4.1
Identities = 22/133 (16%), Positives = 46/133 (34%), Gaps = 18/133 (13%)
Query: 152 IQAAHEVTEVRIKYL--LKTLFNCCPSDSILIVGTQGRTVSGGFRSDICDEQVRVKWEHK 209
+Q + + + KY+ L+ +F P+D TQ + G S + V + +
Sbjct: 360 VQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLSGEYSKPVPESGDGE 419
Query: 210 VERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGYQQQ---EFKDTMVKYL 266
Q++ + + FK + K E +QQ EF ++ +
Sbjct: 420 RVPEQKEVQ-------------DGIAPRMFKALIGKGHPEFSTNRQQDAQEFFLHLINMV 466
Query: 267 EELMGYQQQVSRI 279
E + + +
Sbjct: 467 ERNCRSSENPNEV 479
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 5.4
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 25/71 (35%)
Query: 200 EQVRVKW-EHKVERCQEDFAAISAMIKREYAGFEASRVQEFKDTMVKYLEELMGYQQQEF 258
E +R KW E + +R QE + AS+V E +E +++
Sbjct: 85 ESIR-KWREEQRKRLQE----------LD----AASKVME---------QEWREKAKKDL 120
Query: 259 KDTMVKYLEEL 269
++ + E++
Sbjct: 121 EEWNQRQSEQV 131
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 0.132 0.372
Gapped
Lambda K H
0.267 0.0498 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,194,105
Number of extensions: 246851
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 432
Number of HSP's successfully gapped: 27
Length of query: 280
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 188
Effective length of database: 4,133,061
Effective search space: 777015468
Effective search space used: 777015468
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: 57 (26.3 bits)