RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16823
(263 letters)
>1k8k_E P21, ARP2/3 complex 21 kDa subunit, P21-ARC; beta-propeller,
structural protein; 2.00A {Bos taurus} SCOP: a.148.1.1
PDB: 1tyq_E* 1u2v_E* 2p9i_E* 2p9k_E* 2p9l_E 2p9n_E*
2p9p_E* 2p9s_E* 2p9u_E* 3dxk_E* 3dxm_E* 3rse_E
Length = 178
Score = 190 bits (485), Expect = 2e-61
Identities = 79/123 (64%), Positives = 105/123 (85%), Gaps = 2/123 (1%)
Query: 1 MPAYHSTLTDFN-QCVGNIAMLPIKTQYRGPAPQFTTGEQDIIEEALYYFKANVFFRTYE 59
MPAYHS+L D + + +GN+A+LPI++Q++GPAP+ T + DI++EA+YYFKANVFF+ YE
Sbjct: 1 MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPR-ETKDTDIVDEAIYYFKANVFFKNYE 59
Query: 60 IKSEADRLLIYITLYITECLKKLQKCPTKAQGQNEMYSLALAKFDLPGEAGFPLNSVYAK 119
IK+EADR LIYITLYI+ECLKKLQKC +K+QG+ EMY+L + F +PGE GFPLN++YAK
Sbjct: 60 IKNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAK 119
Query: 120 PQN 122
P N
Sbjct: 120 PAN 122
Score = 175 bits (446), Expect = 1e-55
Identities = 61/107 (57%), Positives = 83/107 (77%)
Query: 156 IYVIRNCLKKLQKCPTKAQGQNEMYSLALAKFDLPGEAGFPLNSVYAKPQSQNEADLMKN 215
I CLKKLQKC +K+QG+ EMY+L + F +PGE GFPLN++YAKP ++ E ++M+
Sbjct: 72 TLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRA 131
Query: 216 YLTQVRQETGLRVCERVFNTPDGKPSKWWLCFSKKRFMDKSLTALGQ 262
YL Q+RQETGLR+CE+VF+ + KPSKWW CF K++FM+KSL+ GQ
Sbjct: 132 YLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ 178
>3dwl_E Actin-related protein 2/3 complex subunit 3; propellor,
actin-binding, ATP-binding, cytoskeleton, nucleot
binding, WD repeat; HET: ATP; 3.78A {Schizosaccharomyces
pombe}
Length = 174
Score = 185 bits (471), Expect = 2e-59
Identities = 60/124 (48%), Positives = 81/124 (65%), Gaps = 3/124 (2%)
Query: 1 MPAYHSTLTDFN--QCVGNIAMLPIKTQYRGPAPQFTTGEQDIIEEALYYFKANVFFRTY 58
MPAYHS+ GNIAMLP+KT++RGPA + DII+E + F+AN FFR +
Sbjct: 1 MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNF 60
Query: 59 EIKSEADRLLIYITLYITECLKKLQKCPTKAQGQNEMYSLALAKFDLPGEAGFPLNSVYA 118
EIK ADR LIY TL+I+ECL ++ + + ++ SLAL F +PG AGFPLN++YA
Sbjct: 61 EIKGPADRTLIYGTLFISECLGRVNGLNYR-DAERQLNSLALENFSIPGSAGFPLNALYA 119
Query: 119 KPQN 122
P +
Sbjct: 120 PPLS 123
Score = 160 bits (406), Expect = 1e-49
Identities = 46/102 (45%), Positives = 64/102 (62%), Gaps = 1/102 (0%)
Query: 156 IYVIRNCLKKLQKCPTKAQGQNEMYSLALAKFDLPGEAGFPLNSVYAKPQSQNEADLMKN 215
I CL ++ + + ++ SLAL F +PG AGFPLN++YA P S +A++M+
Sbjct: 74 TLFISECLGRVNGLNYR-DAERQLNSLALENFSIPGSAGFPLNALYAPPLSPQDAEIMRT 132
Query: 216 YLTQVRQETGLRVCERVFNTPDGKPSKWWLCFSKKRFMDKSL 257
YLTQ RQE R+ V+ T PSKWW CFSK+RFM+K+L
Sbjct: 133 YLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL 174
>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 = 43.9 bits (103), Expect = 4e-05
Identities = 36/202 (17%), Positives = 73/202 (36%), Gaps = 48/202 (23%)
Query: 58 YEIKSEADRLLIYITLYITECLKKLQKC-PTKAQGQNEMYSLALAKFDLPGEAGFP---L 113
+ +A +L +I + C + P + ++ + L G P L
Sbjct: 293 FVSVRKAITVLFFIGV---RC----YEAYPNTS------LPPSILEDSLENNEGVPSPML 339
Query: 114 NSVYAKPQNLLFKAKKLKEANGYKFVWVRDCKIMI-RKNESSRIYVI----------RNC 162
S+ Q + + + N + ++ I N ++ V+
Sbjct: 340 -SISNLTQEQVQDY--VNKTNSHLP---AGKQVEISLVN-GAKNLVVSGPPQSLYGLNLT 392
Query: 163 LKKLQKCPTKAQGQNEM-YSLALAKFD---LPGEAGFPLNSVYAKP-QSQNEADLMKNYL 217
L+K K P+ Q+ + +S KF LP + P +S P DL+KN +
Sbjct: 393 LRKA-KAPSG-LDQSRIPFSERKLKFSNRFLPVAS--PFHSHLLVPASDLINKDLVKNNV 448
Query: 218 TQVRQETGLRVCERVFNTPDGK 239
+ ++ +++ V++T DG
Sbjct: 449 SFNAKD--IQI--PVYDTFDGS 466
Score = 40.0 bits (93), Expect = 7e-04
Identities = 35/230 (15%), Positives = 60/230 (26%), Gaps = 84/230 (36%)
Query: 29 GPAPQFTTGEQDIIEEALYYFKANVFFRTYEIKSEADRLLIYITLYITECLKKLQKCPTK 88
QF ++ L F+ + +I + A +LL + + K+L K
Sbjct: 75 SKVGQFD----QVLNLCLTEFENC-YLEGNDIHALAAKLLQENDTTLVK-TKELIKN--- 125
Query: 89 AQGQNEMYSLALAKFDLPGEAGFPLNSVYAKPQNLLFKAKKLKEANGYKFVWVRDCKIMI 148
Y A A P + K + LF+A A
Sbjct: 126 -------YITARI------MAKRPFDK---KSNSALFRAVGEGNA--------------- 154
Query: 149 RKNESSRIYVIRNCLKKLQKCPTKAQGQNEMYSLALAKFDLPGEAGFPLNSVYAKPQS-- 206
++ I QG + Y F+ E L +Y
Sbjct: 155 ------QLVAIFG-----------GQGNTDDY------FE---E----LRDLYQTYHVLV 184
Query: 207 ----QNEADLMKNYLTQVRQETGLRVCERVFN------TPDGKPSKWWLC 246
+ A+ + + +V + N P P K +L
Sbjct: 185 GDLIKFSAETLSELIRTTLDAE--KVFTQGLNILEWLENPSNTPDKDYLL 232
>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 = 42.9 bits (100), Expect = 7e-05
Identities = 44/308 (14%), Positives = 81/308 (26%), Gaps = 98/308 (31%)
Query: 20 MLPIKTQYRGPAPQFTTGEQDIIEEALYYFKANVFFRTYEIKSEADRLLIYITLYITECL 79
M PIKT+ R P+ + IE+ + N F Y + RL Y+ L + L
Sbjct: 95 MSPIKTEQRQPSMM----TRMYIEQRDRLYNDNQVFAKYNVS----RLQPYLKL--RQAL 144
Query: 80 KKLQKCP------------------------TKAQGQNEMYSLALAKFDLPGEAGFPLNS 115
+L+ + + +++ L L + P L
Sbjct: 145 LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204
Query: 116 VYAK---------------PQNL---------LFKAKKLKEA-----NGYKFVWVRD--- 143
+ + + L K+K + N V
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN----VQNAKAWN 260
Query: 144 -----CKIMIRKNESSRIYVIRNCLKKLQKCPTKAQGQNEMYSLAL-AKF------DLPG 191
CKI++ + + +L K+ DLP
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320
Query: 192 EA--GFPLN-SVYAKPQSQNEADLMKNY--LTQVRQETGLRVCERVFNTPDGKPSKWWLC 246
E P S+ A+ ++ N+ + + T + V +
Sbjct: 321 EVLTTNPRRLSIIAE-SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAE--------- 370
Query: 247 FSKKRFMD 254
+K F
Sbjct: 371 -YRKMFDR 377
Score = 36.0 bits (82), Expect = 0.013
Identities = 42/258 (16%), Positives = 79/258 (30%), Gaps = 74/258 (28%)
Query: 61 KSEADRLLIYITLYITECLKKLQKCPTKAQGQNEMYSLALAKF------DLPGEA--GFP 112
K D L T +I+ L T E+ SL L K+ DLP E P
Sbjct: 275 KQVTDFLSAATTTHIS--LDHHSMTLTPD----EVKSL-LLKYLDCRPQDLPREVLTTNP 327
Query: 113 LNSVYAKPQNLLFKAKKLKEA----NGYKFVWVRDCKIMIRKNESS----RIYVIRNCLK 164
+ + A+ +++ + +K V +C + ESS R
Sbjct: 328 R--RLS-----II-AESIRDGLATWDNWKHV---NCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 165 KLQ------KCPTKA--------------QGQNEMYSLALAKFDLPGEAGFPLNSVY--A 202
+L PT N+++ +L + P E+ + S+Y
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ-PKESTISIPSIYLEL 435
Query: 203 KPQSQNEADLMKNYLTQVRQETGLRVCERVFNTPDG-------------KPSKWWLCFSK 249
K + +NE L ++ + + + D + + F
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495
Query: 250 K----RFMDKSLTALGQS 263
RF+++ + +
Sbjct: 496 VFLDFRFLEQKIRHDSTA 513
Score = 34.1 bits (77), Expect = 0.046
Identities = 39/255 (15%), Positives = 77/255 (30%), Gaps = 60/255 (23%)
Query: 34 FTTGEQ-----DIIEEALYYFKANVFFRTYEI---------KSEADRLL-----IYITLY 74
F TGE DI+ F N F ++ K E D ++ + TL
Sbjct: 9 FETGEHQYQYKDILSVFEDAFVDN--FDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 75 ITECLKKLQKCPTKAQGQNEMYSLALAKFDLPGEAGFPLNSVYAKPQNLLFKAKKLKEAN 134
+ L L K Q EM + + F ++ + + + + +
Sbjct: 67 LFWTL--LSK-------QEEMVQKFVEEVLRI-NYKFLMSPIKTEQRQ---PSMMTRMYI 113
Query: 135 GYKFVWVRDCKIMIRKNESSR---IYVIRNCLKKLQKCPTKA---QGQNEMY-----SLA 183
+ D ++ K SR +R L +L+ P K G + +A
Sbjct: 114 EQRDRLYNDNQV-FAKYNVSRLQPYLKLRQALLELR--PAKNVLIDG---VLGSGKTWVA 167
Query: 184 L-AKFDLPGEAGFPLNSVYAKPQSQNEADL----MKNYLTQVRQETGLRVCERVFNTPDG 238
L + + ++ N + ++ L Q+ R ++ +
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN----WTSRSDHSSNI 223
Query: 239 KPSKWWLCFSKKRFM 253
K + +R +
Sbjct: 224 KLRIHSIQAELRRLL 238
>3e19_A FEOA; transcriptional regulator, metal-binding, iron uptake, beta-
transcription regulator, metal binding protein; HET:
GOL; 2.00A {Thermococcus thioreducens}
Length = 77
Score = 29.1 bits (66), Expect = 0.32
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 139 VWVRDCKIMIRKNESSRIYV 158
+ V + I K + R+ V
Sbjct: 55 ISVGGVRFAIGKGLAGRVMV 74
>4g4f_A Tumor necrosis factor ligand superfamily member 1;
glucocorticoid-induced TNF receptor ligand, immune
system, T structural genomics; 1.85A {Otolemur
garnettii}
Length = 126
Score = 29.6 bits (66), Expect = 0.44
Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 11/67 (16%)
Query: 14 CVGNIAMLPIKTQYRGPAPQ----FTTGEQDIIEEALYYFKANVFFRT-------YEIKS 62
C+ +L K Q P G+ I+++ LY V T + ++
Sbjct: 8 CLAKFELLTSKWQMTSRKPPCVNSLPEGKLKILQDGLYLIYGQVAPSTAYKGVAPFAVQL 67
Query: 63 EADRLLI 69
+ ++
Sbjct: 68 RKNEAML 74
>2k5l_A FEOA; structure, NESG, structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium; NMR {Clostridium thermocellum atcc 27405}
Length = 81
Score = 26.9 bits (60), Expect = 2.0
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 139 VWVRDCKIMIRKNESSRIYV 158
+ VR ++ +RK+ + I V
Sbjct: 53 INVRGYELSLRKSAAEMIEV 72
>3mhx_A Putative ferrous iron transport protein A; FEOA, zinc binding,
prokaryotic SH3 stenotrophomonus maltophilia, metal
transport; 1.70A {Stenotrophomonas maltophilia}
Length = 85
Score = 26.6 bits (59), Expect = 2.6
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 139 VWVRDCKIMIRKNESSRIYV 158
V V + +R +E+ R+ V
Sbjct: 57 VQVGFTRFALRISEAKRVVV 76
>2k4y_A FEOA-like protein; GFT structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium, NESG; NMR {Clostridium acetobutylicum}
Length = 86
Score = 26.1 bits (58), Expect = 4.3
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 139 VWVRDCKIMIRKNESSRIYV 158
+ +R + +RK+E+ I V
Sbjct: 56 LRLRGYSLSLRKSEAKDILV 75
>2q8o_A GITR ligand; TNF, dimer, unknown function; 1.75A {Mus musculus}
SCOP: b.22.1.1 PDB: 3fc0_A 2qdn_A 3b9i_A
Length = 136
Score = 26.6 bits (58), Expect = 4.9
Identities = 11/89 (12%), Positives = 26/89 (29%), Gaps = 6/89 (6%)
Query: 14 CVGNIAMLPIKTQYRGPAP----QFTTGEQDIIEEALYYFKANVFFRTYEIKSEADRLLI 69
C+ + K P P + G+ I++ Y V + + ++
Sbjct: 15 CMVKFELSSSKWHMTSPKPHCVNTTSDGKLKILQSGTYLIYGQVIPVDKKYIKDNAPFVV 74
Query: 70 YITLYITECLKKLQKCPTKAQGQNEMYSL 98
+Y + + + +Y L
Sbjct: 75 Q--IYKKNDVLQTLMNDFQILPIGGVYEL 101
>2fok_A R.FOKI, FOKI restriction endonuclease; nucleic acid recognition,
DNA-binding protein, type IIS restriction endonuclease;
2.30A {Planomicrobium okeanokoites} SCOP: a.4.5.12
a.4.5.12 a.4.5.12 c.52.1.12 PDB: 1fok_A*
Length = 579
Score = 27.0 bits (59), Expect = 7.3
Identities = 10/49 (20%), Positives = 17/49 (34%), Gaps = 13/49 (26%)
Query: 201 YAKPQSQNEADLMKNYLTQVRQETGLRVCERVFNTPDGKPSKWWLCFSK 249
Y P Q AD M+ Y+ + + P++WW +
Sbjct: 475 YNLPIGQ--ADEMQRYVEENQTRNKHI-----------NPNEWWKVYPS 510
>3iuk_A Uncharacterized protein; PF05960.1, DUF885, M32
carboxypeptidase-like fold, PSI, MCSG structural
genomics, protein structure initiative; 1.85A
{Arthrobacter aurescens}
Length = 562
Score = 26.9 bits (59), Expect = 8.8
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 43 EEALYYFKANVFFRTYEIKSEADR 66
E+ + KAN+ +++ E R
Sbjct: 483 EKGFDFLKANLDISEGQLQFEFTR 506
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 0.408
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,850,981
Number of extensions: 214291
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 436
Number of HSP's successfully gapped: 20
Length of query: 263
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 171
Effective length of database: 4,133,061
Effective search space: 706753431
Effective search space used: 706753431
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: 56 (25.8 bits)