RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4906
(144 letters)
>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 = 33.0 bits (74), Expect = 0.014
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 13/32 (40%)
Query: 50 KKEIKKLQ-RLR----DQ-----IKSWIASAE 71
K+ +KKLQ L+ D IK A+ E
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIK---ATME 47
>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 = 33.3 bits (75), Expect = 0.022
Identities = 17/144 (11%), Positives = 46/144 (31%), Gaps = 15/144 (10%)
Query: 7 GRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEA-DLKKEIKKLQRLRDQIKS 65
+ L+ + + I + ++ + K ++ E+++L + +
Sbjct: 190 KNCNSPETVLEMLQK---LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 66 WIASAEIKDKSTL--LDY--RKLIETQMERFKVVERETKTKAYSKEGLGAVQK-MDPAQK 120
+ +++ + + L+ T RFK V + L + P
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTT---RFKQVTDFLSAATTTHISLDHHSMTLTPD-- 301
Query: 121 EKEEI-STWLVTSIDALNIQVSSV 143
E + + +L L +V +
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTT 325
Score = 30.2 bits (67), Expect = 0.22
Identities = 21/129 (16%), Positives = 40/129 (31%), Gaps = 36/129 (27%)
Query: 10 GEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIAS 69
GE K + + FED + + + K +Q D KS ++
Sbjct: 12 GEHQYQYKDI---LSVFED---------------AFVDNF--DCKDVQ---DMPKSILSK 48
Query: 70 AEIKD----KSTLLDYRKLI-------ETQMERFKVVERETKTKAYSKEGLGAVQKMDPA 118
EI K + +L E +++F V E + + ++ P+
Sbjct: 49 EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF-VEEVLRINYKFLMSPI-KTEQRQPS 106
Query: 119 QKEKEEIST 127
+ I
Sbjct: 107 MMTRMYIEQ 115
Score = 26.7 bits (58), Expect = 3.4
Identities = 24/122 (19%), Positives = 44/122 (36%), Gaps = 36/122 (29%)
Query: 16 LKKV--SEGVETFEDI-----W--QKV-HNATNSN----------QKEKYEADLKKEIKK 55
LK + E + F + + QK+ H++T N Q + Y+ + K
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540
Query: 56 LQRLRDQIKSWIASAE---IKDKSTLLDYRKLIETQMERFKVVERETKTKAYSKEGLGAV 112
+RL + I ++ E I K Y L+ + + +A +E V
Sbjct: 541 YERLVNAILDFLPKIEENLICSK-----YTDLLRIAL--------MAEDEAIFEEAHKQV 587
Query: 113 QK 114
Q+
Sbjct: 588 QR 589
Score = 26.4 bits (57), Expect = 4.4
Identities = 8/96 (8%), Positives = 30/96 (31%), Gaps = 26/96 (27%)
Query: 16 LKKVSEGVETFEDIWQKVHNATNSNQKEKYEA------DLKKEIKKLQRLRDQIKSWIAS 69
K++ +E+ ++ + ++ ++ L + W
Sbjct: 352 CDKLTTIIESS------LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI------WFDV 399
Query: 70 AEIKDKSTLLDYRKLIETQMERFKVVERETKTKAYS 105
+ ++ ++ ++ +VE++ K S
Sbjct: 400 IKSDVM--------VVVNKLHKYSLVEKQPKESTIS 427
>3rpw_A ABC transporter; structural genomics, PSI-biology, protein
structure initiati midwest center for structural
genomics, MCSG; HET: MSE; 1.65A {Rhodopseudomonas
palustris}
Length = 365
Score = 31.6 bits (72), Expect = 0.067
Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 43 EKYEADLKKEIKKLQRLRDQIKS-WIASAEIKDK 75
+ Y D+ + +KKL+ ++ + W +A+
Sbjct: 195 KLYPIDMDRALKKLKEIKPHVVKWWTTAAQPPQL 228
>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 = 31.6 bits (71), Expect = 0.077
Identities = 30/166 (18%), Positives = 43/166 (25%), Gaps = 62/166 (37%)
Query: 3 RTYP--GRQGEIDRCLKKVSEGVETFEDIWQKVHNATNSNQKEKYE---ADLKKEI-KKL 56
+ G QG D + E + ++ Y DL K + L
Sbjct: 155 QLVAIFGGQGNTDDYFE---ELRDLYQT----------------YHVLVGDLIKFSAETL 195
Query: 57 QRL-RD------------QIKSWIASAEIK-DKSTLLDYR---KLIE-TQMERFKVVERE 98
L R I W+ + DK LL LI Q+ + V +
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL 255
Query: 99 TKTKAYSKEGLGAVQKMDPAQKEKEEISTWLVTSIDALNIQVSSVA 144
LG P E L V++VA
Sbjct: 256 ----------LG----FTPG--ELRSYLKGATGHSQGL---VTAVA 282
>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex,
MERR-family transcription activator, MU binding protein;
HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3
d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A*
3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A*
3d6y_A* 1bow_A 2bow_A*
Length = 278
Score = 28.2 bits (63), Expect = 1.0
Identities = 8/91 (8%), Positives = 31/91 (34%), Gaps = 2/91 (2%)
Query: 43 EKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERETKTK 102
+ E +++++ L L I + + + L +++ E ++++ E +
Sbjct: 85 TEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLD--EEEIRIIQTEAEGI 142
Query: 103 AYSKEGLGAVQKMDPAQKEKEEISTWLVTSI 133
+ K+ + + + +
Sbjct: 143 GPENVLNASYSKLKKFIESADGFTNNSYGAT 173
>1ri5_A MRNA capping enzyme; methyltransferase, M7G, messenger RNA CAP,
structural genomics, PSI, protein structure initiative;
2.10A {Encephalitozoon cuniculi} SCOP: c.66.1.34 PDB:
1ri2_A* 1ri3_A* 1ri1_A* 1ri4_A 1z3c_A* 2hv9_A*
Length = 298
Score = 27.0 bits (59), Expect = 2.2
Identities = 9/54 (16%), Positives = 24/54 (44%)
Query: 27 EDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLD 80
E +++ NS ++ E+ + + ++ + IK+ + K ++LD
Sbjct: 17 EGKKEEIREHYNSIRERGRESRQRSKTINIRNANNFIKACLIRLYTKRGDSVLD 70
>2prs_A High-affinity zinc uptake system protein ZNUA; protein consists of
two (beta/ALFA)4 domains, metal transport; 1.70A
{Escherichia coli} PDB: 2osv_A 2ps0_A 2ps3_A 2ps9_A
2ogw_A 2xy4_A* 2xqv_A* 2xh8_A
Length = 284
Score = 27.0 bits (60), Expect = 2.4
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 41 QKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
+ K +A+LK +L Q+ + +A + K
Sbjct: 143 SRAKLDANLKDFEAQLASTETQVGNELAPLKGKG 176
>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress,
MERR family, activator; HET: DNA; 2.80A {Escherichia
coli} PDB: 2zhh_A
Length = 154
Score = 25.8 bits (57), Expect = 5.1
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 47 ADLKKEIKKLQRLRDQIKSWIA 68
+L + I L LRD++ I
Sbjct: 100 EELDRRIHTLVALRDELDGCIG 121
>1pq4_A Periplasmic binding protein component of AN ABC T uptake
transporter; ZNUA, loop, metal-binding, metal binding
protein; 1.90A {Synechocystis SP} SCOP: c.92.2.2 PDB:
2ov3_A 2ov1_A
Length = 291
Score = 25.8 bits (57), Expect = 5.5
Identities = 7/34 (20%), Positives = 18/34 (52%)
Query: 41 QKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
+++YEA+L + +L+RL ++ + +
Sbjct: 159 NRDQYEANLAAFLAELERLNQELGQILQPLPQRK 192
>3lo3_A Uncharacterized conserved protein; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; 2.38A {Colwellia psychrerythraea}
Length = 94
Score = 24.9 bits (55), Expect = 5.6
Identities = 5/27 (18%), Positives = 10/27 (37%)
Query: 66 WIASAEIKDKSTLLDYRKLIETQMERF 92
I KD L Y + + + ++
Sbjct: 7 IIVGLTPKDAEKLQQYGARVASTLAKY 33
>3pu5_A Extracellular solute-binding protein; structural genomics, PSI-2,
protein structure initiative; 2.05A {Bordetella
parapertussis}
Length = 333
Score = 25.8 bits (57), Expect = 5.6
Identities = 5/26 (19%), Positives = 12/26 (46%)
Query: 44 KYEADLKKEIKKLQRLRDQIKSWIAS 69
D++ I L+R++ I + +
Sbjct: 169 SGYGDIEASIATLERMKPHIFKFFTA 194
>2fiu_A Conserved hypothetical protein; alpha-beta, dimeric alpha-beta
barrels, structural genomics, protein structure
initiative; 2.00A {Agrobacterium tumefaciens str} SCOP:
d.58.4.16
Length = 99
Score = 24.9 bits (55), Expect = 6.8
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 66 WIASAEIKDKSTLLDYRKLIETQMERF--KVVERETKTKAYSKEG 108
WIA +++D DY + ERF + R EG
Sbjct: 8 WIAQVDVRDSERYKDYVSTAKPAFERFGANFLARGGSVTEL--EG 50
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.5 bits (55), Expect = 7.6
Identities = 11/70 (15%), Positives = 29/70 (41%), Gaps = 16/70 (22%)
Query: 42 KEKYEADLKK----EIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVER 97
+E+ L++ Q R++ A ++++ + + Q+E+ K+ R
Sbjct: 91 REEQRKRLQELDAASKVMEQEWREK-----AKKDLEE------WNQRQSEQVEKNKINNR 139
Query: 98 ETKTKAYSKE 107
KA+ ++
Sbjct: 140 IAD-KAFYQQ 148
>2riq_A Poly [ADP-ribose] polymerase 1; Zn-binding domain, Zn ribbon, Zn
finger, ADP-ribosylation, D damage, DNA repair,
DNA-binding, glycosyltransferase; 1.70A {Homo sapiens}
PDB: 2jvn_A
Length = 160
Score = 25.0 bits (54), Expect = 7.8
Identities = 7/35 (20%), Positives = 20/35 (57%)
Query: 40 NQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
++ K E LK + + ++D++K ++ ++K+
Sbjct: 15 DKDSKLEKALKAQNDLIWNIKDELKKVCSTNDLKE 49
>2o1e_A YCDH; alpha-beta protein, structural genomics, PSI-2, protein
structure initiative, northeast structural genomics
consortium, NESG; 2.60A {Bacillus subtilis}
Length = 312
Score = 25.4 bits (56), Expect = 7.8
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 42 KEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
KE YE + K+ I KLQ L ++ AE K+
Sbjct: 160 KEYYEKNSKEYIAKLQDLDKLYRTTAKKAEKKE 192
>3tk8_A 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
succinyltransferase; ssgcid; 1.80A {Burkholderia
pseudomallei}
Length = 316
Score = 25.6 bits (55), Expect = 8.4
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 34 HNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
H+++ S+ L++ I R ++ ASAEI++
Sbjct: 31 HSSSTSSIATNMSQQLQQIIDNAWENRAELSPKAASAEIRE 71
>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11,
conformation, nucleotide, ATP-binding, microtubule,
motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP:
c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*
Length = 369
Score = 25.3 bits (56), Expect = 8.5
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 32 KVHNATNSNQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
+ N + N K A LKK + ++Q E+++
Sbjct: 326 SIVNDPSKNVSSKEVARLKKLVSY---WKEQAGRKGDDEELEE 365
>3c3r_A Programmed cell death 6-interacting protein; ALIX BRO1 CHMP4C
amphipathic-helix, apoptosis, HOST-virus interaction,
protein transport, transport; 2.02A {Homo sapiens} PDB:
2oew_A 3c3o_A 3c3q_A
Length = 380
Score = 25.6 bits (55), Expect = 8.8
Identities = 11/54 (20%), Positives = 18/54 (33%)
Query: 47 ADLKKEIKKLQRLRDQIKSWIASAEIKDKSTLLDYRKLIETQMERFKVVERETK 100
A + ++L +LR TLL Y I + +F E +
Sbjct: 58 AQYCRAAEELSKLRRAAVGRPLDKHEGALETLLRYYDQICSIEPKFPFSENQIC 111
>1q08_A Zn(II)-responsive regulator of ZNTA; MERR family transcriptional
regulator; 1.90A {Escherichia coli} SCOP: a.6.1.3 PDB:
1q09_A 1q0a_A
Length = 99
Score = 24.6 bits (53), Expect = 8.9
Identities = 3/27 (11%), Positives = 14/27 (51%)
Query: 43 EKYEADLKKEIKKLQRLRDQIKSWIAS 69
++ +++ I +LQ ++ ++ +
Sbjct: 45 QERLQEVEARIAELQSMQRSLQRLNDA 71
>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome
condensation, condensin, SMC, N subunit, ABC-type
ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus
ducreyi} PDB: 3euk_A*
Length = 483
Score = 25.2 bits (54), Expect = 9.0
Identities = 11/87 (12%), Positives = 26/87 (29%), Gaps = 7/87 (8%)
Query: 18 KVSEGVETFEDIWQKVHNATNS---NQKEKYEADLKKEIKKLQRLRDQIKSWIASAEIKD 74
+ + + H +QK + L K++ + +
Sbjct: 293 NIRDTHSILLNALSDQHEQHKDLFESQKLSFSEALAMLYKRINPHIELGQR----MPQTI 348
Query: 75 KSTLLDYRKLIETQMERFKVVERETKT 101
LLDYR ++ ++E + +
Sbjct: 349 GEELLDYRNYLDLEVETLRGAYGWMRA 375
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
0.311 0.126 0.345
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,083,091
Number of extensions: 110514
Number of successful extensions: 336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 330
Number of HSP's successfully gapped: 66
Length of query: 144
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,328,508
Effective search space: 255381972
Effective search space used: 255381972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.5 bits)