RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10473
(124 letters)
>2cy7_A Cysteine protease APG4B; papain-like fold, autophagy, hydrolase;
1.90A {Homo sapiens} SCOP: d.3.1.22 PDB: 2d1i_A 2zzp_A
2z0d_A 2z0e_A
Length = 396
Score = 70.3 bits (171), Expect = 1e-15
Identities = 36/112 (32%), Positives = 51/112 (45%), Gaps = 12/112 (10%)
Query: 14 DSEKKLDSTYHCPQAS-RLHILHMDPSIAVCFLCKTENDFASLCSQIRAELRP-EQQPLF 71
D D ++HC R+ I +DPSIAV F CKTE+DF C Q++ P+F
Sbjct: 293 DGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMF 352
Query: 72 ELIEDPIEDWTPTQPRPSNLGGTSSPSCSSMRRQPRRVSGVGEGSDDDFEFL 123
EL+E +PS+L + S R+ + D+DFE L
Sbjct: 353 ELVEQ----------QPSHLACPDVLNLSLDSSDVERLERFFDSEDEDFEIL 394
>2p82_A Cysteine protease ATG4A; autophagy, hydrolase, protein transport,
thiol Pro transport, UBL conjugation pathway, structural
genomics; 2.10A {Homo sapiens} SCOP: d.3.1.22
Length = 355
Score = 68.0 bits (165), Expect = 9e-15
Identities = 26/70 (37%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 13 QDSEKKLDSTYHCPQ-ASRLHILHMDPSIAVCFLCKTENDFASLCSQIRAELRPEQQPLF 71
+++ D T+HC Q R++IL++DPS+A+ F CK E DF + CS ++ E+ E +F
Sbjct: 286 EENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMF 345
Query: 72 ELIEDPIEDW 81
EL++ W
Sbjct: 346 ELVQKHPSHW 355
>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 = 34.5 bits (78), Expect = 0.003
Identities = 7/34 (20%), Positives = 16/34 (47%), Gaps = 12/34 (35%)
Query: 12 EQDSEKKLDST---YHCPQASRLHILHMDPSIAV 42
E+ + KKL ++ Y ++ P++A+
Sbjct: 18 EKQALKKLQASLKLY-ADDSA--------PALAI 42
>2o90_A DHNA, dihydroneopterin aldolase; monapterin, drug design, atomic
resolution, X-RAY crystallography, lyase; HET: NEU;
1.07A {Escherichia coli} PDB: 2o9m_A*
Length = 122
Score = 26.8 bits (60), Expect = 1.3
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 27/80 (33%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI---LHMDPSIAVCFLCKTEN-----DFASL 55
IGVY D E+ + Q +L + D A K+++ +A +
Sbjct: 13 TTIGVY----DWEQTI------EQ--KLVFDIEMAWDNRKA----AKSDDVADCLSYADI 56
Query: 56 CSQIRAELRPEQQPLFELIE 75
+ + + E F L+E
Sbjct: 57 AETVVSHV--EGAR-FALVE 73
>3o1k_A Dihydroneopterin aldolase FOLB, putative; structural genomics,
center for structural genomics of infec diseases,
csgid; 1.95A {Vibrio cholerae o1 biovar el tor}
Length = 132
Score = 26.8 bits (60), Expect = 1.3
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 27/80 (33%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI---LHMDPSIAVCFLCKTEN-----DFASL 55
IGVY D E+++ Q +L + + D A K+++ D+A +
Sbjct: 28 TTIGVY----DWEQQI------KQ--KLVLDLEMAHDNRAA----GKSDDVADALDYAQV 71
Query: 56 CSQIRAELRPEQQPLFELIE 75
+ + EQ F L+E
Sbjct: 72 SQAVLEHI--EQGR-FLLVE 88
>1dhn_A DHNA, 7,8-dihydroneopterin aldolase; pterin binding, folate
biosynthesis, antibiotic target, beta; 1.65A
{Staphylococcus aureus} SCOP: d.96.1.3 PDB: 1rri_A*
1rrw_A* 1rry_A* 1rs2_A* 1rs4_A* 1rsd_A* 1rsi_A* 1u68_A*
2dhn_A* 2nm2_A* 2nm3_A*
Length = 121
Score = 26.4 bits (59), Expect = 1.6
Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 23/78 (29%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI-LHMDPSIAVCFLCKTEN-----DFASLCS 57
G+ G +E ++ + ++ + L +D S A +T+N + +
Sbjct: 14 GYHGAL----SAENEIGQIF------KVDVTLKVDLSEA----GRTDNVIDTVHYGEVFE 59
Query: 58 QIRAELRPEQQPLFELIE 75
++++ + + L+E
Sbjct: 60 EVKSIM---EGKAVNLLE 74
>1nbu_A DHNA, probable dihydroneopterin aldolase; anti-parallel,
beta-sheet, two alpha helices, structural genomics,
PSI; HET: PH2; 1.60A {Mycobacterium tuberculosis} SCOP:
d.96.1.3 PDB: 1nbu_B* 1nbu_C*
Length = 119
Score = 26.4 bits (59), Expect = 1.7
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 23/78 (29%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI-LHMDPSIAVCFLCKTEN-----DFASLCS 57
G GVY D E+ + + + + +D + A +++ D+ L S
Sbjct: 14 GRHGVY----DHERVAGQRF------VIDVTVWIDLAEA----ANSDDLADTYDYVRLAS 59
Query: 58 QIRAELRPEQQPLFELIE 75
+ + P +LIE
Sbjct: 60 RAAEIV--AGPP-RKLIE 74
>1z9w_A DHNA, dihydroneopterin aldolase; FOLB, structural genomics, TB ST
genomics; 2.50A {Mycobacterium tuberculosis H37RV}
SCOP: d.96.1.3
Length = 133
Score = 26.1 bits (58), Expect = 2.5
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 23/78 (29%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI-LHMDPSIAVCFLCKTEN-----DFASLCS 57
G GVY D E+ + + + + +D + A +++ D+ L S
Sbjct: 14 GRHGVY----DHERVAGQRF------VIDVTVWIDLAEA----ANSDDLADTYDYVRLAS 59
Query: 58 QIRAELRPEQQPLFELIE 75
+ + P +LIE
Sbjct: 60 RAAEIV--AGPP-RKLIE 74
>3r2e_A Dihydroneopterin aldolase; structural genomics, IDP90567, center
for structural genomic infectious diseases, csgid,
bifunctional; 2.15A {Yersinia pestis}
Length = 143
Score = 26.1 bits (58), Expect = 2.5
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 27/80 (33%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI---LHMDPSIAVCFLCKTEN-----DFASL 55
IGVY D E+ + Q +L + D A +++ +A +
Sbjct: 37 TTIGVY----DWEQTI------QQ--KLVFDIEMGWDNRKA----AGSDDVNDCLSYADI 80
Query: 56 CSQIRAELRPEQQPLFELIE 75
+ + ++ F L+E
Sbjct: 81 SEAVIQHVGSQR---FALVE 97
>1sql_A Dihydroneopterin aldolase; tetrahydrofolate biosynthesis,
aldolase classes, retroaldol reaction, purin binding,
schiff base, lyase; HET: GUN; 2.20A {Arabidopsis
thaliana} SCOP: d.96.1.3
Length = 146
Score = 26.1 bits (58), Expect = 2.6
Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 23/78 (29%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI-LHMDPSIAVCFLCKTEN-----DFASLCS 57
G G E+ L + + I + A +++N + + S
Sbjct: 33 GFHGAI----AEERTLGQMF------LVDIDAWVSLKKA----GESDNLEDTISYVDIFS 78
Query: 58 QIRAELRPEQQPLFELIE 75
+ + E P L+E
Sbjct: 79 LAKEIV--EGSP-RNLLE 93
>2hq7_A Protein, related to general stress protein 26(GS2 B.subtilis;
NP_350077.1, structural genomics, joint center for
structural genomics; 2.00A {Clostridium acetobutylicum}
SCOP: b.45.1.1
Length = 146
Score = 26.1 bits (57), Expect = 2.7
Identities = 11/76 (14%), Positives = 22/76 (28%), Gaps = 10/76 (13%)
Query: 34 LHMDPSIAVCFLCKTENDFASLCSQIRAELRPEQQPLFELIEDPIEDWTPTQPRPSNLGG 93
L + I + F+ + L E+ ++ L D E + P G
Sbjct: 62 LKKNNKICLYFVDDNKFAGLMLVG--TIEILHDRASKEMLWTDGCEIYYP--------LG 111
Query: 94 TSSPSCSSMRRQPRRV 109
P +++
Sbjct: 112 IDDPDYTALCFTAEWG 127
>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 = 26.6 bits (58), Expect = 3.0
Identities = 12/76 (15%), Positives = 22/76 (28%), Gaps = 15/76 (19%)
Query: 16 EKKLDST-YHCPQASRLHI-LHMDPSIAVCFLCKTENDFASLCSQIRAELRP-------- 65
+ ++ T H P ++ I L V + L +R P
Sbjct: 350 QDYVNKTNSHLPAGKQVEISLVNGAKNLV--VSGPPQSLYGLNLTLRKAKAPSGLDQSRI 407
Query: 66 ---EQQPLFELIEDPI 78
E++ F P+
Sbjct: 408 PFSERKLKFSNRFLPV 423
>1dxy_A D-2-hydroxyisocaproate dehydrogenase; D-2-hydroxycarboxylate
dehydrogenase, D-lactate dehydrogenas oxidoreductase;
HET: NAD; 1.86A {Lactobacillus casei} SCOP: c.2.1.4
c.23.12.1
Length = 333
Score = 26.0 bits (58), Expect = 3.6
Identities = 12/56 (21%), Positives = 13/56 (23%), Gaps = 30/56 (53%)
Query: 1 VGTGHIG---------------VYDKEQDSEKKLDSTY---------------HCP 26
+GTGHIG YD D Y H P
Sbjct: 151 MGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDHPDFDYVSLEDLFKQSDVIDLHVP 206
>1b9l_A Protein (epimerase); isomerase; 2.90A {Escherichia coli} SCOP:
d.96.1.3
Length = 120
Score = 25.3 bits (56), Expect = 4.9
Identities = 11/78 (14%), Positives = 29/78 (37%), Gaps = 23/78 (29%)
Query: 4 GHIGVYDKEQDSEKKLDSTYHCPQASRLHI-LHMDPSIAVCFLCKTEN-----DFASLCS 57
IG+ ++E ++ Q +++ +H A +E+ ++ ++
Sbjct: 17 TFIGIKEEEINN----------RQDIVINVTIHYPADKA----RTSEDINDALNYRTVTK 62
Query: 58 QIRAELRPEQQPLFELIE 75
I + + F L+E
Sbjct: 63 NIIQHVENNR---FSLLE 77
>1nu0_A Hypothetical protein YQGF; structural genomics, structure 2
function project, S2F, unknown function; 1.60A
{Escherichia coli} SCOP: c.55.3.8 PDB: 1nmn_A 1ovq_A
Length = 138
Score = 25.2 bits (56), Expect = 5.5
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 64 RPEQQPLFELIEDPIEDWTPTQ-----PRPSNLGGTSSPSCSSMRR 104
+ P + +IE +++W P + P N+ GT P + R+
Sbjct: 35 AQDGTPDWNIIERLLKEWQPDEIIVGLPL--NMDGTEQPLTARARK 78
>1vgy_A Succinyl-diaminopimelate desuccinylase; structural genomics,
unknown function; HET: MSE; 1.90A {Neisseria
meningitidis} SCOP: c.56.5.4 d.58.19.1
Length = 393
Score = 24.9 bits (55), Expect = 7.7
Identities = 7/27 (25%), Positives = 11/27 (40%)
Query: 69 PLFELIEDPIEDWTPTQPRPSNLGGTS 95
L ++ I + + S GGTS
Sbjct: 303 KLTDVARAAIAETCGIEAELSTTGGTS 329
>3isz_A Succinyl-diaminopimelate desuccinylase; DAPE, Zn-binding,
metallopeptidase, structural genomics, PSI-2, protein
struc initiative; 2.00A {Haemophilus influenzae} PDB:
3ic1_A
Length = 377
Score = 24.9 bits (55), Expect = 8.2
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 69 PLFELIEDPIEDWTPTQPRPSNLGGTS 95
L + I IE+ P+ GGTS
Sbjct: 300 KLLDSITSAIEETIGITPKAETGGGTS 326
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
0.316 0.135 0.417
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: 1,887,631
Number of extensions: 94661
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 212
Number of HSP's successfully gapped: 23
Length of query: 124
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 42
Effective length of database: 4,412,271
Effective search space: 185315382
Effective search space used: 185315382
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 (21.6 bits)
S2: 51 (23.9 bits)