RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 025777
(248 letters)
>2pkp_A Homoaconitase small subunit; beta barrel, amino-acid biosynthesis,
leucine biosynthesis, structural genomics, NPPSFA; 2.10A
{Methanocaldococcus jannaschii}
Length = 170
Score = 184 bits (469), Expect = 2e-59
Identities = 57/180 (31%), Positives = 95/180 (52%), Gaps = 17/180 (9%)
Query: 70 FHGLCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKT 129
G + GD++DTD IIP YL ++P E L S+ + G+ + +
Sbjct: 3 IKGRAHKFGDDVDTDAIIPGPYLRT--TDPYE---LASHCMAGIDENFPKKV-------K 50
Query: 130 KYKIIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARL 189
+ +I+AG NFGCGSSRE A +A+ G AV+A+S+ARIF+RN++ G + P+ +
Sbjct: 51 EGDVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVG-LIPIIAN--- 106
Query: 190 CEECSTGDVVTIEIAESRLINHTTGKEYKLKPIGD-LGPVIDAGGIFAYARKTGMIASRN 248
+E GD+V I++ + ++ K K + ++ AGG+ Y +K +I S+
Sbjct: 107 TDEIKDGDIVEIDLDKEEIVITNKNKTIKCETPKGLEREILAAGGLVNYLKKRKLIQSKK 166
>1v7l_A 3-isopropylmalate dehydratase small subunit; beta barrel, lyase;
1.98A {Pyrococcus horikoshii} SCOP: c.8.2.1
Length = 163
Score = 178 bits (453), Expect = 5e-57
Identities = 56/179 (31%), Positives = 84/179 (46%), Gaps = 19/179 (10%)
Query: 70 FHGLCYVVGDNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKT 129
G + GD+I TD+I P Y + +P E L A I + +
Sbjct: 3 TTGKVWKFGDDISTDEITPGRYN--LTKDPKE---LAKIAFIEVRPDFARNV-------R 50
Query: 130 KYKIIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNSVATGEIYPLDSEARL 189
+++AG NFG GSSRE A +AL A G + V+AES+ RIF+RN++ G I L +
Sbjct: 51 PGDVVVAGKNFGIGSSRESAALALKALGIAGVIAESFGRIFYRNAINIG-IPLLLGKT-- 107
Query: 190 CEECSTGDVVTIEIAESRLINHTTGKEYKLKPIGD-LGPVIDAGGIFAYARKTGMIASR 247
E GD+VT+ + + +P+ D L ++ GGI Y R+ G + R
Sbjct: 108 -EGLKDGDLVTVNWETGEVRK--GDEILMFEPLEDFLLEIVREGGILEYIRRRGDLCIR 163
>2hcu_A 3-isopropylmalate dehydratase small subunit; beta barrel, lyase;
2.10A {Streptococcus mutans}
Length = 213
Score = 92.7 bits (231), Expect = 3e-23
Identities = 40/107 (37%), Positives = 55/107 (51%), Gaps = 22/107 (20%)
Query: 79 DNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENET--------KTK 130
DNIDTDQI+P ++L L+ + + G Y + Y R++D N T + +
Sbjct: 34 DNIDTDQILPKQFLKLI-----DKKGFGKYLM------YEWRYLDNNYTENPDFIFNQPE 82
Query: 131 Y---KIIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNS 174
Y I+I G NFG GSSREHA AL G +VA S+ I + N
Sbjct: 83 YREASILITGDNFGAGSSREHAAWALADYGFKVIVAGSFGDIHYNND 129
>3h5j_A 3-isopropylmalate dehydratase small subunit; leucine biosynthesis,
isopropylmalate isomerase, LEUD, amino-acid
biosynthesis; 1.20A {Mycobacterium tuberculosis} PDB:
3h5h_A 3h5e_A
Length = 171
Score = 90.3 bits (225), Expect = 1e-22
Identities = 31/96 (32%), Positives = 43/96 (44%), Gaps = 7/96 (7%)
Query: 79 DNIDTDQIIPAEYLTLVPSNPDEYEKLGSYALIGLPATYTTRFIDENETKTKYKIIIAGG 138
N+DTDQIIPA +L V G F+ + +++AG
Sbjct: 20 SNVDTDQIIPAVFLKRV-----TRTGFEDGLFAGW--RSDPAFVLNLSPFDRGSVLVAGP 72
Query: 139 NFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNS 174
+FG GSSREHA AL G V++ + IF N+
Sbjct: 73 DFGTGSSREHAVWALMDYGFRVVISSRFGDIFRGNA 108
>3q3w_A 3-isopropylmalate dehydratase small subunit; structural genomics,
center for structural genomics of infec diseases, csgid,
isomerase; HET: MSE; 1.89A {Campylobacter jejuni}
Length = 203
Score = 90.3 bits (225), Expect = 2e-22
Identities = 39/110 (35%), Positives = 54/110 (49%), Gaps = 27/110 (24%)
Query: 79 DNIDTDQIIPAEYLTLVPSNPDEYEK--LGSYALIGLPATYTTRFIDENETKTK------ 130
NIDTDQIIP ++L V K G + + R++D+ E+
Sbjct: 20 ANIDTDQIIPKQFLLAV-------SKQGFGKHLF------HDLRYLDDKESVLNMDFNLN 66
Query: 131 ---Y---KIIIAGGNFGCGSSREHAPVALGAAGCSAVVAESYARIFFRNS 174
Y I+++ NFG GSSREHAP AL G A++A S+A IF N+
Sbjct: 67 KKEYQNSSILVSFENFGSGSSREHAPWALVDYGIRAIIAPSFADIFKNNA 116
>1c96_A Mitochondrial aconitase; lyase, tricarboxylic acid cycle,
iron-sulfur, mitochondrion, transit peptide, 4Fe-4S,
3D-structure; HET: FLC; 1.81A {Bos taurus} SCOP: c.8.2.1
c.83.1.1 PDB: 1c97_A* 1b0k_A* 1b0j_A* 7acn_A* 6acn_A*
5acn_A* 1b0m_A* 1ami_A* 1amj_A 8acn_A* 1fgh_A* 1aco_A*
1nis_A* 1nit_A
Length = 753
Score = 63.8 bits (156), Expect = 7e-12
Identities = 43/201 (21%), Positives = 65/201 (32%), Gaps = 44/201 (21%)
Query: 75 YVVGDNIDTDQIIPA-EYLTLVPSNPDEYEKLGSYALIGLPATYT-----TRFIDENETK 128
V TD I A +L + D + + LIG R E
Sbjct: 558 IKVKGKCTTDHISAAGPWLKF-RGHLD---NISNNLLIGAINIENRKANSVRNAVTQEFG 613
Query: 129 T------KYK------IIIAGGNFGCGSSREHAPVALGA--AGCSAVVAESYARIFFRNS 174
YK ++I N+G G+SREH+ AL G A++ +S+ARI N
Sbjct: 614 PVPDTARYYKQHGIRWVVIGDENYGEGASREHS--ALEPRHLGGRAIITKSFARIHETNL 671
Query: 175 VATGEIYPL---DSEARLCEECSTGDVVTIEIAESRL--------INHTTGKEYKLKPIG 223
G + PL D + D +TI+ + I H G + +
Sbjct: 672 KKQG-LLPLTFADPADY--NKIHPVDKLTIQGLKDFAPGKPLKCIIKHPNGTQETILLNH 728
Query: 224 DLGP----VIDAGGIFAYARK 240
AG ++
Sbjct: 729 TFNETQIEWFRAGSALNRMKE 749
>2b3y_A Iron-responsive element binding protein 1; IRP1 IRE-IRP1 aconitase
activity, lyase; 1.85A {Homo sapiens} SCOP: c.8.2.1
c.83.1.1 PDB: 2b3x_A 3snp_A 3sn2_A 2ipy_A
Length = 888
Score = 49.5 bits (119), Expect = 4e-07
Identities = 36/140 (25%), Positives = 50/140 (35%), Gaps = 52/140 (37%)
Query: 76 VVGDNIDTDQIIPA----------EYLTLVPSNPDEYEKLGSYA---------------- 109
+GD++ TD I PA YLT + + SY
Sbjct: 669 NLGDSVTTDHISPAGNIARNSPAARYLT---NRGLTPREFNSYGSRRGNDAVMARGTFAN 725
Query: 110 ------LIGLPATYTTRFIDENETKT------KYK------IIIAGGNFGCGSSREHAPV 151
+ A T + E +Y+ I++AG +G GSSR+ A
Sbjct: 726 IRLLNRFLNKQAPQT-IHLPSGEILDVFDAAERYQQAGLPLIVLAGKEYGAGSSRDWA-- 782
Query: 152 ALGAA--GCSAVVAESYARI 169
A G G AV+AESY RI
Sbjct: 783 AKGPFLLGIKAVLAESYERI 802
>1l5j_A Aconitate hydratase 2; molecular recognition, RNA binding, citric
acid cycle, heat- like domain, lyase; HET: TRA; 2.40A
{Escherichia coli} SCOP: a.118.15.1 c.8.2.1 c.83.1.1
Length = 865
Score = 42.9 bits (101), Expect = 6e-05
Identities = 32/170 (18%), Positives = 56/170 (32%), Gaps = 31/170 (18%)
Query: 75 YVVGDNIDTDQIIPAEYLTLVPSNPD--------EYEKLGSYALIGLPATYTTRFIDENE 126
+ V +TD + PA S PD + I+ +
Sbjct: 171 FKVTGETNTDDLSPAPDAW---SRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQ 227
Query: 127 TKTKYKIIIAGGNFGCGSSREHAPVALGAAG------------CSAVVAESYARIFFRNS 174
K + + G G GSSR+ A ++ + A IFF
Sbjct: 228 QK-GFPLAYVGDVVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTM 286
Query: 175 VATGEIYPLDSEARLCEECSTGDVVTIEIAESRLINHTTGK---EYKLKP 221
G + P++ + + GDV+ + + + NH TG+ ++LK
Sbjct: 287 EDAGAL-PIEVD---VSNLNMGDVIDVYPYKGEVRNHETGELLATFELKT 332
>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 = 38.9 bits (90), Expect = 0.001
Identities = 31/197 (15%), Positives = 60/197 (30%), Gaps = 69/197 (35%)
Query: 23 TKPLFIPHSLKFTTGNGRAAVTFQRAVSVIPKATSADSRATK----------EPTATFHG 72
T+PL + H G ++P T++ A++ EPT F
Sbjct: 6 TRPLTLSH--------GSLEHVL-----LVP--TASFFIASQLQEQFNKILPEPTEGFAA 50
Query: 73 LCYVVGDNIDTDQIIPAE----YLTLV-----PSNPDEYEKLGSYALIGLPATYTTRFID 123
D + PAE +L V PS +++++ + L + +++
Sbjct: 51 ---------DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCL----TEFENCYLE 97
Query: 124 ENETKTKYKIIIAGGNFGCGSSREHAPVA--LGAAGCSAVVAESYARIFFRNSVATGEIY 181
N+ I HA A L + V + + + + +
Sbjct: 98 GND--------I------------HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPF 137
Query: 182 PLDSEARLCEECSTGDV 198
S + L G+
Sbjct: 138 DKKSNSALFRAVGEGNA 154
Score = 35.0 bits (80), Expect = 0.023
Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 21/93 (22%)
Query: 39 GRAAVTF-QRAVSVIPKATSADSRATKEPTATFHGLCYVVGDNIDTDQIIPA------EY 91
GR A +F Q A+ + + + L +V N++ Q + A +
Sbjct: 1815 GRVAASFSQEALQYVVERVGKRTG----------WLVEIVNYNVENQQYVAAGDLRALDT 1864
Query: 92 LTLVPSNPDEYEKLGSYALIGLPATYTTRFIDE 124
+T V + + KL +I L + + ++
Sbjct: 1865 VTNVLN----FIKLQKIDIIELQKSLSLEEVEG 1893
>3bxp_A Putative lipase/esterase; putative carboxylesterase, structural
genomics, joint center structural genomics, JCSG; HET:
EPE; 1.70A {Lactobacillus plantarum WCFS1} PDB: 3d3n_A*
Length = 277
Score = 32.1 bits (73), Expect = 0.13
Identities = 16/34 (47%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 133 IIIAGGNFGCGSSREHAPVA--LGAAGCSAVVAE 164
II GG F S RE AP+A + AAG VV
Sbjct: 39 IICPGGGFTYHSGREEAPIATRMMAAGMHTVVLN 72
>3hxk_A Sugar hydrolase; alpha-beta protein., structural genomics, PSI-2,
protein structure initiative; 3.20A {Lactococcus lactis
subsp}
Length = 276
Score = 30.9 bits (70), Expect = 0.30
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 2/34 (5%)
Query: 133 IIIAGGNFGCGSSREHAPVA--LGAAGCSAVVAE 164
II GG + S RE P+A A G ++
Sbjct: 47 IICPGGGYQHISQRESDPLALAFLAQGYQVLLLN 80
>3bjr_A Putative carboxylesterase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; 2.09A {Lactobacillus plantarum WCFS1}
Length = 283
Score = 30.2 bits (68), Expect = 0.47
Identities = 8/34 (23%), Positives = 13/34 (38%), Gaps = 2/34 (5%)
Query: 133 IIIAGGNFGCGSSREHAPVA--LGAAGCSAVVAE 164
II+ GG++ + +A G A E
Sbjct: 54 IIVPGGSYTHIPVAQAESLAMAFAGHGYQAFYLE 87
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.9 bits (64), Expect = 1.2
Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 16/55 (29%)
Query: 177 TGEIYPLDSEARLCEEC-----------STGDVVTIE---IAESRLINHTTGKEY 217
G P + C EC S GDVV + +L++ T E+
Sbjct: 11 AGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVD--TRSEW 63
>2f8l_A Hypothetical protein LMO1582; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: MSE SAM; 2.20A {Listeria monocytogenes}
SCOP: c.66.1.45
Length = 344
Score = 27.4 bits (61), Expect = 5.2
Identities = 5/30 (16%), Positives = 9/30 (30%), Gaps = 2/30 (6%)
Query: 16 TSSPIPKTKP--LFIPHSLKFTTGNGRAAV 43
+ LFI +++T G
Sbjct: 225 LCREEGHSFAHFLFIEQGMRYTKPGGYLFF 254
>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis,
nucleotide-B transferase; HET: MSE; 2.01A
{Staphylococcus aureus}
Length = 219
Score = 26.5 bits (59), Expect = 8.2
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 112 GLPATYTTRFIDENETKTKYKIIIAGGN 139
G ++ T R I+ K II+ G N
Sbjct: 169 GSSSSRTQRLINGKPAKIDDPIILVGAN 196
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 0.133 0.385
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,732,497
Number of extensions: 224437
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 459
Number of HSP's successfully gapped: 34
Length of query: 248
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 157
Effective length of database: 4,160,982
Effective search space: 653274174
Effective search space used: 653274174
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: 56 (25.2 bits)