BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 030768
(171 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OL2|B Chain B, Receptor-Ligand Structure Of Human Semaphorin 4d With
Plexin B1
Length = 528
Score = 31.6 bits (70), Expect = 0.23, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 14/89 (15%)
Query: 37 DMSCECKSKPISKLISWGRRLTNGAKSLCLAKPASGYVPMDQDPIREKP--------VSV 88
D++ +C P+ L ++ S P + VP++ PI E P V++
Sbjct: 343 DVNSDCAQLPVDTLDAYP------CGSDHTPSPMASRVPLEATPILEWPGIQLTAVAVTM 396
Query: 89 PKGHLAVYVGQKDGDFHRVLVPVIYFNHP 117
GH ++G G HRV + HP
Sbjct: 397 EDGHTIAFLGDSQGQLHRVYLGPGSDGHP 425
>pdb|2B9W|A Chain A, Crystal Structure Of Cla-Producing Fatty Acid Isomerase
From P. Acnes
pdb|2B9X|A Chain A, Crystal Structure Of Cla-Producing Fatty Acid Isomerase
From P. Acnes
pdb|2B9Y|A Chain A, Crystal Structure Of Cla-Producing Fatty Acid Isomerase
From P. Acnes
pdb|2BA9|A Chain A, Crystal Structure Of Cla-Producing Fatty Acid Isomerase
From P. Acnes
pdb|2BAB|A Chain A, Crystal Structure Of Cla-Producing Fatty Acid Isomerase
From P. Acnes
pdb|2BAC|A Chain A, Crystal Structure Of Cla-Producing Fatty Acid Isomerase
From P. Acnes
Length = 424
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 10/60 (16%)
Query: 65 CLAKP---ASGYVPMDQDPIREKPVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGK 121
CL K SGYVP + P R GH+ VY + D H+++ + NHP +
Sbjct: 286 CLVKEYPTISGYVPDNMRPER-------LGHVMVYYHRWADDPHQIITTYLLRNHPDYAD 338
>pdb|3E04|A Chain A, Crystal Structure Of Human Fumarate Hydratase
pdb|3E04|B Chain B, Crystal Structure Of Human Fumarate Hydratase
pdb|3E04|C Chain C, Crystal Structure Of Human Fumarate Hydratase
pdb|3E04|D Chain D, Crystal Structure Of Human Fumarate Hydratase
Length = 490
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 39 SCECKSKPISKLISWGRRLTNGAKSLCLAKPASGYV 74
+ + KSK +++I GR T A L L + SGYV
Sbjct: 197 ALDAKSKEFAQIIKIGRTHTQDAVPLTLGQEFSGYV 232
>pdb|1K5H|A Chain A, 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase
pdb|1K5H|B Chain B, 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase
pdb|1K5H|C Chain C, 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase
pdb|1ONN|A Chain A, Ispc Apo Structure
pdb|1ONN|B Chain B, Ispc Apo Structure
pdb|1ONO|A Chain A, Ispc Mn2+ Complex
pdb|1ONO|B Chain B, Ispc Mn2+ Complex
pdb|1ONP|A Chain A, Ispc Complex With Mn2+ And Fosmidomycin
pdb|1ONP|B Chain B, Ispc Complex With Mn2+ And Fosmidomycin
Length = 398
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 25 RGGSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
+ GS +LG PDM PI+ ++W R+ +G K L K
Sbjct: 263 QDGSVLAQLGEPDMR-----TPIAHTMAWPNRVNSGVKPLDFCK 301
>pdb|1T1R|A Chain A, Crystal Structure Of The Reductoisomerase Complexed With A
Bisphosphonate
pdb|1T1R|B Chain B, Crystal Structure Of The Reductoisomerase Complexed With A
Bisphosphonate
pdb|1T1S|A Chain A, Crystal Structure Of The Reductoisomerase Complexed With A
Bisphosphonate
pdb|1T1S|B Chain B, Crystal Structure Of The Reductoisomerase Complexed With A
Bisphosphonate
Length = 398
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 25 RGGSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
+ GS +LG PDM PI+ ++W R+ +G K L K
Sbjct: 263 QDGSVLAQLGEPDMR-----TPIAHTMAWPNRVNSGVKPLDFCK 301
>pdb|1Q0L|A Chain A, Crystal Structure Of Dxr In Complex With Fosmidomycin
pdb|1Q0Q|A Chain A, Crystal Structure Of Dxr In Complex With The Substrate 1-
Deoxy-D-Xylulose-5-Phosphate
pdb|1Q0Q|B Chain B, Crystal Structure Of Dxr In Complex With The Substrate 1-
Deoxy-D-Xylulose-5-Phosphate
Length = 406
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 25 RGGSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
+ GS +LG PDM PI+ ++W R+ +G K L K
Sbjct: 271 QDGSVLAQLGEPDMR-----TPIAHTMAWPNRVNSGVKPLDFCK 309
>pdb|3R0I|A Chain A, Ispc In Complex With An N-Methyl-Substituted Hydroxamic
Acid
pdb|3R0I|B Chain B, Ispc In Complex With An N-Methyl-Substituted Hydroxamic
Acid
Length = 410
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 25 RGGSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
+ GS +LG PDM PI+ ++W R+ +G K L K
Sbjct: 275 QDGSVLAQLGEPDMR-----TPIAHTMAWPNRVNSGVKPLDFCK 313
>pdb|3ANL|A Chain A, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase (Dxr) Complexed With
Pyridin-2-Ylmethylphosphonic Acid
pdb|3ANL|B Chain B, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase (Dxr) Complexed With
Pyridin-2-Ylmethylphosphonic Acid
pdb|3ANM|A Chain A, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase (Dxr) Complexed With
5-Phenylpyridin-2-Ylmethylphosphonic Acid
pdb|3ANM|B Chain B, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase (Dxr) Complexed With
5-Phenylpyridin-2-Ylmethylphosphonic Acid
pdb|3ANN|A Chain A, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase (Dxr) Complexed With
Quinolin-2-Ylmethylphosphonic Acid
pdb|3ANN|B Chain B, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase (Dxr) Complexed With
Quinolin-2-Ylmethylphosphonic Acid
Length = 420
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 25 RGGSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
+ GS +LG PDM PI+ ++W R+ +G K L K
Sbjct: 273 QDGSVLAQLGEPDMR-----TPIAHTMAWPNRVNSGVKPLDFCK 311
>pdb|2EGH|A Chain A, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase Complexed With A Magnesium Ion, Nadph
And Fosmidomycin
pdb|2EGH|B Chain B, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase Complexed With A Magnesium Ion, Nadph
And Fosmidomycin
Length = 424
Score = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 25 RGGSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
+ GS +LG PDM PI+ ++W R+ +G K L K
Sbjct: 273 QDGSVLAQLGEPDMR-----TPIAHTMAWPNRVNSGVKPLDFCK 311
>pdb|1R0K|A Chain A, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase From Zymomonas Mobilis
pdb|1R0K|B Chain B, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase From Zymomonas Mobilis
pdb|1R0K|C Chain C, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase From Zymomonas Mobilis
pdb|1R0K|D Chain D, Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate
Reductoisomerase From Zymomonas Mobilis
pdb|1R0L|A Chain A, 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From
Zymomonas Mobilis In Complex With Nadph
pdb|1R0L|B Chain B, 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From
Zymomonas Mobilis In Complex With Nadph
pdb|1R0L|C Chain C, 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From
Zymomonas Mobilis In Complex With Nadph
pdb|1R0L|D Chain D, 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From
Zymomonas Mobilis In Complex With Nadph
Length = 388
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 27 GSGYQRLGAPDMSCECKSKPISKLISWGRRLTNGAKSLCLAK 68
GS ++G+PDM PI ++W +R+ A+SL K
Sbjct: 255 GSILAQIGSPDMRT-----PIGHTLAWPKRMETPAESLDFTK 291
>pdb|2DF4|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
Complexed With Mn2+
pdb|2DQN|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
Complexed With Asn
pdb|2G5H|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
pdb|2G5I|A Chain A, Structure Of Trna-dependent Amidotransferase Gatcab
Complexed With Adp-alf4
pdb|3IP4|A Chain A, The High Resolution Structure Of Gatcab
pdb|2F2A|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
Complexed With Gln
Length = 485
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 57 LTNGAKSLCLAKPASGYVPMDQDPIREK 84
+TNG ++ C +K G+VP+ + + EK
Sbjct: 83 ITNGLETTCASKMLEGFVPIYESTVMEK 110
>pdb|2OGA|A Chain A, X-Ray Crystal Structure Of S. Venezuelae Desv In Complex
With Ketimine Intermediate
pdb|2OGA|B Chain B, X-Ray Crystal Structure Of S. Venezuelae Desv In Complex
With Ketimine Intermediate
pdb|2OGA|C Chain C, X-Ray Crystal Structure Of S. Venezuelae Desv In Complex
With Ketimine Intermediate
pdb|2OGA|D Chain D, X-Ray Crystal Structure Of S. Venezuelae Desv In Complex
With Ketimine Intermediate
Length = 399
Score = 26.6 bits (57), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 66 LAKPASGYVPMDQDPIREKPVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRD 125
LA A+G P+ +P + P P + V + R L+PV + HP LR+
Sbjct: 118 LAVSATGATPVPVEPHEDHPTLDP-----LLVEKAITPRTRALLPVHLYGHPADMDALRE 172
Query: 126 AEEEYGFN 133
+ +G +
Sbjct: 173 LADRHGLH 180
>pdb|2OGE|A Chain A, X-Ray Structure Of S. Venezuelae Desv In Its Internal
Aldimine Form
pdb|2OGE|B Chain B, X-Ray Structure Of S. Venezuelae Desv In Its Internal
Aldimine Form
pdb|2OGE|C Chain C, X-Ray Structure Of S. Venezuelae Desv In Its Internal
Aldimine Form
pdb|2OGE|D Chain D, X-Ray Structure Of S. Venezuelae Desv In Its Internal
Aldimine Form
Length = 399
Score = 26.6 bits (57), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 66 LAKPASGYVPMDQDPIREKPVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRD 125
LA A+G P+ +P + P P + V + R L+PV + HP LR+
Sbjct: 118 LAVSATGATPVPVEPHEDHPTLDP-----LLVEKAITPRTRALLPVHLYGHPADMDALRE 172
Query: 126 AEEEYGFN 133
+ +G +
Sbjct: 173 LADRHGLH 180
>pdb|4FC6|A Chain A, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC6|B Chain B, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC6|C Chain C, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC6|D Chain D, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC7|A Chain A, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC7|B Chain B, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC7|C Chain C, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
pdb|4FC7|D Chain D, Studies On Dcr Shed New Light On Peroxisomal
Beta-Oxidation: Crystal Structure Of The Ternary Complex
Of Pdcr
Length = 277
Score = 26.2 bits (56), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 10 GKRLVRVTRWIIRKTRGGSGYQRLGAPDMSCECK--SKPISKLISWGRRLTNGAKSLCLA 67
G + +RV G G +RLG P S K + P+ +L G + L LA
Sbjct: 196 GPQNIRVNSLAPGPISGTEGLRRLGGPQASLSTKVTASPLQRL---GNKTEIAHSVLYLA 252
Query: 68 KPASGYV 74
P + YV
Sbjct: 253 SPLASYV 259
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.140 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,653,557
Number of Sequences: 62578
Number of extensions: 237162
Number of successful extensions: 432
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 429
Number of HSP's gapped (non-prelim): 16
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)