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= psy10773
(290 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZXC|A Chain A, Seramidase Complexed With C2
pdb|2ZXC|B Chain B, Seramidase Complexed With C2
pdb|2ZWS|A Chain A, Crystal Structure Analysis Of Neutral Ceramidase From
Pseudomonas Aeruginosa
Length = 646
Score = 95.9 bits (237), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 66/173 (38%), Positives = 83/173 (47%), Gaps = 40/173 (23%)
Query: 49 SISRAHNNLQKGRLFVSKGELLDANINRSPTAYLQNPEEERMRYEHDVDKGMVQLQFISA 108
SI RA LQ GRLF GEL +A+ NRS ++L+NP+ YE +D M L F+ A
Sbjct: 133 SIERAQARLQPGRLFYGSGELRNASRNRSLLSHLKNPD--IAGYEDGIDPQMSVLSFVDA 190
Query: 109 EDRPLGVINWFAVHPTSMNNTNRLVSSDN---------------GKFVAAFASTNLGDVS 153
G I+WF VH TSM N N L+S DN FVAAFA TN G++S
Sbjct: 191 NGELAGAISWFPVHSTSMTNANHLISPDNKGYASYHWEHDVSRKSGFVAAFAQTNAGNLS 250
Query: 154 PNIKGPKCLLTGVDCDIDTSACPKQGDSCVASGPGRDMFESTRLIAERMYRKA 206
PN+ L G SGP + F++TR I R + KA
Sbjct: 251 PNLN----LKPG-------------------SGPFDNEFDNTREIGLRQFAKA 280
Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 41/71 (57%)
Query: 211 PHQWQPNTVSTQLVRIGHLVLVGVPGELTTMAGRRLRRALQDELGLLMESDVIIAGLANT 270
P+ W P + Q+ RIG L L+G P E T MAG R+RRA+Q V+ G AN
Sbjct: 385 PYPWTPTVLPIQMFRIGQLELLGAPAEFTVMAGVRIRRAVQAASEAAGIRHVVFNGYANA 444
Query: 271 YADYVTTPEEY 281
YA YVTT EEY
Sbjct: 445 YASYVTTREEY 455
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 1 MGYAKMEQKGVGIHLRLFSRAFIIDDGE--RRFVFVSVDSGMIGYNIRAESISR 52
MGY+ +EQK GIH+R ++RAF+I++ RR V+V+ D GMI + + ++R
Sbjct: 24 MGYSSLEQKTAGIHMRQWARAFVIEEAASGRRLVYVNTDLGMIFQAVHLKVLAR 77
>pdb|3RHY|A Chain A, Crystal Structure Of The Dimethylarginine
Dimethylaminohydrolase Adduct With
4-Chloro-2-Hydroxymethylpyridine
pdb|3RHY|B Chain B, Crystal Structure Of The Dimethylarginine
Dimethylaminohydrolase Adduct With
4-Chloro-2-Hydroxymethylpyridine
Length = 254
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 15/86 (17%)
Query: 11 VGIHLRLFSRAFIIDDGERRFVFVSVDSGMIGYNIRAESISR--------AHNNLQKGRL 62
VG H + A +G R+ + + G+ G +R E + HNNL
Sbjct: 121 VGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLHLKTGLAYLEHNNLLAAGE 180
Query: 63 FVSKGELLDANINRSPTAYLQNPEEE 88
FVSK E D NI ++ PEEE
Sbjct: 181 FVSKPEFQDFNI-------IEIPEEE 199
>pdb|1H70|A Chain A, Ddah From Pseudomonas Aeruginosa. C249s Mutant Complexed
With Citrulline
Length = 255
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 15/86 (17%)
Query: 11 VGIHLRLFSRAFIIDDGERRFVFVSVDSGMIGYNIRAESISR--------AHNNLQKGRL 62
VG H + A +G R+ + + G+ G +R E + HNNL
Sbjct: 122 VGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLHLKTGLAYLEHNNLLAAGE 181
Query: 63 FVSKGELLDANINRSPTAYLQNPEEE 88
FVSK E D NI ++ PEEE
Sbjct: 182 FVSKPEFQDFNI-------IEIPEEE 200
>pdb|3BPB|A Chain A, Crystal Structure Of The Dimethylarginine
Dimethylaminohydrolase H162g Adduct With S-Methyl-L-
Thiocitrulline
pdb|3BPB|B Chain B, Crystal Structure Of The Dimethylarginine
Dimethylaminohydrolase H162g Adduct With S-Methyl-L-
Thiocitrulline
Length = 254
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 15/86 (17%)
Query: 11 VGIHLRLFSRAFIIDDGERRFVFVSVDSGMIGYNIRAESI--------SRAHNNLQKGRL 62
VG H + A +G R+ + + G+ G +R E + HNNL
Sbjct: 121 VGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLGLKTGLAYLEHNNLLAAGE 180
Query: 63 FVSKGELLDANINRSPTAYLQNPEEE 88
FVSK E D NI ++ PEEE
Sbjct: 181 FVSKPEFQDFNI-------IEIPEEE 199
>pdb|1L1L|A Chain A, Crystal Structure Of B-12 Dependent (Class Ii)
Ribonucleotide Reductase
pdb|1L1L|B Chain B, Crystal Structure Of B-12 Dependent (Class Ii)
Ribonucleotide Reductase
pdb|1L1L|C Chain C, Crystal Structure Of B-12 Dependent (Class Ii)
Ribonucleotide Reductase
pdb|1L1L|D Chain D, Crystal Structure Of B-12 Dependent (Class Ii)
Ribonucleotide Reductase
Length = 739
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 50/108 (46%), Gaps = 25/108 (23%)
Query: 165 GVDCDID-TSACPKQGDSCVASGPGRDMFESTRLIAERM-------------YRKALMNV 210
G+D D++ T+ C G+ +A+G ++FE LIAE Y K +
Sbjct: 397 GIDGDVEGTNPC---GEISLANGEPCNLFEVFPLIAEEQGWDLQEVFALAARYAKRVTFS 453
Query: 211 PHQWQPNTVSTQLV----RIGHLVLVGVPGELTTMAGRRLRRALQDEL 254
P+ W+ +S +++ RIG + + G+ L T G R+ +D+
Sbjct: 454 PYDWE---ISREIIQKNRRIG-ISMSGIQDWLLTRLGNRVVTGFKDDF 497
>pdb|2F9F|A Chain A, Crystal Structure Of The Putative Mannosyl Transferase
(Wbaz-1)from Archaeoglobus Fulgidus, Northeast
Structural Genomics Target Gr29a
Length = 177
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 101 VQLQ-FISAEDRPLGVINWFAV--HPTSMNNTNRLVSSDNGKFVAAFASTNLGDVSPNIK 157
+QL+ F +D L ++ WF+ H ++ DN KF+ + + L D+ K
Sbjct: 40 LQLEVFKKLQDEKLYIVGWFSKGDHAERYARKIXKIAPDNVKFLGSVSEEELIDLYSRCK 99
Query: 158 GPKC 161
G C
Sbjct: 100 GLLC 103
>pdb|2IYQ|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate And Adp
pdb|2IYR|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate
pdb|2IYR|B Chain B, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate
pdb|2IYS|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate, Open Lid (Conf. A)
pdb|2IYT|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Unliganded State, Open Lid (conf. A)
pdb|2IYU|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Adp, Open Lid (Conf. A)
pdb|2IYV|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Adp, Open Lid (Conf. B)
pdb|2IYW|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Mgatp, Open Lid (Conf. B)
pdb|2IYX|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate And So4
pdb|2IYY|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate-3-Phosphate And So4
pdb|2IYZ|A Chain A, Shikimate Kinase From Mycobacterium Tuberculosis In
Complex With Shikimate-3-Phosphate And Adp
Length = 184
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 24/35 (68%), Gaps = 3/35 (8%)
Query: 230 VLVGVPGELTTMAGRRLRRALQDELGLLMESDVII 264
VLVG+PG + GRRL +AL +GLL ++DV I
Sbjct: 6 VLVGLPGSGKSTIGRRLAKALG--VGLL-DTDVAI 37
>pdb|1L4U|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Mgadp And Pt(Ii) At 1.8
Angstrom Resolution
pdb|1L4Y|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Mgadp At 2.0 Angstrom
Resolution
pdb|1U8A|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Shikimate
Kinase In Complex With Shikimate And Adp At 2.15
Angstrom Resolution
pdb|1WE2|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Mgadp And Shikimic Acid
pdb|1ZYU|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Shikimate
Kinase In Complex With Shikimate And Amppcp At 2.85
Angstrom Resolution
pdb|2G1J|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Shikimate
Kinase At 2.0 Angstrom Resolution
pdb|2G1J|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Shikimate
Kinase At 2.0 Angstrom Resolution
pdb|2G1K|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Shikimate
Kinase In Complex With Shikimate At 1.75 Angstrom
Resolution
pdb|2DFN|A Chain A, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Shikimate At 1.9
Angstrons Of Resolution
pdb|2DFT|A Chain A, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|2DFT|B Chain B, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|2DFT|C Chain C, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|2DFT|D Chain D, Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis Complexed With Adp And Mg At 2.8 Angstrons
Of Resolution
pdb|3BAF|A Chain A, Crystal Structure Of Shikimate Kinase From Mycobacterium
Tuberculosis In Complex With Amp-Pnp
Length = 176
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 24/35 (68%), Gaps = 3/35 (8%)
Query: 230 VLVGVPGELTTMAGRRLRRALQDELGLLMESDVII 264
VLVG+PG + GRRL +AL +GLL ++DV I
Sbjct: 6 VLVGLPGSGKSTIGRRLAKALG--VGLL-DTDVAI 37
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
0.319 0.135 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,416,991
Number of Sequences: 62578
Number of extensions: 329353
Number of successful extensions: 682
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 674
Number of HSP's gapped (non-prelim): 10
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)