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= 029051
(200 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NZE|A Chain A, Crystal Structure Of Psbq Polypeptide Of Photosystem Ii
From Higher Plants
pdb|1VYK|A Chain A, Crystal Structure Of Psbq Protein Of Photosystem Ii From
Higher Plants
Length = 149
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 63/121 (52%)
Query: 80 GTRSFLKERFFEPGLSPEDAVARIKQTAEGMHSLREMVDRMAWRYVIFYIRLKQAYLSQD 139
GT + K+RF+ L P +A R K +A + ++++ +DR AW + +RL+ +YL D
Sbjct: 29 GTLPYTKDRFYLQPLPPTEAAQRAKVSASEILNVKQFIDRKAWPSLQNDLRLRASYLRYD 88
Query: 140 LKTAFSTLPEVRRREYVNTANDLIDNMAEFDYYVRTPKVYESYLYYEKALKNLDDIVAMF 199
LKT S P+ ++ + L ++ D+ + E+ YY + + N+++++A
Sbjct: 89 LKTVISAKPKDEKKSLQELTSKLFSSIDNLDHAAKIKSPTEAEKYYGQTVSNINEVLAKL 148
Query: 200 A 200
Sbjct: 149 G 149
>pdb|3BEZ|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
pdb|3BEZ|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
pdb|3BEZ|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
pdb|3BEZ|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Semet Crystals
Length = 593
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 32/125 (25%)
Query: 47 VTTLISTSLALVGLHGDGIGSSSGASVALAESWGTRSFLKERFFEPGLSPEDAVAR-IKQ 105
V T + SL +G+H DG+ +S A V++ TR+ E LS E+ R I
Sbjct: 412 VITTVENSLDSIGVHTDGVSTSPLADVSI-----TRALPPEAQLXXQLSIENGYKRFITL 466
Query: 106 TAEGMHSLREMVDRMAWRYVIFYIRLKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDN 165
A+ HS E +D++A +V + QD K AN L+D+
Sbjct: 467 VADARHSTPEQIDKIAQGHV---------WTGQDAK-----------------ANGLVDS 500
Query: 166 MAEFD 170
+ +FD
Sbjct: 501 LGDFD 505
>pdb|3BF0|A Chain A, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
pdb|3BF0|B Chain B, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
pdb|3BF0|C Chain C, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
pdb|3BF0|D Chain D, Crystal Structure Of Escherichia Coli Signal Peptide
Peptidase (Sppa), Native Crystals
Length = 593
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 40/144 (27%), Positives = 61/144 (42%), Gaps = 36/144 (25%)
Query: 47 VTTLISTSLALVGLHGDGIGSSSGASVALAESWGTRSFLKERFFEPGLSPEDAVAR-IKQ 105
V T + SL +G+H DG+ +S A V++ TR+ E LS E+ R I
Sbjct: 412 VITTVENSLDSIGVHTDGVSTSPLADVSI-----TRALPPEAQLMMQLSIENGYKRFITL 466
Query: 106 TAEGMHSLREMVDRMAWRYVIFYIRLKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDN 165
A+ HS E +D++A +V + QD K AN L+D+
Sbjct: 467 VADARHSTPEQIDKIAQGHV---------WTGQDAK-----------------ANGLVDS 500
Query: 166 MAEFDYYV----RTPKVYESYLYY 185
+ +FD V KV + +L Y
Sbjct: 501 LGDFDDAVAKAAELAKVKQWHLEY 524
>pdb|1JE6|A Chain A, Structure Of The Mhc Class I Homolog Micb
Length = 275
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 73 VALAESWGTRSFLKERFFEPGLSPEDAVARIKQTAEGMHSLREMV-----DRMAWRYVIF 127
V AE+W T + E E G + IK G+HSL+E+ + + R
Sbjct: 54 VLGAETWDTET---EDLTENGQDLRRTLTHIKDQKGGLHSLQEIRVCEIHEDSSTRGSRH 110
Query: 128 YIRLKQAYLSQDLKTAFSTLPEVRR 152
+ + +LSQ+L+T ST+P+ R
Sbjct: 111 FYYNGELFLSQNLETQESTVPQSSR 135
>pdb|2WYB|B Chain B, The Quorum Quenching N-Acyl Homoserine Lactone Acylase
Pvdq With A Covalently Bound Dodecanoic Acid
pdb|2WYC|B Chain B, The Quorum Quenching N-Acyl Homoserine Lactone Acylase
Pvdq In Complex With 3-Oxo-Lauric Acid
pdb|2WYD|B Chain B, The Quorum Quenching N-Acyl Homoserine Lactone Acylase
Pvdq In Complex With Dodecanoic Acid
pdb|2WYE|B Chain B, The Quorum Quenching N-Acyl Homoserine Lactone Acylase
Pvdq Is An Ntn-Hydrolase With An Unusual
Substrate-Binding Pocket
pdb|3L91|B Chain B, Structure Of Pseudomonas Aerugionsa Pvdq Bound To
Octanoate
pdb|3L94|B Chain B, Structure Of Pvdq Covalently Acylated With Myristate
pdb|3SRA|B Chain B, Structure Of Pseudomonas Aerugionsa Pvdq Covalently
Acylated With Myristic Acid From Pvdiq
pdb|3SRB|B Chain B, Structure Of Pseudomonas Aeruginosa Pvdq Bound To Smer28
pdb|3SRC|B Chain B, Structure Of Pseudomonas Aeruginosa Pvdq Bound To Ns2028
Length = 546
Score = 30.0 bits (66), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 89 FFEPGLSPEDAVARIKQTAEGMHSLREMVDRMAWRYVIFYIRLKQAYLSQDLKTAFSTLP 148
+ +P L P A+ ++ AEG+ +L+ R AW + +Q T + LP
Sbjct: 208 YLKPELIPACAIPQL--VAEGLPALQGQDSRCAWS--------RDPAAAQAGITPAAQLP 257
Query: 149 EVRRREYVNTAND 161
+ RR++V +ND
Sbjct: 258 VLLRRDFVQNSND 270
>pdb|2WY3|A Chain A, Structure Of The Hcmv Ul16-Micb Complex Elucidates Select
Binding Of A Viral Immunoevasin To Diverse Nkg2d Ligands
pdb|2WY3|C Chain C, Structure Of The Hcmv Ul16-Micb Complex Elucidates Select
Binding Of A Viral Immunoevasin To Diverse Nkg2d Ligands
Length = 319
Score = 30.0 bits (66), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 76 AESWGTRSFLKERFFEPGLSPEDAVARIKQTAEGMHSLREMV-----DRMAWRYVIFYIR 130
AE+W T + E E G + IK G+HSL+E+ + + R +
Sbjct: 57 AETWDTET---EDLTENGQDLRRTLTHIKDQKGGLHSLQEIRVCEIHEDSSTRGSRHFYY 113
Query: 131 LKQAYLSQDLKTAFSTLPEVRR 152
+ +LSQ+L+T ST+P+ R
Sbjct: 114 NGELFLSQNLETQESTVPQSSR 135
>pdb|3MAS|B Chain B, Crystal Structure Of Heterodimeric R132h Mutant Of Human
Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In
Complex With Nadp And Isocitrate
Length = 419
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 131 LKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDNMAE 168
++ ++++DL LP V+R +Y+NT + +D + E
Sbjct: 372 IEAGFMTKDLAACIKGLPNVQRSDYLNTF-EFMDKLGE 408
>pdb|3INM|A Chain A, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase R132h Mutant In Complex With
Nadph, Alpha-Ketoglutarate And Calcium(2+)
pdb|3INM|B Chain B, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase R132h Mutant In Complex With
Nadph, Alpha-Ketoglutarate And Calcium(2+)
pdb|3INM|C Chain C, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase R132h Mutant In Complex With
Nadph, Alpha-Ketoglutarate And Calcium(2+)
Length = 425
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 131 LKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDNMAE 168
++ ++++DL LP V+R +Y+NT + +D + E
Sbjct: 367 IEAGFMTKDLAACIKGLPNVQRSDYLNTF-EFMDKLGE 403
>pdb|3MAP|A Chain A, Crystal Structure Of Homodimeric R132h Mutant Of Human
Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In
Complex With Nadp And Isocitrate
pdb|3MAP|B Chain B, Crystal Structure Of Homodimeric R132h Mutant Of Human
Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In
Complex With Nadp And Isocitrate
pdb|3MAR|A Chain A, Crystal Structure Of Homodimeric R132h Mutant Of Human
Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In
Complex With Nadp
pdb|3MAR|B Chain B, Crystal Structure Of Homodimeric R132h Mutant Of Human
Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In
Complex With Nadp
pdb|3MAS|A Chain A, Crystal Structure Of Heterodimeric R132h Mutant Of Human
Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In
Complex With Nadp And Isocitrate
Length = 422
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 131 LKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDNMAE 168
++ ++++DL LP V+R +Y+NT + +D + E
Sbjct: 367 IEAGFMTKDLAACIKGLPNVQRSDYLNTF-EFMDKLGE 403
>pdb|1T09|A Chain A, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase In Complex Nadp
pdb|1T09|B Chain B, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase In Complex Nadp
pdb|1T0L|A Chain A, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase In Complex With Nadp,
Isocitrate, And Calcium(2+)
pdb|1T0L|B Chain B, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase In Complex With Nadp,
Isocitrate, And Calcium(2+)
pdb|1T0L|C Chain C, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase In Complex With Nadp,
Isocitrate, And Calcium(2+)
pdb|1T0L|D Chain D, Crystal Structure Of Human Cytosolic Nadp(+)-Dependent
Isocitrate Dehydrogenase In Complex With Nadp,
Isocitrate, And Calcium(2+)
Length = 414
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 131 LKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDNMAE 168
++ ++++DL LP V+R +Y+NT + +D + E
Sbjct: 367 IEAGFMTKDLAACIKGLPNVQRSDYLNTF-EFMDKLGE 403
>pdb|2CMJ|A Chain A, Crystal Structure Of Mouse Cytosolic Isocitrate
Dehydrogenase
pdb|2CMJ|B Chain B, Crystal Structure Of Mouse Cytosolic Isocitrate
Dehydrogenase
pdb|2CMV|A Chain A, Crystal Structure Of Mouse Cytosolic Isocitrate
Dehydrogenase Complexed With Cadmium And Citrate
pdb|2CMV|B Chain B, Crystal Structure Of Mouse Cytosolic Isocitrate
Dehydrogenase Complexed With Cadmium And Citrate
Length = 410
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 131 LKQAYLSQDLKTAFSTLPEVRRREYVNTANDLIDNMAE 168
++ ++++DL LP V+R +Y+NT + +D + E
Sbjct: 364 IEAGFMTKDLAACIKGLPNVQRSDYLNTF-EFMDKLGE 400
>pdb|1B3J|A Chain A, Structure Of The Mhc Class I Homolog Mic-A, A Gammadelta T
Cell Ligand
Length = 274
Score = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 100 VARIKQTAEGMHSLREMV-----DRMAWRYVIFYIRLKQAYLSQDLKTAFSTLPEVRR 152
+A IK EG+HSL+E+ + + R + + +LSQ+L+T T+P+ R
Sbjct: 77 LAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSQHFYYDGELFLSQNLETKEWTMPQSSR 134
>pdb|1HYR|C Chain C, Crystal Structure Of Human Mica In Complex With Natural
Killer Cell Receptor Nkg2d
Length = 275
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 100 VARIKQTAEGMHSLREMV-----DRMAWRYVIFYIRLKQAYLSQDLKTAFSTLPEVRR 152
+A IK EG+HSL+E+ + + R + + +LSQ+L+T T+P+ R
Sbjct: 78 LAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSQHFYYDGELFLSQNLETKEWTMPQSSR 135
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
0.317 0.130 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,561,207
Number of Sequences: 62578
Number of extensions: 211554
Number of successful extensions: 541
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 531
Number of HSP's gapped (non-prelim): 20
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)