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= psy7866
(109 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WYT|A Chain A, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Apo Form
pdb|1WYT|C Chain C, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Apo Form
pdb|1WYU|A Chain A, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|C Chain C, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|E Chain E, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYU|G Chain G, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Holo Form
pdb|1WYV|A Chain A, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|C Chain C, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|E Chain E, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
pdb|1WYV|G Chain G, Crystal Structure Of Glycine Decarboxylase (P-Protein) Of
The Glycine Cleavage System, In Inhibitor-Bound Form
Length = 438
Score = 78.2 bits (191), Expect = 1e-15, Method: Composition-based stats.
Identities = 42/103 (40%), Positives = 68/103 (66%), Gaps = 2/103 (1%)
Query: 8 LGEHELLEEIQSIANKN-EIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIA 66
L E ++LEE++ +A +N ++++G G + VP V+Q L ++T YTPYQPE++
Sbjct: 45 LPEWKVLEELRRLAAQNLPAHKAFLGGGVRSHHVPPVVQA-LAARGEFLTAYTPYQPEVS 103
Query: 67 QGRLESLLNFQTMVSDLTGLSVANASLLDEATAAAEAMSICHR 109
QG L++ +QTM+++L GL +ANAS+ D ATA AE + + R
Sbjct: 104 QGVLQATFEYQTMIAELAGLEIANASMYDGATALAEGVLLALR 146
>pdb|3LIA|A Chain A, Crystal Structure Of The Extracellular Domain Of The
Putative Histidine Kinase Mmhk1s-Z2
pdb|3LIA|B Chain B, Crystal Structure Of The Extracellular Domain Of The
Putative Histidine Kinase Mmhk1s-Z2
Length = 291
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 42 TVIQRNLFENPGWVTQYTPYQPEIAQGRLESLLN 75
++I+R L ENP + Y Y+P+ GR ++ +N
Sbjct: 60 SIIKRILNENPQLIGVYLGYEPDAFDGRDKNYIN 93
>pdb|3LI8|A Chain A, Crystal Structure Of The Extracellular Domain Of The
Putative Histidine Kinase Mmhk1s-Z2
pdb|3LI9|A Chain A, Crystal Structure Of The Extracellular Domain Of The
Putative Histidine Kinase Mmhk1s-Z2
Length = 291
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 42 TVIQRNLFENPGWVTQYTPYQPEIAQGRLESLLN 75
++I+R L ENP + Y Y+P+ GR ++ +N
Sbjct: 60 SIIKRILNENPQLIGVYLGYEPDAFDGRDKNYIN 93
>pdb|3B81|A Chain A, Crystal Structure Of Predicted Dna-Binding
Transcriptional Regulator Of TetrACRR FAMILY
(NP_350189.1) FROM CLOSTRIDIUM ACETOBUTYLICUM AT 2.10 A
Resolution
Length = 203
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 24 NEIWRSYIGLGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQGRLESLLNF 76
N+IW +I GY N + +I + L + G + Y + E A +E+ + F
Sbjct: 18 NKIWDIFIANGYENTTLAFIINK-LGISKGALYHYFSSKEECADAAIENRVAF 69
>pdb|3QSI|B Chain B, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|C Chain C, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|D Chain D, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|A Chain A, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|F Chain F, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|G Chain G, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|H Chain H, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|E Chain E, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|J Chain J, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
pdb|3QSI|I Chain I, Nickel Binding Domain Of Nikr From Helicobacter Pylori
Disclosing Partial Metal Occupancy
Length = 88
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 16 EIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFE 50
+IQ + + + ++I + HNCL ++Q N FE
Sbjct: 25 DIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFE 59
>pdb|2Y3Y|A Chain A, Holo-Ni(Ii) Hpnikr Is A Symmetric Tetramer Containing
Four Canonic Square-Planar Ni(Ii) Ions At Physiological
Ph
pdb|2Y3Y|B Chain B, Holo-Ni(Ii) Hpnikr Is A Symmetric Tetramer Containing
Four Canonic Square-Planar Ni(Ii) Ions At Physiological
Ph
pdb|2Y3Y|C Chain C, Holo-Ni(Ii) Hpnikr Is A Symmetric Tetramer Containing
Four Canonic Square-Planar Ni(Ii) Ions At Physiological
Ph
pdb|2Y3Y|D Chain D, Holo-Ni(Ii) Hpnikr Is A Symmetric Tetramer Containing
Four Canonic Square-Planar Ni(Ii) Ions At Physiological
Ph
Length = 91
Score = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 16 EIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFE 50
+IQ + + + ++I + HNCL ++Q N FE
Sbjct: 28 DIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFE 62
>pdb|3C67|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Glucose
pdb|3C67|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Glucose
pdb|3C68|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Mannose
pdb|3C68|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Mannose
pdb|3C69|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Galactose
pdb|3C69|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Galactose
Length = 761
Score = 25.8 bits (55), Expect = 6.8, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 17 IQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGW-------VTQYTPYQPEIAQGR 69
+++I N WRS G N + P+V R N W + P+IA+
Sbjct: 285 VKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKEN 344
Query: 70 LESLLNFQTMVSD 82
+ ++ ++Q D
Sbjct: 345 IRAVFSWQIQPGD 357
>pdb|3D3I|A Chain A, Crystal Structural Of Escherichia Coli K12 Ygjk, A
Glucosidase Belonging To Glycoside Hydrolase Family 63
pdb|3D3I|B Chain B, Crystal Structural Of Escherichia Coli K12 Ygjk, A
Glucosidase Belonging To Glycoside Hydrolase Family 63
Length = 761
Score = 25.8 bits (55), Expect = 6.8, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 17 IQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFENPGW-------VTQYTPYQPEIAQGR 69
+++I N WRS G N + P+V R N W + P+IA+
Sbjct: 285 VKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAXAHFNPDIAKEN 344
Query: 70 LESLLNFQTMVSD 82
+ ++ ++Q D
Sbjct: 345 IRAVFSWQIQPGD 357
>pdb|1OHF|A Chain A, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|B Chain B, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|C Chain C, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|D Chain D, The Refined Structure Of Nudaurelia Capensis Omega Virus
Length = 644
Score = 25.8 bits (55), Expect = 7.2, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 33 LGYHNCLVPTVIQRNLFENPGWVTQYTPYQPEIAQG 68
+G H L P +N E G+V + +P IA G
Sbjct: 261 IGGHYALTPIATTQNAVEGSGFVHPFNVTRPGIAAG 296
>pdb|2CA9|A Chain A, Apo-Nikr From Helicobacter Pylori In Closed Trans-
Conformation
pdb|2CA9|B Chain B, Apo-Nikr From Helicobacter Pylori In Closed Trans-
Conformation
pdb|2CAD|A Chain A, Nikr From Helicobacter Pylori In Closed Trans-Conformation
And Nickel Bound To 2f, 2x And 2i Sites.
pdb|2CAD|B Chain B, Nikr From Helicobacter Pylori In Closed Trans-Conformation
And Nickel Bound To 2f, 2x And 2i Sites.
pdb|2CAJ|A Chain A, Nikr From Helicobacter Pylori In Closed Trans-Conformation
And Nickel Bound To 4 Intermediary Sites
pdb|2CAJ|B Chain B, Nikr From Helicobacter Pylori In Closed Trans-Conformation
And Nickel Bound To 4 Intermediary Sites
pdb|3LGH|A Chain A, Crystal Structure Of Nikr From Helicobacter Pylori With
Variable Ni Site Coordination
pdb|3LGH|B Chain B, Crystal Structure Of Nikr From Helicobacter Pylori With
Variable Ni Site Coordination
pdb|3LGH|C Chain C, Crystal Structure Of Nikr From Helicobacter Pylori With
Variable Ni Site Coordination
pdb|3LGH|D Chain D, Crystal Structure Of Nikr From Helicobacter Pylori With
Variable Ni Site Coordination
Length = 148
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 16 EIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFE 50
+IQ + + + ++I + HNCL ++Q N FE
Sbjct: 85 DIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFE 119
>pdb|3PHT|A Chain A, Crystal Structure Of H74a Mutant Of Helicobacter Pylori
Nikr
pdb|3PHT|B Chain B, Crystal Structure Of H74a Mutant Of Helicobacter Pylori
Nikr
Length = 148
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 16 EIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFE 50
+IQ + + + ++I + HNCL ++Q N FE
Sbjct: 85 DIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFE 119
>pdb|2WVC|A Chain A, Structural And Mechanistic Insights Into Helicobacter
Pylori Nikr Function
pdb|2WVC|B Chain B, Structural And Mechanistic Insights Into Helicobacter
Pylori Nikr Function
pdb|2WVF|A Chain A, Structural And Mechanistic Insights Into Helicobacter
Pylori Nikr Function
pdb|2WVF|B Chain B, Structural And Mechanistic Insights Into Helicobacter
Pylori Nikr Function
Length = 148
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 9 GEHEL---LEEIQSIANKNEIWRSYIGLGYHNCLVPTVIQRNLFE 50
G+ EL + +IQ + + + ++I + HNCL ++Q N FE
Sbjct: 75 GQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFE 119
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
0.318 0.132 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,153,309
Number of Sequences: 62578
Number of extensions: 114907
Number of successful extensions: 244
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 232
Number of HSP's gapped (non-prelim): 15
length of query: 109
length of database: 14,973,337
effective HSP length: 73
effective length of query: 36
effective length of database: 10,405,143
effective search space: 374585148
effective search space used: 374585148
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: 45 (21.9 bits)