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= 033814
(111 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2G8S|A Chain A, Crystal Structure Of The Soluble Aldose Sugar
Dehydrogenase (Asd) From Escherichia Coli In The
Apo-Form
pdb|2G8S|B Chain B, Crystal Structure Of The Soluble Aldose Sugar
Dehydrogenase (Asd) From Escherichia Coli In The
Apo-Form
Length = 353
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 6/88 (6%)
Query: 30 GKGSRLPNRGKFPDELGVVASYSGQGRIADFGFRNPK------WVDGELLQLNGKGMGPY 83
GK RL ++G+ PD+ + + I +G RNP+ W + L +G G
Sbjct: 164 GKLVRLTDQGEIPDDNPFIKESGVRAEIWSYGIRNPQGXAXNPWSNALWLNEHGPRGGDE 223
Query: 84 VKGADLGFLYVVPEQSFLVLFNRLKLPD 111
+ G Y P ++ + ++ K+P+
Sbjct: 224 INIPQKGKNYGWPLATWGINYSGFKIPE 251
>pdb|3SSA|A Chain A, Crystal Structure Of Subunit B Mutant N157t Of The A1ao
Atp Synthase
pdb|3SSA|B Chain B, Crystal Structure Of Subunit B Mutant N157t Of The A1ao
Atp Synthase
Length = 460
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 DELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVK 85
D LG + S SG+ R D G P+ V +LL +NG M PY +
Sbjct: 83 DLLGRILSGSGEPR--DGG---PRIVPDQLLDINGAAMNPYAR 120
>pdb|3TIV|A Chain A, Crystal Structure Of Subunit B Mutant N157a Of The A1ao
Atp Synthase
pdb|3TIV|B Chain B, Crystal Structure Of Subunit B Mutant N157a Of The A1ao
Atp Synthase
Length = 460
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 DELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVK 85
D LG + S SG+ R D G P+ V +LL +NG M PY +
Sbjct: 83 DLLGRILSGSGEPR--DGG---PRIVPDQLLDINGAAMNPYAR 120
>pdb|2C61|A Chain A, Crystal Structure Of The Non-Catalytic B Subunit Of A-Type
Atpase From M. Mazei Go1
pdb|2C61|B Chain B, Crystal Structure Of The Non-Catalytic B Subunit Of A-Type
Atpase From M. Mazei Go1
pdb|3DSR|A Chain A, Adp In Transition Binding Site In The Subunit B Of The
Energy Converter A1ao Atp Synthase
pdb|3DSR|B Chain B, Adp In Transition Binding Site In The Subunit B Of The
Energy Converter A1ao Atp Synthase
Length = 469
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 DELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVK 85
D LG + S SG+ R D G P+ V +LL +NG M PY +
Sbjct: 92 DLLGRILSGSGEPR--DGG---PRIVPDQLLDINGAAMNPYAR 129
>pdb|3TGW|A Chain A, Crystal Structure Of Subunit B Mutant H156a Of The A1ao
Atp Synthase
pdb|3TGW|B Chain B, Crystal Structure Of Subunit B Mutant H156a Of The A1ao
Atp Synthase
Length = 460
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 DELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVK 85
D LG + S SG+ R D G P+ V +LL +NG M PY +
Sbjct: 83 DLLGRILSGSGEPR--DGG---PRIVPDQLLDINGAAMNPYAR 120
>pdb|2RKW|A Chain A, Intermediate Position Of Atp On Its Trail To The Binding
Pocket Inside The Subunit B Mutant R416w Of The Energy
Converter A1ao Atp Synthase
pdb|2RKW|B Chain B, Intermediate Position Of Atp On Its Trail To The Binding
Pocket Inside The Subunit B Mutant R416w Of The Energy
Converter A1ao Atp Synthase
pdb|3B2Q|A Chain A, Intermediate Position Of Atp On Its Trail To The Binding
Pocket Inside The Subunit B Mutant R416w Of The Energy
Converter A1ao Atp Synthase
pdb|3B2Q|B Chain B, Intermediate Position Of Atp On Its Trail To The Binding
Pocket Inside The Subunit B Mutant R416w Of The Energy
Converter A1ao Atp Synthase
pdb|3EIU|A Chain A, A Second Transient Position Of Atp On Its Trail To The
Nucleotide- Binding Site Of Subunit B Of The Motor
Protein A1ao Atp Synthase
pdb|3EIU|B Chain B, A Second Transient Position Of Atp On Its Trail To The
Nucleotide- Binding Site Of Subunit B Of The Motor
Protein A1ao Atp Synthase
Length = 469
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 43 DELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVK 85
D LG + S SG+ R D G P+ V +LL +NG M PY +
Sbjct: 92 DLLGRILSGSGEPR--DGG---PRIVPDQLLDINGAAMNPYAR 129
>pdb|1LEA|A Chain A, Solution Structure Of The Lexa Repressor Dna Binding
Determined By 1h Nmr Spectroscopy
pdb|1LEB|A Chain A, Solution Structure Of The Lexa Repressor Dna Binding
Determined By 1h Nmr Spectroscopy
Length = 84
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 60 FGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQSFLVLFNRL 107
GFR+P + L L KG+ V GA G + E+ L L R+
Sbjct: 35 LGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRV 82
>pdb|1PRN|A Chain A, Refined Structure Of Porin From Rhodopseudomonas Blastica
And Comparison With The Porin From Rhodobacter
Capsulatus
Length = 289
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%)
Query: 40 KFPDELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQS 99
+ E+G AS G + + F + + G L NG + + G +L YV P+Q+
Sbjct: 95 TYDSEMGYEASSFGDAQSSFFAYNSKYDASGALDNYNGIAVTYSISGVNLYLSYVDPDQT 154
>pdb|1H6S|1 Chain 1, Asymmetric Conductivity Of Engineered Proteins
Length = 307
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%)
Query: 40 KFPDELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQS 99
+ E+G AS G + + F + + G L NG + + G +L YV P+Q+
Sbjct: 95 TYDSEMGYEASSFGDAQSSFFAYNSKYDASGALDNYNGIAVTYSISGVNLYLSYVDPDQT 154
>pdb|6PRN|A Chain A, E1m, K50a, R52a Mutant Of Rh. Blastica Porin
Length = 289
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%)
Query: 40 KFPDELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQS 99
+ E+G AS G + + F + + G L NG + + G +L YV P+Q+
Sbjct: 95 TYDSEMGYEASSFGDAQSSFFAYNSKYDASGALDNYNGIAVTYSISGVNLYLSYVDPDQT 154
>pdb|3JSO|A Chain A, Classic Protein With A New Twist: Crystal Structure Of A
Lexa Repressor Dna Complex
pdb|3JSO|B Chain B, Classic Protein With A New Twist: Crystal Structure Of A
Lexa Repressor Dna Complex
pdb|3JSP|A Chain A, Classic Protein With A New Twist: Crystal Structure Of A
Lexa Repressor Dna Complex
pdb|3JSP|B Chain B, Classic Protein With A New Twist: Crystal Structure Of A
Lexa Repressor Dna Complex
pdb|3K3R|E Chain E, Unrefined Crystal Structure Of A Lexa-Dna Complex
pdb|3K3R|F Chain F, Unrefined Crystal Structure Of A Lexa-Dna Complex
Length = 202
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 60 FGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQSFLVLFNRL 107
GFR+P + L L KG+ V GA G + E+ L L R+
Sbjct: 35 LGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRV 82
>pdb|1JHF|A Chain A, Lexa G85d Mutant
pdb|1JHF|B Chain B, Lexa G85d Mutant
Length = 202
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 60 FGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQSFLVLFNRL 107
GFR+P + L L KG+ V GA G + E+ L L R+
Sbjct: 35 LGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRV 82
>pdb|1JHH|A Chain A, Lexa S119a Mutant
pdb|1JHH|B Chain B, Lexa S119a Mutant
Length = 202
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 60 FGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQSFLVLFNRL 107
GFR+P + L L KG+ V GA G + E+ L L R+
Sbjct: 35 LGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRV 82
>pdb|1J6O|A Chain A, Crystal Structure Of Tatd-related Deoxyribonuclease
(tm0667) From Thermotoga Maritima At 1.8 A Resolution
Length = 268
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 6 YVEAVKLTGDLNVPAGEVTFRAKIGKGSRLPNRGKFPDELGVVASYSGQ----GRIADFG 61
+VE ++L G LN+P V R + + P++ GV+ ++S + D G
Sbjct: 122 FVEQIELAGKLNLPLV-VHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKKFIDLG 180
Query: 62 F 62
F
Sbjct: 181 F 181
>pdb|3G0Q|A Chain A, Crystal Structure Of Muty Bound To Its Inhibitor Dna
Length = 352
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 78 KGMGPYVKGADLGFLYVVPE 97
KG+GPY GA L Y VPE
Sbjct: 113 KGVGPYTVGAVLSLAYGVPE 132
>pdb|1RRQ|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An
A:oxog Pair
Length = 369
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 78 KGMGPYVKGADLGFLYVVPE 97
KG+GPY GA L Y VPE
Sbjct: 124 KGVGPYTVGAVLSLAYGVPE 143
>pdb|1RRS|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An
Abasic Site
pdb|1VRL|A Chain A, Muty Adenine Glycosylase In Complex With Dna And Soaked
Adenine Free Base
Length = 369
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 78 KGMGPYVKGADLGFLYVVPE 97
KG+GPY GA L Y VPE
Sbjct: 124 KGVGPYTVGAVLSLAYGVPE 143
>pdb|3FSP|A Chain A, Muty Adenine Glycosylase Bound To A Transition State
Analog (1n) Paired With Dg In Duplexed Dna
pdb|3FSQ|A Chain A, Muty Adenine Glycosylase Bound To A Transition State
Analog (1n) Paired With D(8-Oxog) In Duplexed Dna
Length = 369
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 78 KGMGPYVKGADLGFLYVVPE 97
KG+GPY GA L Y VPE
Sbjct: 124 KGVGPYTVGAVLSLAYGVPE 143
>pdb|1BH3|A Chain A, E1m, A116k Mutant Of Rh. Blastica Porin
Length = 289
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 27/60 (45%)
Query: 40 KFPDELGVVASYSGQGRIADFGFRNPKWVDGELLQLNGKGMGPYVKGADLGFLYVVPEQS 99
+ E+G AS G + + F + + G L NG + + G +L YV P+Q+
Sbjct: 95 TYDSEMGYEASSFGDAQSSFFKYNSKYDASGALDNYNGIAVTYSISGVNLYLSYVDPDQT 154
>pdb|1LFW|A Chain A, Crystal Structure Of Pepv
Length = 470
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 7/93 (7%)
Query: 18 VPAGE----VTFRAKIGKGSRLPNRGKFPDELGVVASYSGQGRIADFGFRNPKWVD---G 70
VPAGE F+ +I + R+ RG D+ + +Y G + + GF+ K +D G
Sbjct: 91 VPAGEGWTRDPFKMEIDEEGRIYGRGSADDKGPSLTAYYGMLLLKEAGFKPKKKIDFVLG 150
Query: 71 ELLQLNGKGMGPYVKGADLGFLYVVPEQSFLVL 103
+ N G+ Y+K + P+ + ++
Sbjct: 151 TNEETNWVGIDYYLKHEPTPDIVFSPDAEYPII 183
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
0.321 0.145 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,877,671
Number of Sequences: 62578
Number of extensions: 177512
Number of successful extensions: 321
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 304
Number of HSP's gapped (non-prelim): 24
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
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: 45 (21.9 bits)