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= 020860
(320 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1BP1|A Chain A, Crystal Structure Of Bpi, The Human Bactericidal
Permeability-Increasing Protein
Length = 456
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 59/283 (20%), Positives = 122/283 (43%), Gaps = 9/283 (3%)
Query: 30 VNEGGYISAVISKKGLDFFKNYLINKATSSIIPLELPDIEKSKKIPLIGKVHMALSNIII 89
VN G + IS+KGLD+ + +++PD S KI +GK H + ++ I
Sbjct: 1 VNPG--VVVRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDI 58
Query: 90 YSVEIDSSYVETGDPDLLLAVSGATADCGMNWEYSYGSWLLPTISDSGAAXXXXXXXXXX 149
++ SS + P++ L S + A+ ++ ++ L +S +
Sbjct: 59 REFQLPSSQISMV-PNVGLKFSISNANIKISGKWKAQKRFL-KMSGNFDLSIEGMSISAD 116
Query: 150 XXXXXKEQGGIVKVILVDCGSHVRDISIKV-DGGASWLYQALFEAFEGKIKSAVESAVTK 208
G + C SH+ + + + WL Q + E +++ + S V +
Sbjct: 117 LKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALRNKMNSQVCE 176
Query: 209 KISELI-TKLDSIFQSLPKQIPVSDIASMNTSFVRSPVLSDSSVEVEINGLFTAISGTSM 267
K++ + +KL FQ+LP + +A +N V P + +++V++ G F + + +
Sbjct: 177 KVTNSVSSKLQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHNP 236
Query: 268 LNYYHKGFESSASCSSPAKMIGIQLNENVFSSGALVYFNSGTV 310
+ E A+ +M+ + L++ F++ LVY +G +
Sbjct: 237 PPFAPPVMEFPAAHD---RMVYLGLSDYFFNTAGLVYQEAGVL 276
>pdb|1EWF|A Chain A, The 1.7 Angstrom Crystal Structure Of Bpi
Length = 456
Score = 61.2 bits (147), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 58/283 (20%), Positives = 122/283 (43%), Gaps = 9/283 (3%)
Query: 30 VNEGGYISAVISKKGLDFFKNYLINKATSSIIPLELPDIEKSKKIPLIGKVHMALSNIII 89
VN G + IS+KGLD+ + +++PD S KI +GK H + ++ I
Sbjct: 1 VNPG--VVVRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDI 58
Query: 90 YSVEIDSSYVETGDPDLLLAVSGATADCGMNWEYSYGSWLLPTISDSGAAXXXXXXXXXX 149
++ SS + P++ L S + A+ ++ ++ L +S +
Sbjct: 59 REFQLPSSQISMV-PNVGLKFSISNANIKISGKWKAQKRFL-KMSGNFDLSIEGMSISAD 116
Query: 150 XXXXXKEQGGIVKVILVDCGSHVRDISIKV-DGGASWLYQALFEAFEGKIKSAVESAVTK 208
G + C SH+ + + + WL Q + E +++ + S V +
Sbjct: 117 LKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALRNKMNSQVCE 176
Query: 209 KISELI-TKLDSIFQSLPKQIPVSDIASMNTSFVRSPVLSDSSVEVEINGLFTAISGTSM 267
K++ + ++L FQ+LP + +A +N V P + +++V++ G F + + +
Sbjct: 177 KVTNSVSSELQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHNP 236
Query: 268 LNYYHKGFESSASCSSPAKMIGIQLNENVFSSGALVYFNSGTV 310
+ E A+ +M+ + L++ F++ LVY +G +
Sbjct: 237 PPFAPPVMEFPAAHD---RMVYLGLSDYFFNTAGLVYQEAGVL 276
>pdb|2NYF|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Nostoc Punctiforme
Length = 567
Score = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 23 PTSA---HVQVNEGGYISAVISKKGLDFFKNYL 52
PT A + +N GYISA ++++ +D F+NY+
Sbjct: 442 PTHAEQFNQNINSQGYISANLTRRSVDIFQNYM 474
>pdb|2OBD|A Chain A, Crystal Structure Of Cholesteryl Ester Transfer Protein
pdb|4EWS|A Chain A, Crystal Structure Of Cholesteryl Ester Transfer Protein In
Complex With Inhibitors
pdb|4F2A|A Chain A, Crystal Structure Of Cholestryl Esters Transfer Protein In
Complex With Inhibitors
Length = 476
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 54/273 (19%), Positives = 98/273 (35%), Gaps = 21/273 (7%)
Query: 52 LINKATSSIIPLEL-----PDIEKSKKIPLIGKVHMALSNIIIYSVEIDSSYVETGDP-- 104
++N T+ +I PDI K + L+G+V L NI I + I SS VE +
Sbjct: 22 VLNHETAKVIQTAFQRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIASSQVELVEAKS 81
Query: 105 -DLLLAVSGATADCGMNWEYSYGSWLLPTISDSGAAXXXXXXXXXXXXXXXKEQGGIVKV 163
D+ + + + Y+ WL D G V+
Sbjct: 82 IDVSIQDVSVVFKGTLKYGYTTAWWLG---IDQSIDFEIDSAIDLQINTQLTADSGRVRT 138
Query: 164 ILVDCGSHVRDISIKVDGGAS--WLYQALFEAFEGKIKSAVESAVTKKISELITKLDSIF 221
DC + + + G W+ Q +K ++ + K+I+ + +
Sbjct: 139 DAPDCYLSFHKLLLHLQGEREPGWIKQLFTNFISFTLKLVLKGQICKEINVISNIMADFV 198
Query: 222 QSLPKQIPVSDIASMNTSFVRSPVLSDSSVEVEING--LFTAISGTSMLNYYHKGFESSA 279
Q+ I ++ S PV++ S +E G ++ +S L + S
Sbjct: 199 QTRAASILSDGDIGVDISLTGDPVITASYLESHHKGHFIYKDVSEDLPLPTF------SP 252
Query: 280 SCSSPAKMIGIQLNENVFSSGALVYFNSGTVVF 312
+ ++M+ +E VF S A V F G ++
Sbjct: 253 TLLGDSRMLYFWFSERVFHSLAKVAFQDGRLML 285
>pdb|2NYN|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
pdb|2NYN|B Chain B, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
pdb|2NYN|C Chain C, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
pdb|2NYN|D Chain D, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Anabaena Variabilis
Length = 565
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 23 PTSA---HVQVNEGGYISAVISKKGLDFFKNYLINKATSSIIPLELPDIEKSKK 73
PT A + +N GY SA ++++ +D F+NY+ A + + ++ D+ KK
Sbjct: 442 PTHAEQFNQNINSQGYTSATLARRSVDIFQNYV---AIALMFGVQAVDLRTYKK 492
>pdb|3CZO|A Chain A, Crystal Structure Of Double Mutant Phenylalanine
Ammonia-Lyase From Anabaena Variabilis
pdb|3CZO|B Chain B, Crystal Structure Of Double Mutant Phenylalanine
Ammonia-Lyase From Anabaena Variabilis
pdb|3CZO|C Chain C, Crystal Structure Of Double Mutant Phenylalanine
Ammonia-Lyase From Anabaena Variabilis
pdb|3CZO|D Chain D, Crystal Structure Of Double Mutant Phenylalanine
Ammonia-Lyase From Anabaena Variabilis
Length = 539
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 23 PTSA---HVQVNEGGYISAVISKKGLDFFKNYL 52
PT A + +N GY SA ++++ +D F+NY+
Sbjct: 418 PTHAEQFNQNINSQGYTSATLARRSVDIFQNYV 450
>pdb|3C1J|A Chain A, Substrate Binding, Deprotonation And Selectivity At The
Periplasmic Entrance Of The E. Coli Ammonia Channel Amtb
Length = 424
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 259 FTAISGTSMLNYYHKGFESSASCSSPAKMIGIQLNENVFSSGALVYFNSGTVVFLWLQL 317
TA+ G S+ Y H F+ SA+C + ++G L E + S L++ V +WL L
Sbjct: 88 LTAVMG-SIYQYIHVAFQGSAACITVGLIVG-ALAERIRFSAVLIF------VVVWLTL 138
>pdb|3C1H|A Chain A, Substrate Binding, Deprotonation And Selectivity At The
Periplasmic Entrance Of The E. Coli Ammonia Channel Amtb
Length = 424
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 259 FTAISGTSMLNYYHKGFESSASCSSPAKMIGIQLNENVFSSGALVYFNSGTVVFLWLQL 317
TA+ G S+ Y H F+ SA+C + ++G L E + S L++ V +WL L
Sbjct: 88 LTAVMG-SIYQYIHVAFQGSAACITVGLIVG-ALAERIRFSAVLIF------VVVWLTL 138
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 0.134 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,614,077
Number of Sequences: 62578
Number of extensions: 322019
Number of successful extensions: 773
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 767
Number of HSP's gapped (non-prelim): 10
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
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: 51 (24.3 bits)