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= 023079
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DME|A Chain A, Crystal Structure Of Conserved Exported Protein From
Bordetella Pertussis. Northeast Structural Genomics
Target Ber141
pdb|3DME|B Chain B, Crystal Structure Of Conserved Exported Protein From
Bordetella Pertussis. Northeast Structural Genomics
Target Ber141
Length = 369
Score = 250 bits (638), Expect = 6e-67, Method: Compositional matrix adjust.
Identities = 132/284 (46%), Positives = 177/284 (62%), Gaps = 24/284 (8%)
Query: 2 KRGTANGVHGLRMLEGFEAMKMEPELQCVKALLSPASGIVDSHSLMLSLVGEAENHGTTF 61
+R ANGV L+ ++G A ++EP L C AL+SP++GIVDSH+LML+ G+AE+ G
Sbjct: 108 RRAGANGVDDLQHIDGAAARRLEPALHCTAALVSPSTGIVDSHALMLAYQGDAESDGAQL 167
Query: 62 SNNTSVIGGHLEGNCMNVYISESKNLRNWDGVSPLQPELTLIPKLVVNSAGLSAPALAKR 121
+T +I G + E ++ G P+ TL ++++N+AGL AP LA+R
Sbjct: 168 VFHTPLIAGRVR--------PEGGFELDFGGAEPM----TLSCRVLINAAGLHAPGLARR 215
Query: 122 FIGLDNVFIPPAYYARGCYFSLANTKVAPFKHLIYPIPEDGGLGVHVTLDLDGQIKFGPD 181
G+ IPP Y +G YF+LA APF LIYP+P+ GLGVH+TLDL GQ KFGPD
Sbjct: 216 IEGIPRDSIPPEYLCKGSYFTLAGR--APFSRLIYPVPQHAGLGVHLTLDLGGQAKFGPD 273
Query: 182 VEWIDGIDDTLSFLNRFDYSVNANRAERFYPEIRKYYPDLRDGSLQPSYAGIRPKLSGPR 241
EWI DY+++ RA+ FY +R Y+P L DG+L P Y GIRPK+SGP
Sbjct: 274 TEWI----------ATEDYTLDPRRADVFYAAVRSYWPALPDGALAPGYTGIRPKISGPH 323
Query: 242 QSPIDFVIQGDDTHGVPGLVNLFGIESPGLTSSMAIAEYVAAKF 285
+ DF I G +HGV GLVNL+GIESPGLT+S+AIAE A+
Sbjct: 324 EPAADFAIAGPASHGVAGLVNLYGIESPGLTASLAIAEETLARL 367
>pdb|3RIM|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis
Transketolase (rv1449c)
pdb|3RIM|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis
Transketolase (rv1449c)
pdb|3RIM|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis
Transketolase (rv1449c)
pdb|3RIM|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis
Transketolase (rv1449c)
Length = 700
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 41/96 (42%), Gaps = 20/96 (20%)
Query: 81 ISESKNLRNWDGVSPLQPELTLIPKLVVNSA----GLSAP---ALAKRFIGLDNVFIPPA 133
+S+ ++LR W +P PE P + + + GL++ A+A R
Sbjct: 103 LSDIESLRTWGSKTPGHPEFRHTPGVEITTGPLGQGLASAVGMAMASR------------ 150
Query: 134 YYARGCYFSLANTKVAPFKHLIYPIPEDGGLGVHVT 169
Y RG + A +PF H IY I DG + VT
Sbjct: 151 -YERGLFDPDAEPGASPFDHYIYVIASDGDIEEGVT 185
>pdb|3CJ8|A Chain A, Crystal Structure Of
2,3,4,5-Tetrahydropyridine-2-Carboxylate N-
Succinyltransferase From Enterococcus Faecalis V583
pdb|3CJ8|B Chain B, Crystal Structure Of
2,3,4,5-Tetrahydropyridine-2-Carboxylate N-
Succinyltransferase From Enterococcus Faecalis V583
pdb|3CJ8|C Chain C, Crystal Structure Of
2,3,4,5-Tetrahydropyridine-2-Carboxylate N-
Succinyltransferase From Enterococcus Faecalis V583
Length = 236
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 25/45 (55%)
Query: 208 ERFYPEIRKYYPDLRDGSLQPSYAGIRPKLSGPRQSPIDFVIQGD 252
E +PE K + + + G+L +A ++P L ++ D+V++ D
Sbjct: 32 EVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVEND 76
>pdb|1DE4|C Chain C, Hemochromatosis Protein Hfe Complexed With Transferrin
Receptor
pdb|1DE4|F Chain F, Hemochromatosis Protein Hfe Complexed With Transferrin
Receptor
pdb|1DE4|I Chain I, Hemochromatosis Protein Hfe Complexed With Transferrin
Receptor
pdb|3KAS|A Chain A, Machupo Virus Gp1 Bound To Human Transferrin Receptor 1
Length = 640
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 203 NANRAERFYPEIRKYYPDLRDGSLQPSYAGIRPKLSGPRQSPIDFVIQGDDTHGVPGLV 261
NA + +RF + L D ++ Y + P +S P++SP V G +H +P L+
Sbjct: 542 NAEKTDRFVMK------KLNDRVMRVEYHFLSPYVS-PKESPFRHVFWGSGSHTLPALL 593
>pdb|1CX8|A Chain A, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|B Chain B, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|C Chain C, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|D Chain D, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|E Chain E, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|F Chain F, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|G Chain G, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1CX8|H Chain H, Crytal Structure Of The Ectodomain Of Human Transferrin
Receptor
pdb|1SUV|A Chain A, Structure Of Human Transferrin Receptor-transferrin
Complex
pdb|1SUV|B Chain B, Structure Of Human Transferrin Receptor-transferrin
Complex
pdb|2NSU|A Chain A, Crystal Structure Of The Ectodomain Of Human Transferrin
Receptor Fitted Into A Cryo-Em Reconstruction Of Canine
Parvovirus And Feline Transferrin Receptor Complex
pdb|2NSU|B Chain B, Crystal Structure Of The Ectodomain Of Human Transferrin
Receptor Fitted Into A Cryo-Em Reconstruction Of Canine
Parvovirus And Feline Transferrin Receptor Complex
Length = 639
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 203 NANRAERFYPEIRKYYPDLRDGSLQPSYAGIRPKLSGPRQSPIDFVIQGDDTHGVPGLV 261
NA + +RF + L D ++ Y + P +S P++SP V G +H +P L+
Sbjct: 541 NAEKTDRFVMK------KLNDRVMRVEYHFLSPYVS-PKESPFRHVFWGSGSHTLPALL 592
>pdb|3S9L|A Chain A, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 2
pdb|3S9L|B Chain B, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 2
pdb|3S9M|A Chain A, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 1
pdb|3S9M|B Chain B, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Cryocooled 1
pdb|3S9N|A Chain A, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Room Temperature
pdb|3S9N|B Chain B, Complex Between Transferrin Receptor 1 And Transferrin
With Iron In The N-Lobe, Room Temperature
Length = 654
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 203 NANRAERFYPEIRKYYPDLRDGSLQPSYAGIRPKLSGPRQSPIDFVIQGDDTHGVPGLV 261
NA + +RF + L D ++ Y + P +S P++SP V G +H +P L+
Sbjct: 556 NAEKTDRFVMK------KLNDRVMRVEYHFLSPYVS-PKESPFRHVFWGSGSHTLPALL 607
>pdb|1WD3|A Chain A, Crystal Structure Of Arabinofuranosidase
pdb|1WD4|A Chain A, Crystal Structure Of Arabinofuranosidase Complexed With
Arabinose
Length = 482
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 48/101 (47%), Gaps = 11/101 (10%)
Query: 163 GLGVHVTLDLDGQIKFGPDVEWIDGIDDTLSFLNRFDYSVNANRAERFYPEIRKYYPDLR 222
G G + +D++ + G D + G D ++S+ RF + A+++ IR +
Sbjct: 194 GDGPWIMVDMENNLFSGADEGYNSG-DPSISY--RFVTAAVKGGADKW--AIRG--ANAA 246
Query: 223 DGSLQPSYAGIRPKLSG----PRQSPIDFVIQGDDTHGVPG 259
GSL Y+G RP SG ++ I I GD+++G G
Sbjct: 247 SGSLSTYYSGARPDYSGYNPMSKEGAIILGIGGDNSNGAQG 287
>pdb|2B43|A Chain A, Crystal Structure Of The Norwalk Virus Rna Dependent Rna
Polymerase From Strain HuNLVDRESDEN1741997GE
pdb|2B43|B Chain B, Crystal Structure Of The Norwalk Virus Rna Dependent Rna
Polymerase From Strain HuNLVDRESDEN1741997GE
pdb|2B43|C Chain C, Crystal Structure Of The Norwalk Virus Rna Dependent Rna
Polymerase From Strain HuNLVDRESDEN1741997GE
pdb|2B43|D Chain D, Crystal Structure Of The Norwalk Virus Rna Dependent Rna
Polymerase From Strain HuNLVDRESDEN1741997GE
Length = 526
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 47 MLSLVGEAENHGTTF-SNNTSVIGGHLEGNCMNVYISESKNLRNW---DGVSPLQPELTL 102
++SL+GEA HG F S + ++ L+ M+ Y+ + + W +S + + L
Sbjct: 441 LMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNL 500
Query: 103 IPKLVVNSAGLSAPALA 119
P VN G+ LA
Sbjct: 501 APSF-VNEDGVEVDKLA 516
>pdb|3U46|L Chain L, Ch04hCH02L P212121
pdb|3U46|B Chain B, Ch04hCH02L P212121
pdb|3U4B|L Chain L, Ch04hCH02L FAB P4
Length = 215
Score = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 10/60 (16%)
Query: 104 PKLVVNSAGLSAPALAKRFIGLDNVFIPPAYYARGCYFSLANTKVAPFKHLIYPIPEDGG 163
P+L+++S A +A RF G + G +F+L T+V P +Y + GG
Sbjct: 45 PRLLIHSGSTRAAGIADRFSGGGS----------GMHFTLTITRVEPEDFAVYFCQQYGG 94
>pdb|3TQO|A Chain A, Structure Of The Cysteinyl-Trna Synthetase (Cyss) From
Coxiella Burnetii
Length = 462
Score = 27.3 bits (59), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 200 YSVNANRAERFYPEIRKY--YPDLRDGSLQPSYAGIRPKLSGPRQSPIDFVIQGDDTHGV 257
Y+ + F+ ++R++ Y L L AG R ++S ++ P+DFV+ G
Sbjct: 136 YAYTGQNGDVFF-DVRRFKDYGKLSHRHLDELQAGARVEVSDSKRDPLDFVLWKKAKPGE 194
Query: 258 PGLVNLFGIESPG 270
P + +G PG
Sbjct: 195 PKWDSPWGEGRPG 207
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 0.139 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,223,479
Number of Sequences: 62578
Number of extensions: 407719
Number of successful extensions: 838
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 831
Number of HSP's gapped (non-prelim): 11
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)