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= psy13410
(493 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%)
Query: 47 TQDTLSTWALTPQLNWVCTQDTLSTWAQAFFFCGAIVGGLVFGWVADRFGRVPALVLTNL 106
T ++L+T + PQ ++L + A G I+GG + G+ ++RFGR +L + +
Sbjct: 34 TVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAV 93
Query: 107 VGFIFGVITA 116
+ FI GV +A
Sbjct: 94 LFFISGVGSA 103
Score = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 380 DYDHSDIPYTTIATELNWVCTQDTLSTWAQAFF-FC------GAIVGGLVFGWVADRFGR 432
YD + I T + +V Q+ + A + FC G I+GG + G+ ++RFGR
Sbjct: 25 GYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYCSNRFGR 84
Query: 433 VPALVLTNLVGFIFGVVTA 451
+L + ++ FI GV +A
Sbjct: 85 RDSLKIAAVLFFISGVGSA 103
>pdb|3SE8|L Chain L, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc03 In Complex With Hiv-1 Gp120
Length = 209
Score = 32.0 bits (71), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 23/53 (43%)
Query: 403 TLSTWAQAFFFCGAIVGGLVFGWVADRFGRVPALVLTNLVGFIFGVVTAFTKS 455
+LS A FC A GG W R G+VP L++ + GV F S
Sbjct: 12 SLSPGETATLFCKASQGGNAMTWYQKRRGQVPRLLIYDTSRRASGVPDRFVGS 64
>pdb|2R9U|A Chain A, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|B Chain B, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|C Chain C, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
pdb|2R9U|D Chain D, Crystal Structure Of Lamprey Variable Lymphocyte Receptor
2913 Ectodomain
Length = 174
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 304 VYFSQIFITVIPEHYWCRVPELSHLDFEQRKLISIPQIGAAFDSCR 349
+YF+ +T IP + ++ +L+ LD L SIP+ AFD+ +
Sbjct: 62 LYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPR--GAFDNLK 105
>pdb|3BLW|A Chain A, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|C Chain C, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|E Chain E, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|G Chain G, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|I Chain I, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|K Chain K, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|M Chain M, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLW|O Chain O, Yeast Isocitrate Dehydrogenase With Citrate And Amp Bound
In The Regulatory Subunits
pdb|3BLX|A Chain A, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|C Chain C, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|E Chain E, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|G Chain G, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|I Chain I, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|K Chain K, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|M Chain M, Yeast Isocitrate Dehydrogenase (Apo Form)
pdb|3BLX|O Chain O, Yeast Isocitrate Dehydrogenase (Apo Form)
Length = 349
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 217 KEESHEEADTIAESYIKRNHTGDRGLHNSPRSST-HGSLN 255
K+ H+E A +KRN G +GL ++P T HGSLN
Sbjct: 55 KQTDHKEGVYEAVESLKRNKIGLKGLWHTPADQTGHGSLN 94
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
0.329 0.141 0.477
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,172,033
Number of Sequences: 62578
Number of extensions: 630888
Number of successful extensions: 1435
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1423
Number of HSP's gapped (non-prelim): 22
length of query: 493
length of database: 14,973,337
effective HSP length: 103
effective length of query: 390
effective length of database: 8,527,803
effective search space: 3325843170
effective search space used: 3325843170
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 bits)