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= 041620
(172 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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 61/157 (38%), Gaps = 24/157 (15%)
Query: 15 SQLLTTFISSLYITGILASLIASSVTRALGRKVSILIGGVAFL---AGSA---LGVCAFN 68
+ LL ++S I I+ + + GR+ S+ I V F GSA LG + N
Sbjct: 54 NSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSIN 113
Query: 69 ------IYM------LIFGRLLLGVGIGFGNQSVPLYLSEMTTPKYRGTFNIGFQLCAAI 116
+Y+ + R++ G+G+G + P+Y++E+ RG Q
Sbjct: 114 PDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIF 173
Query: 117 GLLSANLLN--CTQKIKGGW----GWRISLAMAAAPA 147
G L +N + W GWR A PA
Sbjct: 174 GQLLVYCVNYFIARSGDASWLNTDGWRYMFASECIPA 210
>pdb|2FX7|H Chain H, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With A 16-Residue Peptide Encompassing The 4e10
Epitope On Gp41
Length = 228
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 66 AFNIYMLIFGRLLLGVGIGFGNQSVPLYLSEMTTPKYRGTFNIGFQLCAAIGLLSANLLN 125
+F+ Y L + R G G+ + +PL P+++G I + L N L
Sbjct: 28 SFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLR 87
Query: 126 --------CTQKIKGGWGW 136
C ++ GWGW
Sbjct: 88 PEDTAVYYCAREGTTGWGW 106
>pdb|1TZG|H Chain H, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With A 13-residue Peptide Containing The 4e10
Epitope On Gp41
pdb|1TZG|I Chain I, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With A 13-residue Peptide Containing The 4e10
Epitope On Gp41
Length = 232
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 66 AFNIYMLIFGRLLLGVGIGFGNQSVPLYLSEMTTPKYRGTFNIGFQLCAAIGLLSANLLN 125
+F+ Y L + R G G+ + +PL P+++G I + L N L
Sbjct: 28 SFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLR 87
Query: 126 --------CTQKIKGGWGW 136
C ++ GWGW
Sbjct: 88 PEDTAVYYCAREGTTGWGW 106
>pdb|2FX8|H Chain H, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With An Aib-Induced Peptide Encompassing The
4e10 Epitope On Gp41
pdb|2FX8|I Chain I, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With An Aib-Induced Peptide Encompassing The
4e10 Epitope On Gp41
pdb|2FX8|J Chain J, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With An Aib-Induced Peptide Encompassing The
4e10 Epitope On Gp41
pdb|2FX8|K Chain K, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With An Aib-Induced Peptide Encompassing The
4e10 Epitope On Gp41
pdb|2FX9|H Chain H, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With A Thioether-Linked Peptide Encompassing The
4e10 Epitope On Gp41
pdb|2FX9|I Chain I, Crystal Structure Of Hiv-1 Neutralizing Human Fab 4e10 In
Complex With A Thioether-Linked Peptide Encompassing The
4e10 Epitope On Gp41
Length = 227
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 66 AFNIYMLIFGRLLLGVGIGFGNQSVPLYLSEMTTPKYRGTFNIGFQLCAAIGLLSANLLN 125
+F+ Y L + R G G+ + +PL P+++G I + L N L
Sbjct: 28 SFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLR 87
Query: 126 --------CTQKIKGGWGW 136
C ++ GWGW
Sbjct: 88 PEDTAVYYCAREGTTGWGW 106
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
0.324 0.138 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,441,847
Number of Sequences: 62578
Number of extensions: 160114
Number of successful extensions: 494
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 489
Number of HSP's gapped (non-prelim): 8
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)