BLASTP 2.2.18 [Mar-02-2008]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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. Schäffer, and Yi-Kuo Yu (2005) "Protein database
searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= SODEF17
(71 letters)
Database: pdb_seqres.txt
180,722 sequences; 42,776,091 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
1gps_A mol:protein length:47 GAMMA-1-P THIONIN 37 0.011
1gpt_A mol:protein length:47 GAMMA-1-H THIONIN 35 0.020
1mr4_A mol:protein length:47 Nicotiana alata plant defensin 1 (... 35 0.027
>1gps_A mol:protein length:47 GAMMA-1-P THIONIN
Length = 47
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 8 ICKSRSHEYKGRCIQDMDCNAACVKESESYTGGFCNGRPPFKQCFCTKPC 57
IC+ RS +KG C+ + +C C + E + GG C+G PF++C C + C
Sbjct: 2 ICRRRSAGFKGPCMSNKNCAQVC--QQEGWGGGNCDG--PFRRCKCIRQC 47
>1gpt_A mol:protein length:47 GAMMA-1-H THIONIN
Length = 47
Score = 35.4 bits (80), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 8 ICKSRSHEYKGRCIQDMDCNAACVKESESYTGGFCNGRPPFKQCFCTKPC 57
IC+ RS +KG C+ + +C C++ E + GG C+G P ++C C + C
Sbjct: 2 ICRRRSAGFKGPCVSNKNCAQVCMQ--EGWGGGNCDG--PLRRCKCMRRC 47
>1mr4_A mol:protein length:47 Nicotiana alata plant defensin 1
(NaD1)
Length = 47
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 9 CKSRSHEYKGRCIQDMDCNAACVKESESYTGGFCNGRPPFKQCFCTKPC 57
CK+ S+ + G CI C AC+ SE +T G C+ ++C CTKPC
Sbjct: 3 CKTESNTFPGICITKPPCRKACI--SEKFTDGHCSK--ILRRCLCTKPC 47
Database: pdb_seqres.txt
Posted date: Dec 1, 2010 5:40 PM
Number of letters in database: 42,776,091
Number of sequences in database: 180,722
Lambda K H
0.323 0.136 0.486
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 180722
Number of Hits to DB: 7,404,841
Number of extensions: 311123
Number of successful extensions: 218
Number of sequences better than 1.0e-01: 4
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 4
Length of query: 71
Length of database: 42,776,091
Length adjustment: 41
Effective length of query: 30
Effective length of database: 35,366,489
Effective search space: 1060994670
Effective search space used: 1060994670
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 75 (33.5 bits)