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= 042263
(159 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 7/55 (12%)
Query: 16 QDLFDCPIWYQALKVPVSQSINGHIICSSCLAKVNN------KCPACRSCVMLRS 64
Q + +CPI + +K PVS + HI C C+ K+ N +CP C++ + RS
Sbjct: 19 QKILECPICLELIKEPVSTKCD-HIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS 72
>pdb|3OL2|B Chain B, Receptor-Ligand Structure Of Human Semaphorin 4d With
Plexin B1
Length = 528
Score = 30.8 bits (68), Expect = 0.36, Method: Composition-based stats.
Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 4/35 (11%)
Query: 28 LKVPVSQSINGHIICSSCLAKVNNKCPACRSCVML 62
LKVPV+ S H+ C+SCLA ++ P C CV+L
Sbjct: 459 LKVPVA-SCAQHLDCASCLA---HRDPYCGWCVLL 489
>pdb|2A25|A Chain A, Crystal Structure Of Siah1 Sbd Bound To The Peptide
Ekpaavvapittg From Sip
Length = 193
Score = 29.3 bits (64), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 72 EKTMSFGENKDHERNCQCAP--CACPLLDCNFLGSASQLYLYFSWKNGKTFVSFTYKKRV 129
E T+ E DHE C+ P C CP C + GS + + ++ +
Sbjct: 17 EITLPHTEKADHEELCEFRPYSCPCPGASCKWQGSLDAVMPH-----------LMHQHKS 65
Query: 130 KVTLNVNDSVFL 141
TL D VFL
Sbjct: 66 ITTLQGEDIVFL 77
>pdb|3KNV|A Chain A, Crystal Structure Of The Ring And First Zinc Finger
Domains Of Traf2
Length = 141
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 6/87 (6%)
Query: 34 QSINGHIICSSCLAKVNNKCPA-CRSCVMLRSRVMDIA-LEKTMSFGENKDHERNCQCAP 91
Q+ GH CS CLA + + P C +CV I+ LE + +F +N R + P
Sbjct: 46 QAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISILESSSAFPDNAAR-REVESLP 104
Query: 92 CACPLLDCNFLGSASQLYLYFSWKNGK 118
CP C + G+ L Y S G+
Sbjct: 105 AVCPSDGCTWKGT---LKEYESCHEGR 128
>pdb|1K2F|A Chain A, Siah, Seven In Absentia Homolog
pdb|1K2F|B Chain B, Siah, Seven In Absentia Homolog
Length = 190
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 72 EKTMSFGENKDHERNCQCAP--CACPLLDCNFLGSASQLYLYFSWKNGKTFVSFTYKKRV 129
E T+ E +HE C+ P C CP C + GS + + ++ +
Sbjct: 14 EITLPHTEKAEHEELCEFRPYSCPCPGASCKWQGSLDAVMPH-----------LMHQHKS 62
Query: 130 KVTLNVNDSVFL 141
TL D VFL
Sbjct: 63 ITTLQGEDIVFL 74
>pdb|2AN6|A Chain A, Protein-Peptide Complex
pdb|2AN6|B Chain B, Protein-Peptide Complex
pdb|2AN6|C Chain C, Protein-Peptide Complex
pdb|2AN6|D Chain D, Protein-Peptide Complex
Length = 191
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 72 EKTMSFGENKDHERNCQCAP--CACPLLDCNFLGSASQLYLYFSWKNGKTFVSFTYKKRV 129
E T+ E +HE C+ P C CP C + GS + + ++ +
Sbjct: 15 EITLPHTEKAEHEELCEFRPYSCPCPGASCKWQGSLDAVMPH-----------LMHQHKS 63
Query: 130 KVTLNVNDSVFL 141
TL D VFL
Sbjct: 64 ITTLQGEDIVFL 75
>pdb|3I2D|A Chain A, Crystal Structure Of S. Cerevisiae Sumo E3 Ligase Siz1
Length = 371
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 44/96 (45%), Gaps = 19/96 (19%)
Query: 1 LRSCKNGSITSTISDQDLFDCPIWYQALKVPVSQSIN-GHIICSSCLAKVNN-------K 52
LR + +T+T + L CPI Y +K P S+SIN H+ C L +++ +
Sbjct: 233 LREDEEMGLTTTSTIMSL-QCPISYTRMKYP-SKSINCKHLQCFDALWFLHSQLQIPTWQ 290
Query: 53 CPACRSCVMLRSRVMDIALEKTMSFGENKDHERNCQ 88
CP C+ +DIALE D +NCQ
Sbjct: 291 CPVCQ---------IDIALENLAISEFVDDILQNCQ 317
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 26.6 bits (57), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 21/97 (21%)
Query: 19 FDCPIWYQALKVPVSQSINGHIICSSCLAK----VNNKCP----------------ACRS 58
++CPI AL+ V Q+ GH C +C+ K +KCP A R
Sbjct: 19 YECPICLMALREAV-QTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKRE 77
Query: 59 CVMLRSRVMDIALEKTMSFGENKDHERNCQCAPCACP 95
+ L + + M +DH+ +C+ A CP
Sbjct: 78 ILSLMVKCPNEGCLHKMELRHLEDHQAHCEFALMDCP 114
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 0.135 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,441,063
Number of Sequences: 62578
Number of extensions: 155196
Number of successful extensions: 766
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 761
Number of HSP's gapped (non-prelim): 22
length of query: 159
length of database: 14,973,337
effective HSP length: 91
effective length of query: 68
effective length of database: 9,278,739
effective search space: 630954252
effective search space used: 630954252
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: 47 (22.7 bits)