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= 031041
(167 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VE3|A Chain A, Retinoic Acid Bound Cyanobacterial Cyp120a1
pdb|2VE3|B Chain B, Retinoic Acid Bound Cyanobacterial Cyp120a1
pdb|2VE4|A Chain A, Substrate Free Cyanobacterial Cyp120a1
pdb|2VE4|B Chain B, Substrate Free Cyanobacterial Cyp120a1
Length = 444
Score = 29.6 bits (65), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 103 QDEDKIQVRVDLTGDATQRV--FDKVLTNLARSAPPIPGFRRE 143
Q+++K+Q+ +LT + +++ D+VL + R PP+ G RE
Sbjct: 282 QEQNKLQLSQELTAETLKKMPYLDQVLQEVLRLIPPVGGGFRE 324
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 28.1 bits (61), Expect = 2.1, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 38 KSVNFFHFQNSSCFFVRPSLYCNPLMRRVQHVLKTVSAVDSGVEVSITEPEDLI 91
K F +F+ P P M++V H + ++ + S E EPE+L+
Sbjct: 51 KGFGFLEVDAQKSYFIPP-----PQMKKVMHGDRIIAVIHSEKERESAEPEELV 99
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 28.1 bits (61), Expect = 2.1, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 38 KSVNFFHFQNSSCFFVRPSLYCNPLMRRVQHVLKTVSAVDSGVEVSITEPEDLI 91
K F +F+ P P M++V H + ++ + S E EPE+L+
Sbjct: 50 KGFGFLEVDAQKSYFIPP-----PQMKKVMHGDRIIAVIHSEKERESAEPEELV 98
>pdb|2AAR|7 Chain 7, Structure Of Trigger Factor Binding Domain In Biologically
Homologous Complex With Eubacterial Ribosome
Length = 113
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 102 SQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFR 141
S++ +K++ +V + R +D+V LAR +PGFR
Sbjct: 5 SKEGNKVEFKVSVPAAEVNRAYDQVWAGLARDV-RVPGFR 43
>pdb|2D3O|1 Chain 1, Structure Of Ribosome Binding Domain Of The Trigger Factor
On The 50s Ribosomal Subunit From D. Radiodurans
Length = 112
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 102 SQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFR 141
S++ +K++ +V + R +D+V LAR +PGFR
Sbjct: 6 SKEGNKVEFKVSVPAAEVNRAYDQVWAGLARDV-RVPGFR 44
>pdb|1R8S|E Chain E, Arf1[delta1-17]-Gdp In Complex With A Sec7 Domain Carrying
The Mutation Of The Catalytic Glutamate To Lysine
Length = 203
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 11 IPSKFQNIELFSPRSCRNYTLCHPNAPKSVNFFHFQNSSCFFVRPSLYCNPLMRRVQHVL 70
+P K Q I+ + Y LC+P +S + + + S + L+ NP +R + L
Sbjct: 104 LPGKAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSYSVIMLNTDLH-NPNVRD-KMGL 161
Query: 71 KTVSAVDSGVEVSITEPEDLI 91
+ A++ G+ PE+L+
Sbjct: 162 ERFVAMNRGINEGGDLPEELL 182
>pdb|3GVX|A Chain A, Crystal Structure Of Glycerate Dehydrogenase Related
Protein From Thermoplasma Acidophilum
pdb|3GVX|B Chain B, Crystal Structure Of Glycerate Dehydrogenase Related
Protein From Thermoplasma Acidophilum
Length = 290
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 17/107 (15%)
Query: 64 RRVQHVLK---------TVSAVDSGVEVSITEPEDLITVKD-AKIVVESQDEDKIQVRVD 113
RRV H+ K T S+VD V+V P DL D I + D+ + V
Sbjct: 135 RRVAHLAKAFGXRVIAYTRSSVDQNVDVISESPADLFRQSDFVLIAIPLTDKTRGXVNSR 194
Query: 114 LTGDATQRVFDKVLTNLAR----SAPPIPGFRREKGGKTTKVSIFWH 156
L +A + + + N+AR S P GF +E+ ++W+
Sbjct: 195 LLANARKNL---TIVNVARADVVSKPDXIGFLKERSDVWYLSDVWWN 238
>pdb|4AE2|A Chain A, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
pdb|4AE2|B Chain B, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
pdb|4AE2|C Chain C, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
pdb|4AK3|A Chain A, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
Length = 256
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 24 RSCRNYTLCHPNAPKSVNFFHFQNSSCFFVRPSLYCN 60
R+CR+ CHP KS ++ N C ++CN
Sbjct: 50 RNCRDLKFCHPEL-KSGEYWVDPNQGCKLDAIKVFCN 85
>pdb|4AEJ|A Chain A, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
pdb|4AEJ|B Chain B, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
pdb|4AEJ|C Chain C, Crystal Structure Of Human Fibrillar Procollagen Type
Iii C- Propeptide Trimer
Length = 256
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 24 RSCRNYTLCHPNAPKSVNFFHFQNSSCFFVRPSLYCN 60
R+CR+ CHP KS ++ N C ++CN
Sbjct: 50 RNCRDLKFCHPEL-KSGEYWVDPNQGCKLDAIKVFCN 85
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
0.322 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,535,041
Number of Sequences: 62578
Number of extensions: 162250
Number of successful extensions: 393
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 17
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)