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= 029406
(194 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PBR|A Chain A, Crystal Structure Of Thymidylate Kinase (Aq_969) From
Aquifex Aeolicus Vf5
pdb|2PBR|B Chain B, Crystal Structure Of Thymidylate Kinase (Aq_969) From
Aquifex Aeolicus Vf5
Length = 195
Score = 30.4 bits (67), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 39/145 (26%), Positives = 65/145 (44%), Gaps = 20/145 (13%)
Query: 42 LAEFQRQDQVFLCM-------KLYDVVRKEIWYRPDMFFYRDMLMMLARNKKVVEAKQVW 94
L E+ +Q F+ + K+ +V+R EI ++ ++L+ A K++E K +
Sbjct: 20 LYEYLKQKGYFVSLYREPGGTKVGEVLR-EILLTEELDERTELLLFEASRSKLIEEK-II 77
Query: 95 EDLKREEV-LFDQHTFGDIIRAFSDSGLPSEAMFIYNEMRSSPATP-----ISLPFRVIL 148
DLKR++V + D+ I GL E + NE + P + +P + L
Sbjct: 78 PDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIAL 137
Query: 149 KGL-----IPYPEFREKVKDDFLEL 168
+ L EF EKV+ FLEL
Sbjct: 138 RRLKEKNRFENKEFLEKVRKGFLEL 162
>pdb|2FAU|A Chain A, Crystal Structure Of Human Vps26
Length = 341
Score = 30.0 bits (66), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 123 SEAMFIYNEMRSSPATPISLPFRVILKGLIPYPEFREKVKDDFLELFPDMIVYDPPED-- 180
+E + Y M +P S+P R+ L G P P R+ K + F ++++ D ED
Sbjct: 229 TETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVD-EEDRR 287
Query: 181 LFEDQE---WRR 189
F+ QE WR+
Sbjct: 288 YFKQQEIILWRK 299
>pdb|3CH4|B Chain B, The Crystal Structure Of Human Phosphomavelonate Kinase At
1.8 A Resolution
Length = 202
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 16 QSHPVRFDRFIKSHVSR-LLKSDLVSVLAEFQRQDQVFLCMKLYDVVRKEIWY------R 68
Q H + F R + + + + D++ E ++ D F C K+ + + + IW
Sbjct: 55 QEHGLNFQRLLDTSTYKEAFRKDMIRWGEEKRQADPGFFCRKIVEGISQPIWLVSDTRRV 114
Query: 69 PDMFFYRDMLMMLARNKKVVEAKQ 92
D+ ++R+ + + +VV +Q
Sbjct: 115 SDIQWFREAYGAVTQTVRVVALEQ 138
>pdb|3F3S|A Chain A, The Crystal Structure Of Human Lambda-Crystallin, Cryl1
pdb|3F3S|B Chain B, The Crystal Structure Of Human Lambda-Crystallin, Cryl1
Length = 313
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 122 PSEAMFIYNEMRSSPATPISLPFRVILKGLIPYPEFR----EKVKDDFLELFPDMIVYDP 177
P E M + E S S + +L+ P PEF EKV D M V D
Sbjct: 234 PLETMHLNAEGMLSYCDRYSEGIKHVLQTFGPIPEFSRATAEKVNQDMC-----MKVPDD 288
Query: 178 PEDLFEDQEWRRES 191
PE L ++WR E
Sbjct: 289 PEHLAARRQWRDEC 302
>pdb|3DPG|A Chain A, Sgrai With Noncognate Dna Bound
pdb|3DPG|B Chain B, Sgrai With Noncognate Dna Bound
pdb|3DVO|A Chain A, Sgrai With Cognate Dna And Calcium Bound
pdb|3DVO|B Chain B, Sgrai With Cognate Dna And Calcium Bound
pdb|3DVO|C Chain C, Sgrai With Cognate Dna And Calcium Bound
pdb|3DVO|D Chain D, Sgrai With Cognate Dna And Calcium Bound
pdb|3DW9|A Chain A, Sgrai With Cognate Dna And Manganese Bound
pdb|3DW9|B Chain B, Sgrai With Cognate Dna And Manganese Bound
pdb|3MQ6|A Chain A, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|B Chain B, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|C Chain C, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|D Chain D, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|E Chain E, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|F Chain F, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|G Chain G, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQ6|H Chain H, Domain Swapped Sgrai With Dna And Calcium Bound
pdb|3MQY|A Chain A, Sgrai With Cleaved Dna And Magnesium Bound
pdb|3MQY|B Chain B, Sgrai With Cleaved Dna And Magnesium Bound
pdb|3N78|A Chain A, Sgrai Bound To Secondary Site Dna And Mg(Ii)
pdb|3N78|B Chain B, Sgrai Bound To Secondary Site Dna And Mg(Ii)
pdb|3N7B|A Chain A, Sgrai Bound To Secondary Site Dna And Ca(Ii)
pdb|3N7B|B Chain B, Sgrai Bound To Secondary Site Dna And Ca(Ii)
Length = 338
Score = 27.3 bits (59), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 156 EFREKVKDDFLEL---FPDMIVYDPPEDLFEDQEWRRE 190
EFR ++ D L L PD+ V PE+ D+ WR E
Sbjct: 169 EFRAGLRKDGLGLPTSTPDLAVVVLPEEFQNDEMWREE 206
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 0.140 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,764,478
Number of Sequences: 62578
Number of extensions: 229443
Number of successful extensions: 843
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 841
Number of HSP's gapped (non-prelim): 12
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
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: 49 (23.5 bits)