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= 046070
(309 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GOC|A Chain A, Crystal Structure Of The Endonuclease V (Sav1684) From
Streptomyces Avermitilis. Northeast Structural Genomics
Consortium Target Svr196
pdb|3GOC|B Chain B, Crystal Structure Of The Endonuclease V (Sav1684) From
Streptomyces Avermitilis. Northeast Structural Genomics
Consortium Target Svr196
Length = 237
Score = 109 bits (272), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 71/180 (39%), Positives = 98/180 (54%), Gaps = 18/180 (10%)
Query: 123 TLQIVYEDYSLLRLQVPYVPGFLAFREAPVLLSLLDNMKKRANHFYPQVLMVDGNGLLHP 182
TL +V E ++ + PYVPG LAFRE P +L+ LD + P +++ DG G+ HP
Sbjct: 67 TLDVVAEATAVGEVSFPYVPGLLAFREIPTVLAALDALP-----CPPGLIVCDGYGVAHP 121
Query: 183 RGFGLASHIGVLANLTTIGVGKNLHHVDGLTHSGVRQLLDAKENNNEDIIPLMGGSGSTW 242
R FGLASH+GVL L TIGV KN T S + PL+ G+
Sbjct: 122 RRFGLASHLGVLTGLPTIGVAKNP-----FTFS-----YEDPGAPRGSAAPLLAGADEV- 170
Query: 243 GVAMRSTPDTLKPIFISVGHCISLDTAVM-IVKMTCKYRVPEPIRQADIRSRDYLQKHQS 301
G A+R T +KP+F+SVGH + LD A + +T KYR+PE R+AD R L++ +
Sbjct: 171 GRALR-TQSGVKPVFVSVGHRVDLDHACAHTLALTPKYRIPETTRRADSLCRRALKEATA 229
>pdb|3GA2|A Chain A, Crystal Structure Of The Endonuclease_v (Bsu36170) From
Bacillus Subtilis, Northeast Structural Genomics
Consortium Target Sr624
Length = 246
Score = 102 bits (253), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 69/210 (32%), Positives = 109/210 (51%), Gaps = 22/210 (10%)
Query: 98 GGVDMSFSKED--PSIACGCIVVLDLQTLQIVYEDYSLLRLQVPYVPGFLAFREAPVLLS 155
GVD+++ ++D P C CI+V+D T +++ + +S R+ VPYV GFLAFRE P+++
Sbjct: 43 AGVDLAYWEQDGEPYGVC-CIIVIDADTKEVIEKVHSXGRISVPYVSGFLAFRELPLIIE 101
Query: 156 LLDNMKKRANHFYPQVLMVDGNGLLHPRGFGLASHIGVLANLTTIGVGKNLHHVDGLTHS 215
++ P V + DGNG LH G+A+H TIG+ K + G
Sbjct: 102 AAKKLETE-----PDVFLFDGNGYLHYNHXGVATHAAFFLGKPTIGIAKTYLKIKGCDFV 156
Query: 216 GVRQLLDAKENNNEDIIPLMGGSGSTWGVAMRSTPDTLKPIFISVGHCISLDTAVMIVK- 274
+ A DII G +G A+R+ D +KPIF+S G+ I LD++ I
Sbjct: 157 TPEIEVGAY----TDIII----DGEVYGRALRTRRD-VKPIFLSCGNYIDLDSSYQITXS 207
Query: 275 -MTCKYRVPEPIRQADIRS---RDYLQKHQ 300
+ + R+P P+R AD+ + R + QK+
Sbjct: 208 LINQESRLPIPVRLADLETHVLRTFYQKNH 237
>pdb|2W35|A Chain A, Structures Of Endonuclease V With Dna Reveal Initiation Of
Deaminated Adenine Repair
pdb|2W35|B Chain B, Structures Of Endonuclease V With Dna Reveal Initiation Of
Deaminated Adenine Repair
Length = 225
Score = 97.8 bits (242), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 64/207 (30%), Positives = 107/207 (51%), Gaps = 33/207 (15%)
Query: 95 KYIGGVDMSFSKEDPSIACGCIVVLDLQTLQIVYEDYSLLRLQVPYVPGFLAFREAPVLL 154
+Y+ GVD+SF ++ +A IVVL+ + +I+ + PY+PG LAFRE P+ L
Sbjct: 37 EYVAGVDLSFPGKEEGLAV--IVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFL 94
Query: 155 SLLDNMKKRANHFYPQVLMVDGNGLLHPRGFGLASHIGVLANLTTIGVGKNLHHVDGLTH 214
+ ++ + P V++ DG GL HPR G+ASH+G+ + TIGV K+ +
Sbjct: 95 KAWEKLRTK-----PDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLY------ 143
Query: 215 SGVRQLLDAKE------NNNEDIIPLMGGSGSTWGVAMRSTPDTLKPIFISVGHCISLDT 268
G ++ + K + E+II G +R T + PIF+S GH + +++
Sbjct: 144 -GTFKMPEDKRCSWSYLYDGEEII----------GCVIR-TKEGSAPIFVSPGHLMDVES 191
Query: 269 AVMIVKMTC--KYRVPEPIRQADIRSR 293
+ ++K R+PEP R A I ++
Sbjct: 192 SKRLIKAFTLPGRRIPEPTRLAHIYTQ 218
>pdb|3HD0|A Chain A, Crystal Structure Of Tm1865, An Endonuclease V From
Thermotoga Maritima
pdb|3HD0|B Chain B, Crystal Structure Of Tm1865, An Endonuclease V From
Thermotoga Maritima
pdb|3HD0|D Chain D, Crystal Structure Of Tm1865, An Endonuclease V From
Thermotoga Maritima
Length = 237
Score = 94.7 bits (234), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 64/207 (30%), Positives = 104/207 (50%), Gaps = 33/207 (15%)
Query: 95 KYIGGVDMSFSKEDPSIACGCIVVLDLQTLQIVYEDYSLLRLQVPYVPGFLAFREAPVLL 154
+Y+ GVD+SF ++ +A IVVL+ + +I+ + PY+PG LAFRE P+ L
Sbjct: 49 EYVAGVDLSFPGKEEGLAV--IVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFL 106
Query: 155 SLLDNMKKRANHFYPQVLMVDGNGLLHPRGFGLASHIGVLANLTTIGVGKNLHHVDGLTH 214
+ ++ + P V++ DG GL HPR G+ASH G+ + TIGV K+ +
Sbjct: 107 KAWEKLRTK-----PDVVVFDGQGLAHPRKLGIASHXGLFIEIPTIGVAKSRLY------ 155
Query: 215 SGVRQLLDAKE------NNNEDIIPLMGGSGSTWGVAMRSTPDTLKPIFISVGHCISLDT 268
G + + K + E+II G +R T + PIF+S GH +++
Sbjct: 156 -GTFKXPEDKRCSWSYLYDGEEII----------GCVIR-TKEGSAPIFVSPGHLXDVES 203
Query: 269 AVMIVKMTC--KYRVPEPIRQADIRSR 293
+ ++K R+PEP R A I ++
Sbjct: 204 SKRLIKAFTLPGRRIPEPTRLAHIYTQ 230
>pdb|2W36|A Chain A, Structures Of Endonuclease V With Dna Reveal Initiation Of
Deaminated Adenine Repair
pdb|2W36|B Chain B, Structures Of Endonuclease V With Dna Reveal Initiation Of
Deaminated Adenine Repair
Length = 225
Score = 94.7 bits (234), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 63/207 (30%), Positives = 106/207 (51%), Gaps = 33/207 (15%)
Query: 95 KYIGGVDMSFSKEDPSIACGCIVVLDLQTLQIVYEDYSLLRLQVPYVPGFLAFREAPVLL 154
+Y+ GV +SF ++ +A IVVL+ + +I+ + PY+PG LAFRE P+ L
Sbjct: 37 EYVAGVALSFPGKEEGLAV--IVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFL 94
Query: 155 SLLDNMKKRANHFYPQVLMVDGNGLLHPRGFGLASHIGVLANLTTIGVGKNLHHVDGLTH 214
+ ++ + P V++ DG GL HPR G+ASH+G+ + TIGV K+ +
Sbjct: 95 KAWEKLRTK-----PDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLY------ 143
Query: 215 SGVRQLLDAKE------NNNEDIIPLMGGSGSTWGVAMRSTPDTLKPIFISVGHCISLDT 268
G ++ + K + E+II G +R T + PIF+S GH + +++
Sbjct: 144 -GTFKMPEDKRCSWSYLYDGEEII----------GCVIR-TKEGSAPIFVSPGHLMDVES 191
Query: 269 AVMIVKMTC--KYRVPEPIRQADIRSR 293
+ ++K R+PEP R A I ++
Sbjct: 192 SKRLIKAFTLPGRRIPEPTRLAHIYTQ 218
>pdb|3G5B|A Chain A, The Structure Of Unc5b Cytoplasmic Domain
Length = 405
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 4/96 (4%)
Query: 184 GFGLASHIGVLANLTTI-GVGKNLHHVDGLTHSGVRQLLDAKENNNEDIIPLMGGSGSTW 242
G ++ G L TI G G +L +G G L + N E +PL GS +
Sbjct: 2 GSSVSGTFGCLGGRLTIPGTGVSLLVPNGAIPQGKFYDLYLRINKTESTLPLSEGSQTVL 61
Query: 243 GVAMRSTPDTL---KPIFISVGHCISLDTAVMIVKM 275
++ P L +P+ ++V HC + I ++
Sbjct: 62 SPSVTCGPTGLLLCRPVVLTVPHCAEVIAGDWIFQL 97
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
0.321 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,217,961
Number of Sequences: 62578
Number of extensions: 364855
Number of successful extensions: 780
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 762
Number of HSP's gapped (non-prelim): 8
length of query: 309
length of database: 14,973,337
effective HSP length: 99
effective length of query: 210
effective length of database: 8,778,115
effective search space: 1843404150
effective search space used: 1843404150
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)