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= 025373
(254 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PZK|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmg In Complex With Nad
pdb|2PZK|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmg In Complex With Nad
pdb|2PZL|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmg In Complex With Nad And Udp
pdb|2PZL|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmg In Complex With Nad And Udp
pdb|2PZM|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmg In Complex With Nad And Udp
pdb|2PZM|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
Wbmg In Complex With Nad And Udp
Length = 330
Score = 34.3 bits (77), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 133 DTFRLSKCVQIARLYLEDDD-----AVNAEAFINKASFLVSSSQQEVLNLQYKVCYAR 185
D+F+ + V A Y + DD A N + IN A + + +LN Q +CY R
Sbjct: 85 DSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGR 142
>pdb|2VF7|A Chain A, Crystal Structure Of Uvra2 From Deinococcus Radiodurans
pdb|2VF7|B Chain B, Crystal Structure Of Uvra2 From Deinococcus Radiodurans
pdb|2VF7|C Chain C, Crystal Structure Of Uvra2 From Deinococcus Radiodurans
pdb|2VF8|A Chain A, Crystal Structure Of Uvra2 From Deinococcus Radiodurans
pdb|2VF8|B Chain B, Crystal Structure Of Uvra2 From Deinococcus Radiodurans
Length = 842
Score = 29.3 bits (64), Expect = 2.3, Method: Composition-based stats.
Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 13/97 (13%)
Query: 22 KHILSSVISSNDIVQAKKFIDHMLSDDVPLVVSRQLLQ-----TFA----QELGRLEPET 72
+H+L + ++ K+ +M+S++ PL ++L Q TFA EL RL
Sbjct: 260 RHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLAR 319
Query: 73 QKEIANYTLAQIQP----RVVSFEEQVLIIREKLADL 105
E+ + +P RV + EQ + ++ ADL
Sbjct: 320 VSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADL 356
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 129 RVIDDTFRLSKCVQIARLYLEDDDAVNAE--AFINKASFLVSSSQQEVLNLQY 179
+++ DTF + + D D N++ AFIN ASF S + E +N QY
Sbjct: 20 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY 72
>pdb|3O53|A Chain A, Crystal Structure Of Lrim1 Leucine-Rich Repeat Domain
pdb|3O53|B Chain B, Crystal Structure Of Lrim1 Leucine-Rich Repeat Domain
Length = 317
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 38/92 (41%), Gaps = 19/92 (20%)
Query: 123 DLDSGMRVIDDTFRLSKCVQIARLYLEDDDAVNAEAFINKASFLVSSSQQEVLNLQYKVC 182
DLD G R VQ L L + D VN A SS E LNLQY
Sbjct: 137 DLDEGCR---------SRVQYLDLKLNEIDTVNF------AELAASSDTLEHLNLQYNFI 181
Query: 183 YARILDLKRKFLEAALRYYDISQIQKRQIGDE 214
Y D+K + + A L+ D+S + +G E
Sbjct: 182 Y----DVKGQVVFAKLKTLDLSSNKLAFMGPE 209
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 47/194 (24%), Positives = 85/194 (43%), Gaps = 24/194 (12%)
Query: 24 ILSSVISSNDIVQAKKFIDHMLSDDVPLVVSRQLLQTF-----AQELGRLEPETQKEIAN 78
+ ++ S V ++ I + +++ P+ V R L+ TF A+ R+ +KE+
Sbjct: 28 VAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEALEKELVQ 87
Query: 79 YTLAQIQPRVVSFEEQV-LIIREKLADLYESEQQWSKAAQMLSGIDLDSGMRVIDDTFRL 137
+P + Q+ L+ R ++ L+ Q K L IDLD G R+ D T
Sbjct: 88 ------RPGSLHIRRQLSLLNRASISTLHSFCLQVLKKYYYL--IDLDPGFRIADQTEGE 139
Query: 138 SKCVQIARLYLEDDDAVNAEAFINKASFLVS--SSQQEVLNLQYKVC----YARILDLKR 191
++ ED+ A +AF LV ++ + L+LQ+ V Y+R
Sbjct: 140 LIGDEVLDELFEDEYAKGEKAFFE----LVDRYTTDRHDLDLQFLVKQVYEYSRSHPNPE 195
Query: 192 KFLEAALRYYDISQ 205
+LE+ + YD+S+
Sbjct: 196 AWLESFVHLYDVSE 209
>pdb|3OJA|A Chain A, Crystal Structure Of Lrim1APL1C COMPLEX
Length = 487
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 38/92 (41%), Gaps = 19/92 (20%)
Query: 123 DLDSGMRVIDDTFRLSKCVQIARLYLEDDDAVNAEAFINKASFLVSSSQQEVLNLQYKVC 182
DLD G R VQ L L + D VN A SS E LNLQY
Sbjct: 137 DLDEGCR---------SRVQYLDLKLNEIDTVNF------AELAASSDTLEHLNLQYNFI 181
Query: 183 YARILDLKRKFLEAALRYYDISQIQKRQIGDE 214
Y D+K + + A L+ D+S + +G E
Sbjct: 182 Y----DVKGQVVFAKLKTLDLSSNKLAFMGPE 209
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
0.318 0.130 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,948,323
Number of Sequences: 62578
Number of extensions: 204272
Number of successful extensions: 561
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 559
Number of HSP's gapped (non-prelim): 11
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)