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= 021622
(310 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
Length = 360
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 36/160 (22%), Positives = 69/160 (43%), Gaps = 30/160 (18%)
Query: 108 EAESTVKKVSASMKEKISAATEEVKGTFRTGSTDTSAKHDDDVRDGFKASSGEEKQK--- 164
+AE+ + + A++++ + AT + G FR G HD D F + EE Q+
Sbjct: 158 DAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQ---GHDVD----FLITHPEEGQEVGL 210
Query: 165 -----QTVSSDTAETFYGKLKSSISSPKFTLAFQKLKEAKVVDLAKKGYDIVKDELSGSP 219
+ S ++ +S ++ L + + +D+ ++ + I+ G P
Sbjct: 211 LPKVMSCLQSQGLVLYHQYHRSHLADSAHNLR----QRSSTMDVFERSFCIL-----GLP 261
Query: 220 SKRKHL---EYTPSPSWTGEKSTRTDLVVTPSKKSMWSKL 256
++ P P+W K+ R DLVVTPS + ++ L
Sbjct: 262 QPQQAALAGALPPCPTW---KAVRVDLVVTPSSQFPFALL 298
>pdb|2ON7|A Chain A, Structure Of Nagst-1
pdb|2ON7|B Chain B, Structure Of Nagst-1
pdb|2ON7|C Chain C, Structure Of Nagst-1
pdb|2ON7|D Chain D, Structure Of Nagst-1
Length = 206
Score = 31.6 bits (70), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 195 LKEAKVVDLAKKGYDIVKDELSGSPSKRKHLEYTPSPSWTGEKSTRTDLVVTPSKKSMWS 254
++E V L K+ +D+ G +K L+ +PS G+ T DL+V+ +M +
Sbjct: 112 MREGDVEQLKKEVLLPARDKFFGFITK--FLKKSPSGFLVGDSLTWVDLLVSEHNATMLT 169
Query: 255 KLKEKMQGYP 264
+ E ++GYP
Sbjct: 170 FVPEFLEGYP 179
>pdb|3OI8|A Chain A, The Crystal Structure Of Functionally Unknown Conserved
Protein Domain From Neisseria Meningitidis Mc58
pdb|3OI8|B Chain B, The Crystal Structure Of Functionally Unknown Conserved
Protein Domain From Neisseria Meningitidis Mc58
Length = 156
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 198 AKVVDLAKKGYDIV---KDELSGSPSKRKHLEYTPSPSWTGEKSTRTDLVVTPSKKSMWS 254
A V+D A + ++ KDE+ G + L+Y +P KS V P KS+ +
Sbjct: 64 AYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYXFNPEQFHLKSILRPAVFVPEGKSLTA 123
Query: 255 KLKE 258
LKE
Sbjct: 124 LLKE 127
>pdb|1NT2|B Chain B, Crystal Structure Of FibrillarinNOP5P COMPLEX
Length = 258
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 65 EFKHSVKELKKKAEEIKGVKE-ELKERTKQTTEQLYKQVDGVWMEAESTVKKVSASMKEK 123
E S+ L +K E+I+ VKE E+ E+ ++ +L + V E E ++K++ +M E
Sbjct: 86 EIDESINMLNEKLEDIRAVKESEITEKFEKKIRELRELRRDVEREIEEVMEKIAPNMTEL 145
Query: 124 ISA 126
+ A
Sbjct: 146 VGA 148
>pdb|4HCH|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Tartrate
pdb|4HCH|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Tartrate
pdb|4HCL|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Lyxarohydroxamate
pdb|4HCL|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Lyxarohydroxamate
Length = 402
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 235 GEKSTRTDLVVTPSKKSMWSKLKEKMQGYPVFKRITGISEPVVTKGQEVCSNRL 288
G + TD + ++W L + G PV+K I G + V+ G +C + L
Sbjct: 111 GSAAQLTDRTLAVVDCALWD-LAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDEL 163
>pdb|2QE7|G Chain G, Crystal Structure Of The F1-Atpase From The
Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
Length = 286
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 259 KMQGYPVFKRITGISE-PVVTKGQEVCSNRL 288
K +GYPV + +TGIS+ P +T+ Q++ + +
Sbjct: 127 KKRGYPVVEEVTGISDTPSLTEIQDIAQSAI 157
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
0.310 0.125 0.344
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,601,163
Number of Sequences: 62578
Number of extensions: 347478
Number of successful extensions: 1193
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 1176
Number of HSP's gapped (non-prelim): 48
length of query: 310
length of database: 14,973,337
effective HSP length: 99
effective length of query: 211
effective length of database: 8,778,115
effective search space: 1852182265
effective search space used: 1852182265
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (24.3 bits)