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= 026608
(236 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LNJ|A Chain A, Solution Structure Of Cyanobacterial Psbp (Cyanop) From
Synechocystis Sp. Pcc 6803
Length = 170
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 41/159 (25%), Positives = 64/159 (40%), Gaps = 24/159 (15%)
Query: 88 DKKASAEYIYDVPDGWKERLVSKVEKGTNGTDSEFYNPKKRTEKEYLTFLAGFRQLAPKD 147
D K E++Y P+GW + V+ + G D F + +R E L+ P D
Sbjct: 19 DTKDGYEFLY--PNGW---IGVDVKGASPGVDVVFRDLIERDEN-----LSVIISEIPSD 68
Query: 148 AVLNNLAL-SDVDLQDLLASAD--------KVASEEKKDDKGQLYYVYEI-----DGVGS 193
L +L +DV + + D ++ + E +D+ GQ+YY E D V
Sbjct: 69 KTLTDLGTATDVGYRFMKTVNDASQGDRQAELINAEARDEDGQVYYTLEYRVLVGDNVER 128
Query: 194 HSLISVTCANNKLYAHFVNAPTPEWNRDEETLRHVHESF 232
H L SVT KL ++ W+ + V SF
Sbjct: 129 HDLASVTTNRGKLITFDLSTAEDRWDTVKSLFDTVASSF 167
>pdb|2XB3|A Chain A, The Structure Of Cyanobacterial Psbp
Length = 165
Score = 34.3 bits (77), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 165 ASADKVASEEKKDDKGQLYYVYE----IDGVGS-----HSLISVTCANNKLYAHFVNAPT 215
+SA A+ +K DDK YY+ E + G G+ H+L S+ + K+Y V+AP
Sbjct: 88 SSALIAATSQKADDK--TYYILEYAVTLPGDGNTAQQRHNLSSIAVSRGKVYTLSVSAPE 145
Query: 216 PEWNRDEETLRHVHESF 232
W + E+ + + SF
Sbjct: 146 ERWPKVEDQFKTIVSSF 162
>pdb|3CYV|A Chain A, Crystal Structure Of Uroporphyrinogen Decarboxylase From
Shigella Flexineri: New Insights Into Its Catalytic
Mechanism
Length = 354
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 94 EYIYDVPDGWKERLVSKVEKGTNGTDSEFYNPKKRTEKEYLTFLAGF 140
++ D+ D + R+ +KV N S Y P R E+E T LAGF
Sbjct: 270 DWTTDIADA-RRRVGNKVALQGNMDPSMLYAPPARIEEEVATILAGF 315
>pdb|2VTV|A Chain A, Phaz7 Depolymerase From Paucimonas Lemoignei
pdb|2VTV|B Chain B, Phaz7 Depolymerase From Paucimonas Lemoignei
pdb|2X5X|A Chain A, The Crystal Structure Of Phaz7 At Atomic (1.2 Angstrom)
Resolution Reveals Details Of The Active Site And
Suggests A Substrate Binding Mode
pdb|2X76|A Chain A, The Crystal Structure Of Phaz7 At Atomic (1.2 Angstrom)
Resolution Reveals Details Of The Active Site And
Suggests A Substrate Binding Mode
Length = 342
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 100 PDGWKERL-VSKVEKGTNGTDSEFYNPKKRTEKEYLTFLAGFR 141
P+GW + VS G+ T+S P KRT + T AGF+
Sbjct: 199 PEGWYYGVWVSNPWTGSGSTNSMRDMPAKRTAVSFYTLSAGFK 241
>pdb|1S96|A Chain A, The 2.0 A X-Ray Structure Of Guanylate Kinase From E.Coli
pdb|1S96|B Chain B, The 2.0 A X-Ray Structure Of Guanylate Kinase From E.Coli
Length = 219
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 25/74 (33%), Gaps = 6/74 (8%)
Query: 166 SADKVASEEKKDDKGQLYYVYEIDGVGSHSLISVTCANNKLY------AHFVNAPTPEWN 219
+DK+ +G LY V G G SLI LY +H P P
Sbjct: 2 GSDKIHHHHHHXAQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEV 61
Query: 220 RDEETLRHVHESFK 233
E H+ FK
Sbjct: 62 HGEHYFFVNHDEFK 75
>pdb|3QPF|A Chain A, Analysis Of A New Family Of Widely Distributed
Metal-Independent Alpha-Mannosidases Provides Unique
Insight Into The Processing Of N- Linked Glycans,
Streptococcus Pneumoniae Sp_2144 Apo-Structure
pdb|3QPF|B Chain B, Analysis Of A New Family Of Widely Distributed
Metal-Independent Alpha-Mannosidases Provides Unique
Insight Into The Processing Of N- Linked Glycans,
Streptococcus Pneumoniae Sp_2144 Apo-Structure
pdb|3QRY|B Chain B, Analysis Of A New Family Of Widely Distributed
Metal-Independent Alpha Mannosidases Provides Unique
Insight Into The Processing Of N-Linked Glycans,
Streptococcus Pneumoniae Sp_2144 1-Deoxymannojirimycin
Complex
pdb|3QRY|A Chain A, Analysis Of A New Family Of Widely Distributed
Metal-Independent Alpha Mannosidases Provides Unique
Insight Into The Processing Of N-Linked Glycans,
Streptococcus Pneumoniae Sp_2144 1-Deoxymannojirimycin
Complex
pdb|3QSP|A Chain A, Analysis Of A New Family Of Widely Distributed
Metal-Independent Alpha Mannosidases Provides Unique
Insight Into The Processing Of N-Linked Glycans,
Streptococcus Pneumoniae Sp_2144 Non-Productive
Substrate Complex With Alpha-1,6-Mannobiose
pdb|3QSP|B Chain B, Analysis Of A New Family Of Widely Distributed
Metal-Independent Alpha Mannosidases Provides Unique
Insight Into The Processing Of N-Linked Glycans,
Streptococcus Pneumoniae Sp_2144 Non-Productive
Substrate Complex With Alpha-1,6-Mannobiose
Length = 426
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 9/53 (16%)
Query: 154 ALSDVDLQDLLASADKVASEEKK---------DDKGQLYYVYEIDGVGSHSLI 197
AL+ D Q ++A A ++ E ++ + KG+ Y +E+DG+G+ S++
Sbjct: 246 ALNLADSQSVIADAKRLQDEIQEGIKNYAYTTNSKGEKIYAFEVDGLGNASIM 298
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
0.312 0.129 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,406,615
Number of Sequences: 62578
Number of extensions: 204252
Number of successful extensions: 431
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 428
Number of HSP's gapped (non-prelim): 12
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)