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= 043250
(507 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana
Length = 176
Score = 114 bits (285), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 69/163 (42%), Positives = 96/163 (58%), Gaps = 8/163 (4%)
Query: 2 YDVFLSFRGEDTRDNFTSILHYVLSLKSIKTFIDD-QLIRGENISHSLLDTIEAXXXXXX 60
YDVFLSFRG DTR NF S L+ L +SI+TF DD +L G+ S L IE
Sbjct: 9 YDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAVV 68
Query: 61 XXXQRYASSRWCLDELLKILECKHNYGQIVIPVFYHVDPSHVRSQSQ--DSSFGKYFSEL 118
+ YA+S WCLDEL+ I++ + V+P+FY V+P+HVR Q+ F K+ S
Sbjct: 69 VVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASRE 128
Query: 119 EKCYPENMQRWKNALTEAANLSGFDSHVIRSESKLIEEIANDV 161
+ PE + +W+ ALT A LSG S +SKL+++IAN++
Sbjct: 129 D---PEKVLKWRQALTNFAQLSGDCSG--DDDSKLVDKIANEI 166
>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
pdb|3OZI|B Chain B, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
Length = 204
Score = 95.1 bits (235), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 55/145 (37%), Positives = 85/145 (58%), Gaps = 7/145 (4%)
Query: 2 YDVFLSFRGEDTRDNFTSILHYVLSLKSIKTF-IDDQLIRGENISHSLLDTIEAXXXXXX 60
Y+VFLSFRG DTR+ FT L+ L I TF DD+L++G+ I +LL I+
Sbjct: 36 YEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYVP 95
Query: 61 XXXQRYASSRWCLDELLKILECK-HNYGQIVIPVFYHVDPSHVRSQSQ--DSSFGKYFSE 117
YA S+WCL EL +I+ + + +I++P+FY VDPS VR Q+ +F K+ ++
Sbjct: 96 IISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHANK 155
Query: 118 LEKCYPENMQRWKNALTEAANLSGF 142
+ + +Q WK+AL + +L G+
Sbjct: 156 FDG---QTIQNWKDALKKVGDLKGW 177
>pdb|2CYA|A Chain A, Crystal Structure Of Tyrosyl-Trna Synthetase From
Aeropyrum Pernix
Length = 364
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 48/118 (40%), Gaps = 21/118 (17%)
Query: 260 RRNIESQLNRLARKKVLIVFDDVSHRRQIESLIGCLDELASGSRV--IITTRDKQVLKTC 317
R ++E + NR+AR V IV + E L G LASG+R+ I V
Sbjct: 3 RVDVEERFNRIARNTVEIVTE--------EELKGL---LASGARIKGYIGYEPSGVAHIG 51
Query: 318 WASQIYQMKELVYADAHKLFCQCAF--------GGDHPDASHTELTDRAIKYAQGVPL 367
W +Y++K+LV A + + GGD R + A GVP+
Sbjct: 52 WLVWMYKVKDLVEAGVDFSVLEATWHAYINDKLGGDMDLIRAAARIVRRVMEAAGVPV 109
>pdb|2HX6|A Chain A, Solution Structure Analysis Of The Phage T4
Endoribonuclease Regb
Length = 153
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 219 NKISRHFEGSYFALN--VREAEETGGIKDLQKKLLSELLNDGNRRNIE 264
NK+ RHFE + +N +REA + G+ K LL+ +R I+
Sbjct: 12 NKLRRHFESEFRQINNEIREASKAAGVSSFHLKYSQALLDRAIQREID 59
>pdb|2A5H|A Chain A, 2.1 Angstrom X-Ray Crystal Structure Of
Lysine-2,3-Aminomutase From Clostridium Subterminale
Sb4, With Michaelis Analog (L-Alpha-Lysine External
Aldimine Form Of Pyridoxal-5'-Phosphate).
pdb|2A5H|B Chain B, 2.1 Angstrom X-Ray Crystal Structure Of
Lysine-2,3-Aminomutase From Clostridium Subterminale
Sb4, With Michaelis Analog (L-Alpha-Lysine External
Aldimine Form Of Pyridoxal-5'-Phosphate).
pdb|2A5H|C Chain C, 2.1 Angstrom X-Ray Crystal Structure Of
Lysine-2,3-Aminomutase From Clostridium Subterminale
Sb4, With Michaelis Analog (L-Alpha-Lysine External
Aldimine Form Of Pyridoxal-5'-Phosphate).
pdb|2A5H|D Chain D, 2.1 Angstrom X-Ray Crystal Structure Of
Lysine-2,3-Aminomutase From Clostridium Subterminale
Sb4, With Michaelis Analog (L-Alpha-Lysine External
Aldimine Form Of Pyridoxal-5'-Phosphate)
Length = 416
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 328 LVYADAHKLFCQ-CA---FGGDHPDASHTELTDRAIKYAQGVPLALKVL--GCHLCGRSK 381
L+ D +C+ C F G D+ E D+AI Y + P VL G S
Sbjct: 119 LLITDXCSXYCRHCTRRRFAGQSDDSXPXERIDKAIDYIRNTPQVRDVLLSGGDALLVSD 178
Query: 382 EEWESAMRKLEVIPHEEI 399
E E + KL IPH EI
Sbjct: 179 ETLEYIIAKLREIPHVEI 196
>pdb|2DY3|A Chain A, Crystal Structure Of Alanine Racemase From Corynebacterium
Glutamicum
pdb|2DY3|B Chain B, Crystal Structure Of Alanine Racemase From Corynebacterium
Glutamicum
pdb|2DY3|C Chain C, Crystal Structure Of Alanine Racemase From Corynebacterium
Glutamicum
pdb|2DY3|D Chain D, Crystal Structure Of Alanine Racemase From Corynebacterium
Glutamicum
Length = 361
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 373 GCHLCGRSKEEWESAMRKLEVIPHEEIQGVL 403
G H G ++EWE L PH E+ G+
Sbjct: 126 GLHRSGVDEQEWEGVFSALAAAPHIEVTGMF 156
>pdb|3UOQ|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
Length = 534
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 346 HPDASHTELTDRAIKYAQGVPLALKVLGCHLCGRSKEEW 384
HPDA T +T++ + + Q + A V G +K +W
Sbjct: 21 HPDAGKTTITEKVLLFGQAIQTAGTVKGRGSNQHAKSDW 59
>pdb|2H5E|A Chain A, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
pdb|2H5E|B Chain B, Crystal Structure Of E.Coli Polypeptide Release Factor Rf3
pdb|2O0F|A Chain A, Docking Of The Modified Rf3 X-Ray Structure Into Cryo-Em
Map Of E.Coli 70s Ribosome Bound With Rf3
pdb|3ZVO|Y Chain Y, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3SFS|W Chain W, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
Length = 529
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 346 HPDASHTELTDRAIKYAQGVPLALKVLGCHLCGRSKEEW 384
HPDA T +T++ + + Q + A V G +K +W
Sbjct: 21 HPDAGKTTITEKVLLFGQAIQTAGTVKGRGSNQHAKSDW 59
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
0.320 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,049,070
Number of Sequences: 62578
Number of extensions: 535300
Number of successful extensions: 1177
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1163
Number of HSP's gapped (non-prelim): 15
length of query: 507
length of database: 14,973,337
effective HSP length: 103
effective length of query: 404
effective length of database: 8,527,803
effective search space: 3445232412
effective search space used: 3445232412
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)