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= 016486
(388 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NWJ|A Chain A, Crystal Structure Of Shikimate Kinase From Arabidopsis
Thaliana (Atsk2)
pdb|3NWJ|B Chain B, Crystal Structure Of Shikimate Kinase From Arabidopsis
Thaliana (Atsk2)
Length = 250
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 3/105 (2%)
Query: 184 LKGTSIFLVGDSTEVNEKVALELAVGLGYTPLSTKELLETFAKQTIDSWMLAEGSDSVVN 243
L G S++LVG V +A LGYT L+E K T + + +SV
Sbjct: 46 LNGRSMYLVGMMGSGKTTVGKIMARSLGYTFFDCDTLIEQAMKGTSVAEIFEHFGESVFR 105
Query: 244 -GECDVLESLSSHVRAVVATLGGQQGAAARADKWQHLYAGFTVWL 287
E + L+ LS VV + GG GA R W++++ G ++WL
Sbjct: 106 EKETEALKKLSLMYHQVVVSTGG--GAVIRPINWKYMHKGISIWL 148
>pdb|1SHK|A Chain A, The Three-dimensional Structure Of Shikimate Kinase From
Erwinia Chrysanthemi
pdb|2SHK|A Chain A, The Three-Dimensional Structure Of Shikimate Kinase From
Erwinia Chrysanthemi Complexed With Adp
pdb|1SHK|B Chain B, The Three-dimensional Structure Of Shikimate Kinase From
Erwinia Chrysanthemi
pdb|2SHK|B Chain B, The Three-Dimensional Structure Of Shikimate Kinase From
Erwinia Chrysanthemi Complexed With Adp
Length = 173
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 189 IFLVGDSTEVNEKVALELAVGLGYTPLSTKELLETFAKQTIDSWMLAEGSDSVVNGECDV 248
IF+VG V ELA LGY + T ++ + T+ + AEG E +
Sbjct: 5 IFMVGARGCGKTTVGRELARALGYEFVDTDIFMQHTSGMTVADVVAAEGWPGFRRRESEA 64
Query: 249 LESLSSHVRAVVATLGG 265
L+++++ R VVAT GG
Sbjct: 65 LQAVATPNR-VVATGGG 80
>pdb|1E6C|A Chain A, K15m Mutant Of Shikimate Kinase From Erwinia Chrysanthemi
pdb|1E6C|B Chain B, K15m Mutant Of Shikimate Kinase From Erwinia Chrysanthemi
Length = 173
Score = 31.2 bits (69), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 189 IFLVGDSTEVNEKVALELAVGLGYTPLSTKELLETFAKQTIDSWMLAEGSDSVVNGECDV 248
IF+VG V ELA LGY + T ++ + T+ + AEG E +
Sbjct: 5 IFMVGARGCGMTTVGRELARALGYEFVDTDIFMQHTSGMTVADVVAAEGWPGFRRRESEA 64
Query: 249 LESLSSHVRAVVATLGG 265
L+++++ R VVAT GG
Sbjct: 65 LQAVATPNR-VVATGGG 80
>pdb|1Q25|A Chain A, Crystal Structure Of N-terminal 3 Domains Of Ci-mpr
pdb|1SYO|A Chain A, N-Terminal 3 Domains Of Ci-Mpr Bound To Mannose
6-Phosphate
pdb|1SYO|B Chain B, N-Terminal 3 Domains Of Ci-Mpr Bound To Mannose
6-Phosphate
pdb|1SZ0|A Chain A, N-Terminal 3 Domains Of Ci-Mpr Bound To Mannose
6-Phosphate
pdb|1SZ0|B Chain B, N-Terminal 3 Domains Of Ci-Mpr Bound To Mannose
6-Phosphate
Length = 432
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 32/140 (22%), Positives = 59/140 (42%), Gaps = 16/140 (11%)
Query: 21 ISKSETQHFSSPRHSVSIFKPIFISSSLHKSTNVVPIKTHDRRRFTCSNSLSSIPANTSQ 80
++ ++ H+ R + + K IF K+ VP DR + L+ + +
Sbjct: 106 VTATDCVHYFEWRTTAACKKNIF------KANKEVPCYAFDRELK--KHDLNPLIKTSGA 157
Query: 81 YEFSDGSAEIELRLQLGSLEIQSSKDIFVDADGTCLTVRVNRSGSFITLIETNQLFDKIK 140
Y D + SL I +DI V + VRV +G+ L+ ++ FD +
Sbjct: 158 YLVDDSDPDT-------SLFINVCRDIEV-LRASSPQVRVCPTGAAACLVRGDRAFDVGR 209
Query: 141 PTETIWYIDEDQLVINLKKQ 160
P E + + D+LV++ K+
Sbjct: 210 PQEGLKLVSNDRLVLSYVKE 229
>pdb|1WTD|A Chain A, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Dna- Free Form
pdb|1WTD|B Chain B, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Dna- Free Form
pdb|1WTE|A Chain A, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Complexed With Cognate Dna
pdb|1WTE|B Chain B, Crystal Structure Of Type Ii Restrcition Endonuclease,
Ecoo109i Complexed With Cognate Dna
Length = 272
Score = 28.1 bits (61), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 278 HLYAG--FTVWLSQTEAMDENSAKEEARRHVKDGKLGYSNADVVVKLQ 323
H+YAG F WL+ EA ++ E R VK+ + N D++ K +
Sbjct: 196 HVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFK 243
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
0.313 0.128 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,147,975
Number of Sequences: 62578
Number of extensions: 429313
Number of successful extensions: 830
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 828
Number of HSP's gapped (non-prelim): 10
length of query: 388
length of database: 14,973,337
effective HSP length: 101
effective length of query: 287
effective length of database: 8,652,959
effective search space: 2483399233
effective search space used: 2483399233
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: 52 (24.6 bits)