GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Desulfovibrio vulgaris Miyazaki F

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 8500663 DvMF_1411 aminotransferase class I and II (RefSeq)

Query= BRENDA::Q8YTF2
         (403 letters)



>FitnessBrowser__Miya:8500663
          Length = 394

 Score =  362 bits (930), Expect = e-105
 Identities = 177/381 (46%), Positives = 250/381 (65%), Gaps = 3/381 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           R+ +LPPYVFA ++ELK + R Q +D++DLGMGNPD  TPQ +VD  ++A     NH Y 
Sbjct: 6   RMHRLPPYVFATVNELKMQLRRQNVDIVDLGMGNPDIPTPQHIVDKLVEASGKGVNHRYS 65

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
              G  + R+AI +WY RR+GV LDPD+EA+  +G+KEGLSHL++A ++PGDVV  P P 
Sbjct: 66  VSRGIPNLRKAICDWYMRRFGVYLDPDTEAVATMGAKEGLSHLSLAMLSPGDVVFAPDPT 125

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H   P+IAG  V  + +    D+  DL     +   + K+L+ +YP NPT   A  E
Sbjct: 126 YPIHTYAPIIAGADVRRIPIGRGRDFFEDLLVATRQTWPQPKLLFISYPHNPTCEIAAPE 185

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           FF+++V FA++++I ++HD  YA+LAFDG+ P S ++  GAKD+GVEF ++SK+Y+MAGW
Sbjct: 186 FFQKVVDFAKEHKIYVIHDFAYADLAFDGHMPPSFMQAEGAKDVGVEFFSMSKSYSMAGW 245

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           RVGF VGNR ++  L  +K+ LDYG F  +Q AA  AL  P   + E+   YR RRD LI
Sbjct: 246 RVGFCVGNRDLVYALTRIKSYLDYGHFQPIQIAATVALNGPQECVTEIVDTYRKRRDVLI 305

Query: 311 QGLGELGWDVPKTKATMYLWVKCPV---GMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +GLG  GW VP  K TM++W + P     MGS +F+  LL++  V V+PG  FG  G+ +
Sbjct: 306 EGLGRAGWVVPPPKGTMFVWAQIPEEFRAMGSVEFSKLLLKEGHVAVSPGLGFGAHGDDH 365

Query: 368 VRISLIADCDRLGEALDRIKQ 388
           VR +LI +  R  +A+  IK+
Sbjct: 366 VRFALIENEHRTKQAMKGIKK 386


Lambda     K      H
   0.321    0.140    0.427 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 485
Number of extensions: 24
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 403
Length of database: 394
Length adjustment: 31
Effective length of query: 372
Effective length of database: 363
Effective search space:   135036
Effective search space used:   135036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory