GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Pseudomonas simiae WCS417

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate GFF4291 PS417_21975 glutamate-pyruvate aminotransferase

Query= BRENDA::Q8YTF2
         (403 letters)



>lcl|FitnessBrowser__WCS417:GFF4291 PS417_21975 glutamate-pyruvate
           aminotransferase
          Length = 403

 Score =  357 bits (916), Expect = e-103
 Identities = 176/380 (46%), Positives = 248/380 (65%), Gaps = 3/380 (0%)

Query: 11  RIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHGYP 70
           RI +LPPYVF    ELK  AR +G D+IDL MGNPDG TP  +V+  +Q  Q    HGY 
Sbjct: 12  RIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGPTPPHIVEKLVQVAQREDTHGYS 71

Query: 71  PFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPSPA 130
             +G    RRAI+ WY  RY V +DP+SEA+  +GSKEGL+HL +A ++ GD VLVP+P+
Sbjct: 72  TSKGIPRLRRAISRWYKDRYEVDIDPESEAIVTIGSKEGLAHLMLATLDQGDTVLVPNPS 131

Query: 131 YPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAPRE 190
           YP H  G VIAG  V S+ L P  D+  +L         K K++   +PSNPT      +
Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVPGVDFFAELERAIRGSIPKPKMMILGFPSNPTAQCVELD 191

Query: 191 FFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMAGW 250
           FFE ++A A++Y++L++HDL YA++ +DG++  S++++PGAKDI VEF TLSK+YNMAGW
Sbjct: 192 FFERVIALAKQYDVLVIHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKSYNMAGW 251

Query: 251 RVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDFLI 310
           R+GF+VGN  ++  L  +K+  DYG F  LQ AA  AL+     + ++ ++YR RR+ L+
Sbjct: 252 RIGFMVGNPELVNALARIKSYHDYGTFTPLQVAAIAALEGDQQCVKDIAEQYRQRRNVLV 311

Query: 311 QGLGELGWDVPKTKATMYLWVKCP---VGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGY 367
           +GL ELGW V   KA+MY+W K P     +GS +FA  LL +  V V+PG  FG  G+ +
Sbjct: 312 KGLHELGWMVENPKASMYVWAKIPEQYAALGSLEFAKKLLLEAKVCVSPGIGFGEYGDDH 371

Query: 368 VRISLIADCDRLGEALDRIK 387
           VR +LI + DR+ +A+  I+
Sbjct: 372 VRFALIENQDRIRQAVRGIR 391


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: 488
Number of extensions: 28
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: 403
Length adjustment: 31
Effective length of query: 372
Effective length of database: 372
Effective search space:   138384
Effective search space used:   138384
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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