GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Phaeobacter inhibens BS107

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate GFF2997 PGA1_c30460 D-alanine aminotransferase Dat

Query= curated2:Q58414
         (288 letters)



>FitnessBrowser__Phaeo:GFF2997
          Length = 286

 Score =  150 bits (380), Expect = 2e-41
 Identities = 91/272 (33%), Positives = 146/272 (53%), Gaps = 3/272 (1%)

Query: 3   IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62
           +Y+NG ++ E DAK+S+FD G L  DGV+E      G +   + H  RL  S   L +  
Sbjct: 5   VYVNGDYLPEGDAKISIFDRGFLMADGVYEVTSVLGGKLIDFEGHAVRLKRSLDELEMAE 64

Query: 63  PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGV-GDLG-LDPRKCGKPTIFCIAIPMPPL 120
           P +KEE++++  + + +N + +  + L VTRG  GD   + P    KPTI       P L
Sbjct: 65  PCSKEELLEIHRKLVALNEIEEGLVYLQVTRGSDGDRDFVFPSADTKPTIVLFTQNKPGL 124

Query: 121 LGEDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEG 180
                 +     +    +      +K++  L   + K+ A  AG D+A++++D G V EG
Sbjct: 125 ADSPAAKKGAKIISIEDIRWGRRDIKTVQLLYPSMGKMMAKKAGADDAWMIED-GHVTEG 183

Query: 181 TGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFI 240
           T +N + VKNGV+ T P+   IL GITR  V+++A+E  +++ E   T+ +   ADE F 
Sbjct: 184 TSNNAYFVKNGVIVTRPLSNDILHGITRKAVLRMAEEAQMKIEERLFTIEEAKEADEAFT 243

Query: 241 TGTAAEIVPVFEIDGRVINNKQVGEITKKLKE 272
           T  +A ++PV EIDG  + +   G I K+L+E
Sbjct: 244 TSASAFVMPVVEIDGVALGDGTPGPIAKRLRE 275


Lambda     K      H
   0.321    0.143    0.411 

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: 241
Number of extensions: 13
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: 288
Length of database: 286
Length adjustment: 26
Effective length of query: 262
Effective length of database: 260
Effective search space:    68120
Effective search space used:    68120
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: 47 (22.7 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