GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate AZOBR_RS23800 AZOBR_RS23800 2-keto-4-methylthiobutyrate aminotransferase

Query= CharProtDB::CH_012531
         (298 letters)



>FitnessBrowser__azobra:AZOBR_RS23800
          Length = 270

 Score =  148 bits (374), Expect = 1e-40
 Identities = 103/275 (37%), Positives = 144/275 (52%), Gaps = 13/275 (4%)

Query: 6   IFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEI 65
           ++LNG  +P +EA++   D G+  GDG+FE IRV  G    L  HL RL +SA  + L +
Sbjct: 4   VWLNGCLLPAEEARIDPADRGFTLGDGLFETIRVAGGTARHLGRHLARLADSAALLGLPL 63

Query: 66  PYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQ 125
           P+    +       I       G +R+ ++RG G  G+ P     P ++     ++L P 
Sbjct: 64  PHDAAALAVAAEALIAAQGRVEGVLRITLTRGTGARGVLPPVDAVPTLL-----MTLAPA 118

Query: 126 EYYEKGIP-VVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVA 184
                 +  V+   TRRN    LS +VKSLNYL++IL R EA   G  EAL+LN  G +A
Sbjct: 119 PPPAGPVEAVIARTTRRNEHSPLS-RVKSLNYLDSILARQEAATRGAGEALLLNGAGRLA 177

Query: 185 EGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEV 244
           E S  N+FIV+  + +TPP + GAL GI R  ILE G     D  E   +  D+  A+E 
Sbjct: 178 ESSVANLFIVRDGRPLTPPVAEGALPGIRRALILERG-----DAGEAPLSVTDLLGAEEA 232

Query: 245 FLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEE 279
           FLT     +  +  VDGR IG G  GP T  LL++
Sbjct: 233 FLTNILG-LRPLLRVDGRAIGAGTVGPVTAALLKD 266


Lambda     K      H
   0.317    0.138    0.390 

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: 185
Number of extensions: 7
Number of successful extensions: 3
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: 298
Length of database: 270
Length adjustment: 26
Effective length of query: 272
Effective length of database: 244
Effective search space:    66368
Effective search space used:    66368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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