GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate AZOBR_RS06555 AZOBR_RS06555 GntR family transcriptional regulator

Query= reanno::azobra:AZOBR_RS06555
         (404 letters)



>FitnessBrowser__azobra:AZOBR_RS06555
          Length = 404

 Score =  806 bits (2081), Expect = 0.0
 Identities = 404/404 (100%), Positives = 404/404 (100%)

Query: 1   VTVDWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQ 60
           VTVDWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQ
Sbjct: 1   VTVDWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQ 60

Query: 61  SNSGAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGP 120
           SNSGAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGP
Sbjct: 61  SNSGAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGP 120

Query: 121 GEKILVTRPTYLGALQAFSPYEPQYLSVPGDAEGPDLAAVEAALEQKPKFFYLVPDFQNP 180
           GEKILVTRPTYLGALQAFSPYEPQYLSVPGDAEGPDLAAVEAALEQKPKFFYLVPDFQNP
Sbjct: 121 GEKILVTRPTYLGALQAFSPYEPQYLSVPGDAEGPDLAAVEAALEQKPKFFYLVPDFQNP 180

Query: 181 NGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLF 240
           NGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLF
Sbjct: 181 NGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLF 240

Query: 241 CGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIRR 300
           CGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIRR
Sbjct: 241 CGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHIRR 300

Query: 301 LRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAF 360
           LRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAF
Sbjct: 301 LRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAF 360

Query: 361 VPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLLQTVAA 404
           VPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLLQTVAA
Sbjct: 361 VPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLLQTVAA 404


Lambda     K      H
   0.320    0.138    0.410 

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: 796
Number of extensions: 17
Number of successful extensions: 1
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: 404
Length of database: 404
Length adjustment: 31
Effective length of query: 373
Effective length of database: 373
Effective search space:   139129
Effective search space used:   139129
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