Alignments for a candidate for agx1 in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Azospirillum brasilense Sp245

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate AZOBR_RS07830 AZOBR_RS07830 aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__azobra:AZOBR_RS07830
          Length = 424

 Score =  414 bits (1063), Expect = e-120
 Identities = 207/390 (53%), Positives = 270/390 (69%), Gaps = 4/390 (1%)

Query: 7   FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66
           F ++K+LP YVFA VN +K + R  GEDI+DLGMGNPD P  QHI+DKL E    P  H 
Sbjct: 6   FHRIKRLPPYVFAEVNAMKARARAAGEDIIDLGMGNPDQPTPQHIVDKLIEAVRDPKTHR 65

Query: 67  YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126
           YS S+GIP LRKA   +YKRR+ V++DPE   I+TIG+KEG ++L  A+  PGD ++VPN
Sbjct: 66  YSNSRGIPGLRKAHAAYYKRRFNVDVDPESECIVTIGSKEGLANLAQAITSPGDIILVPN 125

Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFP---EVFLRRLYDLIKTSFRKPKAVVLSFPHN 183
           P+YPIH +  I+ G     +P+          + F+  L   ++ S  KP A+VL++P N
Sbjct: 126 PSYPIHPFGFILAGASVRHLPVGQANGTSTDIDSFMIMLERAVRHSVPKPLALVLNYPSN 185

Query: 184 PTTLCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSM 243
           PT   V L+F++ +V+  ++ GI+I+ D AYA++ FDG  PPSIL++  A +VAVE  SM
Sbjct: 186 PTAEVVGLDFYRPIVEFCRKHGIYILSDLAYAEVFFDGEPPPSILEIPEAREVAVEFTSM 245

Query: 244 SKGFSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREI 303
           SK +SMAGWR+ F  GN+ LI  LA +KSYLDYG FTPIQVA+  AL  P E VE+ R +
Sbjct: 246 SKTYSMAGWRIGFATGNKKLITALARIKSYLDYGAFTPIQVAATAALNGPQECVEQVRTM 305

Query: 304 YRRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVSPGI 362
           YR+RRDV++EGL   GW V  P  SMF WA +PE    + SL+FS  LL+EAKVAV+PGI
Sbjct: 306 YRQRRDVMIEGLASAGWTVPSPSASMFAWAPIPEPFAHLGSLEFSKLLLQEAKVAVAPGI 365

Query: 363 GFGEYGEGYVRFALVENEHRIRQAVRGIKK 392
           GFGEYG+G+VR ALVEN HRIRQA R IK+
Sbjct: 366 GFGEYGDGHVRLALVENVHRIRQATRNIKE 395


Lambda     K      H
   0.322    0.141    0.425 

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: 477
Number of extensions: 19
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: 402
Length of database: 424
Length adjustment: 31
Effective length of query: 371
Effective length of database: 393
Effective search space:   145803
Effective search space used:   145803
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 (21.9 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for Amino acid biosynthesis