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_RS24065 AZOBR_RS24065 aspartate aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__azobra:AZOBR_RS24065
          Length = 392

 Score =  163 bits (412), Expect = 9e-45
 Identities = 115/360 (31%), Positives = 180/360 (50%), Gaps = 10/360 (2%)

Query: 32  GEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYSASKGIPRLRKAICDFYKRRYGVE 91
           GED++ L +G+PD      + D      +  + H Y+   G P LR A+     RR G+ 
Sbjct: 31  GEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTH-YTPIPGRPELRAALARDVARRTGLP 89

Query: 92  LDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPNPTYPIHYYAPIICGGDAISVPILPE 151
           ++PE N I+  GA+ G  +  L ++E GD V+VP P Y + Y A +   G A  VP+ P+
Sbjct: 90  VEPE-NVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMY-LTYEACVRASG-ATLVPVAPD 146

Query: 152 EDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTTLCVDLEFFQEVVKLAKQEGIWIVHD 211
                +    L   +     + +A+ L+ P NPT + +  E  + V  LA++  +W+V D
Sbjct: 147 AATLRLDPAALAAAVTP---RTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVAD 203

Query: 212 FAYADLGFDGYTPPSILQVEGALDVAVELYSMSKGFSMAGWRVAFVVGNEMLIKNLAHLK 271
             YA L FD      I  + G  +  V + S+SK  +M GWR  +VV    L+ ++  L 
Sbjct: 204 EVYASLTFDR-PHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLA 262

Query: 272 SYLDYGVFTPIQVASIIALESPYEVVEKNREIYRRRRDVLVEGLNRV-GWEVKKPKGSMF 330
             + YG+   +Q A+++A+E   E V   RE YRRRRD+ +E L  V G    KP+  MF
Sbjct: 263 LCMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMF 322

Query: 331 VWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGFGEYGEGYVRFALVENEHRIRQAVRGI 390
           +   V    G+ +++F+  L RE  V+V     FG    G VR +   +E  + +A R I
Sbjct: 323 MLVDV-RGTGLPTMEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAELAEACRRI 381


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: 344
Number of extensions: 22
Number of successful extensions: 5
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: 392
Length adjustment: 31
Effective length of query: 371
Effective length of database: 361
Effective search space:   133931
Effective search space used:   133931
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.

Links

Downloads

Related tools

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