Alignments for a candidate for tyrB in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for tyrB in Azospirillum brasilense Sp245

Align Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase; Aspartate 4-decarboxylase; Asd; AsdP; EC 2.6.1.1; EC 4.1.1.12 (characterized)
to candidate AZOBR_RS30390 AZOBR_RS30390 aspartate aminotransferase

Query= SwissProt::Q53IZ1
         (531 letters)



>FitnessBrowser__azobra:AZOBR_RS30390
          Length = 543

 Score =  783 bits (2023), Expect = 0.0
 Identities = 381/524 (72%), Positives = 444/524 (84%)

Query: 2   SKDYRSLANLSPFELKDELIKVASGKANRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAE 61
           S DY   A LSPFELKDELIK+ASG+ NRLMLNAGRGNPNFLAT PRRAFFRLGLFA AE
Sbjct: 3   SIDYSRYAKLSPFELKDELIKLASGRENRLMLNAGRGNPNFLATLPRRAFFRLGLFAVAE 62

Query: 62  SELSYSYMTVGVGGLAKLDGIEGRFERFIAEHRDQEGVKFLGKSLSYVRDQLGLDPAAFL 121
           +ELS+SYM  GVGGL +L+GIEGRFER+++EHRDQEGV FLG++LSYVRDQLGL  + FL
Sbjct: 63  AELSFSYMPNGVGGLPRLEGIEGRFERYVSEHRDQEGVVFLGRALSYVRDQLGLSGSGFL 122

Query: 122 HEMVDGILGCNYPVPPRMLTVSEQIVRQYIVREMAGGAVPPESVDLFAVEGGTAAMAYIF 181
           HEMV+G+LG NYPVPPRML +SE +VR Y+V+EM GG +PP SVDLFAVEGGTAAM YIF
Sbjct: 123 HEMVEGVLGANYPVPPRMLAISEDVVRHYLVKEMVGGFLPPGSVDLFAVEGGTAAMTYIF 182

Query: 182 ESLRISGLLKAGDKVAIGMPVFTPYIEIPELAQYDLKEVPIHADPDNGWQYSDAELDKLK 241
            S++ +GL++ GDKVAIG+PVFTPYIEIPEL +Y L EV I+ADP  GWQY DAELDKLK
Sbjct: 183 NSMKQNGLVERGDKVAIGLPVFTPYIEIPELDEYGLTEVAINADPAKGWQYPDAELDKLK 242

Query: 242 DPDVKIFFCVNPSNPPSVKMDQRSLDRVRAIVAEQRPDLLILTDDVYGTFADEFQSLFSV 301
           DP VK+FFCVNPSNPPSVKMD RSLDR+ AIV  +R DL+ILTDDVYGTFAD F+SLF+V
Sbjct: 243 DPAVKVFFCVNPSNPPSVKMDDRSLDRIAAIVKNERKDLIILTDDVYGTFADNFRSLFAV 302

Query: 302 CPRNTLLVYSFSKYFGATGWRLGVIAAHKDNVFDHALSQLPESAKKALDHRYRSLLPDVR 361
           CP NT+LVYSFSKYFGATGWRLGVIA HK NV D  ++ LPE  K ALD RY SL+PDVR
Sbjct: 303 CPENTMLVYSFSKYFGATGWRLGVIATHKTNVCDQRIAALPEERKAALDRRYGSLVPDVR 362

Query: 362 SLKFIDRLVADSRVVALNHTAGLSTPQQVQMVLFSLFALMDEADAYKQALKQLIRRREAT 421
            L+FIDRLVADSR VALNHTAGLSTPQQVQMVLFSLFALMDE D YK  LK++IRRREA 
Sbjct: 363 GLRFIDRLVADSRTVALNHTAGLSTPQQVQMVLFSLFALMDEQDGYKAELKKVIRRREAA 422

Query: 422 LYRELGMPPLENPNSVNYYTLIDLQNVTCRLYGEAFSQWAVQQSSTGDMLFRVADETGIV 481
           LYRELG+P L +PN+V+YYTL+DL+++  +LYG  ++ W        D+LFR+A ETGIV
Sbjct: 423 LYRELGLPTLSDPNAVDYYTLLDLEDIALKLYGPDYAAWVKANFVPNDLLFRIAAETGIV 482

Query: 482 LLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRRLADELYEQY 525
           LLPG+GFG+ +P+ R SLANLNEYEYAAIGR+LR +AD+ +E++
Sbjct: 483 LLPGKGFGTLQPAARVSLANLNEYEYAAIGRSLRGMADQSHEEF 526


Lambda     K      H
   0.321    0.138    0.400 

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: 909
Number of extensions: 27
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: 531
Length of database: 543
Length adjustment: 35
Effective length of query: 496
Effective length of database: 508
Effective search space:   251968
Effective search space used:   251968
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Candidates (tab-delimited)
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
the source code
instructions for running GapMind on your computer
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