Alignments for a candidate for aceA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Azospirillum brasilense Sp245

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate AZOBR_RS03245 AZOBR_RS03245 malate synthase

Query= SwissProt::Q10663
         (968 letters)



>FitnessBrowser__azobra:AZOBR_RS03245
          Length = 534

 Score =  592 bits (1527), Expect = e-173
 Identities = 295/519 (56%), Positives = 369/519 (71%), Gaps = 5/519 (0%)

Query: 452 GDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQG 511
           G E ILTP+AL FL +L   F   RLRLL  R + +A I+     PDF  ET  +R +  
Sbjct: 17  GVETILTPEALAFLAELEGRFGSERLRLLDVRTKRRALIDQG-HRPDFLPETRAIR-EAD 74

Query: 512 WKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLY 571
           W  A +P DL DRRVEITGP DRKMVINA+NSGA VFMADFEDS+ P+W N +EGQ NL 
Sbjct: 75  WTIAPLPHDLLDRRVEITGPVDRKMVINALNSGAKVFMADFEDSSCPSWANLIEGQANLR 134

Query: 572 DAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVF 631
           DAVR  I++  P + K+Y LN+K AVLKVRPRGWHL EKHV    +P SG+LFDF L+ F
Sbjct: 135 DAVRRTIAFDDPVSGKKYRLNDKTAVLKVRPRGWHLAEKHVRFDGEPVSGALFDFALYAF 194

Query: 632 HNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASF 691
           HNA+ L+A+GSGPYFYLPKL+S  EA+LW +VF   ED L +  G+IK TVL+E +LA+F
Sbjct: 195 HNAQELLARGSGPYFYLPKLESHFEARLWNEVFSVAEDYLKIPHGSIKATVLVETILAAF 254

Query: 692 QLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVI 751
           ++ EI++ L+D+  GLNCGRWDYIFS+IKTF+N    +LPDR ++ M  PF+++YSL  +
Sbjct: 255 EMDEILYELRDHSAGLNCGRWDYIFSFIKTFRNDPAAVLPDRAEVTMATPFLQSYSLLAV 314

Query: 752 KACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLA 811
           K CH RG  A+GGMAA IP+K D  AN+ AF+ VRADKERE ++GHDGTWVAHPGLVP+A
Sbjct: 315 KTCHRRGAPAIGGMAAYIPVKDDPAANETAFSKVRADKEREVSNGHDGTWVAHPGLVPVA 374

Query: 812 KRVFDQMMPKPNQISKNLTRANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRGTG 871
           + VFD  M KPNQI +     + T  DL  +PEG +TE G R+N++V +GYL++WLRG G
Sbjct: 375 REVFDAYMRKPNQIDRKRADVSVTAADLLAVPEGPKTERGLRNNVAVAIGYLEAWLRGIG 434

Query: 872 CVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAETERRLIRAGSV 931
           CVPL+NLMEDAATAEISR QLWQW+HH A L+DGR +   LV +TIA E      R G  
Sbjct: 435 CVPLFNLMEDAATAEISRTQLWQWVHHRATLDDGRPVTMELVDETIAEELAAWKARVGDR 494

Query: 932 V---NRIPEAADLLEKFVTEEKMSDFLTTDAYDRLVSEG 967
                   EAA +L   V  +   DFLT  AYDR+V++G
Sbjct: 495 AFDHGLYEEAAVMLRDLVERDDFVDFLTLPAYDRIVAQG 533


Lambda     K      H
   0.319    0.134    0.402 

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: 1184
Number of extensions: 44
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: 968
Length of database: 534
Length adjustment: 40
Effective length of query: 928
Effective length of database: 494
Effective search space:   458432
Effective search space used:   458432
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: 55 (25.8 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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