Alignments for a candidate for aceA in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Kyrpidia tusciae DSM 2912

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate WP_041303752.1 BTUS_RS05060 malate synthase A

Query= SwissProt::Q10663
         (968 letters)



>NCBI__GCF_000092905.1:WP_041303752.1
          Length = 534

 Score =  576 bits (1485), Expect = e-168
 Identities = 291/512 (56%), Positives = 365/512 (71%), Gaps = 8/512 (1%)

Query: 455 KILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQGWKG 514
           +ILTP AL F+ DL+ +FN RR  LL++R + QA I+     PDF  ET  LR    W  
Sbjct: 23  EILTPGALEFVADLHRQFNGRRQALLAERQKRQAAIDGGQ-MPDFPAETAELRQAD-WTV 80

Query: 515 AEIPRDLQDRRVEITGPT-DRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLYDA 573
           A IP DL DRRVEITGP  DRKMVINA+NSGA  FMADFED+NSPTW N + GQINL DA
Sbjct: 81  APIPADLLDRRVEITGPAGDRKMVINALNSGAKTFMADFEDANSPTWENTVGGQINLRDA 140

Query: 574 VRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVFHN 633
           VR  I Y  P  K+ Y L ++ AVL VRPRGWHLPEKHVL+  +P SG+LFDFGL+ FHN
Sbjct: 141 VRRTIRYVSPEGKR-YELKDRTAVLIVRPRGWHLPEKHVLVDGEPISGALFDFGLYFFHN 199

Query: 634 AKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASFQL 693
            + L+ +G+GPYFYLPK++S  EA+LW DVF   +D+LG+ RGTIK TVLIE +LA+F++
Sbjct: 200 VRELLERGTGPYFYLPKMESRFEARLWNDVFNVAQDRLGIPRGTIKATVLIETILAAFEM 259

Query: 694 HEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVIKA 753
            EI++ L+D+  GLNCGRWDYIFS+IK F+N  + +LPDR  + MTAPFMR Y+   IK 
Sbjct: 260 DEILYELRDHAAGLNCGRWDYIFSFIKRFRNRPEVILPDRGLVTMTAPFMRAYTQLTIKT 319

Query: 754 CHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLAKR 813
           CH RG  A+GGMAAQIP+K+D  AN++AFA VRADKEREATDGHDGTWVAHPGLVP+A  
Sbjct: 320 CHRRGAMAIGGMAAQIPVKNDPAANEEAFAKVRADKEREATDGHDGTWVAHPGLVPVAME 379

Query: 814 VFDQMMPKPNQISKNLTRANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRGTGCV 873
           VFD++MP PNQ+ +     + +  DL  +PEG  TE G R NISV + Y+++WLRG+G V
Sbjct: 380 VFDRLMPTPNQLDRKREDVHVSAADLIRVPEGPITEQGLRTNISVGIQYIEAWLRGSGAV 439

Query: 874 PLYNLMEDAATAEISRAQLWQWLHHD-AKLEDGRTIDAGLVKQTIAAETERRLIRAGS-- 930
           P++NLMEDAATAEISRAQ+WQW+ H    LEDGR +   L +Q +  E  +     G   
Sbjct: 440 PIFNLMEDAATAEISRAQVWQWIRHPRGVLEDGRKVTVELFRQVLDEELNKIKAELGEDR 499

Query: 931 -VVNRIPEAADLLEKFVTEEKMSDFLTTDAYD 961
               R  EAA+L  +  T +  ++FLT   Y+
Sbjct: 500 FAGGRYSEAAELFSRLTTSDSFAEFLTLPGYE 531


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: 1239
Number of extensions: 69
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: 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 10 2024. The underlying query database was built on Apr 09 2024.

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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