Aligments for a candidate for aceA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Aligments for a candidate for aceA in Escherichia coli BW25113

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate 18042 b4014 malate synthase (NCBI)

Query= SwissProt::Q10663
         (968 letters)



>lcl|FitnessBrowser__Keio:18042 b4014 malate synthase (NCBI)
          Length = 533

 Score =  495 bits (1275), Expect = e-144
 Identities = 263/513 (51%), Positives = 336/513 (65%), Gaps = 9/513 (1%)

Query: 453 DEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQGW 512
           +++ILT +A+ FL +L T F P+R +LL+ R Q Q DI+N    PDF  ET  +R D  W
Sbjct: 21  EKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGT-LPDFISETASIR-DADW 78

Query: 513 KGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLYD 572
           K   IP DL+DRRVEITGP +RKMVINA+N+   VFMADFEDS +P W   ++GQINL D
Sbjct: 79  KIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPDWNKVIDGQINLRD 138

Query: 573 AVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVFH 632
           AV   ISYT+   K  Y L    AVL  R RG HLPEKHV    +   GSLFDF L+ FH
Sbjct: 139 AVNGTISYTNEAGKI-YQLKPNPAVLICRVRGLHLPEKHVTWRGEAIPGSLFDFALYFFH 197

Query: 633 NAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASFQ 692
           N +AL+A+GSGPYFYLPK QS +EA  W++VF Y ED+  L RGTIK T+LIE L A FQ
Sbjct: 198 NYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLPAVFQ 257

Query: 693 LHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVIK 752
           + EI+HAL+D+IVGLNCGRWDYIFSYIKT +N+   +LPDR  + M  PF+  YS  +IK
Sbjct: 258 MDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIK 317

Query: 753 ACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLAK 812
            CH RG  AMGGMAA IP K D+  N++    V+ADK  EA +GHDGTW+AHPGL   A 
Sbjct: 318 TCHKRGAFAMGGMAAFIPSK-DEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAM 376

Query: 813 RVFDQMM-PKPNQISKNLTR-ANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRGT 870
            VF+ ++  + NQ+     + A  T + L    +G RTE G R NI V + Y+++W+ G 
Sbjct: 377 AVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRANIRVAVQYIEAWISGN 436

Query: 871 GCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAETERRLIRAGS 930
           GCVP+Y LMEDAATAEISR  +WQW+HH   L +G+ +   L +Q +  E +      G 
Sbjct: 437 GCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFRQMLGEEMKVIASELGE 496

Query: 931 ---VVNRIPEAADLLEKFVTEEKMSDFLTTDAY 960
                 R  +AA L+E+  T +++ DFLT   Y
Sbjct: 497 ERFSQGRFDDAARLMEQITTSDELIDFLTLPGY 529


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: 1200
Number of extensions: 49
Number of successful extensions: 6
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: 533
Length adjustment: 40
Effective length of query: 928
Effective length of database: 493
Effective search space:   457504
Effective search space used:   457504
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, 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