Alignments for a candidate for aceA in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Amycolatopsis halophila YIM 93223

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate WP_034273407.1 AMYHA_RS19760 malate synthase A

Query= SwissProt::Q10663
         (968 letters)



>NCBI__GCF_000504245.1:WP_034273407.1
          Length = 524

 Score =  461 bits (1185), Expect = e-134
 Identities = 247/517 (47%), Positives = 342/517 (66%), Gaps = 12/517 (2%)

Query: 452 GDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQG 511
           GDE ILTP+AL F+ +L+  F  RR  L+  R   + +    +   DF  ET+ +R    
Sbjct: 14  GDE-ILTPEALAFVGELHKAFAARRNELVRARTD-RRNAAAKVGKLDFLPETKDVREGD- 70

Query: 512 WKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLY 571
           W+ A  P  L++RRVEITGPTDRKM INAMNSGA V++AD ED+N+P W N + GQ+NLY
Sbjct: 71  WQVAGAPEALRNRRVEITGPTDRKMTINAMNSGAKVWLADLEDANTPHWSNVVSGQVNLY 130

Query: 572 DAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVF 631
           DA R  IS      K E   + +   + VRPRGWHLPE+++ +  +   G+L DFGL  F
Sbjct: 131 DAARETISLDTGAKKYELRDDVERPTIVVRPRGWHLPERNITVDGETAVGALVDFGLHFF 190

Query: 632 HNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASF 691
           HNAK L  +G+GP++YLPK++S  EA+LW DVF + + +LG+  GT++ TVLIE + A+F
Sbjct: 191 HNAKYLTEKGTGPFYYLPKMESHLEARLWNDVFTHAQAELGIPHGTVRATVLIETIPAAF 250

Query: 692 QLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQN-HRKFLLPDRFQIGMTAPFMRNYSLEV 750
           ++ EI++ L+D+  GLN GRWDY+FS IK F++  +KF LPDR  + MTAPFMR Y+  +
Sbjct: 251 EMEEILYELRDHAAGLNAGRWDYLFSVIKYFRDAGQKFTLPDRNSVTMTAPFMRAYTELL 310

Query: 751 IKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPL 810
           ++ CH RG  A+GGMAA IP K  +V N+KA+A V  DK REA DG DG+WVAHPG+V L
Sbjct: 311 VRTCHKRGAMAIGGMAAFIPSKDPEV-NEKAYAKVTDDKNREANDGFDGSWVAHPGMVSL 369

Query: 811 AKRVFDQMM-PKPNQISKNLTRANCTKEDLTVIPE--GTRTEAGFRHNISVTLGYLDSWL 867
            +  FD+++  KPNQ+ +     + T E L  + E  G+ TEAG R  + V + Y+ SWL
Sbjct: 370 CREQFDKVLGDKPNQVDRKREDVSVTAEQLLAVEETPGSCTEAGLRGAVDVGVRYIASWL 429

Query: 868 RGTGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAETERRLIR 927
            G G   ++NLMEDAATAEISR+QLWQW+++  +LE G  + A LV++ + AET + L  
Sbjct: 430 GGNGAAAIHNLMEDAATAEISRSQLWQWVNNGVELEGGVKVTADLVRE-VLAETRKEL-- 486

Query: 928 AGSV-VNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963
           AG +    +  AA+L E+    ++  DFLT  AYDR+
Sbjct: 487 AGEIDTELLDPAAELFEQVALADEFPDFLTLPAYDRI 523


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: 1202
Number of extensions: 64
Number of successful extensions: 7
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: 524
Length adjustment: 39
Effective length of query: 929
Effective length of database: 485
Effective search space:   450565
Effective search space used:   450565
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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 2024 update 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 original 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