Alignments for a candidate for aceA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Shewanella loihica PV-4

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate 5208773 Shew_1275 malate synthase (RefSeq)

Query= SwissProt::Q10663
         (968 letters)



>FitnessBrowser__PV4:5208773
          Length = 544

 Score =  487 bits (1253), Expect = e-141
 Identities = 261/532 (49%), Positives = 334/532 (62%), Gaps = 9/532 (1%)

Query: 438 QDEEILSLTAQNVAGDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFP 497
           Q E  LS+    V G E +L   AL  L  L  +F     +LL  R Q Q  I+     P
Sbjct: 10  QLETGLSILGAPVPGQEIVLNEGALSLLEVLCDQFAAEVPKLLEMRRQKQELIDKGS-LP 68

Query: 498 DFNKETEVLRSDQGWKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNS 557
           DF  ET  +R D  W+   IP+DLQDRRVEITGP DRKM+INA+N+   VFMADFEDS +
Sbjct: 69  DFLPETRAIR-DGDWQIRGIPQDLQDRRVEITGPVDRKMIINALNANVKVFMADFEDSLA 127

Query: 558 PTWRNQLEGQINLYDAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQ 617
           P+W   ++GQINL DAVR  I YT P T K YTL++  AVL  R RG HL EKHV  + +
Sbjct: 128 PSWIKVIQGQINLRDAVRGEIEYTAPETGKHYTLDDDPAVLIARVRGLHLKEKHVAFNGE 187

Query: 618 PTSGSLFDFGLFVFHNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGT 677
              G+LFDF L+ +HN + L+ +GSGPYFY+PKL+S  EA+ WA VF Y E++  L  GT
Sbjct: 188 AIPGALFDFCLYFYHNYRQLLEKGSGPYFYIPKLESHVEARWWAKVFAYVEERFCLTPGT 247

Query: 678 IKCTVLIEHLLASFQLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIG 737
           IKCT LIE L A F++ EI++ L+ NIV LNCGRWDYIFSYIKT + H   +LPDR  + 
Sbjct: 248 IKCTCLIETLPAVFEMEEILYELRSNIVALNCGRWDYIFSYIKTLKKHSDRILPDRQAVT 307

Query: 738 MTAPFMRNYSLEVIKACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGH 797
           M  PF+  YS  +IK CH RG  AMGGMAA IP K DQ  N+     VR DKE EA +GH
Sbjct: 308 MDKPFLSAYSRLLIKTCHKRGALAMGGMAAFIPAK-DQAQNEAVLVKVRGDKELEARNGH 366

Query: 798 DGTWVAHPGLVPLAKRVFDQMMPKPNQISKNLTR---ANCTKEDLTVIPEGTRTEAGFRH 854
           DGTWVAHPGL   A  +F++ + + +    ++TR   A     DL +  EG RTE+G R 
Sbjct: 367 DGTWVAHPGLADTAMGIFNEYIGEDHVNQLHITRDVDAPILARDLLMPCEGERTESGMRL 426

Query: 855 NISVTLGYLDSWLRGTGCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVK 914
           NI + L Y+++W+RG GCVP+Y LMEDAATAEISR  +WQW+ H+ KL +G+ +   L K
Sbjct: 427 NIRIALQYIEAWIRGNGCVPIYGLMEDAATAEISRTSIWQWIQHEQKLSNGKLVTKALFK 486

Query: 915 QTIAAETERRLIRAGS---VVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963
           + +  E     +  G          +AA LLE+  T +++ DFLT   Y+ L
Sbjct: 487 EMLVEELANVKLEVGPDRFTHGSFTQAAVLLEEITTADELVDFLTLPGYEIL 538


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: 1203
Number of extensions: 45
Number of successful extensions: 4
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: 544
Length adjustment: 40
Effective length of query: 928
Effective length of database: 504
Effective search space:   467712
Effective search space used:   467712
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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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