Alignments for a candidate for aceA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Dyella japonica UNC79MFTsu3.2

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate N515DRAFT_4124 N515DRAFT_4124 malate synthase

Query= SwissProt::Q10663
         (968 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4124
          Length = 543

 Score =  540 bits (1390), Expect = e-157
 Identities = 283/524 (54%), Positives = 345/524 (65%), Gaps = 15/524 (2%)

Query: 452 GDEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQG 511
           G E ILTP AL FL DL+  FN RRL LL+ R   QA  +     PDF  +T  +R  + 
Sbjct: 22  GHESILTPAALAFLADLHHRFNDRRLDLLAARRTRQARYDAGE-LPDFRADTLAIREGR- 79

Query: 512 WKGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLY 571
           W   +IP  LQDRRVEITGP +RKM+INA+NSGA VFMADFEDS++PT  NQ +GQINL 
Sbjct: 80  WTVGKIPAALQDRRVEITGPVERKMIINALNSGAKVFMADFEDSSAPTLANQFDGQINLR 139

Query: 572 DAVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVF 631
           DAV   I YT P  K  Y +    AVL VRPRGWHLPE+H+ +  +P SG+L DFGL+ F
Sbjct: 140 DAVNGTIGYTSPEGKT-YRVGHDPAVLVVRPRGWHLPERHLTVDGEPMSGALVDFGLYAF 198

Query: 632 HNAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASF 691
           HNA+AL A+  GPYFYLPKL++ EEA LW +     E+ LGL    +K TVLIE L A F
Sbjct: 199 HNARALQARDRGPYFYLPKLEAMEEAALWHEAMAAAEEALGLPAHCMKATVLIETLPAVF 258

Query: 692 QLHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVI 751
           Q+HEI+HAL++  VGLNCGRWDYIFSY+KTF+ HR  LLP+R Q+ MT PF++ YS  +I
Sbjct: 259 QMHEILHALRERAVGLNCGRWDYIFSYLKTFRGHRDRLLPERGQVLMTVPFLKAYSELLI 318

Query: 752 KACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLA 811
           + CH RG  AMGGMAAQIPIK D+ AN+ A A VRADK RE   GHDGTWVAHP LVP+A
Sbjct: 319 QTCHRRGAFAMGGMAAQIPIKGDEAANEAALAKVRADKLREVQAGHDGTWVAHPALVPVA 378

Query: 812 KRVFDQMMPKPNQISKNLTRANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRGTG 871
           + +FDQ MP PNQ++        +++ L     GT + AGF +N+ V L Y  +WL G G
Sbjct: 379 REIFDQYMPSPNQLNVARADVQASRDQLIAPCAGTISRAGFDNNVEVALRYTAAWLDGLG 438

Query: 872 CVPLYNLMEDAATAEISRAQLWQWLHHDA------------KLEDGRTIDAGLVKQTIAA 919
           CVP+++LMEDAATAEI+RAQLWQWLHH              +  D   ID  L  Q +AA
Sbjct: 439 CVPIHHLMEDAATAEIARAQLWQWLHHPGNPAGGTPAGDGLEFTDHAPIDFALFDQALAA 498

Query: 920 ETERRLIRAGSVVNRIPEAADLLEKFVTEEKMSDFLTTDAYDRL 963
            T R          R  +AA LL      E++ DFLT  AYDRL
Sbjct: 499 HTHRLRASTHPGAARADDAAALLATLTHAEQLGDFLTLPAYDRL 542


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: 1251
Number of extensions: 51
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: 543
Length adjustment: 40
Effective length of query: 928
Effective length of database: 503
Effective search space:   466784
Effective search space used:   466784
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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Candidates (tab-delimited)
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