Alignments for a candidate for mcmA in Brevundimonas sp. GW460-12-10-14-LB2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Brevundimonas sp. GW460-12-10-14-LB2

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_066550723.1 A4249_RS02490 methylmalonyl-CoA mutase

Query= BRENDA::Q84FZ1
         (721 letters)



>NCBI__GCF_001636925.1:WP_066550723.1
          Length = 719

 Score =  989 bits (2556), Expect = 0.0
 Identities = 499/716 (69%), Positives = 581/716 (81%), Gaps = 3/716 (0%)

Query: 6   PDFASVAYAADGFKAPPPPAGEPWMTPEGIPVKGFYGPEDREGCEGIDSFPGLPPYLRGP 65
           PDF+ +A   D       P  +PW+TPEG+ V+  YGP+  E  +     PG  P++RGP
Sbjct: 4   PDFSKIALNLDA--TGQGPTRDPWLTPEGLTVETAYGPDSTEALDHPHGLPGFAPFVRGP 61

Query: 66  YPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVSG 125
           YP MY   PWTIRQYAGFSTAE+SNAFYRRNLAAGQKGLS+AFDLATHRGYDSDHPRV G
Sbjct: 62  YPTMYAGNPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSIAFDLATHRGYDSDHPRVKG 121

Query: 126 DVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIVAAEEQGVPPEKLAG 185
           DVGMAGVAIDSIYDMRTLF GIPLD+M+VSMTMNGAVLP +ALY+VAAEEQGVP  KL G
Sbjct: 122 DVGMAGVAIDSIYDMRTLFDGIPLDQMSVSMTMNGAVLPILALYVVAAEEQGVPHAKLTG 181

Query: 186 TIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISISGYHMQEAGATQDL 245
           TIQNDILKEFMVRNTYIYPP+ SMRII+DIF +T++  PKFNSISISGYHMQEAGA+ D+
Sbjct: 182 TIQNDILKEFMVRNTYIYPPEPSMRIIADIFAWTAQETPKFNSISISGYHMQEAGASADI 241

Query: 246 ELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAKMRAARLIWAKLVKE 305
           ELAYTLADG+EY++AG+AAG+ ID+FAPRLSFFWAIGMN+FME+AKMRA RL+WA+ V++
Sbjct: 242 ELAYTLADGIEYLRAGVAAGMPIDRFAPRLSFFWAIGMNYFMEVAKMRAGRLLWAEAVRK 301

Query: 306 FEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGTQSLHTNALDEALAL 365
                 KSL LR H QTSGWSL AQDVFNNV RT +EAMAA  G TQSLHTNALDEALAL
Sbjct: 302 EGGVDPKSLSLRAHCQTSGWSLAAQDVFNNVPRTMVEAMAAAGGQTQSLHTNALDEALAL 361

Query: 366 PTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARAWEHIREVEALGGMA 425
           PTDFSARIARNTQ+ LQQE+G TR+IDPWGGS+YVERLT ++A RA  H+ EVEALGGMA
Sbjct: 362 PTDFSARIARNTQILLQQETGLTRVIDPWGGSFYVERLTHELAERARAHMAEVEALGGMA 421

Query: 426 KAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDLLRVDNADVRAKQID 485
           KAIEAGIPKLRIEE+AA+ QARID+G+QT+VG+NKY       I +L+VDNA V A QID
Sbjct: 422 KAIEAGIPKLRIEESAAKTQARIDTGQQTVVGVNKYLNPVVDDIPMLKVDNAAVLAAQID 481

Query: 486 KLKRLRAERNQADVDAALAALTKAADGEGNLLELAVNAARAKATVGEISEALEKAWGRHR 545
           KLKRLRAER+QA  DAAL ALT+ A G  NLLELAV AARAKATVGEIS+ALE A+GRH 
Sbjct: 482 KLKRLRAERDQATTDAALNALTEGARGNANLLELAVQAARAKATVGEISDALEAAFGRHV 541

Query: 546 AQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAKMGQDGHDRGQKVIAS 605
           A ++++SGVY +E  G      + R +V  F ENDG  PRIL+AK+GQDGHDRGQKV+A+
Sbjct: 542 ATVQTVSGVYAKE-AGKDARFARAREMVATFVENDGGPPRILIAKLGQDGHDRGQKVVAT 600

Query: 606 AFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTLVPELKAALKQEGRDD 665
            + DLGFDV  G LF TP EAA++AVE  VH VG SSLAAGHLTLVPELKA L++ GR D
Sbjct: 601 GYGDLGFDVTAGSLFQTPSEAAQEAVEKGVHAVGASSLAAGHLTLVPELKAELEKLGRPD 660

Query: 666 VMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNTRLGYGERQAAE 721
           +MIVVGGVIPP D   L   GA+A++PPG+ IA+ AV+L+ +LN RLGY +   A+
Sbjct: 661 IMIVVGGVIPPSDVQPLLDMGAAAVYPPGSAIADTAVDLIEKLNQRLGYAQPAPAK 716


Lambda     K      H
   0.318    0.134    0.391 

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: 1390
Number of extensions: 40
Number of successful extensions: 2
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: 721
Length of database: 719
Length adjustment: 40
Effective length of query: 681
Effective length of database: 679
Effective search space:   462399
Effective search space used:   462399
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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 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

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 catabolism of small carbon sources