Alignments for a candidate for mcmA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Rhodomicrobium vannielii ATCC 17100

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_013419773.1 RVAN_RS10880 methylmalonyl-CoA mutase

Query= BRENDA::Q84FZ1
         (721 letters)



>NCBI__GCF_000166055.1:WP_013419773.1
          Length = 720

 Score = 1061 bits (2743), Expect = 0.0
 Identities = 536/713 (75%), Positives = 604/713 (84%), Gaps = 3/713 (0%)

Query: 3   SRIPDFASVAYAADGFKAPPPPAGEPWMTPEGIPVKGFYGPEDREGCEGIDSFPGLPPYL 62
           S +PDF+ + +            G P  TPEGI +K  YGP+D +G + ++++PG+ P+L
Sbjct: 4   SPLPDFSKIEWQTPSLAGSS--FGAPAETPEGIKLKPAYGPDDIDGLDFLNTYPGVAPFL 61

Query: 63  RGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPR 122
           RGPYP MYV QPWT+RQYAGFSTAEDSNAFYRRNLAAGQKGLS+AFDLATHRGYDSDHPR
Sbjct: 62  RGPYPTMYVQQPWTVRQYAGFSTAEDSNAFYRRNLAAGQKGLSIAFDLATHRGYDSDHPR 121

Query: 123 VSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIVAAEEQGVPPEK 182
           V GDVGMAGVAIDSIYDMRTLF GIPL EM+VSMTMNGAVLP +AL+IVA EEQGV P +
Sbjct: 122 VRGDVGMAGVAIDSIYDMRTLFDGIPLSEMSVSMTMNGAVLPILALFIVAGEEQGVKPAQ 181

Query: 183 LAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISISGYHMQEAGAT 242
           L+GTIQNDILKEFMVRNTYIYPP  SMRIISDIF YTS+NMPKFNSISISGYHMQEAGAT
Sbjct: 182 LSGTIQNDILKEFMVRNTYIYPPLPSMRIISDIFAYTSQNMPKFNSISISGYHMQEAGAT 241

Query: 243 QDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAKMRAARLIWAKL 302
            DLELAYTLADGVEY +AG AAGL ID FAPRLSFFWAIGMN+FME+AKMRA R +WA+L
Sbjct: 242 ADLELAYTLADGVEYARAGKAAGLGIDAFAPRLSFFWAIGMNYFMEVAKMRAGRALWARL 301

Query: 303 VKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGTQSLHTNALDEA 362
           +K    KS KS+ LR H QTSGWSLTAQDVFNNVTRTC+EA AAT GGTQSLHTNALDEA
Sbjct: 302 MKAEGAKSSKSMSLRAHCQTSGWSLTAQDVFNNVTRTCVEAFAATHGGTQSLHTNALDEA 361

Query: 363 LALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARAWEHIREVEALG 422
           LALPTDFSARIARNTQLF++ E+GTTR IDPWGGSYYVERLT ++A +AWEHI EVE LG
Sbjct: 362 LALPTDFSARIARNTQLFIEYETGTTRTIDPWGGSYYVERLTYELAKKAWEHIEEVERLG 421

Query: 423 GMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDLLRVDNADVRAK 482
           GMAKAI+AG+PKLRIEEAAAR QARIDSG+Q IVG+N+++P DE  I++L+VDN+ VRA 
Sbjct: 422 GMAKAIDAGVPKLRIEEAAARTQARIDSGKQIIVGVNRFQPVDEAPIEVLKVDNSAVRAA 481

Query: 483 QIDKLKRLRAERNQADVDAALAALTK-AADGEGNLLELAVNAARAKATVGEISEALEKAW 541
           QI+KL+RLRAER+ A V A L ALT  AA G GNLL LAV+AARA ATVGEIS+ALEK +
Sbjct: 482 QIEKLERLRAERDGAKVAATLEALTNAAASGSGNLLALAVDAARAMATVGEISDALEKVY 541

Query: 542 GRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAKMGQDGHDRGQK 601
           GRHRA+ R+ISGVY+ EVG M   V  V  + +AFE+ DGRRPR+LVAK+GQDGHDRGQK
Sbjct: 542 GRHRAETRAISGVYRAEVGSMENKVPHVIAMCQAFEKEDGRRPRLLVAKVGQDGHDRGQK 601

Query: 602 VIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTLVPELKAALKQE 661
           VIASAFADLGFDVDIG LFATP E ARQAVENDVHIVGVSSLAAGHLTLVPELK  L+ +
Sbjct: 602 VIASAFADLGFDVDIGALFATPAEVARQAVENDVHIVGVSSLAAGHLTLVPELKRELEAQ 661

Query: 662 GRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNTRLGY 714
           GR D++IV GGVIPP DYDALY  GA AIF PGT I EA+ +LLG+LN  LGY
Sbjct: 662 GRPDILIVAGGVIPPDDYDALYKGGAVAIFGPGTNIVEASTDLLGKLNAHLGY 714


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: 1346
Number of extensions: 42
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: 720
Length adjustment: 40
Effective length of query: 681
Effective length of database: 680
Effective search space:   463080
Effective search space used:   463080
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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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