Alignments for a candidate for mcmA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Bacteroides thetaiotaomicron VPI-5482

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 351618 BT2090 methylmalonyl-CoA mutase large subunit (NCBI ptt file)

Query= BRENDA::Q84FZ1
         (721 letters)



>FitnessBrowser__Btheta:351618
          Length = 715

 Score =  935 bits (2417), Expect = 0.0
 Identities = 472/678 (69%), Positives = 552/678 (81%), Gaps = 2/678 (0%)

Query: 29  WMTPEGIPVKGFYGPEDREGCEGIDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAED 88
           W TPE I VK  Y  ED EG E +    GLPPYLRGPY  MY  +PWTIRQYAGFSTAE+
Sbjct: 32  WNTPEHIDVKPVYTKEDLEGMEHLGYAAGLPPYLRGPYSVMYTLRPWTIRQYAGFSTAEE 91

Query: 89  SNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIP 148
           SNAFYRRNLA+GQKGLSVAFDLATHRGYD DH RV GDVG AGV+I S+ +M+ LF GIP
Sbjct: 92  SNAFYRRNLASGQKGLSVAFDLATHRGYDPDHERVVGDVGKAGVSICSLENMKVLFDGIP 151

Query: 149 LDEMTVSMTMNGAVLPGVALYIVAAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGS 208
           L +M+VSMTMNGAVLP +A YI A  EQG   E++AGTIQNDILKEFMVRNTYIYPP  S
Sbjct: 152 LSKMSVSMTMNGAVLPIMAFYINAGLEQGAKLEEMAGTIQNDILKEFMVRNTYIYPPAFS 211

Query: 209 MRIISDIFGYTSKNMPKFNSISISGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTI 268
           M+IISDIF YTS+ MPKFNSISISGYHMQEAGAT D+ELAYTLADG+EY++AG AAG+ I
Sbjct: 212 MKIISDIFEYTSQKMPKFNSISISGYHMQEAGATADIELAYTLADGLEYLRAGTAAGIDI 271

Query: 269 DQFAPRLSFFWAIGMNFFMEIAKMRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLT 328
           D FAPRLSFFWAIG N FMEIAKMRAAR++WAK+VK+F PK+ KSL LRTHSQTSGWSLT
Sbjct: 272 DAFAPRLSFFWAIGTNHFMEIAKMRAARMLWAKIVKQFNPKNPKSLALRTHSQTSGWSLT 331

Query: 329 AQDVFNNVTRTCIEAMAATQGGTQSLHTNALDEALALPTDFSARIARNTQLFLQQESGTT 388
            QD FNNV RTCIEAMAA  G TQSLHTNALDEA+ALPTDFSARIARNTQ+++Q+E+   
Sbjct: 332 EQDPFNNVGRTCIEAMAAALGHTQSLHTNALDEAIALPTDFSARIARNTQIYIQEETYIC 391

Query: 389 RIIDPWGGSYYVERLTRDIAARAWEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARI 448
           + +DPWGGSYYVE LT ++A +AWE I EVE LGGMAKAIE GIPK+RIEEAAAR QARI
Sbjct: 392 KNVDPWGGSYYVEALTNELAHKAWERIEEVEKLGGMAKAIETGIPKMRIEEAAARTQARI 451

Query: 449 DSGRQTIVGINKYKPDDEMKIDLLRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTK 508
           DSG QTIVG+NKY+ + E  ID+L +DN  VR +QI+ LKRL+  RNQA+VD ALAA+T+
Sbjct: 452 DSGSQTIVGVNKYRLEKEAPIDILEIDNTAVRLEQIENLKRLKEGRNQAEVDKALAAITE 511

Query: 509 AAD-GEGNLLELAVNAARAKATVGEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVE 567
             + G+GNLLELAV AAR +AT+GEIS A EK  GR++A IR+ISGVY  E        +
Sbjct: 512 CVETGKGNLLELAVEAARVRATLGEISYACEKVVGRYKAIIRTISGVYSSESKNDGD-FK 570

Query: 568 KVRGLVEAFEENDGRRPRILVAKMGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAA 627
           +   L E F + +GR+PRI+VAKMGQDGHDRG KV+A+ +AD GFDVD+GPLF TP EAA
Sbjct: 571 RACELAEKFAKKEGRQPRIMVAKMGQDGHDRGAKVVATGYADCGFDVDMGPLFQTPAEAA 630

Query: 628 RQAVENDVHIVGVSSLAAGHLTLVPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGA 687
           R+AVENDVH+VGVSSLAAGH TL+P++   LK+ GR+D++++ GGVIP  DYD LY AG 
Sbjct: 631 REAVENDVHVVGVSSLAAGHKTLIPQIMEELKKLGREDIVVIAGGVIPAQDYDFLYKAGV 690

Query: 688 SAIFPPGTVIAEAAVNLL 705
           +AIF PGT +A+AA  +L
Sbjct: 691 AAIFGPGTPVAKAACQIL 708


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: 1289
Number of extensions: 42
Number of successful extensions: 3
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: 715
Length adjustment: 40
Effective length of query: 681
Effective length of database: 675
Effective search space:   459675
Effective search space used:   459675
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 Sep 17 2021. 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)
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

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