Aligments for a candidate for mcmA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Paraburkholderia bryophila 376MFSha3.1

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_01038 H281DRAFT_01038 methylmalonyl-CoA mutase

Query= reanno::PS:Dsui_0519
         (721 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01038 H281DRAFT_01038
           methylmalonyl-CoA mutase
          Length = 703

 Score =  651 bits (1680), Expect = 0.0
 Identities = 334/663 (50%), Positives = 448/663 (67%), Gaps = 2/663 (0%)

Query: 45  VKPLYTKKDVEDLPYADTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKA 104
           +K +YT+ D+E + + D++PG AP++RGP A+MY  +PWTIRQYAG++ A ++N  +R A
Sbjct: 14  LKRVYTRADIEGIAHIDSMPGEAPFVRGPFASMYTQKPWTIRQYAGYAQASDTNLAFRTA 73

Query: 105 LAAGGQGVSVAFDLATHRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSM 164
           LA G QG+SVAFDL T RGYDSD+P V  DVG  GVAID+VEDM  LF+ I LD++SVSM
Sbjct: 74  LAEGAQGLSVAFDLPTQRGYDSDDPAVSADVGMTGVAIDTVEDMTRLFEDIALDRVSVSM 133

Query: 165 TMNGAVLPILAGYIVAAEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIF 224
           TMNGAVLP+LA +IVAAEE GV   QL GTIQNDILKEFMVRNT I+ P+PS++I +D+ 
Sbjct: 134 TMNGAVLPVLAAFIVAAEESGVGASQLRGTIQNDILKEFMVRNTSIFAPEPSLRIAADVV 193

Query: 225 GYTAQHMPKFNSISISGYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLS 284
            Y  +++P+FN++S+SGYH QEAGA+  +ELA T+A+  +Y+      G+  D    R+S
Sbjct: 194 EYLGKNVPRFNALSVSGYHFQEAGADPVLELALTMANARKYITALAGRGMQADDVCQRMS 253

Query: 285 FFWAVGMNFYLEIAKMRAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNV 344
           FF+ VGM+FY+EIAK+RA R+LW  I S     S ++  LR H QTSGWSLT Q P NNV
Sbjct: 254 FFFGVGMDFYVEIAKLRAARILWADIASASGATSDRARALRMHCQTSGWSLTAQKPMNNV 313

Query: 345 VRTTIEAMAAVFGGTQSLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAG 404
           VRTT+EA+AAVFGGTQSLHTN  DEA++LP   ++R+AR+TQL++Q ET +C+VVDPWAG
Sbjct: 314 VRTTVEALAAVFGGTQSLHTNGYDEALSLPCADASRLARDTQLVLQHETGVCDVVDPWAG 373

Query: 405 SYMMEKLTQDMADKAWSIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIV 464
           SYMMEK T ++  KA +++ EIE  GG+   VESGW + Q+   A + QA I+S K  +V
Sbjct: 374 SYMMEKFTAEICQKALTVMAEIERRGGVVDVVESGWVRDQIHRSALNIQAEIESRKRTVV 433

Query: 465 GVNKYKL-AKEDQIDILDIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEG 523
           GVN +     ED  +   +D   VR  Q  RL  I+A RD   V+  LDALT+ A   +G
Sbjct: 434 GVNDFMTGCDEDLGEPQTVDGRRVRVLQTQRLAHIKARRDPTRVRNTLDALTRAARGRDG 493

Query: 524 NLLDLSVKAIRLRATVGEVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAK 583
           NLL+L+V  +R RATVGE + ALE V+ R++     +   YG  +E  + W+     +A 
Sbjct: 494 NLLELTVACMRARATVGECTQALEAVWPRYQIGLPLLRDHYGANLESDKDWQDTCRAVAD 553

Query: 584 FAEEEGRRPRIMIAKLGQDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDV 643
             +  GR PR++IAKLGQDGHDRGA+++A A +D GF +  G +F +P +  + A    V
Sbjct: 554 ATKRLGRAPRVLIAKLGQDGHDRGARIIAAALSDAGFAVFTGSMFASPSDTVQLAEGERV 613

Query: 644 HAIGVSSLAAGHKTLLPALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGT 703
             IGVSSLA     L+ AL + L  +G   I +  GG+I       L  +G  A F  GT
Sbjct: 614 DVIGVSSLAGAQNDLITALHDQLTVRGL-RIPIVVGGIIDQASQLVLRRSGVAACFPAGT 672

Query: 704 RIE 706
            I+
Sbjct: 673 PIK 675


Lambda     K      H
   0.317    0.132    0.380 

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: 1122
Number of extensions: 39
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: 703
Length adjustment: 39
Effective length of query: 682
Effective length of database: 664
Effective search space:   452848
Effective search space used:   452848
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 (21.6 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)
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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 preprint on GapMind for carbon sources, or view the source code.

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