Alignments for a candidate for mcm-large in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Desulfobulbus mediterraneus DSM 13871

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_028585562.1 G494_RS0117545 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000429965.1:WP_028585562.1
          Length = 725

 Score =  917 bits (2369), Expect = 0.0
 Identities = 462/725 (63%), Positives = 561/725 (77%), Gaps = 8/725 (1%)

Query: 5   PRFDSVDLGNAPVPADA---ARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWL 61
           P F  ++L     P D    A   ++    +    AW+T EQI V  L+  D Y+ +D L
Sbjct: 4   PDFSKMNLNPGKAPMDYQSWAAAVQQETGMSAEELAWKTVEQIDVKPLYRRDDYQGLDHL 63

Query: 62  DTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPT 121
              AGI P++ GPYATM+  RPWT+RQYAGFSTA+ESNAFYRRNLAAGQKGLS+AFDL T
Sbjct: 64  SYMAGIAPYLRGPYATMFVMRPWTVRQYAGFSTAEESNAFYRRNLAAGQKGLSIAFDLAT 123

Query: 122 HRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVT 181
           HRGYDSD+PRV GDVG AGVA+DSI DM  LF GIPLD+M+VSMTMNGAVLPI++ Y+V 
Sbjct: 124 HRGYDSDHPRVVGDVGKAGVAVDSILDMNILFDGIPLDEMTVSMTMNGAVLPIISFYIVA 183

Query: 182 AEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISIS 241
           AEEQGVK  QL GTIQNDILKE+MVRNTYIYPP  SM+IIS+IFAYTS +MPK+NSISIS
Sbjct: 184 AEEQGVKQSQLGGTIQNDILKEYMVRNTYIYPPAQSMKIISDIFAYTSEHMPKYNSISIS 243

Query: 242 GYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKL 301
           GYHM+EAGAT+DIEMAYTLADG DY RAG + G+++D FAPRLSFFW  GMN++ME+AK+
Sbjct: 244 GYHMEEAGATSDIEMAYTLADGWDYARAGVNAGMDIDTFAPRLSFFWAQGMNYYMEIAKM 303

Query: 302 RAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQ 361
           RAAR+LWA+++  F PKN KS++LRTHSQTSGWSLT  D +NNV RT IE MAA  GHTQ
Sbjct: 304 RAARVLWARIIKTFNPKNVKSLALRTHSQTSGWSLTEGDPFNNVCRTVIEGMAAALGHTQ 363

Query: 362 SLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAW 421
           S+HTNSLDEAIALPT+FSARIARNTQL+LQ E+   R  DPW+GS Y+E LT  +  + W
Sbjct: 364 SMHTNSLDEAIALPTEFSARIARNTQLYLQDETNILRPADPWAGSYYLEALTGAIMERGW 423

Query: 422 GHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVL 481
             IQEVE++GGMAKAIE G+PKMRIEEAAAR QA IDSGR+ +IGVN Y LE E  LD L
Sbjct: 424 SLIQEVEQLGGMAKAIETGLPKMRIEEAAARRQAGIDSGREKIIGVNSYCLEQEDALDTL 483

Query: 482 KVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRA 541
           +VDN+ V   Q  +L KL+A RD  K +  L+ +T +A     +  + NLL L I+A RA
Sbjct: 484 EVDNTAVREAQLERLAKLKAMRDETKCQETLNALTRSA-----ESGEGNLLALSIEAARA 538

Query: 542 MATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRIL 601
            A++GE+S ALEK +GR+TA IR+I+GVY  E     EVE+   L +EFE+ EGRRPRI+
Sbjct: 539 RASLGEISFALEKSWGRHTAVIRSIAGVYKAEFSEKEEVEKVVRLTKEFEEKEGRRPRIM 598

Query: 602 LAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGH 661
           +AK+GQDGHDRG KVI+TA+ADLGFDVD+GPLFQTPEE ARQAVE D H++G SSLA GH
Sbjct: 599 VAKLGQDGHDRGAKVISTAFADLGFDVDIGPLFQTPEEAARQAVENDAHIIGFSSLAAGH 658

Query: 662 LTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKK 721
            TL+PAL +EL+KLGRPDI+  +GGVIP  D+D LR+ GA  I+ PGTVIP +A  ++++
Sbjct: 659 KTLLPALVEELEKLGRPDIMCVIGGVIPAPDYDYLRERGAAAIFGPGTVIPVAAQKVLEE 718

Query: 722 LRASL 726
           L   L
Sbjct: 719 LNIRL 723


Lambda     K      H
   0.317    0.133    0.389 

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: 1406
Number of extensions: 45
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: 728
Length of database: 725
Length adjustment: 40
Effective length of query: 688
Effective length of database: 685
Effective search space:   471280
Effective search space used:   471280
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 24 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