Alignments for a candidate for mcm-large in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Williamsia sterculiae CPCC 203464

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_076477891.1 BW971_RS07055 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_900156495.1:WP_076477891.1
          Length = 759

 Score =  971 bits (2509), Expect = 0.0
 Identities = 504/721 (69%), Positives = 579/721 (80%), Gaps = 14/721 (1%)

Query: 16  PVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDW----------LDTYA 65
           P P  A    E+   +      W T EQI V  +F      D D           LD+  
Sbjct: 23  PSPESADVPVEDRTPRPEAQTLWTTPEQIDVPPVFTR---ADRDAVATSGEHPYPLDSVP 79

Query: 66  GIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGY 125
           G  PF+ GPY TMY  +PWTIRQYAGFSTA ESNAFYRRNLAAGQKGLSVAFDL THRGY
Sbjct: 80  GAVPFLRGPYPTMYVNQPWTIRQYAGFSTAAESNAFYRRNLAAGQKGLSVAFDLATHRGY 139

Query: 126 DSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQ 185
           DSD+PRVAGDVGMAGVAIDSI DMR+LF GI L  +SVSMTMNGAVLPILALYVV AEEQ
Sbjct: 140 DSDHPRVAGDVGMAGVAIDSILDMRQLFDGIDLGSVSVSMTMNGAVLPILALYVVAAEEQ 199

Query: 186 GVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHM 245
           GV  E+LAGTIQNDILKEFMVRNTYIYPP+PSMRIIS+IF +TS  MP++NSISISGYH+
Sbjct: 200 GVPAEKLAGTIQNDILKEFMVRNTYIYPPEPSMRIISDIFKFTSTEMPRFNSISISGYHI 259

Query: 246 QEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAAR 305
           QEAGATAD+E+AYTLADGV+YIRAG + GL+VD+FAPRLSFFWGIGMNFFMEVAKLRAAR
Sbjct: 260 QEAGATADLELAYTLADGVEYIRAGLAAGLDVDKFAPRLSFFWGIGMNFFMEVAKLRAAR 319

Query: 306 MLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHT 365
           +LW++LV QF P+NPKS+SLRTHSQTSGWSLTAQD +NNV RTCIEAMAATQGHTQSLHT
Sbjct: 320 LLWSELVAQFEPENPKSLSLRTHSQTSGWSLTAQDPFNNVARTCIEAMAATQGHTQSLHT 379

Query: 366 NSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQ 425
           N+LDEA+ALPTDFSARIARNTQL LQQESGTTR IDPW GS YVE LT  LA +A  HI 
Sbjct: 380 NALDEALALPTDFSARIARNTQLLLQQESGTTRPIDPWGGSNYVEWLTAQLADRARAHIA 439

Query: 426 EVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDN 485
           EVE+ GGMA+AI +G+PK+RIEEAAARTQARIDSG+Q +IG+N+Y++  +  +DVLKV+N
Sbjct: 440 EVEEAGGMAQAINEGLPKLRIEEAAARTQARIDSGQQTVIGINRYQVTEDQEIDVLKVEN 499

Query: 486 STVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATV 545
           S V AEQ  KL +LRAERD   V  ALD ++ AAG+      + NLL L I+A R  ATV
Sbjct: 500 SKVRAEQLDKLDRLRAERDEAAVSRALDDLSRAAGDTSG-GRENNLLALAIEAARHQATV 558

Query: 546 GEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKM 605
           GE+S ALEKV+GR+ A+I+TISGVY  E  +   +++A   VE F  AEGRRPR+L+AKM
Sbjct: 559 GEISTALEKVYGRHQAEIKTISGVYRHEAGSVSNIDDAIAAVERFADAEGRRPRVLIAKM 618

Query: 606 GQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLV 665
           GQDGHDRGQKVIATA+ADLGFDVDVGPLFQTP+E ARQA + DVHVVGVSSLA GHLTLV
Sbjct: 619 GQDGHDRGQKVIATAFADLGFDVDVGPLFQTPDEVARQAADNDVHVVGVSSLAAGHLTLV 678

Query: 666 PALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRAS 725
           PALR  L ++GRPDI+I VGGVIP  DFDEL + GA  I+ PGTVI +SA+ L+ KL ++
Sbjct: 679 PALRNALAEVGRPDIMIVVGGVIPPGDFDELYQAGAAAIFPPGTVIADSALELIDKLGSA 738

Query: 726 L 726
           L
Sbjct: 739 L 739


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: 1525
Number of extensions: 50
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: 728
Length of database: 759
Length adjustment: 40
Effective length of query: 688
Effective length of database: 719
Effective search space:   494672
Effective search space used:   494672
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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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