Alignments for a candidate for mcm-large in Desulfatiglans anilini DSM 4660

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Desulfatiglans anilini DSM 4660

Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_035255576.1 H567_RS0120695 methylmalonyl-CoA mutase family protein

Query= BRENDA::O74009
         (563 letters)



>NCBI__GCF_000422285.1:WP_035255576.1
          Length = 560

 Score =  721 bits (1862), Expect = 0.0
 Identities = 363/546 (66%), Positives = 441/546 (80%), Gaps = 3/546 (0%)

Query: 12  IKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYMEKLGFPGEY 71
           I +  K+W +   KK + K PERK  F+   G  IKR+Y+P D   +  Y+E+LGFPGE+
Sbjct: 11  IADNAKKWSDGVEKK-INKHPERKANFINPSGIPIKRLYSPVDT-YNVGYIEELGFPGEF 68

Query: 72  PFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDLPTQLGYDSD 131
           PFTRGV  TMYR + WTMRQYAG+A+AEESN+RYK+LL QGQTGLSVAFDLPTQ+GYDSD
Sbjct: 69  PFTRGVQPTMYRTQYWTMRQYAGFASAEESNRRYKFLLEQGQTGLSVAFDLPTQIGYDSD 128

Query: 132 HPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYILVAEEQGVS 191
             +A GEVGKVGVAIDSL DM ILF+GIPLD VSTSMTIN+ AA LLAMYI+V E+QGVS
Sbjct: 129 DDMAIGEVGKVGVAIDSLKDMEILFNGIPLDTVSTSMTINAPAAVLLAMYIVVGEKQGVS 188

Query: 192 QEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPISISGYHIREA 251
            +KLRGT+QNDILKEY ARGTYIFPP+PSMR+ TDI  YCA NVP WN ISISGYHIREA
Sbjct: 189 SDKLRGTIQNDILKEYSARGTYIFPPKPSMRVITDIFSYCASNVPLWNTISISGYHIREA 248

Query: 252 GANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKFRAARRLW 311
           G+ AVQE+AFTLADGI YV+A I  G+DVD FAPRLSFFF AH++F EEIAK+RAAR+LW
Sbjct: 249 GSTAVQEIAFTLADGIAYVEAAITAGLDVDTFAPRLSFFFNAHSDFFEEIAKYRAARKLW 308

Query: 312 AYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNS 371
           A IMKE F AKNP+SMM+RFHTQTAG TLTAQQP+NNIVRVA QALAAVLGGTQSLHTNS
Sbjct: 309 AKIMKERFGAKNPKSMMMRFHTQTAGCTLTAQQPKNNIVRVAFQALAAVLGGTQSLHTNS 368

Query: 372 YDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKI 431
            DEAL LP+E++V++ALRTQQ+IA+E+G  DTVDPLGG+YY+E LT+ I ++A  YI+KI
Sbjct: 369 MDEALCLPSEEAVQVALRTQQLIAHETGAGDTVDPLGGSYYLENLTNEICQKAEAYIQKI 428

Query: 432 QKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEPIEVEILKVDPSI 491
            KMGG +  IE G++Q+EI E+AYK+Q+EIE+ KR++VG+N+F  +E  E ++ +VDP +
Sbjct: 429 DKMGGAVEVIENGFIQREIQESAYKWQQEIEQKKRVVVGMNSFHVEEEKEGDLQRVDPQV 488

Query: 492 REKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTDVLR 551
           R  QIE L  L+  RD  KV+ +L  L N A  +D NLMPYI+E+ R  ATL E+  VL+
Sbjct: 489 RLTQIEALNSLKLTRDRYKVESSLTSLENCARGKD-NLMPYILESVRSYATLGEICRVLK 547

Query: 552 EIWGEY 557
            ++GEY
Sbjct: 548 SVFGEY 553


Lambda     K      H
   0.318    0.134    0.388 

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: 881
Number of extensions: 27
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: 563
Length of database: 560
Length adjustment: 36
Effective length of query: 527
Effective length of database: 524
Effective search space:   276148
Effective search space used:   276148
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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 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