Alignments for a candidate for mcmA in Halioglobus japonicus S1-36

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Halioglobus japonicus S1-36

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_084199764.1 C0029_RS11185 methylmalonyl-CoA mutase

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



>NCBI__GCF_002869505.1:WP_084199764.1
          Length = 719

 Score = 1057 bits (2734), Expect = 0.0
 Identities = 522/709 (73%), Positives = 593/709 (83%)

Query: 12  NSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYADTLPGFAPYLR 71
           N+   DAWA+ A K   G  ++ L W TPE + VKPLYT  D EDL YADT+PG +PY+R
Sbjct: 10  NTATPDAWAELATKQLRGKPLDDLTWQTPEDIDVKPLYTAADTEDLEYADTMPGMSPYIR 69

Query: 72  GPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDNPRV 131
           GPQATMYA RPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSD+PRV
Sbjct: 70  GPQATMYAGRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHRGYDSDHPRV 129

Query: 132 LGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAEEQGVSQEQL 191
            GDVGKAGVAIDSVEDMKILFDGIPLDK+SVSMTMNGAVLP+LAGYIVAAEEQGVSQ+QL
Sbjct: 130 SGDVGKAGVAIDSVEDMKILFDGIPLDKVSVSMTMNGAVLPVLAGYIVAAEEQGVSQDQL 189

Query: 192 SGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISGYHIQEAGANQ 251
           +GTIQNDILKEFMVRNTYIYPP PSMKII DI  Y + +MPKFN+ISISGYHIQEAGAN 
Sbjct: 190 AGTIQNDILKEFMVRNTYIYPPAPSMKIIGDIIAYCSGNMPKFNTISISGYHIQEAGANA 249

Query: 252 AIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMRAGRMLWHRIM 311
           A+ELA+TLADG EY+RT +A+GLD+D FA RLSFFW +GMNFY+EIAKMRA R+LW +I+
Sbjct: 250 ALELAYTLADGKEYIRTALAAGLDIDQFAPRLSFFWGIGMNFYMEIAKMRAARLLWAKIV 309

Query: 312 SQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAI 371
            +FNP + KS MLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAI
Sbjct: 310 GEFNPGNPKSSMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAI 369

Query: 372 ALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWSIIQEIEAMGG 431
           ALPTEFSARIARNTQLIIQEE+ I NVVDPW GSYMME LTQD+ADKAW +I+EIE  GG
Sbjct: 370 ALPTEFSARIARNTQLIIQEESGITNVVDPWGGSYMMESLTQDIADKAWELIEEIEEAGG 429

Query: 432 MTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILDIDNHAVREAQ 491
           M KA+E+G  K+++E  AA KQARID G DVIVGVNKY L +ED I+ L++DN AVRE+Q
Sbjct: 430 MAKAIETGLPKLKIEEAAARKQARIDRGDDVIVGVNKYTLDEEDAIETLEVDNQAVRESQ 489

Query: 492 IARLKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVGEVSDALEKVFG 551
           +ARL  IR SRD AAV+A L+ + Q A SGEGNLL L+V+A R RATVGE+S A+E+ FG
Sbjct: 490 LARLATIRGSRDEAAVEAILEDIYQAAVSGEGNLLALAVEATRRRATVGEISFAMEREFG 549

Query: 552 RFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLGQDGHDRGAKVV 611
           RF A  QT+SGVYG      E W+ I  DI  F +  GRRPR+++ K+GQDGHDRGAKVV
Sbjct: 550 RFNAQAQTVSGVYGSAFAEDEEWQGISKDIDDFVDHHGRRPRMLVCKMGQDGHDRGAKVV 609

Query: 612 ATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLPALVNSLKEQGA 671
           ATAFAD+GFDID+ P+F TPEE ARQA+ENDVH +G SSLAAGHKTL+P LV  LK+QGA
Sbjct: 610 ATAFADVGFDIDLSPMFSTPEEVARQAIENDVHVVGASSLAAGHKTLVPELVEELKKQGA 669

Query: 672 DDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSR 720
           DDI+V AGGVIP QDYD LY AG K IFGPGT I   A+ VL+ +   +
Sbjct: 670 DDIVVIAGGVIPRQDYDYLYGAGVKCIFGPGTPIPACAREVLDAVNSQQ 718


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: 1479
Number of extensions: 53
Number of successful extensions: 1
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: 719
Length adjustment: 40
Effective length of query: 681
Effective length of database: 679
Effective search space:   462399
Effective search space used:   462399
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 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 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