Alignments for a candidate for mcmA in Chryseobacterium arthrosphaerae CC-VM-7

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Chryseobacterium arthrosphaerae CC-VM-7

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_065401015.1 BBI00_RS21385 methylmalonyl-CoA mutase

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



>NCBI__GCF_001684965.1:WP_065401015.1
          Length = 707

 Score =  913 bits (2359), Expect = 0.0
 Identities = 453/677 (66%), Positives = 552/677 (81%), Gaps = 1/677 (0%)

Query: 41  EGLTVKPLYTKKDVEDLPYADTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAF 100
           +GL +K  Y KKDV+D     T PG  PYLRGP +TMY  +PWTIRQYAGFSTAEESNAF
Sbjct: 27  DGLELKSSYEKKDVKDESLTQTSPGIEPYLRGPYSTMYVQKPWTIRQYAGFSTAEESNAF 86

Query: 101 YRKALAAGGQGVSVAFDLATHRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKI 160
           YR+ LAAG +G+SVAFDLATHRGYDSD+ RV+GDVGKAGVAIDSVEDMKILF+ IPLD+I
Sbjct: 87  YRRNLAAGQKGLSVAFDLATHRGYDSDHSRVVGDVGKAGVAIDSVEDMKILFNEIPLDQI 146

Query: 161 SVSMTMNGAVLPILAGYIVAAEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKII 220
           SVSMTMNGAVLPIL+ YIVAAEEQGV QEQLSGTIQNDILKEFMVRNTYIYPP PSMKII
Sbjct: 147 SVSMTMNGAVLPILSFYIVAAEEQGVKQEQLSGTIQNDILKEFMVRNTYIYPPAPSMKII 206

Query: 221 SDIFGYTAQHMPKFNSISISGYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFA 280
           +DIF YT+Q++PKFNSISISGYH+QEAGA   +E+A+TLADG+EYVRTGI +G++VD FA
Sbjct: 207 ADIFEYTSQNIPKFNSISISGYHMQEAGATPVLEMAYTLADGLEYVRTGIKAGMNVDDFA 266

Query: 281 GRLSFFWAVGMNFYLEIAKMRAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDP 340
            RLSFFWA+GMN ++EIAKMRA R +W  ++ QFNP++ KSL LRTHSQTSGWSLTEQ+P
Sbjct: 267 PRLSFFWAIGMNHFMEIAKMRAARYIWANLLKQFNPQNPKSLALRTHSQTSGWSLTEQEP 326

Query: 341 YNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVD 400
           +NN+ RT IEA+++  GGTQSLHTNALDEAIALPT++SA+IARNTQ+I+Q+E+ IC+VVD
Sbjct: 327 FNNITRTAIEALSSALGGTQSLHTNALDEAIALPTDYSAKIARNTQIILQQESGICDVVD 386

Query: 401 PWAGSYMMEKLTQDMADKAWSIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGK 460
           P  GS ++E LTQ M ++A   I E+E  GGMTKA+E+G  KM++E  AA KQA+IDSG+
Sbjct: 387 PMGGSNLVESLTQQMIEEAMRYIDEVEQEGGMTKAIEAGIPKMRIEEAAAKKQAKIDSGE 446

Query: 461 DVIVGVNKYKLA-KEDQIDILDIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAE 519
           + I+GVN +K + K+D I+ILDIDN  VR  QI RL  I+A R+S AV   L+ + + A+
Sbjct: 447 EFIIGVNSFKSSLKQDAIEILDIDNTEVRRKQIERLNNIKAERNSEAVTQILNDIRESAK 506

Query: 520 SGEGNLLDLSVKAIRLRATVGEVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKA 579
           +G+GNLL L ++A R R T+GE+SDA+E+ FGR++AN +TISGVY       E +E    
Sbjct: 507 TGKGNLLALCIEAARRRVTLGEMSDAMEETFGRYKANIKTISGVYAMNAGKNEYFEKALH 566

Query: 580 DIAKFAEEEGRRPRIMIAKLGQDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAV 639
              KF EEEGRRPRIM+AK+GQDGHDRGAKVVATAFAD+GFD+D+ PLFQTPEE A+QA+
Sbjct: 567 LTQKFEEEEGRRPRIMVAKMGQDGHDRGAKVVATAFADMGFDVDVAPLFQTPEEVAKQAI 626

Query: 640 ENDVHAIGVSSLAAGHKTLLPALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIF 699
           END+H +GVSSLAAGHKTL+P +V  L + GADDI +  GGVIP QDY+ LYA GA  IF
Sbjct: 627 ENDIHILGVSSLAAGHKTLVPQVVEELSKLGADDITIVVGGVIPQQDYEFLYANGADFIF 686

Query: 700 GPGTRIEDSAKRVLEEI 716
           GPGT +   A  +LE +
Sbjct: 687 GPGTNLPKCAVEILERL 703


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: 1333
Number of extensions: 40
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: 721
Length of database: 707
Length adjustment: 39
Effective length of query: 682
Effective length of database: 668
Effective search space:   455576
Effective search space used:   455576
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