Alignments for a candidate for mcmA in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Ruegeria conchae TW15

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_010441942.1 G7G_RS0113370 methylmalonyl-CoA mutase

Query= SwissProt::Q3J4D7
         (709 letters)



>NCBI__GCF_000192475.1:WP_010441942.1
          Length = 708

 Score = 1159 bits (2998), Expect = 0.0
 Identities = 585/706 (82%), Positives = 637/706 (90%)

Query: 4   DLDAWRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVR 63
           D + W+ LAEKEL+G+  D LT  TLEGI VKPLYT+ D A + H+  LPG  PFTRGV+
Sbjct: 3   DTNDWQVLAEKELRGRPLDDLTKETLEGIDVKPLYTQDDTADLPHMGSLPGFGPFTRGVK 62

Query: 64  ATMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGD 123
           ATMYAGRPWTIRQYAGFSTAE SNAFYR+ LAAGQQGVSVAFDLATHRGYDSDHPRVVGD
Sbjct: 63  ATMYAGRPWTIRQYAGFSTAEESNAFYRRNLAAGQQGVSVAFDLATHRGYDSDHPRVVGD 122

Query: 124 VGKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGT 183
           VGKAGVAIDS+EDMKILF+GIPL+K+SVSMTMNGAVIP+LA+FIV GEEQG  +A LSGT
Sbjct: 123 VGKAGVAIDSVEDMKILFDGIPLDKVSVSMTMNGAVIPVLASFIVAGEEQGHDKAVLSGT 182

Query: 184 IQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQE 243
           IQNDILKEFMVRNTYIYPPEPSM+II+DIIE+TS EMPKFNSISISGYHMQEAGANLVQE
Sbjct: 183 IQNDILKEFMVRNTYIYPPEPSMKIISDIIEFTSNEMPKFNSISISGYHMQEAGANLVQE 242

Query: 244 LAYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSEF 303
           LAYTLADGREYVRAA   GM+VD FAGRLSFFFAIGMNFFME AKLRAAR LWHR+M+EF
Sbjct: 243 LAYTLADGREYVRAATQSGMDVDKFAGRLSFFFAIGMNFFMEIAKLRAARTLWHRVMTEF 302

Query: 304 APKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALP 363
             K   S MLRTHCQTSGVSLQEQDPYNNV+RTAYEAMSA LGGTQSLHTNALDEAIALP
Sbjct: 303 GAKSERSKMLRTHCQTSGVSLQEQDPYNNVVRTAYEAMSAVLGGTQSLHTNALDEAIALP 362

Query: 364 TEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTK 423
           T+FSARIARNTQ++LQEETGVT VVDPLAGSYYVESLT EL EKAWAL+EEVE MGGMTK
Sbjct: 363 TDFSARIARNTQLVLQEETGVTDVVDPLAGSYYVESLTNELVEKAWALMEEVEEMGGMTK 422

Query: 424 AVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIAR 483
           AVASGMPKLRIEESAARRQA IDRGE+VIVGVNKYR  +EDPI+ILD+DNVAVR+AQ+AR
Sbjct: 423 AVASGMPKLRIEESAARRQAMIDRGEEVIVGVNKYRKEQEDPIDILDVDNVAVREAQVAR 482

Query: 484 LEKMRATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGRHRA 543
           LE++RATRDEAACQ ALD LT  A EGGNLL AAV+A+RARASVGEISMAMEK FGRHRA
Sbjct: 483 LERIRATRDEAACQQALDALTTTAREGGNLLAAAVEAARARASVGEISMAMEKEFGRHRA 542

Query: 544 EVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAF 603
           EVKTL+GVYGAAYEGD+GFA IQ+ +E FAE EGRRPR+LVVKMGQDGHDRGAKVIATAF
Sbjct: 543 EVKTLAGVYGAAYEGDEGFAAIQKSIEKFAEAEGRRPRLLVVKMGQDGHDRGAKVIATAF 602

Query: 604 ADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEIL 663
           ADIGFDVDVG LFQTP EAAQDA+DNDVHV+GISS AAGHKTLAP+L+E LK+ GA +I+
Sbjct: 603 ADIGFDVDVGPLFQTPAEAAQDAVDNDVHVIGISSQAAGHKTLAPQLVEELKKAGAEDII 662

Query: 664 VICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREARS 709
           VICGGVIPQQDY FL   GVKAIFGPGTNIP AA+ IL LI EA++
Sbjct: 663 VICGGVIPQQDYQFLYDHGVKAIFGPGTNIPDAAQDILRLIGEAKA 708


Lambda     K      H
   0.318    0.133    0.377 

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: 1441
Number of extensions: 38
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: 709
Length of database: 708
Length adjustment: 39
Effective length of query: 670
Effective length of database: 669
Effective search space:   448230
Effective search space used:   448230
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)
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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