Alignments for a candidate for mcmA in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Rhodospirillum centenum SW SW; ATCC 51521

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_012568263.1 RC1_RS14910 methylmalonyl-CoA mutase

Query= SwissProt::Q3J4D7
         (709 letters)



>NCBI__GCF_000016185.1:WP_012568263.1
          Length = 720

 Score = 1015 bits (2624), Expect = 0.0
 Identities = 519/706 (73%), Positives = 598/706 (84%), Gaps = 6/706 (0%)

Query: 8   WRKLAEKEL---KGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRA 64
           W  LA K+L   +G+  DSL   T EGI +KPLYT ADL  +E   GLPG  P+TRG RA
Sbjct: 12  WETLAAKDLSREEGRPLDSLVSATPEGIAIKPLYTAADLEALEDA-GLPGFPPYTRGPRA 70

Query: 65  TMYAGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDV 124
           TMY  +PWTIRQYAGFSTAE SNAFY+  L AGQ G+SVAFDLATHRGYDSDHPRVVGDV
Sbjct: 71  TMYTVKPWTIRQYAGFSTAEESNAFYKANLKAGQMGLSVAFDLATHRGYDSDHPRVVGDV 130

Query: 125 GKAGVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTI 184
           GKAGVAIDS+EDMKILF+ IPL+++SVSMTMNGAV+PI+A +IV  EEQGVP+A LSGTI
Sbjct: 131 GKAGVAIDSVEDMKILFDDIPLDRMSVSMTMNGAVLPIMAMYIVAAEEQGVPQAKLSGTI 190

Query: 185 QNDILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQEL 244
           QNDILKEFMVRNTYIYPPEPSMRIIADIIEYT+  MPKFNSISISGYHMQEAGA  VQEL
Sbjct: 191 QNDILKEFMVRNTYIYPPEPSMRIIADIIEYTATHMPKFNSISISGYHMQEAGATAVQEL 250

Query: 245 AYTLADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIM-SEF 303
           A+TLADG EYVRAALA+G++VD FA RLSFFF IGM+FFME AKLRAARLLW  +M + F
Sbjct: 251 AFTLADGLEYVRAALAKGLDVDRFAPRLSFFFCIGMDFFMEVAKLRAARLLWAELMQTHF 310

Query: 304 APKKPGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALP 363
            PK P SL LRTHCQTSGVSL EQDPYNN++RT  EAM+A LGGTQSLHTN+ DEA+ LP
Sbjct: 311 QPKDPRSLALRTHCQTSGVSLTEQDPYNNIVRTTVEAMAAILGGTQSLHTNSFDEALGLP 370

Query: 364 TEFSARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTK 423
           T FSARIARNTQ+I+ EETG+ RVVDPL GSYYVE LT  LA +A  LI+EVEA+GGMT+
Sbjct: 371 TPFSARIARNTQLIIAEETGIPRVVDPLGGSYYVEHLTHSLAAEARKLIDEVEALGGMTR 430

Query: 424 AVASGMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIAR 483
           AV SGMPKL+IEE+AARRQA IDRGE+VIVGVNKYR A  D +E+LDIDN  VR+AQIAR
Sbjct: 431 AVESGMPKLKIEEAAARRQARIDRGEEVIVGVNKYRPANPDRVEVLDIDNTVVREAQIAR 490

Query: 484 LEKMRATRDEAACQAALDELTRRAAE-GGNLLEAAVDASRARASVGEISMAMEKVFGRHR 542
           L+++RATRDEAA +AAL  LT  A E  GNLL  AV+A+RARA+VGEIS A+E+VF RHR
Sbjct: 491 LKRIRATRDEAAVRAALAALTAAAREKSGNLLALAVEAARARATVGEISDALEEVFTRHR 550

Query: 543 AEVKTLSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATA 602
           A ++++SGVYGAAY+GD+GFA+I R+VE FA EEGRRPRMLV K+GQDGHDRGAKVIATA
Sbjct: 551 AIIRSVSGVYGAAYDGDEGFARICREVEEFAAEEGRRPRMLVAKLGQDGHDRGAKVIATA 610

Query: 603 FADIGFDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEI 662
           FADIGFDVDVG LFQTPEEAA+ A++NDVH+VG+SSLAAGHKTL P+L+ AL+ +GA ++
Sbjct: 611 FADIGFDVDVGPLFQTPEEAARQAVENDVHIVGVSSLAAGHKTLVPQLVAALRAQGADDV 670

Query: 663 LVICGGVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREAR 708
           LVICGGVIP QDYD L ++G  AIFGPGT+IP AA  IL ++R+ R
Sbjct: 671 LVICGGVIPPQDYDMLLESGAAAIFGPGTHIPRAAAEILGILRDRR 716


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: 1427
Number of extensions: 51
Number of successful extensions: 4
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: 720
Length adjustment: 39
Effective length of query: 670
Effective length of database: 681
Effective search space:   456270
Effective search space used:   456270
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 Apr 09 2024. 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 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