Alignments for a candidate for mcmA in Azoarcus sp. BH72

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Azoarcus sp. BH72

Align Methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011764420.1 AZO_RS03440 methylmalonyl-CoA mutase

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



>NCBI__GCF_000061505.1:WP_011764420.1
          Length = 721

 Score = 1235 bits (3195), Expect = 0.0
 Identities = 616/718 (85%), Positives = 664/718 (92%), Gaps = 1/718 (0%)

Query: 3   ADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYADT 62
           ++A+ P  P  D L+AW KAAAK AP G ++ LNWITPEGLTVKPLYTK D  DLP+ADT
Sbjct: 2   SNANLPAYPQPD-LEAWNKAAAKQAPDGQLDKLNWITPEGLTVKPLYTKADTADLPHADT 60

Query: 63  LPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHR 122
           LPGF P+LRGPQ TMYAV+PWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHR
Sbjct: 61  LPGFEPFLRGPQPTMYAVKPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLATHR 120

Query: 123 GYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAE 182
           GYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAE
Sbjct: 121 GYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAE 180

Query: 183 EQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISISGY 242
           EQGV+Q++LSGTIQNDILKEFMVRNTYIYPP PSMKII+DIF YT+ HMPKFNSISISGY
Sbjct: 181 EQGVAQDKLSGTIQNDILKEFMVRNTYIYPPTPSMKIIADIFQYTSSHMPKFNSISISGY 240

Query: 243 HIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKMRA 302
           HIQEAGANQAIELAFTLADG+EYVRTGIA+G+DVD FAGRLSFFWAVGMNFYLEIAKMRA
Sbjct: 241 HIQEAGANQAIELAFTLADGLEYVRTGIAAGMDVDTFAGRLSFFWAVGMNFYLEIAKMRA 300

Query: 303 GRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSL 362
            R+LW RIM QFNPKS KS+MLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSL
Sbjct: 301 ARLLWWRIMKQFNPKSPKSMMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSL 360

Query: 363 HTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWSI 422
           HTNALDEAIALPTEFSARIARNTQ+IIQEETHICNVVDPWAGSYMMEKLTQDMADKAW++
Sbjct: 361 HTNALDEAIALPTEFSARIARNTQIIIQEETHICNVVDPWAGSYMMEKLTQDMADKAWAL 420

Query: 423 IQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDILDI 482
           I+EIEAMGGMTKAVESGWAKM+VE CAADKQARIDSGKDVIVGVNKYKLAKED I+ILDI
Sbjct: 421 IEEIEAMGGMTKAVESGWAKMKVEECAADKQARIDSGKDVIVGVNKYKLAKEDPIEILDI 480

Query: 483 DNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVGEV 542
           DNHAVREAQIARL KIRA+RDSAAVQAALDALTQCAESGEGNLLDL+VKA+RLRA+VGE+
Sbjct: 481 DNHAVREAQIARLTKIRATRDSAAVQAALDALTQCAESGEGNLLDLAVKAVRLRASVGEI 540

Query: 543 SDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLGQD 602
           SDALEKVFGR+RAN Q +SGVYG VVE    W+ +KA+I  F  EEGRRPRIMIAKLGQD
Sbjct: 541 SDALEKVFGRYRANPQAVSGVYGAVVEDDADWKELKAEIEAFIAEEGRRPRIMIAKLGQD 600

Query: 603 GHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLPAL 662
           GHDRGAKVVA+AFADLGFDID+GPLFQTPEEAAR AVENDVHA+G SSLAAGHKTL+PA+
Sbjct: 601 GHDRGAKVVASAFADLGFDIDIGPLFQTPEEAARHAVENDVHAVGCSSLAAGHKTLVPAI 660

Query: 663 VNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSR 720
           +  LK  GA+DII F GGVIPAQDYD LYAAGAK IFGPGT I  +A+ VL++IR ++
Sbjct: 661 IAELKRLGAEDIITFVGGVIPAQDYDALYAAGAKGIFGPGTPIPKAAREVLKQIRAAK 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: 1535
Number of extensions: 45
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: 721
Length adjustment: 40
Effective length of query: 681
Effective length of database: 681
Effective search space:   463761
Effective search space used:   463761
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)
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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