Aligments for a candidate for mcmA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Echinicola vietnamensis KMM 6221, DSM 17526

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Echvi_4683 Echvi_4683 Methylmalonyl-CoA mutase, N-terminal domain/subunit

Query= BRENDA::Q84FZ1
         (721 letters)



>FitnessBrowser__Cola:Echvi_4683
          Length = 685

 Score =  872 bits (2252), Expect = 0.0
 Identities = 431/670 (64%), Positives = 527/670 (78%), Gaps = 2/670 (0%)

Query: 40  FYGPEDREGCEGIDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAA 99
           F    DR   + +    G+ P+LRGPY  MY+T+PWT+RQYAGFSTAE SNAFY++NL A
Sbjct: 14  FMEAADRPRPDHVRYAAGIAPFLRGPYSTMYLTRPWTLRQYAGFSTAEASNAFYKKNLEA 73

Query: 100 GQKGLSVAFDLATHRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMN 159
           GQKGLSVAFDLATHRGYDSDHPRV GDVG AGVAIDS+  M+ LF GIPLD+M+VSMTMN
Sbjct: 74  GQKGLSVAFDLATHRGYDSDHPRVQGDVGKAGVAIDSVLGMKLLFDGIPLDKMSVSMTMN 133

Query: 160 GAVLPGVALYIVAAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYT 219
           GAV+P +A YIVAAEEQGVP ++L GTIQNDILKEFMVRNTYIYPP+ S+RII+DIF +T
Sbjct: 134 GAVIPVMAFYIVAAEEQGVPLDQLKGTIQNDILKEFMVRNTYIYPPEPSLRIIADIFAFT 193

Query: 220 SKNMPKFNSISISGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFW 279
           +KNMP FNSISISGYHM EAGAT +LELAYTLADG+EY++ GL AGL ID FAPRLSFFW
Sbjct: 194 AKNMPAFNSISISGYHMLEAGATPELELAYTLADGLEYVRTGLKAGLAIDDFAPRLSFFW 253

Query: 280 AIGMNFFMEIAKMRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRT 339
            +GM+ F EIAK+RA RL+WAKL+KEF P   KSL LR H QTSGWSLT QD FNNV RT
Sbjct: 254 GVGMDHFTEIAKLRAGRLLWAKLMKEFRPTHPKSLKLRAHCQTSGWSLTEQDAFNNVART 313

Query: 340 CIEAMAATQGGTQSLHTNALDEALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYY 399
            IEA+AA  G TQSLHTNA DEA ALPTDFSA IARNTQ+ L++E G  +++DPWGGS  
Sbjct: 314 TIEALAAVMGHTQSLHTNAFDEAFALPTDFSASIARNTQVILREEYGLRKVVDPWGGSVL 373

Query: 400 VERLTRDIAARAWEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGIN 459
           +E LT D+  +AW H++EVE +GGMAKAIEAG+PK  IEEAAAR QA++D G++ +VG+N
Sbjct: 374 LEELTEDLVKKAWAHLQEVEKMGGMAKAIEAGLPKQMIEEAAARRQAKVDQGKEIVVGVN 433

Query: 460 KYKPDDEMKIDLLRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTKAA-DGEGNLLE 518
           ++  D+E   D+L VDN  V  +Q  +L +L+ +R+ A V  +L A+T+AA  GEGNLLE
Sbjct: 434 RFLVDEEEDFDILEVDNEAVLKQQQARLSQLKNDRDAAAVARSLEAITQAAKSGEGNLLE 493

Query: 519 LAVNAARAKATVGEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEE 578
           L+V AAR +AT+GEIS A+EK +GRHRA+ + +SGVY  E G    + ++   L   FE+
Sbjct: 494 LSVEAARERATLGEISMAMEKVYGRHRAKNQVVSGVYSSEAGN-DELFKEALTLTARFEK 552

Query: 579 NDGRRPRILVAKMGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIV 638
            +GRRPRIL+AKMGQDGHDRG KVIAS  AD+GFDVDIGPLF TP+E A+QAVENDVH+V
Sbjct: 553 LEGRRPRILIAKMGQDGHDRGAKVIASGMADMGFDVDIGPLFQTPEEVAKQAVENDVHLV 612

Query: 639 GVSSLAAGHLTLVPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIA 698
           G SSLA GH  L+P+L  AL++ GR D+++V GGVIPP DY+ L   G   +F PGTV+ 
Sbjct: 613 GASSLAGGHKVLIPQLIIALEEMGRPDILVVAGGVIPPHDYEFLKEKGVLEVFGPGTVLT 672

Query: 699 EAAVNLLGEL 708
           +AA+ ++  L
Sbjct: 673 KAAIRIMSVL 682


Lambda     K      H
   0.318    0.134    0.391 

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: 1263
Number of extensions: 48
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: 721
Length of database: 685
Length adjustment: 39
Effective length of query: 682
Effective length of database: 646
Effective search space:   440572
Effective search space used:   440572
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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