GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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