Alignments for a candidate for mcmA in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Rhodomicrobium vannielii ATCC 17100

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_013418817.1 RVAN_RS05750 protein meaA

Query= SwissProt::P27253
         (714 letters)



>NCBI__GCF_000166055.1:WP_013418817.1
          Length = 673

 Score =  410 bits (1053), Expect = e-118
 Identities = 243/645 (37%), Positives = 356/645 (55%), Gaps = 20/645 (3%)

Query: 71  QPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGV 130
           QPW  R YAG ST K SN  Y +NLA GQ GLSVAFDL T  GYDSD+P   G+VGK GV
Sbjct: 19  QPWIFRTYAGHSTPKASNELYLKNLAKGQTGLSVAFDLPTQTGYDSDHPLAKGEVGKVGV 78

Query: 131 AIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDIL 190
            +  + DM+ L   IPL KM+ SMT+N     +L+ Y+  A+EQGV+ ++LTGT+QNDI+
Sbjct: 79  PVAHIGDMRTLLAGIPLGKMNTSMTINATAAWMLSLYVAIADEQGVSRNQLTGTVQNDII 138

Query: 191 KEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLA 250
           KEYL R TY++PP+PSMR+I D+  +C   +PR+N +++  YH+ EAGA  VQ++A+ LA
Sbjct: 139 KEYLSRGTYVFPPQPSMRLIKDVTVFCYREVPRWNPMNVCSYHLQEAGATPVQELAYALA 198

Query: 251 DGIEYIKAAISAG-LKIDDFA---PRLSFFFGIGMDLFMNVAMLRAARYLWSE-AVSGFG 305
                +     +G +  ++F     R+SFF   GM     +  +RA   LW E A   +G
Sbjct: 199 TAQAVLDTVRDSGEIPEEEFGQALARVSFFVNAGMRFVTEMCKMRAFVELWDEIAEKRYG 258

Query: 306 AQDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATL---GGTQSLHTNAFDEALG 362
             DPK    R   Q +   LTE  P NNV R  +E LA  +      +++   A++EALG
Sbjct: 259 VTDPKLRRFRYGVQVNSLGLTEPQPENNVYRILVEMLAVVMSKKARARAVQLPAWNEALG 318

Query: 363 LPTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGM 422
           LP  +  + +   Q I+  E++L    D   GS  I++  + +  +AR  + +I+  GG 
Sbjct: 319 LPRPWDQQWSLRMQQIVAYETDLLEYGDIFDGSREIDAKVEALKAEAREELTRIEAMGGA 378

Query: 423 AKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDHEDETDVLEIDNVM-----V 477
             A+++   K+ + EA+A     I+ G++V+VGVN++              ++M     V
Sbjct: 379 IAAVDSSYMKQRLVEANAARLQKIESGEQVVVGVNRWTETEPSPLSGGVGGSIMTVPEGV 438

Query: 478 RNEQIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDALEV 537
             EQ+ +L+  RA RD  AV A L AL  AAQ   N++  ++  A+   T GE  D L  
Sbjct: 439 EREQVEALKAWRAARDAKAVDATLTALREAAQEGRNIMEPSIACAKAGVTTGEWGDTLRQ 498

Query: 538 AFDRYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGH 597
            F  Y  P    TGV   S   ++ + ++   I A   +  A  GRR ++L+ K G DGH
Sbjct: 499 VFGEYRAP----TGV---SRAAAQGARADLTTIRADVARLSAKLGRRLKLLVGKPGLDGH 551

Query: 598 DRGAKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPELVE 657
             GA+ IA    D G +V    +  TP +I   A+E  VH+VG S L+  H  L+ ++++
Sbjct: 552 SNGAEQIAVRARDSGMEVVYEGIRLTPAQIVNAALEESVHIVGLSILSGSHVPLVRDVMD 611

Query: 658 ALKKWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSV 702
            ++  G  DI VV GG+IP +D A L+  GVAAIY P    L+ +
Sbjct: 612 RMRAAGLSDIPVVVGGIIPLEDEATLKACGVAAIYTPKDFQLNDI 656


Lambda     K      H
   0.318    0.133    0.381 

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: 970
Number of extensions: 50
Number of successful extensions: 6
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: 714
Length of database: 673
Length adjustment: 39
Effective length of query: 675
Effective length of database: 634
Effective search space:   427950
Effective search space used:   427950
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 Apr 09 2024. 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:

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