Alignments for a candidate for mcmA in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Ruegeria conchae TW15

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_010442843.1 G7G_RS0117980 protein meaA

Query= SwissProt::P27253
         (714 letters)



>NCBI__GCF_000192475.1:WP_010442843.1
          Length = 655

 Score =  412 bits (1059), Expect = e-119
 Identities = 249/651 (38%), Positives = 364/651 (55%), Gaps = 23/651 (3%)

Query: 71  QPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGV 130
           +PW IR YAG STAK SNA YR NLA GQ GLSVAFDL T  GYDSD+    G+VGK GV
Sbjct: 8   RPWLIRTYAGHSTAKASNALYRANLAKGQTGLSVAFDLPTQTGYDSDHTLARGEVGKVGV 67

Query: 131 AIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDIL 190
            I  + DM+ LFDQIPL++M+ SMT+N     +LA YI  AEEQG    KL GT+QND++
Sbjct: 68  PICHLGDMRNLFDQIPLEQMNTSMTINATAPWLLALYIAVAEEQGADVSKLQGTVQNDLI 127

Query: 191 KEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLA 250
           KEYL R TY+ PPKPS+++IAD+  +C  N+P++N +++  YH+ EAGA   Q++A+ LA
Sbjct: 128 KEYLSRGTYVCPPKPSLKMIADVAEYCYENVPKWNPMNVCSYHLQEAGATPEQELAYALA 187

Query: 251 DGIEYIKAAISAGLKIDDF---APRLSFFFGIGMDLFMNVAMLRAARYLWSEAVS-GFGA 306
             I  +   +   +  +DF     R+SFF   G+     +  +RA   LW E +   +G 
Sbjct: 188 TAIAVLD-ELRPRVPAEDFPALCGRISFFVNAGIRFVTEMCKMRAFVDLWDEILQRRYGV 246

Query: 307 QDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATL---GGTQSLHTNAFDEALGL 363
           +DPK    R   Q +   LTEQ P NNV R  IE LA TL      +++   A++EALGL
Sbjct: 247 EDPKFRRFRYGVQVNSLGLTEQQPENNVYRILIEMLAVTLSKRARARAVQLPAWNEALGL 306

Query: 364 PTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMA 423
           P  +  + +   Q I+  E++L    D   G+  +++  +++   ARA +  +D  GG  
Sbjct: 307 PRPWDQQWSMRMQQILAYETDLLEYGDLFDGNPVVDAKVEELKNGARAELANLDSMGGAV 366

Query: 424 KAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDH----EDETDVLEIDNVMVRN 479
            +IE    K  + E++A   + I++ + V+VGVNK+        + E   + + +  V  
Sbjct: 367 ASIE--YMKSRLVESNAERLNRIERNETVVVGVNKWTEGEASPLQTEDGGIMVVDPAVEQ 424

Query: 480 EQIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDALEVAF 539
           EQI  L   R  RD+AAV+AAL AL  AAQ   N++  ++ AA+   T GE ++ +  A+
Sbjct: 425 EQIGRLNDWRTVRDNAAVSAALQALREAAQSGANVMEPSIAAAKAGVTTGEWAEEMRKAY 484

Query: 540 DRYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDR 599
             Y  P+  V+G ++      E   +  DA+  +        GRR + L+ K G DGH  
Sbjct: 485 GTYRGPTG-VSGSVSNKTEGLEDLRAAVDAVSDRL-------GRRLKFLVGKPGLDGHSN 536

Query: 600 GAKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEAL 659
           GA+ IA    D G D+    +  TPEEI     E + HV+G S L+  H  L+ +++  L
Sbjct: 537 GAEQIAFRARDCGMDISYEGIRLTPEEIVSAVQETNAHVIGLSILSGSHLPLVKDVMTRL 596

Query: 660 KKWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLD-SVRDVLNLI 709
            + G  DI V+ GG+IP +D   L+  GVA IY P    L+  + D++ L+
Sbjct: 597 TEAGLSDIPVIVGGIIPDEDAEQLRSMGVAKIYTPKNFELNLIIGDIVTLV 647


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: 944
Number of extensions: 41
Number of successful extensions: 7
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: 655
Length adjustment: 39
Effective length of query: 675
Effective length of database: 616
Effective search space:   415800
Effective search space used:   415800
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 24 2021. 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 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