Alignments for a candidate for mcmA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Dinoroseobacter shibae DFL-12

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate 3609471 Dshi_2855 methylmalonyl-CoA mutase, large subunit (RefSeq)

Query= SwissProt::P27253
         (714 letters)



>FitnessBrowser__Dino:3609471
          Length = 657

 Score =  396 bits (1018), Expect = e-114
 Identities = 252/651 (38%), Positives = 356/651 (54%), Gaps = 23/651 (3%)

Query: 71  QPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDVGKAGV 130
           +PW  R YAG STA+ SNA YR NLA GQ GLSVAFDL T  GYDSD+    G+VGK GV
Sbjct: 10  RPWLFRTYAGHSTAEASNALYRGNLAKGQTGLSVAFDLPTQTGYDSDHVLSRGEVGKVGV 69

Query: 131 AIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDKLTGTIQNDIL 190
            +  + DM+ LF  IPLD+M+ SMT+N     +L+ YI  AEEQG    KL GT+QNDI+
Sbjct: 70  PVAHLGDMRALFKDIPLDQMNTSMTINATAPWLLSLYIAVAEEQGADVTKLQGTVQNDII 129

Query: 191 KEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGANCVQQVAFTLA 250
           KEYL R TYI PPKPS+R+I D+ A+   ++P++N +++  YH+ EAGA   Q++AF LA
Sbjct: 130 KEYLSRGTYICPPKPSLRMITDVAAYTREHLPKWNPMNVCSYHLQEAGATPEQELAFALA 189

Query: 251 DG---IEYIKAAISAGLKIDDFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEAV-SGFGA 306
                ++ +K  + A         R+SFF   G+     +  +RA   LW E     +G 
Sbjct: 190 TATAVLDDLKGKVPAE-HFPAMVGRISFFVNAGIRFVTEMCKMRAFVTLWDEICRDRYGV 248

Query: 307 QDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATL---GGTQSLHTNAFDEALGL 363
           +DPK    R   Q +   LTEQ P NNV R  IE LA TL      +++   A++EALGL
Sbjct: 249 EDPKFRRFRYGVQVNSLGLTEQQPENNVYRILIEMLAVTLSKNARARAVQLPAWNEALGL 308

Query: 364 PTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAGGMA 423
           P  +  + +   Q I+  E++L    D   G+  ++    ++++ ARA +  ID  GG  
Sbjct: 309 PRPWDQQWSLRMQQIMALETDLLEFDDLFDGNPAVDRKVAELMEGARAELATIDGMGGAV 368

Query: 424 KAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDHE----DETDVLEIDNVMVRN 479
            AIE    K  + EA++     I+ G+ V+VGVNKY+        D    + + +  V  
Sbjct: 369 AAIE--YMKSRLVEANSDRLGRIEGGETVVVGVNKYQQGEPSPLMDADGGIMVVDPAVEA 426

Query: 480 EQIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDALEVAF 539
           +QIA L+  RA RD+ A   AL  L  AA    N++ A++ AA+   T GE    +  +F
Sbjct: 427 DQIARLQAWRAARDEDAAQKALADLREAALSGANVMPASIAAAKAGVTTGEWGLEIRKSF 486

Query: 540 DRYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDR 599
             Y  P    TGV A   +++E      DA+ A +    A  GR+ + L+ K G DGH  
Sbjct: 487 GEYRAP----TGVSANPSNRTEGLDEIRDAVSAVS----AKLGRKLKFLVGKPGLDGHSN 538

Query: 600 GAKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEAL 659
           GA+ IA+   D G D+    +  TPEEI R A E D HVVG S L+  H  LI EL+  +
Sbjct: 539 GAEQIAARARDCGMDITYEGIRLTPEEIVRAAREQDAHVVGLSILSGSHIPLIEELMGRM 598

Query: 660 KKWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSVR-DVLNLI 709
           ++     I V+ GG+IP  D   L+  GVA +Y P    L+ +  D++ L+
Sbjct: 599 READLTHIPVIVGGIIPEDDAERLRAMGVAKVYTPKDFELNRIMFDIVGLV 649


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: 938
Number of extensions: 38
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: 657
Length adjustment: 39
Effective length of query: 675
Effective length of database: 618
Effective search space:   417150
Effective search space used:   417150
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:

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