Alignments for a candidate for mcmA in Sphingomonas indica Dd16

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Sphingomonas indica Dd16

Align Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 (characterized)
to candidate WP_085218115.1 B9N75_RS06775 methylmalonyl-CoA mutase

Query= SwissProt::Q3J4D7
         (709 letters)



>NCBI__GCF_900177405.1:WP_085218115.1
          Length = 714

 Score =  950 bits (2456), Expect = 0.0
 Identities = 484/701 (69%), Positives = 564/701 (80%), Gaps = 5/701 (0%)

Query: 8   WRKLAEKELKGKSPDSLTWNTLEGIPVKPLYTRADLAGMEHLDGLPGVAPFTRGVRATMY 67
           W  LA KE+KG+    LTW+T EGI VKPLYT  D+A ++   GLPG APFTRGVRA+MY
Sbjct: 11  WEALAAKEVKGRD---LTWHTPEGIAVKPLYTAEDVADID--PGLPGFAPFTRGVRASMY 65

Query: 68  AGRPWTIRQYAGFSTAEASNAFYRKALAAGQQGVSVAFDLATHRGYDSDHPRVVGDVGKA 127
           AGRPWTIRQYAGFSTAE SNAFYR+ LAAGQ+G+SVAFDLATHRGYDSDHPRV GDVGKA
Sbjct: 66  AGRPWTIRQYAGFSTAEESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVTGDVGKA 125

Query: 128 GVAIDSIEDMKILFNGIPLEKISVSMTMNGAVIPILANFIVTGEEQGVPRAALSGTIQND 187
           GVAIDS+EDMKILF+GIPL+K+SVSMTMNGAVIPILA FIV GEEQGV +  L GTIQND
Sbjct: 126 GVAIDSVEDMKILFDGIPLDKMSVSMTMNGAVIPILAFFIVAGEEQGVAQEMLDGTIQND 185

Query: 188 ILKEFMVRNTYIYPPEPSMRIIADIIEYTSKEMPKFNSISISGYHMQEAGANLVQELAYT 247
           ILKEFMVRNTYIYPPEPSMRII+DI  +TS  MPKFNSISISGYHMQEAGA  VQELA+T
Sbjct: 186 ILKEFMVRNTYIYPPEPSMRIISDIFAFTSANMPKFNSISISGYHMQEAGATQVQELAFT 245

Query: 248 LADGREYVRAALARGMNVDDFAGRLSFFFAIGMNFFMEAAKLRAARLLWHRIMSEFAPKK 307
           +ADG EYV+  +A G+++D FAGRLSFFFAIGMNFFME AKLRAAR+LW+R+M+    K 
Sbjct: 246 IADGMEYVKYGVASGLDIDRFAGRLSFFFAIGMNFFMEIAKLRAARVLWYRVMTSLGAKD 305

Query: 308 PGSLMLRTHCQTSGVSLQEQDPYNNVIRTAYEAMSAALGGTQSLHTNALDEAIALPTEFS 367
             S MLRTHCQTSGVSL EQDPYNNV+RT  EAM+A LGGTQSLHTNALDEAIALPT+FS
Sbjct: 306 ERSKMLRTHCQTSGVSLTEQDPYNNVMRTTIEAMAAMLGGTQSLHTNALDEAIALPTDFS 365

Query: 368 ARIARNTQIILQEETGVTRVVDPLAGSYYVESLTAELAEKAWALIEEVEAMGGMTKAVAS 427
           ARIARNTQ+++QEETG+T VVDPL GSYYVE+LT  L ++AWA+IE VEA GGM KAVA+
Sbjct: 366 ARIARNTQLVIQEETGMTNVVDPLGGSYYVEALTQRLVDEAWAIIERVEAEGGMAKAVAA 425

Query: 428 GMPKLRIEESAARRQAAIDRGEDVIVGVNKYRLAKEDPIEILDIDNVAVRDAQIARLEKM 487
           G PK  IEE+AA   A IDRGE VIVGVN+YR A+EDPIEILD+DN AVR+AQI R+ K+
Sbjct: 426 GWPKAMIEEAAAAAAARIDRGEQVIVGVNRYRKAEEDPIEILDVDNHAVREAQIRRIAKV 485

Query: 488 RATRDEAACQAALDELTRRAAEGGNLLEAAVDASRARASVGEISMAMEKVFGRHRAEVKT 547
           +A RDEAACQ+AL  L   A   GNLL  AV+ +R RA++GEIS AME  FGR+      
Sbjct: 486 KAERDEAACQSALGALREGAKRDGNLLALAVECARRRATLGEISSAMEDAFGRYGTNPAP 545

Query: 548 LSGVYGAAYEGDDGFAQIQRDVESFAEEEGRRPRMLVVKMGQDGHDRGAKVIATAFADIG 607
           +SGVYG AY GD  +  +   VE   +  GR+PR+LV KMGQDGHDRGA ++++ F D+G
Sbjct: 546 VSGVYGGAYTGDARWTGLVDGVEMVGKRMGRKPRLLVAKMGQDGHDRGANLVSSMFGDLG 605

Query: 608 FDVDVGTLFQTPEEAAQDAIDNDVHVVGISSLAAGHKTLAPKLIEALKEKGAGEILVICG 667
           F+V  G LFQTP+EAA  A++  V VVG SSLAAGHKTL P+LI  L++ G  +I V+ G
Sbjct: 606 FEVVPGPLFQTPKEAAALAVERQVDVVGASSLAAGHKTLVPELIGHLRDMGRADIKVVVG 665

Query: 668 GVIPQQDYDFLQQAGVKAIFGPGTNIPSAAKHILDLIREAR 708
           GVIP QDYD L++AGV+ IFGPGTN+  AA  +L L+   R
Sbjct: 666 GVIPAQDYDMLREAGVQGIFGPGTNLIDAAGEVLKLLGHNR 706


Lambda     K      H
   0.318    0.133    0.377 

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: 1354
Number of extensions: 49
Number of successful extensions: 3
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: 709
Length of database: 714
Length adjustment: 39
Effective length of query: 670
Effective length of database: 675
Effective search space:   452250
Effective search space used:   452250
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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)
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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