Alignments for a candidate for mcm-large in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Desulfobulbus mediterraneus DSM 13871

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_028584323.1 G494_RS0109360 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000429965.1:WP_028584323.1
          Length = 717

 Score =  803 bits (2073), Expect = 0.0
 Identities = 415/700 (59%), Positives = 519/700 (74%), Gaps = 18/700 (2%)

Query: 27  ELAAKAGTGEA-----WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAF 81
           E+A K   G++     W+T E I V  L+     + M+ + +  G+ P+  GP ATMYA 
Sbjct: 12  EVATKQMKGKSPDTLTWKTPEGIDVKCLYTAADIEGMETVGSMPGMAPYARGPMATMYAG 71

Query: 82  RPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGV 141
           RPWTIRQYAGFSTA ESNAFYRRNLAAGQKGLSVAFDL THRGYDSDNPRVAGD+G AGV
Sbjct: 72  RPWTIRQYAGFSTAAESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPRVAGDIGKAGV 131

Query: 142 AIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDIL 201
           AIDSI DM+ LF GIPLD+MSVSMTMNGAV+PIL +++  AEE GVK EQL GTIQNDIL
Sbjct: 132 AIDSIEDMKILFDGIPLDKMSVSMTMNGAVIPILGMWIAAAEESGVKQEQLMGTIQNDIL 191

Query: 202 KEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLA 261
           KE++ RNTYIYPP PSMRI+S+I  + S NMPK+N+ISISGYH+ EAGA + ++ A+TLA
Sbjct: 192 KEYLTRNTYIYPPTPSMRIVSDIMEFASQNMPKYNTISISGYHIMEAGADSVLQTAFTLA 251

Query: 262 DGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPK 321
           DGV+Y+RA  + G++VD FAPRLSFF+GIGMNFFM++A LRAAR LW +L+ QF P+NPK
Sbjct: 252 DGVEYVRAAIASGMSVDTFAPRLSFFFGIGMNFFMDIAMLRAARFLWHRLMQQFNPENPK 311

Query: 322 SMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSAR 381
           S  LRTH QTSGWSLT QD YNNV+RT +EAM+A  G TQSLHTNS DEA+ LPTDFSAR
Sbjct: 312 SSMLRTHCQTSGWSLTEQDPYNNVIRTTMEAMSAVLGGTQSLHTNSYDEAVCLPTDFSAR 371

Query: 382 IARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGI 441
           IARNTQ+ +Q+ES   +V DP  GS Y+E LT  +  +A   I E+E++GGMAKAIE G+
Sbjct: 372 IARNTQIIIQEESHVCKVADPLGGSYYIEYLTNQIVDEAQKIIDEIEEIGGMAKAIESGM 431

Query: 442 PKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEP-PLDVLKVDNSTVLAEQKAKLVKLR 500
           PKMRIEE+AAR QARID G   ++GVNKYRLE E    D+L+V + TV  EQ  ++ ++R
Sbjct: 432 PKMRIEESAARRQARIDQGSDVIVGVNKYRLEDEKLDFDILEVPD-TVRTEQIDRINEIR 490

Query: 501 AERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYT 560
             R+  + +A L+ +T AA      +   NLL++ I A +A ATVGE+SDA+EKVFGRY 
Sbjct: 491 KTRNEAECQACLEAVTKAA------EGKGNLLEVAIAAAKARATVGEISDAMEKVFGRYV 544

Query: 561 AQIRTISGVYSKEV-----KNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQK 615
           A  + +SG YS E      ++   +E+ R+    F +  GRRPRIL+ KMGQDGHDRG K
Sbjct: 545 ATTQCVSGAYSSEYAEADSESAQVIEDFRKRTGNFLEKTGRRPRILVTKMGQDGHDRGIK 604

Query: 616 VIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKL 675
           V+A+++ADLGFDVD+ P+FQTP+E A+ A+E DVH+VG SSLA GH TLVP L  +L + 
Sbjct: 605 VVASSFADLGFDVDISPMFQTPDEAAKMAIENDVHIVGASSLAAGHKTLVPELIAKLKEQ 664

Query: 676 GRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESA 715
           G  +I +  GGVIP  D+D L + G   ++ PGT I  SA
Sbjct: 665 GAGEIGVVAGGVIPPSDYDFLYEAGTKAVFGPGTPITTSA 704


Lambda     K      H
   0.317    0.133    0.389 

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: 1247
Number of extensions: 37
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: 728
Length of database: 717
Length adjustment: 40
Effective length of query: 688
Effective length of database: 677
Effective search space:   465776
Effective search space used:   465776
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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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