Alignments for a candidate for mcm-large in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Sedimenticola selenatireducens DSM 17993

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_029132301.1 A3GO_RS0103970 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000428045.1:WP_029132301.1
          Length = 716

 Score =  840 bits (2170), Expect = 0.0
 Identities = 435/716 (60%), Positives = 541/716 (75%), Gaps = 9/716 (1%)

Query: 12  LGNAPVPA--DAARRFE-ELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIP 68
           + N P P   D  ++ E EL  +      W+T E I +  L++    + +  +D+  G  
Sbjct: 1   MANTPKPTLDDWKQQAEKELRGRPLEALNWQTPEGIVIKPLYSAADLEGLKHIDSLPGFA 60

Query: 69  PFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSD 128
           P++ GP ATMYA RPWT+RQYAGFSTA+ESNAFY+RNLAAGQ+GLSVAFDL THRGYDSD
Sbjct: 61  PYLRGPRATMYAGRPWTVRQYAGFSTAEESNAFYKRNLAAGQQGLSVAFDLATHRGYDSD 120

Query: 129 NPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVK 188
           +PRV GDVG AGVAIDS+ DM+ LF  IPLDQ+SVSMTMNGAVLP++A Y+V AEEQGV 
Sbjct: 121 HPRVVGDVGKAGVAIDSVEDMKILFDSIPLDQVSVSMTMNGAVLPVMASYIVAAEEQGVP 180

Query: 189 PEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEA 248
           PE+LAGT+QNDILKEFMVRNTYIYPP+PSMRI+++I  YT+ NMPK+NSISISGYHMQEA
Sbjct: 181 PEKLAGTLQNDILKEFMVRNTYIYPPEPSMRIVADIIGYTAENMPKFNSISISGYHMQEA 240

Query: 249 GATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLW 308
           G+T   E+A+T+ADG++Y+RA  + GL+VDQFAPRLSFF+ IGMNFFME AKLRAAR+LW
Sbjct: 241 GSTLVQELAFTIADGLEYVRAALAKGLDVDQFAPRLSFFFAIGMNFFMEAAKLRAARLLW 300

Query: 309 AKLVHQ-FGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNS 367
           ++L+ + F PK+ +S  LRTH QTSG SLTA+D YNNV+RT IEA+AA  G TQSLHTN+
Sbjct: 301 SELMEKHFQPKDERSKMLRTHCQTSGVSLTAKDPYNNVMRTTIEALAAVLGGTQSLHTNA 360

Query: 368 LDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEV 427
            DEA+ALPTD SARIARNTQL +Q+E+G T+V+DP +GS YVE LT  +  +A   I EV
Sbjct: 361 FDEALALPTDNSARIARNTQLVIQEETGITKVVDPLAGSYYVESLTNAMVEEARALIDEV 420

Query: 428 EKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNST 487
           E +GGM KA+E G+PK+RIEEAAA  QARID G + ++GVNKY+L  EP +DVL +DN+ 
Sbjct: 421 EALGGMTKAVESGMPKLRIEEAAALRQARIDRGEEVIVGVNKYQLAQEPEIDVLDIDNTA 480

Query: 488 VLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGE 547
           V   Q A+L ++R  RD    +AALD +  AA     KD   NLL L +DA RA ATVGE
Sbjct: 481 VREAQVARLRRIRDGRDATAHQAALDALVAAA-----KDGSGNLLALAVDAARARATVGE 535

Query: 548 MSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQ 607
           +SDALE V+ R+ A  R++SGVY    +     E+ ++ + +F + +GRRPR+L+ KMGQ
Sbjct: 536 ISDALESVYNRHKAITRSVSGVYGSAYEGDNGFEKIKQEIADFAEEQGRRPRMLVVKMGQ 595

Query: 608 DGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPA 667
           DGHDRG KVIATAYADLGFDVD+GP+FQTPEE ARQA E DVHVVGVSSLA GH TLVPA
Sbjct: 596 DGHDRGAKVIATAYADLGFDVDIGPMFQTPEEAARQAAENDVHVVGVSSLAAGHKTLVPA 655

Query: 668 LRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLR 723
           L + L   G  DIL+  GGVIP +D+  L + G   +Y PGT IP SA  ++  +R
Sbjct: 656 LIQALKAEGAEDILVVCGGVIPPKDYPVLLEMGVAAVYGPGTNIPASAAEMLAFIR 711


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: 1335
Number of extensions: 42
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: 716
Length adjustment: 40
Effective length of query: 688
Effective length of database: 676
Effective search space:   465088
Effective search space used:   465088
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)
SQLite3 databases

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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