Alignments for a candidate for mcm-large in Dechloromonas agitata is5

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Dechloromonas agitata is5

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_027457187.1 K420_RS0105510 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000519045.1:WP_027457187.1
          Length = 716

 Score =  862 bits (2228), Expect = 0.0
 Identities = 436/704 (61%), Positives = 543/704 (77%), Gaps = 10/704 (1%)

Query: 25  FEELAAKAGTGE-----AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMY 79
           +E++AAK   G       W T E + V  L+ +   +++ + DT  G+ P++ GP  TMY
Sbjct: 14  WEKVAAKQSPGGDVNNLVWNTPEGLAVKALYTKKDVENLAFADTLPGVAPYLRGPQPTMY 73

Query: 80  AFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMA 139
           A +PWTIRQYAGFSTA+ SNAFYR+ LAAG +G+SVAFDL THRGYDSDNPRV GDVG A
Sbjct: 74  AVKPWTIRQYAGFSTAEASNAFYRKALAAGGQGVSVAFDLATHRGYDSDNPRVVGDVGKA 133

Query: 140 GVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQND 199
           GVAIDS+ DM+ LF GIPLD++SVSMTMNGAVLPILA Y+V AEEQGVK EQL+GTIQND
Sbjct: 134 GVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVAAEEQGVKQEQLSGTIQND 193

Query: 200 ILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYT 259
           ILKEFMVRNTYIYPP+PSM+II++IF+YT+ NMPK+NSISISGYH+QEAGA   IE+A+T
Sbjct: 194 ILKEFMVRNTYIYPPKPSMKIIADIFSYTAQNMPKFNSISISGYHIQEAGANQAIELAFT 253

Query: 260 LADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKN 319
           LADG++Y+R G + G++VD FA RLSFFW +GMNF++E+AK+RAAR+LW +++  FG KN
Sbjct: 254 LADGMEYVRTGIASGMDVDTFAGRLSFFWAVGMNFYLEIAKMRAARLLWHRIMSGFGAKN 313

Query: 320 PKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFS 379
            KSM LRTHSQTSGWSLT QD YNNVVRT IEAMAA  G TQSLHTN+LDEAIALPT+FS
Sbjct: 314 AKSMMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQSLHTNALDEAIALPTEFS 373

Query: 380 ARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEK 439
           ARIARNTQL +Q+E+  T VIDPW+GS  +E+LT D+A KAWG IQE+E +GGM KA+E 
Sbjct: 374 ARIARNTQLIIQEETHITNVIDPWAGSYMMEKLTQDMADKAWGIIQEIEAMGGMTKAVES 433

Query: 440 GIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKL 499
           G  KM++E  AA  QARIDSG+  ++GVNKY+L  E P+++L +DN  V   Q A+L  +
Sbjct: 434 GWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDPIEILDIDNHAVREAQIARLKNI 493

Query: 500 RAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRY 559
           RA RD   V AALD +T AA     +  + NLL L + A R  ATVGE+SDALEK+FGR+
Sbjct: 494 RATRDTAAVNAALDALTKAA-----ETGEGNLLDLTVKAIRLRATVGEVSDALEKIFGRF 548

Query: 560 TAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIAT 619
            A  +TISGVY   V+     EE +  V +F + EGRRPRI++AK+GQDGHDRG KV+AT
Sbjct: 549 RANNQTISGVYGGVVEGQESWEEIKAAVAKFAEEEGRRPRIMIAKLGQDGHDRGAKVVAT 608

Query: 620 AYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPD 679
           AYADLGFD+D+GPLFQTPEE ARQA+E DVH +G SSLA GH TLVP + + L + G  D
Sbjct: 609 AYADLGFDIDMGPLFQTPEEAARQAIENDVHAIGCSSLAAGHKTLVPQIIQCLKEQGADD 668

Query: 680 ILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLR 723
           I++  GGVIP QD+D L   GA  I+ PGT I +SA  ++++++
Sbjct: 669 IIVFAGGVIPAQDYDALYAAGAKAIFGPGTRIEDSARKVLEEIK 712


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: 1349
Number of extensions: 42
Number of successful extensions: 2
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