Alignments for a candidate for mcm-large in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Rhizobium etli CFN 42

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011427619.1 RHE_RS22800 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>NCBI__GCF_000092045.1:WP_011427619.1
          Length = 712

 Score =  791 bits (2043), Expect = 0.0
 Identities = 404/685 (58%), Positives = 503/685 (73%), Gaps = 5/685 (0%)

Query: 38  WETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKE 97
           W+T E I V  L+  +  +    L +  G  PF  GP ATMYA RPWTIRQYAGFSTA+E
Sbjct: 26  WQTPEGIAVKPLYIAEDLEGAAHLGSLPGFAPFTRGPRATMYAGRPWTIRQYAGFSTAEE 85

Query: 98  SNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIP 157
           SNAFYRRNLAAGQKGLSVAFDL THRGYDSD+PRV GDVG AGVAIDS+ DM+ LF GIP
Sbjct: 86  SNAFYRRNLAAGQKGLSVAFDLATHRGYDSDHPRVEGDVGKAGVAIDSVEDMKILFDGIP 145

Query: 158 LDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPS 217
           L  MSVSMTMNGAV+PILA ++V  EEQGV   +L+GTIQNDILKEFMVRNTYIYPP+PS
Sbjct: 146 LGDMSVSMTMNGAVIPILASFIVAGEEQGVPRAELSGTIQNDILKEFMVRNTYIYPPEPS 205

Query: 218 MRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNV 277
           MRI+++I  YT+  MPK+NSISISGYHMQEAGAT   E+A+TLADG +Y+RA  + GL+V
Sbjct: 206 MRIVADIIEYTAKEMPKFNSISISGYHMQEAGATLVQELAFTLADGREYVRAAIAKGLDV 265

Query: 278 DQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLT 337
           D FA RLSFF+ IGMNFFME AKLRAAR+LW +++ +F P+   S+ LRTH QTSG SL 
Sbjct: 266 DDFAGRLSFFFAIGMNFFMEAAKLRAARLLWTRIMEEFQPRKASSLMLRTHCQTSGVSLQ 325

Query: 338 AQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTT 397
            QD YNN++RT  EAM+A  G TQSLHTNS DEAIALPT+FSARIARNTQL LQ E+G T
Sbjct: 326 EQDPYNNIIRTAFEAMSAVLGGTQSLHTNSFDEAIALPTEFSARIARNTQLILQHETGVT 385

Query: 398 RVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARI 457
           +V+DP +GS YVE LT +LA KAW  I+EVE +GGM KA+ +G+PK  IEEAAAR QA +
Sbjct: 386 KVVDPLAGSYYVESLTKELADKAWALIEEVEALGGMTKAVNEGLPKRLIEEAAARRQAAV 445

Query: 458 DSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITW 517
           D G + ++GVN+YRL++E P+D+L++DNS V   Q  ++ + +  RD   V+  L  +  
Sbjct: 446 DKGEEVIVGVNRYRLDNEQPIDILEIDNSAVRTAQIRRIEETKRRRDGSAVRETLAALAE 505

Query: 518 AAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNT 577
            A     +    NLLK  I+A RA ATVGE+SDA+   FG + A    I GVY +   N 
Sbjct: 506 VA-----RTGSGNLLKAAIEAARARATVGEISDAMRGAFGDHAATPAVIKGVYGEAYDNE 560

Query: 578 PEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTP 637
           PE+   R+ + E  +A G RP+I++AK+GQDGHDRG KVIA+A+ D+GFDV  GPLFQTP
Sbjct: 561 PELAVLRQRMAEVTEAMGYRPKIMVAKLGQDGHDRGAKVIASAFGDIGFDVLAGPLFQTP 620

Query: 638 EETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELR 697
           +E    A++  V+VVGVSSLA GH TL+P L   L + G  DI++  GGVIP QD++ L 
Sbjct: 621 DEAVELALDRKVNVVGVSSLAAGHRTLLPQLVDRLREKGGDDIIVVCGGVIPRQDYEFLH 680

Query: 698 KDGAVEIYTPGTVIPESAISLVKKL 722
           + G   ++ PGT + E+A S++  L
Sbjct: 681 EHGVAAVFGPGTNVLEAANSVLDLL 705


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: 1269
Number of extensions: 40
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: 712
Length adjustment: 40
Effective length of query: 688
Effective length of database: 672
Effective search space:   462336
Effective search space used:   462336
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 Apr 09 2024. 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 2024 update 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