Alignments for a candidate for mcmA in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Bradyrhizobium sp. BTAi1

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_012043162.1 BBTA_RS14110 methylmalonyl-CoA mutase

Query= BRENDA::Q84FZ1
         (721 letters)



>NCBI__GCF_000015165.1:WP_012043162.1
          Length = 718

 Score = 1147 bits (2968), Expect = 0.0
 Identities = 567/717 (79%), Positives = 647/717 (90%), Gaps = 6/717 (0%)

Query: 3   SRIPDFASVAYAADGFKAPPPPAG--EPWMTPEGIPVKGFYGPEDREGCEGIDSFPGLPP 60
           SRIPDFA +A+A     A P PAG  EPW+TPEGIPVK  YG  D  G + +D++PG+ P
Sbjct: 2   SRIPDFADIAFAPT---AAPAPAGSAEPWLTPEGIPVKPAYGEADLAGIDFLDTWPGIAP 58

Query: 61  YLRGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDH 120
           ++RGPYP MYV QPWT+RQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDH
Sbjct: 59  FMRGPYPTMYVNQPWTVRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLATHRGYDSDH 118

Query: 121 PRVSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIVAAEEQGVPP 180
           PRV GDVGMAGVAIDSIYDMRTLF+GIPLD+M+VSMTMNGAVLP +AL++VAAEEQGVPP
Sbjct: 119 PRVGGDVGMAGVAIDSIYDMRTLFAGIPLDQMSVSMTMNGAVLPILALFVVAAEEQGVPP 178

Query: 181 EKLAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISISGYHMQEAG 240
           EKL+GTIQNDILKEFMVRNTYIYPP  SMRIISDIF +TS+ MPKFNSISISGYHMQEAG
Sbjct: 179 EKLSGTIQNDILKEFMVRNTYIYPPTPSMRIISDIFAFTSQKMPKFNSISISGYHMQEAG 238

Query: 241 ATQDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAKMRAARLIWA 300
           ATQDLELAYTLADGVEY++AG+AAGL +D+FAPRLSFFWAIGMNFFME+AK+RAARL+WA
Sbjct: 239 ATQDLELAYTLADGVEYLRAGIAAGLDVDRFAPRLSFFWAIGMNFFMEVAKLRAARLLWA 298

Query: 301 KLVKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGTQSLHTNALD 360
           KL+K F P+  +SL LRTHSQTSGWSLTAQDV+NNV RT +EAMAATQG TQSLHTNALD
Sbjct: 299 KLLKPFNPRDPRSLSLRTHSQTSGWSLTAQDVYNNVVRTAVEAMAATQGHTQSLHTNALD 358

Query: 361 EALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARAWEHIREVEA 420
           EALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRD+AA+AW HI+E+E 
Sbjct: 359 EALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDLAAKAWGHIQEIEE 418

Query: 421 LGGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDLLRVDNADVR 480
           LGGMAKAIEAG+PKLRIEEA+A+ QARID+GRQ+++G+NKYKP DE  +D+L+VDN+ VR
Sbjct: 419 LGGMAKAIEAGVPKLRIEEASAKTQARIDTGRQSVIGVNKYKPTDEPPLDVLKVDNSTVR 478

Query: 481 AKQIDKLKRLRAERNQADVDAALAALTKAA-DGEGNLLELAVNAARAKATVGEISEALEK 539
             QIDKL RL++ER QA+VDAALAALT++A DG GNLL LA++AARAKATVGEIS+ALEK
Sbjct: 479 RLQIDKLSRLKSERKQAEVDAALAALTRSAGDGNGNLLALAIDAARAKATVGEISDALEK 538

Query: 540 AWGRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAKMGQDGHDRG 599
            +GRHRA+I+SI+GVYKRE+  MS   EK++ L+EAFEE +GRRPRILVAK+GQDGHDRG
Sbjct: 539 VFGRHRAEIKSITGVYKREIAAMSGKAEKLQALIEAFEEAEGRRPRILVAKIGQDGHDRG 598

Query: 600 QKVIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTLVPELKAALK 659
           QKVIASAFAD+GFDVDIGPLFAT DEAARQAVENDVHI+GVSSLAA HLT VPELKAALK
Sbjct: 599 QKVIASAFADIGFDVDIGPLFATADEAARQAVENDVHILGVSSLAAAHLTAVPELKAALK 658

Query: 660 QEGRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNTRLGYGE 716
           ++GR+D+MI+VGGV+PP DYDAL  +GA AIFPPGTVIA+AA  L+ +LN RLG+ E
Sbjct: 659 KQGREDIMIIVGGVVPPQDYDALTKSGAEAIFPPGTVIADAAEELIHKLNARLGHSE 715


Lambda     K      H
   0.318    0.134    0.391 

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: 1414
Number of extensions: 41
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: 721
Length of database: 718
Length adjustment: 40
Effective length of query: 681
Effective length of database: 678
Effective search space:   461718
Effective search space used:   461718
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