Aligments for a candidate for mcmA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for mcmA in Azospirillum brasilense Sp245

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS24250 AZOBR_RS24250 methylmalonyl-CoA mutase

Query= BRENDA::Q84FZ1
         (721 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS24250 AZOBR_RS24250
           methylmalonyl-CoA mutase
          Length = 732

 Score = 1080 bits (2793), Expect = 0.0
 Identities = 546/729 (74%), Positives = 622/729 (85%), Gaps = 14/729 (1%)

Query: 5   IPDFASVAYAADGFKAPPP-------------PAGEPWMTPEGIPVKGFYGPEDREGCEG 51
           +PDF+++   A    A P              PA   W TPE + VK  Y   D +G + 
Sbjct: 4   LPDFSTLPLDAAVSNASPAEWSRRFAAETGTDPATALWRTPEMLDVKPLYTAADLDGLDH 63

Query: 52  IDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLA 111
           + + PG+ P+LRGPYP MYV +PWT+RQYAGFSTA++SNAFYRRNLAAGQKGLSVAFDLA
Sbjct: 64  LAAMPGMAPFLRGPYPTMYVDKPWTVRQYAGFSTAQESNAFYRRNLAAGQKGLSVAFDLA 123

Query: 112 THRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIV 171
           THRGYDSDHPRV+GDVGMAGVAIDSI DM+TLF GIPLD+M+VSMTMNGAVLP +A YIV
Sbjct: 124 THRGYDSDHPRVTGDVGMAGVAIDSILDMKTLFDGIPLDQMSVSMTMNGAVLPVLAGYIV 183

Query: 172 AAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISI 231
           AAEEQGV  +KL+GTIQNDILKEFMVRNTYIYPPK SMRIISDIF +TS++MPKFNSISI
Sbjct: 184 AAEEQGVSADKLSGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAFTSQHMPKFNSISI 243

Query: 232 SGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAK 291
           SGYH+QEAGAT DLELAYTLADGVEY +AGLAAGLTIDQFAPRLSFFWAIGMNFFME+AK
Sbjct: 244 SGYHLQEAGATADLELAYTLADGVEYARAGLAAGLTIDQFAPRLSFFWAIGMNFFMEVAK 303

Query: 292 MRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGT 351
           MRA R++WAKL+KEF PKSDKSL LRTHSQTSGWSLTAQDVFNNVTRTCIEAMA+TQG T
Sbjct: 304 MRAGRMLWAKLIKEFAPKSDKSLSLRTHSQTSGWSLTAQDVFNNVTRTCIEAMASTQGHT 363

Query: 352 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARA 411
           QSLHTNALDEALALPTDFSARIARNTQLFLQQESGT R+IDPWGGSYYVERLTR++AARA
Sbjct: 364 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGTCRVIDPWGGSYYVERLTRELAARA 423

Query: 412 WEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDL 471
           W HIREVE  GGMAKAIE GIPK+R+EEAAAR QARIDSGRQT+VG+NKY+ + E  I++
Sbjct: 424 WGHIREVEETGGMAKAIETGIPKMRVEEAAARTQARIDSGRQTVVGVNKYRLEQEEAIEV 483

Query: 472 LRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTK-AADGEGNLLELAVNAARAKATV 530
           L+VDN+ VRA+QI +L+RLRAER+       L ALT  AA G+GNLL L+V+A RA+ATV
Sbjct: 484 LKVDNSAVRAQQIAQLERLRAERDPIRCRQTLEALTNAAAAGDGNLLALSVDAIRARATV 543

Query: 531 GEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAK 590
           GEIS+ALEK +GRH+A+IR+I+G+Y  EVG  S  + +VR LV  F E DGRRPRI+VAK
Sbjct: 544 GEISDALEKVYGRHKAEIRTITGIYAGEVGRQSDAIARVRALVAEFAERDGRRPRIMVAK 603

Query: 591 MGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTL 650
           MGQDGHDRGQKVIA+AFADLGFDVD+GPLF TP+EAARQAVEND HIVGVSSLAAGHLTL
Sbjct: 604 MGQDGHDRGQKVIATAFADLGFDVDVGPLFQTPEEAARQAVENDCHIVGVSSLAAGHLTL 663

Query: 651 VPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNT 710
           VP+LKA L++ G  D++IVVGGV+PP DYDALYAAGA+AIFPPGTVI+EAAV+LL  LN 
Sbjct: 664 VPQLKAELERHGAGDILIVVGGVVPPQDYDALYAAGATAIFPPGTVISEAAVDLLRILNE 723

Query: 711 RLGYGERQA 719
           R GY  + A
Sbjct: 724 RHGYAPKAA 732


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: 1398
Number of extensions: 37
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: 721
Length of database: 732
Length adjustment: 40
Effective length of query: 681
Effective length of database: 692
Effective search space:   471252
Effective search space used:   471252
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 17 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, or view the source code.

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