Alignments for a candidate for mcm-large in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcm-large in Azospirillum brasilense Sp245

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS21115 AZOBR_RS21115 methylmalonyl-CoA mutase

Query= BRENDA::P11653
         (728 letters)



>FitnessBrowser__azobra:AZOBR_RS21115
          Length = 717

 Score =  843 bits (2179), Expect = 0.0
 Identities = 444/713 (62%), Positives = 536/713 (75%), Gaps = 13/713 (1%)

Query: 18  PADAARRFEELAAKA----GTGE--AWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFV 71
           P      ++ LAAK     GT E   W+T E + V  L+  D  + ++ LD+  G PPF 
Sbjct: 5   PKKTQADWQTLAAKDLGANGTLEDLVWKTPEGLDVKALYTADDLEGLE-LDSLPGFPPFT 63

Query: 72  HGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPR 131
            GP ATMYA +PWTIRQYAGFSTA++SNAFY+ NL AGQ GLSVAFDL THRGYDSD+PR
Sbjct: 64  RGPRATMYAVKPWTIRQYAGFSTAEDSNAFYKANLKAGQMGLSVAFDLATHRGYDSDHPR 123

Query: 132 VAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQ 191
           V GDVG AGVAIDS+ DM+ LF GIPLD+MSVSMTMNGAVLPILA Y+V AEEQGV  ++
Sbjct: 124 VVGDVGKAGVAIDSVEDMKILFDGIPLDKMSVSMTMNGAVLPILAGYIVAAEEQGVSQDK 183

Query: 192 LAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGAT 251
           L+GTIQNDILKEFMVRNTYIYPP+PSMRII++I  YT+ NMPK+NSISISGYHMQEAGAT
Sbjct: 184 LSGTIQNDILKEFMVRNTYIYPPEPSMRIIADIIEYTALNMPKFNSISISGYHMQEAGAT 243

Query: 252 ADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKL 311
           A  E+A+T+ADG++Y+RA  S GL VD+FAPRLSFF+ IGMNFFME+AKLRAAR+LW+ L
Sbjct: 244 AVQELAFTIADGLEYVRAAMSKGLPVDKFAPRLSFFFSIGMNFFMEIAKLRAARLLWSTL 303

Query: 312 VHQ-FGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDE 370
           + Q F PK+ +S++LRTH QTSG SLT QD YNNV+RT IEAMAA  G TQSLHTN+ DE
Sbjct: 304 MKQKFDPKDARSLALRTHCQTSGVSLTEQDPYNNVIRTTIEAMAAVLGGTQSLHTNAFDE 363

Query: 371 AIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKV 430
           A+ LPT FSARIARNTQL + +ESG T V+DP  GS Y+E LT  LA  A   I +VE +
Sbjct: 364 ALGLPTKFSARIARNTQLIIAEESGVTNVVDPLGGSYYIENLTHSLANAALDLINKVEDL 423

Query: 431 GGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLA 490
           GGM KA++ G+PK+ IEEAAAR QAR+D   + ++GVNKYR E+   +DVL +DN+ V  
Sbjct: 424 GGMTKAVDSGMPKLLIEEAAARRQARVDRAEEVIVGVNKYRPENPEMVDVLDIDNTAVRE 483

Query: 491 EQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSD 550
            Q A+L  +RA RD  K +AAL+ +T AA      +   NLL L ++A RA ATVGE+SD
Sbjct: 484 SQIARLNSVRANRDDAKCRAALEALTKAA-----TEKSGNLLALAVEATRARATVGEISD 538

Query: 551 ALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGH 610
           ALEK F R+ A IR++SGVY    +     +  +E V  F   EGRRPRIL+ KMGQDGH
Sbjct: 539 ALEKAFTRHVAVIRSVSGVYGAAYEGDEGFKRIQEEVSAFAAEEGRRPRILVVKMGQDGH 598

Query: 611 DRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRK 670
           DRG KVIAT++AD+GFDVD+GPLFQTPEE ARQAVE DVHV+GVSS A GH TLVP L +
Sbjct: 599 DRGAKVIATSFADIGFDVDIGPLFQTPEEAARQAVENDVHVIGVSSQAAGHKTLVPQLVE 658

Query: 671 ELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLR 723
           EL + G  DIL+  GGVIP QD+D L K GA  IY PGT IP++A  ++  LR
Sbjct: 659 ELRRQGAGDILVVCGGVIPPQDYDYLYKAGAAAIYGPGTNIPKAASDILAILR 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: 1346
Number of extensions: 40
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: 717
Length adjustment: 40
Effective length of query: 688
Effective length of database: 677
Effective search space:   465776
Effective search space used:   465776
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
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