Alignments for a candidate for mcmA in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Magnetospirillum magneticum AMB-1

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_011382757.1 AMB_RS01570 protein meaA

Query= BRENDA::Q23381
         (744 letters)



>NCBI__GCF_000009985.1:WP_011382757.1
          Length = 665

 Score =  403 bits (1035), Expect = e-116
 Identities = 228/632 (36%), Positives = 351/632 (55%), Gaps = 14/632 (2%)

Query: 94  QRPWTIRQYAGFSTVEESNKFYKENIKAGQQGLSVAFDLATHRGYDSDNPRVFGDVGMAG 153
           ++PW  R Y+G S+  ESNK Y+ N+  GQ GLS+AFDL T  GYDSD+    G+VG  G
Sbjct: 15  EKPWLFRTYSGHSSAAESNKLYRTNLTKGQTGLSIAFDLPTQTGYDSDHVLAKGEVGKVG 74

Query: 154 VAVDSVEDMRQLFDGINLEKMSVSMTMNGAVVPVLAMYVVAAEEAGVSRKLLAGTIQNDI 213
           V V  + DM  LF+GI LEKM+ SMT+N     +L++Y+ AAE  G +R +L GT QND+
Sbjct: 75  VPVCHLGDMMTLFEGIPLEKMNTSMTINAPAAWLLSLYIAAAERQGANRSVLNGTTQNDV 134

Query: 214 LKEFMVRNTYIYPPEPSMRIIGDIFAYTSREMPKFNSISISGYHMQEAGADAVLEMAFTI 273
           +KE++ R TYI+ P+PS+++ GD+ A+T RE+PK+N +++  YH+QEAGA    E+A+ +
Sbjct: 135 IKEYLSRGTYIFAPQPSLKLTGDVIAFTYREVPKWNPMNVCSYHLQEAGATPEQELAYAL 194

Query: 274 ADGIQYCET--GLNAGLTIDAFAPRLSFFWGISMNFYMEIAKMRAARRLWANLIKERFSP 331
           A  +   +T          +    R+SFF    + F  E+ KMRA   LW  +   R+  
Sbjct: 195 ATAVAVLDTVRPTVPAADFEQVVSRISFFVNAGIRFVTELCKMRAFTELWDEICVGRYGV 254

Query: 332 KSDKSMMLRTHSQTSGWSLTEQDPYNNIIRTTIEAMASVF---GGTQSLHTNSFDEALGL 388
           K +K+   R   Q +   LTEQ P NN+ R  +E +A V       +++   +++EALGL
Sbjct: 255 KDEKARRFRYGVQVNSLGLTEQQPENNVYRIVMEMLAVVLSKNARARAVQLPAWNEALGL 314

Query: 389 PTKFSARIARNTQIIIQEESGICNVADPWGGSYMMESLTDEIYEKALAVIKEIDELGGMA 448
           P  +  + +   Q I+  E+ +    D + GS+ +    + + E A   +  ID +GG  
Sbjct: 315 PRPWDQQWSLRLQQIMAYETDLLEFGDIFDGSHEITRKVEALKEGAREELARIDAMGGAV 374

Query: 449 KAVASGMTKLKIEEAAAKKQARIDAGKDVIVGVNKYRLDHEQQV-----EVLKIDNAKVR 503
            AV S   K K+ E+ A++   I+ G+ ++VGVNK+       +      ++ +D  K  
Sbjct: 375 SAVESSYMKQKLVESNARRIGAIETGEQIVVGVNKWTETEPSPLTTGEGSIMTVD-PKAE 433

Query: 504 EEQCAKLNHIRATRDAEKAQKALDAITEGARGNGNLMELAIEAARARCTVGEISDAMEKV 563
            EQ  +L   RA RDA+   KAL  +   A    N+ME +I AA A  T GE +  +  V
Sbjct: 434 AEQIERLKAFRAARDAKAVDKALAELRSAANEGRNVMEPSIAAAHAGVTTGEWAQCLRDV 493

Query: 564 FNRHAAVNRLVSGAYKSEFGETSEMSQVLERVKSFADRDGRQPRIMVAKMGQDGHDRGAK 623
           F  + A   +   A + + GE  +M  V  +V++ + + GR+ +I+V K G DGH  GA+
Sbjct: 494 FGEYRAPTGVARAAAEVK-GE--KMGAVRAKVEAVSAKLGRRVKILVGKPGLDGHSNGAE 550

Query: 624 VIATGFADLGFDVDVGPLFQTPLEAAQQAVDADVHVIGASSLAAGHLTLIPQLIGELKKL 683
            IA    D G +V    +  TP +    A++  VHV+G S L+  H+ L+ +++  +K  
Sbjct: 551 QIAVRARDAGMEVVYEGIRLTPAQIVNAALEEGVHVVGLSILSGSHVPLVTEVLERMKAA 610

Query: 684 GRPDILVVAGGVIPPQDYKELYDAGVALVFGP 715
           G  DI VVAGG+IPP+D K L  AG A ++ P
Sbjct: 611 GLSDIPVVAGGIIPPEDEKVLLAAGCARIYTP 642


Lambda     K      H
   0.318    0.133    0.382 

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: 1023
Number of extensions: 40
Number of successful extensions: 5
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: 744
Length of database: 665
Length adjustment: 39
Effective length of query: 705
Effective length of database: 626
Effective search space:   441330
Effective search space used:   441330
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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