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

GapMind for catabolism of small carbon sources

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

Align Monocarboxylic acid transporter (characterized)
to candidate WP_011385006.1 AMB_RS13215 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_000009985.1:WP_011385006.1
          Length = 554

 Score =  413 bits (1061), Expect = e-119
 Identities = 237/543 (43%), Positives = 325/543 (59%), Gaps = 39/543 (7%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I++F  F++ T+ +     K T  ++DFYT G   +G QNGLAIAGDY+SAA+ LG+   
Sbjct: 37  IAMFFAFVMGTLGITYWASKRTKSASDFYTAGGGITGFQNGLAIAGDYMSAATLLGLSSM 96

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +   G+DGF+Y+I FFV W + L L+AE LRN+GR+T AD+ S+RL Q  VR  AA G+L
Sbjct: 97  VFATGFDGFIYTISFFVGWPIILFLLAERLRNLGRYTFADIASYRLDQSKVRTFAAMGSL 156

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V  FYLI QM GAG L+ +L  +      AV V IVG++M+ YV  GGM  TT+VQ+IK
Sbjct: 157 TVVCFYLIVQMVGAGQLIKLLFGLD----YAVAVIIVGVLMVVYVTFGGMIATTWVQIIK 212

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
           A LL+GG  ++  L   K    L  +   AVE H A            +I+ P    G  
Sbjct: 213 ACLLLGGGVLLCALALSKFGFSLENVAAKAVESHKAG----------VKIMGP----GTM 258

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322
           L   +  +SL+L L  GTA LPH+LMRF+TVP AKEARKSV  A   IG F+L+  +LG 
Sbjct: 259 LADPVSAVSLSLGLVFGTAALPHILMRFFTVPNAKEARKSVFVASGFIGFFFLIVCILGL 318

Query: 323 GAAALVGPDRVI--------AAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374
            A ++VG D              G  N     LA  LGG IF+  +SAVAFAT+LAVV+G
Sbjct: 319 AAVSIVGTDPQFFEGGKVGGKLLGGGNMPVMHLAKALGGDIFLGFLSAVAFATILAVVSG 378

Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434
           LA+  ++A+ HDIY  VIR G +TEAE++RVS+++ +V+G+++++LGI+   QNVAFLV 
Sbjct: 379 LALAGASAIAHDIYARVIRKGHATEAEEMRVSKLSSLVLGVVAVILGIMFEKQNVAFLVG 438

Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494
           L F +AASAN P +  S+YW+   T GA+     GL+SA+  + LS AV      +V   
Sbjct: 439 LTFGIAASANFPVLFLSMYWRGLTTKGALWGGIAGLVSAVTCVVLSKAV----WVVVLNN 494

Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE------MEVRSLTGVGVEKA 548
              IFP ++P L S+ LAF+   +  +V K D  +   AE        VR+ TG+G   A
Sbjct: 495 PAPIFPYEHPALFSMTLAFL---VTIVVSKLDGSETAKAEKALFDDQYVRAQTGIGAASA 551

Query: 549 VDH 551
            +H
Sbjct: 552 SNH 554


Lambda     K      H
   0.324    0.138    0.393 

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: 661
Number of extensions: 30
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: 551
Length of database: 554
Length adjustment: 36
Effective length of query: 515
Effective length of database: 518
Effective search space:   266770
Effective search space used:   266770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 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