Alignments for a candidate for Dshi_1194 in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Magnetospirillum magneticum AMB-1

Align TRAP transporter (characterized, see rationale)
to candidate WP_011383333.1 AMB_RS04540 C4-dicarboxylate ABC transporter

Query= uniprot:A8LI82
         (743 letters)



>NCBI__GCF_000009985.1:WP_011383333.1
          Length = 687

 Score =  331 bits (849), Expect = 7e-95
 Identities = 212/628 (33%), Positives = 324/628 (51%), Gaps = 62/628 (9%)

Query: 155 LFGLPLIVATAGGIVLSWFHKRARSGFSAPDLVLAICGVAVATYLITIY-----GTLMRN 209
           L  LP+     G ++L  F   A  G   P  V     +   ++++++Y     G L++ 
Sbjct: 50  LSSLPVRSIHVGFLLLMVFALYAAMGRGNPVKVATAWALGGLSFILSLYHLIYEGELVQR 109

Query: 210 STGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVIAGIFLAYVFVGQYLPGFLNAPAV 269
           S       + +    VA   L+ E  RR+ G AL  +  +F+AY   G+ LP  L     
Sbjct: 110 SGDPSTTDLVVGTVMVA---LVFEAARRLMGWALPALCLVFVAYAAFGEILPAPLGHRGY 166

Query: 270 TWQRFFSQVYTDA-GILGPTTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAGQSRG 328
            + +  +Q +    GI G    VS+TYI LFI+F +FL+ + +   F + A    G ++G
Sbjct: 167 GFDQIINQYFLGTEGIFGIPCYVSATYIFLFILFGSFLEQAGMIRLFTDVALGTVGHTKG 226

Query: 329 GPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLMKKVGYHKKTAGAVEAAASTGGQIMP 388
           GPAKVA+  SGLMG ING+   NVV TG+LTIPLMK+ GY  + AGAVEA AS GGQIMP
Sbjct: 227 GPAKVAVVTSGLMGTINGSGIANVVTTGALTIPLMKRFGYRSEFAGAVEATASMGGQIMP 286

Query: 389 PIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVYFMVDLEAAKLGMRGMSRDELPKF 448
           P+MGA AFIMAE   I Y E+  AA IPA+LY+ S  +MV LEA   G+ GM +D+ P  
Sbjct: 287 PVMGAVAFIMAETLNISYAEVCKAAAIPALLYYASAIWMVHLEAGIAGLHGMPKDQCPSA 346

Query: 449 -NKMVRQVYLFLPIIILIYALFMGYSVIRAGTLATVAAAVVSWFTPFR------------ 495
              + RQ YL +P+  L+Y L  G++ + +GT+     A+V   +               
Sbjct: 347 QGALRRQWYLMVPLAALVYLLLAGFTPMFSGTVGLALTAIVILGSSIAANIGGMAGRVVF 406

Query: 496 MGPRSIAKA--FEIAGTMSVQIIAV----------------------------------- 518
            G   IA +  F++   + V  +AV                                   
Sbjct: 407 WGVLGIASSAFFKLGINVVVVTVAVLVGVNFFVRGGRETMRMTVRGLVEGARSAVPVGVA 466

Query: 519 CACAGIIVGVISLTGVGARFSAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAA 578
           C   G I+G ++LTG+   F+  L+ ++  S  L L   M  +++LGMG+PT   Y + +
Sbjct: 467 CTLVGTIIGTMTLTGIAGSFTQGLVSMSGGSLFLTLILTMIASLILGMGIPTIPTYIITS 526

Query: 579 SVVAPGLVQLGIPLLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIG 638
           S+VAP L ++G+PL+ +H +VFYF +L+ +TPPV LA++AAA I+ +N   T   + ++ 
Sbjct: 527 SLVAPMLFKMGVPLVVSHMYVFYFGILADLTPPVGLAAFAAASIARSNFFVTGWWAVRVA 586

Query: 639 IAAFIVPFMFFYNSAILM-DGTWFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVG 697
           +A F+VPFM  Y+ +++M  G+ F+       A++ +    +   G+       W  R  
Sbjct: 587 MAGFVVPFMAVYDPSLMMVSGSLFDTAYVVIKALLAIGLWGAATIGYLWAPMKMW-ERAV 645

Query: 698 LVFAALMLIEGGIMSDLIGVGTAVAIFL 725
            V AA +L+    ++D IG   + A+FL
Sbjct: 646 AVLAAFLLVAAVPLTDEIGFALS-AVFL 672


Lambda     K      H
   0.327    0.140    0.419 

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: 1336
Number of extensions: 85
Number of successful extensions: 4
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: 743
Length of database: 687
Length adjustment: 39
Effective length of query: 704
Effective length of database: 648
Effective search space:   456192
Effective search space used:   456192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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.

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