Alignments for a candidate for glt in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glt in Shewanella oneidensis MR-1

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 201109 SO1948 sodium:dicarboxylate symporter family protein (NCBI ptt file)

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__MR1:201109
          Length = 437

 Score =  674 bits (1740), Expect = 0.0
 Identities = 340/435 (78%), Positives = 391/435 (89%)

Query: 1   MAAAQSSKIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLK 60
           MA +  +K+GLT KILIGM  GI+ GL+LRN F  S +++DYIT+GF HVIGTIFI+SLK
Sbjct: 1   MATSLQNKLGLTSKILIGMATGIIFGLILRNLFPDSIFIKDYITDGFLHVIGTIFISSLK 60

Query: 61  MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASL 120
           MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTT +ALV+A+ AAV+V PG+A+L
Sbjct: 61  MLVVPLVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTVLALVLAVFAAVIVHPGDATL 120

Query: 121 ASESMQYSAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRV 180
           A+E + Y AKEAPS A V+I+++P+NP++A+SEGNMLQIIIFAVIFGFAI+H+GERG R+
Sbjct: 121 ANEKLNYVAKEAPSFAQVIIDMMPTNPVQAMSEGNMLQIIIFAVIFGFAIAHLGERGNRI 180

Query: 181 AALFDDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHG 240
           A LFDDLN VIMRVVTL+MQLAPYGVFALM KLALTLG+ET  SV+KYF LVL +LL H 
Sbjct: 181 AQLFDDLNNVIMRVVTLVMQLAPYGVFALMAKLALTLGLETFGSVVKYFFLVLTLLLIHN 240

Query: 241 FVVYPTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASF 300
           FV Y  LLK FSGL+PL+FIRKMRDVQLFAFSTASSNATLP+T+EASEHRLG DNK+ASF
Sbjct: 241 FVTYSILLKAFSGLNPLIFIRKMRDVQLFAFSTASSNATLPITIEASEHRLGVDNKIASF 300

Query: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLV 360
           TLPLGATINMDGTAIMQGVATVFIAQVFGI+L++TDYA V++TATLASIGTAGVPGVGL+
Sbjct: 301 TLPLGATINMDGTAIMQGVATVFIAQVFGIELSLTDYAAVIVTATLASIGTAGVPGVGLI 360

Query: 361 MLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFNDP 420
           MLAMVLNQVGLPVEGIALI+GVDR+LDMVRTAVNVTGD VATV+IAKSEG  NE VFN+ 
Sbjct: 361 MLAMVLNQVGLPVEGIALIIGVDRLLDMVRTAVNVTGDCVATVIIAKSEGEFNETVFNNT 420

Query: 421 KAGKTAGSFDAEVHR 435
           +AGK A SFD +VH+
Sbjct: 421 QAGKIAPSFDEQVHK 435


Lambda     K      H
   0.325    0.139    0.388 

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: 590
Number of extensions: 14
Number of successful extensions: 1
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: 437
Length of database: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
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 (21.6 bits)
S2: 51 (24.3 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