Alignments for a candidate for Dshi_1194 in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Marinobacter adhaerens HP15

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate GFF744 HP15_723 TRAP transporter, 4TM/12TM fusion protein

Query= uniprot:E4PQE4
         (729 letters)



>FitnessBrowser__Marino:GFF744
          Length = 729

 Score = 1404 bits (3633), Expect = 0.0
 Identities = 729/729 (100%), Positives = 729/729 (100%)

Query: 1   MTTEQDSKDLPDIEVGEDHVLAHNVDEEPVEANRRLFEGGLLKFVALLAIAYSAFHLYSL 60
           MTTEQDSKDLPDIEVGEDHVLAHNVDEEPVEANRRLFEGGLLKFVALLAIAYSAFHLYSL
Sbjct: 1   MTTEQDSKDLPDIEVGEDHVLAHNVDEEPVEANRRLFEGGLLKFVALLAIAYSAFHLYSL 60

Query: 61  NIAPLETWSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRWTTWISAGAMLPALYVLY 120
           NIAPLETWSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRWTTWISAGAMLPALYVLY
Sbjct: 61  NIAPLETWSFRIVHIAGALVLGFVLFAGARFVSSEEGGARHRWTTWISAGAMLPALYVLY 120

Query: 121 QTFSFWQMVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVPDLVLIVC 180
           QTFSFWQMVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVPDLVLIVC
Sbjct: 121 QTFSFWQMVQNGAMRIPVELEVWHFGWPLLAATGVGIVMSWFHQRERSVFSVPDLVLIVC 180

Query: 181 SLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALVIIGLVFL 240
           SLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALVIIGLVFL
Sbjct: 181 SLAVAAYFLVVYNTSMRMSTGTSFAPVGISFAAIAGTALIMELTRRVAGMALVIIGLVFL 240

Query: 241 AYVFAGPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIIFAAFLQSSKV 300
           AYVFAGPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIIFAAFLQSSKV
Sbjct: 241 AYVFAGPYLPGFLGYPGLSVQRFFSQVYTDAGILGPTTAVSSTYIILFIIFAAFLQSSKV 300

Query: 301 GDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQ 360
           GDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQ
Sbjct: 301 GDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNVVSTGSLTIPLMKKVGYSKQ 360

Query: 361 SAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFE 420
           SAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFE
Sbjct: 361 SAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIAAIIPAILYFASVYFMVDFE 420

Query: 421 AAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWL 480
           AAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWL
Sbjct: 421 AAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMGYSVIRAGTLATVSAAVVSWL 480

Query: 481 SPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQL 540
           SPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQL
Sbjct: 481 SPNKMGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISLTGVGARFSVLLLDVAATSQL 540

Query: 541 LALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPP 600
           LALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPP
Sbjct: 541 LALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPP 600

Query: 601 VALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTAT 660
           VALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTAT
Sbjct: 601 VALASYAAAGISGANAMETSVASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTAT 660

Query: 661 FGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQRK 720
           FGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQRK
Sbjct: 661 FGVYMLSGGVLGWFASISASWITRLLLIAAALLMIEGGLWTDLTGIALAVLAFVIQKQRK 720

Query: 721 TRLATAGAL 729
           TRLATAGAL
Sbjct: 721 TRLATAGAL 729


Lambda     K      H
   0.327    0.139    0.410 

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: 1885
Number of extensions: 72
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: 729
Length of database: 729
Length adjustment: 40
Effective length of query: 689
Effective length of database: 689
Effective search space:   474721
Effective search space used:   474721
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.

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