Alignments for a candidate for Dshi_1194 in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Marivita geojedonensis DPG-138

Align TRAP transporter (characterized, see rationale)
to candidate WP_085636380.1 MGEO_RS08950 TRAP transporter fused permease subunit

Query= uniprot:A8LI82
         (743 letters)



>NCBI__GCF_002115805.1:WP_085636380.1
          Length = 756

 Score = 1071 bits (2769), Expect = 0.0
 Identities = 563/757 (74%), Positives = 623/757 (82%), Gaps = 15/757 (1%)

Query: 1   MTDQTKTADDHLIAEGVDEEPTESNRRLFEGRNFILISTFAALYAAFHMAALNGLSISEW 60
           M  ++  AD+ LIAEGVDEEP E NRRLF G     ++ FAALYA FHMAALNG+SIS +
Sbjct: 1   MVQESTQADEGLIAEGVDEEPIEGNRRLFTGWRLQAVAGFAALYALFHMAALNGVSISAY 60

Query: 61  TGIEVPFLPTFPMETWNFRIVHIAGALALGFLLFAARTDFPGPGKETPLLG---YVAYGL 117
           TGI +PFLP FPMETWNFRIVHIAGALALGFL++ A   F     E    G    +AY L
Sbjct: 61  TGITIPFLPQFPMETWNFRIVHIAGALALGFLVYNAMM-FGDSDDEAGRSGPWDKIAYLL 119

Query: 118 MVPALFSLGMAASFSMEIASGVM--WNGIDEGIKF-------NETWLFGLPLIVATAGGI 168
           M+PALF+LG +  F+  IASG +    G+     F        E W FG+PL+ A+ GG+
Sbjct: 120 MLPALFALGTSLWFARTIASGELPEMGGLTTWPAFAGTPIYGQEVWYFGVPLLAASIGGV 179

Query: 169 VLSWFHKRARSGFSAPDLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGT 228
           VL W  K  R  F A D++LAICGVAVA YLI IYGT  RNS GTPF PIG++ AA AGT
Sbjct: 180 VLGWLEKAPRDQFRASDILLAICGVAVAAYLIAIYGTAARNSVGTPFVPIGVAFAATAGT 239

Query: 229 ALIMELTRRVAGMALIVIAGIFLAYVFVGQYLPGFLNAP-AVTWQRFFSQVYTDAGILGP 287
            +I+ELTRRVAG+AL++I G+FL Y F    LPG L    A +WQRFF  VY+DAGILGP
Sbjct: 240 VMILELTRRVAGLALVIITGVFLVYTFTAHLLPGILAVQSAYSWQRFFGHVYSDAGILGP 299

Query: 288 TTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGT 347
           TTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAG++RGGPAKVAIFASGLMGMINGT
Sbjct: 300 TTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAGRARGGPAKVAIFASGLMGMINGT 359

Query: 348 SAGNVVATGSLTIPLMKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYT 407
           SAGNVVATGSLTIPLMKKVGY  K AGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPY 
Sbjct: 360 SAGNVVATGSLTIPLMKKVGYRPKVAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYQ 419

Query: 408 EIALAAIIPAILYFVSVYFMVDLEAAKLGMRGMSRDELPKFNKMVRQVYLFLPIIILIYA 467
           +IA+AAIIPA+LYFVSVYFMVD EAAKLGMRGM  DELPK  KMVRQ+YLF+PIIILI A
Sbjct: 420 DIAIAAIIPAVLYFVSVYFMVDFEAAKLGMRGMREDELPKLAKMVRQLYLFIPIIILIAA 479

Query: 468 LFMGYSVIRAGTLATVAAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVG 527
           LFMGYSVIRAGTLAT+AAA+VSW TPF M  R IAKAFE+AG MS+QIIAVCACAGIIVG
Sbjct: 480 LFMGYSVIRAGTLATIAAAMVSWLTPFPMTLRGIAKAFELAGIMSIQIIAVCACAGIIVG 539

Query: 528 VISLTGVGARFSAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQ 587
           VISLTGVGARFSAVLL +A TSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQ
Sbjct: 540 VISLTGVGARFSAVLLDLAATSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQ 599

Query: 588 LGIPLLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFM 647
           LGIP LTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSV SFK+GIAAFIVPFM
Sbjct: 600 LGIPQLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVVSFKVGIAAFIVPFM 659

Query: 648 FFYNSAILMDGTWFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIE 707
           FFYNSA+LMDGTWFEV+RAG TAV GVF LS GVQGWF+G R+AWF+R+ L+ AAL +IE
Sbjct: 660 FFYNSALLMDGTWFEVIRAGVTAVFGVFLLSGGVQGWFLGQRSAWFIRLALIGAALFMIE 719

Query: 708 GGIMSDLIGVGTAVAIFLIQKLAAPKGGA-IPVRGAD 743
           GG+++DLIG+G   A +L+QKL  P   A IPVRGAD
Sbjct: 720 GGLVTDLIGIGVTGAAWLVQKLFHPDPNAPIPVRGAD 756


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: 1871
Number of extensions: 98
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: 743
Length of database: 756
Length adjustment: 40
Effective length of query: 703
Effective length of database: 716
Effective search space:   503348
Effective search space used:   503348
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 24 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 2024 update 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