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_085638026.1 MGEO_RS12360 TRAP transporter fused permease subunit

Query= uniprot:A8LI82
         (743 letters)



>NCBI__GCF_002115805.1:WP_085638026.1
          Length = 761

 Score = 1082 bits (2797), Expect = 0.0
 Identities = 566/761 (74%), Positives = 631/761 (82%), Gaps = 18/761 (2%)

Query: 1   MTD-QTKTADDH----LIAEGVDEEPTESNRRLFEGRNFILISTFAALYAAFHMAALNGL 55
           MTD +T   DD     ++AEGVDEEP ESNRRLF GR ++L++  +  YAAFHM ALNG+
Sbjct: 1   MTDPKTAPIDDEPDAPVLAEGVDEEPIESNRRLFSGRAYLLMAGLSTFYAAFHMIALNGV 60

Query: 56  SISEWTGIEVPFLPTFPMETWNFRIVHIAGALALGFLLFAART--DFPGPGKETPLLGYV 113
           SIS WTG+++PFLP FP+ETWNFRI HIAGALALGFLLF+A T  D   P KET  +  +
Sbjct: 61  SISAWTGLDLPFLPQFPLETWNFRIAHIAGALALGFLLFSAHTFSDDGPPHKETRAISIL 120

Query: 114 AYGLMVPALFSLGMAASFSMEIASGVM--WNGIDEGIKF-------NETWLFGLPLIVAT 164
           A  L++PAL S   A  F   I SG +    G+     F       +E W FG PL++AT
Sbjct: 121 AAILVLPALVSGVTAIGFLNLINSGTLPEMGGLTTWAAFPGTEIYSSEVWWFGTPLLIAT 180

Query: 165 AGGIVLSWFHKRARSGFSAPDLVLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAA 224
            G I+  WF +R R  F+A D+VLA+CG+ VA YLI IYGT  RNS GTPF PIG++ AA
Sbjct: 181 FGAILTGWFERRGRELFAASDVVLALCGLVVAIYLIGIYGTAARNSVGTPFVPIGVAFAA 240

Query: 225 VAGTALIMELTRRVAGMALIVIAGIFLAYVFVGQYLPGFLNAP-AVTWQRFFSQVYTDAG 283
            AG+A+I+ELTRRVAG+AL++I  +FL Y F    LPG L    A +WQRFF  VY+DAG
Sbjct: 241 TAGSAMILELTRRVAGLALVIITAVFLVYTFTAHLLPGILAVQSAYSWQRFFGHVYSDAG 300

Query: 284 ILGPTTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGM 343
           ILGPTTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFA AG++RGGPAKVAIFASGLMGM
Sbjct: 301 ILGPTTAVSSTYIILFIIFAAFLQASKVGDYFVNFAFATAGRARGGPAKVAIFASGLMGM 360

Query: 344 INGTSAGNVVATGSLTIPLMKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITG 403
           INGTSAGNVVATGSLTIPLMKKVGY KK AGAVEA ASTGGQIMPPIMGAGAFIMAEITG
Sbjct: 361 INGTSAGNVVATGSLTIPLMKKVGYQKKIAGAVEAGASTGGQIMPPIMGAGAFIMAEITG 420

Query: 404 IPYTEIALAAIIPAILYFVSVYFMVDLEAAKLGMRGMSRDELPKFNKMVRQVYLFLPIII 463
           IPYT+IA+AAIIPA+LYFVS+YFMVD EAAKLGMRGM  DELPKFNK+VRQVYLF+PI+I
Sbjct: 421 IPYTDIAIAAIIPAVLYFVSIYFMVDFEAAKLGMRGMREDELPKFNKLVRQVYLFIPILI 480

Query: 464 LIYALFMGYSVIRAGTLATVAAAVVSWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAG 523
           LI ALFMGYSVIRAGTLATVAAAVVSWFTP RMG RSI KAFE+AG MS+QIIAVCACAG
Sbjct: 481 LIAALFMGYSVIRAGTLATVAAAVVSWFTPNRMGLRSILKAFELAGIMSIQIIAVCACAG 540

Query: 524 IIVGVISLTGVGARFSAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAP 583
           IIVGVISLTGVGARFS+VLL +A  SQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAP
Sbjct: 541 IIVGVISLTGVGARFSSVLLDLAGVSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAP 600

Query: 584 GLVQLGIPLLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFI 643
           GLVQLGIP LTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSV SFKIGIAAFI
Sbjct: 601 GLVQLGIPQLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVASFKIGIAAFI 660

Query: 644 VPFMFFYNSAILMDGTWFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAAL 703
           VP+MFFYNSA+LMDGTWFEVLRAG TA +GVF LSSGVQGWF+GGR+AWFLRV L+FAAL
Sbjct: 661 VPYMFFYNSALLMDGTWFEVLRAGVTATIGVFLLSSGVQGWFLGGRSAWFLRVALIFAAL 720

Query: 704 MLIEGGIMSDLIGVGTAVAIFLIQKLA-APKGGAIPVRGAD 743
            +IEGG+++DLIGVG A A F +QK+  A     IPVRGAD
Sbjct: 721 FMIEGGLITDLIGVGIAAATFFVQKVVHARPDATIPVRGAD 761


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: 1875
Number of extensions: 112
Number of successful extensions: 7
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: 761
Length adjustment: 40
Effective length of query: 703
Effective length of database: 721
Effective search space:   506863
Effective search space used:   506863
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)
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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