GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Acidovorax sp. GW101-3H11

Align TRAP dicarboxylate transporter, DctP-2 subunit, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (characterized)
to candidate Ac3H11_3567 TRAP transporter solute receptor, unknown substrate 6

Query= TCDB::D5ALT6
         (365 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3567
          Length = 360

 Score =  410 bits (1055), Expect = e-119
 Identities = 202/361 (55%), Positives = 244/361 (67%), Gaps = 3/361 (0%)

Query: 1   MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60
           MDRRS +  A I G  A   A    AQ+   + WRL SSFPKSLDTIYGGA+V SK V  
Sbjct: 1   MDRRSIIKHAGIAGVLAAGAAPAVHAQAA--IRWRLASSFPKSLDTIYGGADVFSKAVKA 58

Query: 61  ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120
            S G F+I V A  E++P     D    GTVE CHTV YY++GK+PA+ALG+A+PFG +A
Sbjct: 59  MSGGKFEISVHAGGELMPPFGVMDGVQQGTVEMCHTVPYYFYGKNPAFALGSAIPFGFNA 118

Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180
           R MNAW  HG G  L NEF A    I F GGNTG QMGGW+RKEI + AD  G+KMR+GG
Sbjct: 119 RQMNAWMLHGNGRKLMNEFYANYNAISFAGGNTGTQMGGWYRKEIKSPADFKGMKMRLGG 178

Query: 181 -FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWW 239
              G+VM+KLG VPQ + GG+IY ALEKGTLDA EWVGPYDD+KLGF KVAP+YYYPGWW
Sbjct: 179 GLVGEVMQKLGAVPQSIPGGEIYQALEKGTLDAAEWVGPYDDQKLGFNKVAPFYYYPGWW 238

Query: 240 EGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLR 299
           EGGP V F  N+ A++GL    +A++  A      DML KYD  NP ALK LVA   ++ 
Sbjct: 239 EGGPEVDFFVNQKAFDGLSAENKAIIEAATNVAHIDMLAKYDALNPTALKQLVAAKTKVL 298

Query: 300 PFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFMMIQ 359
           PFSQ +++A F A+ EV+AE  A +P +KKIY  M  F+ D  LW + AE  YDTFM  Q
Sbjct: 299 PFSQAVMDASFKASMEVFAENDAKSPEWKKIYADMRTFQRDQILWFRFAEARYDTFMSAQ 358

Query: 360 Q 360
           +
Sbjct: 359 K 359


Lambda     K      H
   0.319    0.134    0.417 

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: 448
Number of extensions: 14
Number of successful extensions: 2
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: 365
Length of database: 360
Length adjustment: 29
Effective length of query: 336
Effective length of database: 331
Effective search space:   111216
Effective search space used:   111216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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