GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Azospirillum brasilense Sp245

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 AZOBR_RS19865 AZOBR_RS19865 ABC transporter substrate-binding protein

Query= TCDB::D5ALT6
         (365 letters)



>FitnessBrowser__azobra:AZOBR_RS19865
          Length = 362

 Score =  450 bits (1158), Expect = e-131
 Identities = 218/355 (61%), Positives = 256/355 (72%), Gaps = 1/355 (0%)

Query: 1   MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60
           M RRSFL  A +G  AA+TLA PA+AQS P+V WRL SSFPKSLDTIYG A+V+S+ V+ 
Sbjct: 1   MKRRSFLASAGVG-VAASTLAAPAIAQSTPEVHWRLASSFPKSLDTIYGAADVISRRVAA 59

Query: 61  ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120
            +D  F I+ FA+ EIVPGLQ  DA   GTVE  HT  YYY GKDP +   A VPFGL+A
Sbjct: 60  ITDNKFTIRPFASGEIVPGLQVLDAVQNGTVECGHTASYYYVGKDPTFTFDATVPFGLNA 119

Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180
           R  NAW   GGG++L  EF     ++ FP GNTG QMGGWFRKEI TV DLSGLK R+GG
Sbjct: 120 RQQNAWILQGGGMELLREFFKGYNVVNFPAGNTGTQMGGWFRKEIKTVQDLSGLKFRIGG 179

Query: 181 FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWWE 240
           FAG+V+ KLG+VPQQ+AGGDIYP+LEKGT+DA EW+GPYDDEKLGF KVA YYYYPGWWE
Sbjct: 180 FAGQVLTKLGVVPQQIAGGDIYPSLEKGTIDAAEWIGPYDDEKLGFNKVAKYYYYPGWWE 239

Query: 241 GGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLRP 300
           GG  V  + N+  +E LPK YQA L  AC    A M  KYD  NP ALK LVA GAQLRP
Sbjct: 240 GGLNVSLLVNQQKWEELPKPYQAALEAACYEALAIMNAKYDADNPAALKRLVAGGAQLRP 299

Query: 301 FSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTF 355
           F +E++EAC+ AA E+Y E    NP F KIY+    FR + YLW +VAE ++D F
Sbjct: 300 FPREVMEACYKAAYELYDETAKNNPEFAKIYEPWKKFRDEEYLWFRVAENSFDNF 354


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: 441
Number of extensions: 15
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: 362
Length adjustment: 29
Effective length of query: 336
Effective length of database: 333
Effective search space:   111888
Effective search space used:   111888
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