GapMind for catabolism of small carbon sources

 

Aligments 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_RS20010 AZOBR_RS20010 ABC transporter substrate-binding protein

Query= TCDB::D5ALT6
         (365 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS20010 AZOBR_RS20010 ABC
           transporter substrate-binding protein
          Length = 365

 Score =  445 bits (1144), Expect = e-129
 Identities = 210/356 (58%), Positives = 260/356 (73%), Gaps = 1/356 (0%)

Query: 1   MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60
           M RR+F+T A +G  AA+TLA PA+AQS P++ WR  SSFPKSLDTIYGGAE ++K V+E
Sbjct: 1   MKRRTFITSAGVG-VAASTLAAPAIAQSNPEIKWRCASSFPKSLDTIYGGAERVAKRVAE 59

Query: 61  ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120
            ++G FQI+ FA+ EIVPGLQ  DA   GTVE  HTV YYY GKDP +A  AA+PFGL+A
Sbjct: 60  MTEGKFQIRTFASGEIVPGLQVLDAVKDGTVECGHTVSYYYVGKDPTFAFDAAMPFGLNA 119

Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180
           R  NAW  HGGG++L  EF     ++ F  GNTG QMGGWFR E+ TV DL GLK R+GG
Sbjct: 120 RQQNAWMTHGGGMELMREFFKGYNIVQFAAGNTGTQMGGWFRNELKTVEDLKGLKFRIGG 179

Query: 181 FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWWE 240
           +AG ++++LG+VPQQ+AGGDIYPALEKGT+DA EWVGPYDDEKLGF KVA YYYYPGWWE
Sbjct: 180 YAGTILQRLGVVPQQIAGGDIYPALEKGTIDAAEWVGPYDDEKLGFNKVAKYYYYPGWWE 239

Query: 241 GGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLRP 300
           GGP V F+ +   +E LPK YQA+L  AC    ADM+ KYD  N  ALK LV  G  L+P
Sbjct: 240 GGPQVSFLVSLPQWEQLPKHYQAILEAACADATADMVGKYDVVNMHALKRLVGAGTVLKP 299

Query: 301 FSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFM 356
           + ++IL+AC+ A  +VY E  A N  F+K+Y+    FR + YLW +VAE  +D F+
Sbjct: 300 YPRDILQACYQATFDVYEEEAAKNEKFRKVYEQWRKFRDEEYLWFRVAENTFDNFV 355


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: 419
Number of extensions: 13
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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