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_RS29770 AZOBR_RS29770 ABC transporter substrate-binding protein

Query= TCDB::D5ALT6
         (365 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS29770 AZOBR_RS29770 ABC
           transporter substrate-binding protein
          Length = 361

 Score =  412 bits (1060), Expect = e-120
 Identities = 197/357 (55%), Positives = 246/357 (68%), Gaps = 1/357 (0%)

Query: 1   MDRRSFLTKAAIGGAAATTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVSE 60
           M RR F   AA+  A A+TLA PA+AQS P + WR  SSFPK+++ +YG AEVL+K ++E
Sbjct: 1   MKRRQFFKGAAVV-AGASTLAAPAIAQSEPTIRWRCVSSFPKNIEVLYGSAEVLAKNIAE 59

Query: 61  ASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLSA 120
           A+DG FQIQVFAA E+VP LQA DA +  TVE  HT  YYY GKDP++A G  +PFGL+ 
Sbjct: 60  ATDGKFQIQVFAAGELVPALQALDAASNDTVEMAHTASYYYVGKDPSFAFGCCLPFGLNT 119

Query: 121 RGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVGG 180
           R  NAW YHG G  L  EF A   L    GGNTG+QMGGWFRKEI    DL GLK R+ G
Sbjct: 120 RQQNAWFYHGEGGKLLEEFYAGHNLKALAGGNTGSQMGGWFRKEIKNAEDLKGLKFRISG 179

Query: 181 FAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWWE 240
             G+++ KLG+VPQQV+GGDIYPALE+GT+DA E+ GPYDDEKLG YK+AP YYYPGWW+
Sbjct: 180 LGGQILSKLGVVPQQVSGGDIYPALERGTIDAAEFNGPYDDEKLGLYKIAPNYYYPGWWD 239

Query: 241 GGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLRP 300
           G    HF  N   +  LPK YQA L +A    + D + +YD  NP ALK +V  GA+LR 
Sbjct: 240 GTSLQHFFINTNRWNSLPKHYQAALTSAAALANVDSVARYDVLNPAALKRVVEKGAKLRA 299

Query: 301 FSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFMM 357
           F Q++L+A   AA E+Y E++  NP FKK Y+S   F+ D  LW Q +EY YD+ ++
Sbjct: 300 FPQDVLQASHKAAMELYDELSDKNPTFKKFYESYRRFQTDSNLWNQASEYAYDSAVL 356


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: 393
Number of extensions: 7
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: 361
Length adjustment: 29
Effective length of query: 336
Effective length of database: 332
Effective search space:   111552
Effective search space used:   111552
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