GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Magnetospirillum magneticum AMB-1

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 WP_011384965.1 AMB_RS13005 ABC transporter substrate-binding protein

Query= TCDB::D5ALT6
         (365 letters)



>NCBI__GCF_000009985.1:WP_011384965.1
          Length = 364

 Score =  474 bits (1221), Expect = e-138
 Identities = 227/358 (63%), Positives = 267/358 (74%), Gaps = 1/358 (0%)

Query: 1   MDRRSFLTKAAIGGAAA-TTLATPALAQSMPKVTWRLTSSFPKSLDTIYGGAEVLSKMVS 59
           M RR FLT AA+G AAA TT+A PA+AQSMP++ WRL SSFPKSLDTIYG  EVL+K V+
Sbjct: 1   MQRRKFLTGAAVGAAAASTTIAAPAIAQSMPEIKWRLASSFPKSLDTIYGAGEVLAKRVA 60

Query: 60  EASDGNFQIQVFAAAEIVPGLQAADATAAGTVEACHTVGYYYWGKDPAWALGAAVPFGLS 119
           EA+DG FQI+VFA  EIVPGLQ  DA   GTVE  HTV YYY GKD  +   A++PFG +
Sbjct: 61  EATDGKFQIRVFAGGEIVPGLQVLDAVQNGTVECGHTVSYYYVGKDATFGFDASMPFGAN 120

Query: 120 ARGMNAWQYHGGGIDLYNEFLATQGLIGFPGGNTGAQMGGWFRKEINTVADLSGLKMRVG 179
            R  N+W YHGGG+ L  EF A   ++ FP GNTG QMGGWFRKEI TV DL GLK R+G
Sbjct: 121 TRQQNSWLYHGGGMALMREFFAKYNMLNFPCGNTGTQMGGWFRKEIKTVEDLKGLKFRIG 180

Query: 180 GFAGKVMEKLGLVPQQVAGGDIYPALEKGTLDATEWVGPYDDEKLGFYKVAPYYYYPGWW 239
           G+AGKV+ KLG+VPQQ+AGGD+YPALEKGT+DA EWVGPYDDEKLGF KVAPYYYYPGWW
Sbjct: 181 GYAGKVLTKLGVVPQQIAGGDLYPALEKGTIDAAEWVGPYDDEKLGFNKVAPYYYYPGWW 240

Query: 240 EGGPTVHFMFNKAAYEGLPKAYQALLRTACQAEDADMLQKYDYKNPLALKSLVANGAQLR 299
           EGGP V  + NK  +E LPK Y+A+   A    + DM  KYD  NP ALK L+ANG QLR
Sbjct: 241 EGGPCVSALVNKNEWEKLPKHYKAVFEAAAAEANLDMSAKYDVLNPPALKRLIANGTQLR 300

Query: 300 PFSQEILEACFNAAQEVYAEMTATNPAFKKIYDSMVAFRADHYLWTQVAEYNYDTFMM 357
           PFS++I+ AC+ AAQE YAE  A NPAFKK++D   A+ A+   W  VAE  +D FM+
Sbjct: 301 PFSKDIMLACYKAAQETYAEECAANPAFKKVFDHWSAYLAEQRSWFSVAEAGFDNFML 358


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: 468
Number of extensions: 20
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: 364
Length adjustment: 29
Effective length of query: 336
Effective length of database: 335
Effective search space:   112560
Effective search space used:   112560
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