GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dhaM in Pseudomonas fluorescens FW300-N2C3

Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate AO356_07335 AO356_07335 PTS fructose transporter subunit IIA

Query= SwissProt::A0A0H3H456
         (472 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07335 AO356_07335 PTS
           fructose transporter subunit IIA
          Length = 954

 Score =  106 bits (265), Expect = 3e-27
 Identities = 100/338 (29%), Positives = 149/338 (44%), Gaps = 34/338 (10%)

Query: 155 DARSVSVVIQNHNGLHVRPASKLVAALAGFNADL---VLEKGGKCVTPDSLNQIALLQVR 211
           D  S  + + N +GLH RPA  L      F+ ++   +++     V+  SL+++  L  R
Sbjct: 281 DWPSARIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGAR 340

Query: 212 RNDTLRLLARGPDADAALAAFQALAAENFGEPTEAAPARRPASADRVE-----GKVVLYP 266
           R   L  +A    A+ AL A  A   E  GE  E  P   P SA R         V+L P
Sbjct: 341 RGQVLEFIAEPSIANDALPALLAAIEEGLGEEVEPLP---PPSAPRETVMAEVATVMLAP 397

Query: 267 QPQDRISRETSA---AIGQQQLRLKRAIDRTLEDLSA-----------------LTTLAE 306
           +    I    +A   AIG   +++ +AID  L   SA                 +  L E
Sbjct: 398 ESGSLIQAVAAAPGIAIGPAHIQVLQAIDYPLRGESAAIERERLQNALNQVRSDIQGLIE 457

Query: 307 ATFSADIAAIFSGHHTLLDDPDLYAAACDIIRDEQCSAAWAWQQVLSDLSQQYRHLDDAY 366
              +  I  IF  H  +LDDP+L       ++  + SA  AW  V+   +++   L DA 
Sbjct: 458 RAKAKAIREIFITHQEMLDDPELTDEVDTRLKLGE-SAQAAWMGVIEAAAKEQEALQDAL 516

Query: 367 LQARYIDIEDILHRTLRHLNERNEALPQFSAPSILVADDIFPSTVLQLNAEQVKGICLQA 426
           L  R  D+ D+  R L  L    E   +   P ILV D++ PS V +L+  +V GI    
Sbjct: 517 LAERAADLRDVGRRVLAQLCGV-ETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTAR 575

Query: 427 GSELSHGAIIARQAGI-AMLCQQSDALTLQDGENVILD 463
           G   +H AI+AR  GI A++   +  L L  G +++LD
Sbjct: 576 GGATAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLD 613


Lambda     K      H
   0.318    0.132    0.372 

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: 843
Number of extensions: 45
Number of successful extensions: 3
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: 472
Length of database: 954
Length adjustment: 38
Effective length of query: 434
Effective length of database: 916
Effective search space:   397544
Effective search space used:   397544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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