GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS34240 in Burkholderia phytofirmans PsJN

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS28205 BPHYT_RS28205 ATPase

Query= uniprot:B2T9V8
         (351 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28205 BPHYT_RS28205 ATPase
          Length = 338

 Score =  167 bits (422), Expect = 5e-46
 Identities = 101/328 (30%), Positives = 174/328 (53%), Gaps = 10/328 (3%)

Query: 21  LALPASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALV 80
           +A P S     + E     E+ L+  L L + +G  +SP FLT ANL +VL     +AL+
Sbjct: 1   MAKPDSALLTRKRETPLQWEVLLVIVLILSLALGRLLSPVFLTGANLSNVLADLTEIALM 60

Query: 81  VLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVI 140
            L  +LI++  + DLS+ S +G + A+  +L        + M  P    ++ ++V GA+ 
Sbjct: 61  ALPMTLIIVAAEIDLSVASVLGASSALMGVL--------WHMGLPMPLVIVLVLVAGALA 112

Query: 141 GFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLG--LP 198
           G +NG ++V+L L +  VT+  L + RG+         + D P ++ A     + G  +P
Sbjct: 113 GLLNGLVIVKLNLPSLAVTIGTLALFRGLAYVLLGDQAVADFPPAYTAFGMDTLGGSFIP 172

Query: 199 LSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASV 258
           L   +      +   +L+    GR+LYAIG NP AA  +GI V +I   +FVL   ++++
Sbjct: 173 LPFVIVIVGAIVFTVLLQSTAFGRSLYAIGANPTAAAFSGIEVAKIRLRLFVLSGAMSAL 232

Query: 259 GGLIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLT 318
            G++ T    +   + G G   +V AA + GG+S+ GG+G+M G L  +L++GV++N LT
Sbjct: 233 AGVVYTLRFTSARGDNGEGFELSVIAAVLFGGVSIFGGRGSMIGVLLSLLIIGVLKNALT 292

Query: 319 LAQVPSFWIQAIYGAIILGSLMVARLAS 346
           L  V S  +  + G ++L S+++  L +
Sbjct: 293 LDDVSSETLTIVTGVLLLASVLIPNLVA 320


Lambda     K      H
   0.326    0.140    0.397 

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: 245
Number of extensions: 7
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: 351
Length of database: 338
Length adjustment: 29
Effective length of query: 322
Effective length of database: 309
Effective search space:    99498
Effective search space used:    99498
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 paper from 2022 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