GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS28205
          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:

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