GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Burkholderia phytofirmans PsJN

Align RhaQ (characterized, see rationale)
to candidate BPHYT_RS28205 BPHYT_RS28205 ATPase

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__BFirm:BPHYT_RS28205
          Length = 338

 Score =  221 bits (563), Expect = 2e-62
 Identities = 123/332 (37%), Positives = 198/332 (59%), Gaps = 7/332 (2%)

Query: 7   QPEKRIIPDRLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEK 66
           +P+  ++  +  TPL+     WEVLL  V +L      L SP FL   NLS+   + TE 
Sbjct: 3   KPDSALLTRKRETPLQ-----WEVLLVIVLILSLALGRLLSPVFLTGANLSNVLADLTEI 57

Query: 67  AMIAFAMALLVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNG 126
           A++A  M L++++ EIDLSVA+++  +S  MG    +G+  P ++++ +  G   G+ NG
Sbjct: 58  ALMALPMTLIIVAAEIDLSVASVLGASSALMGVLWHMGLPMPLVIVLVLVAGALAGLLNG 117

Query: 127 VLVSVLKLPSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVF-SFEFVL 185
           +++  L LPS+ VTIGT++LFRG++Y++LGDQA   +P  +  FG   +   F    FV+
Sbjct: 118 LVIVKLNLPSLAVTIGTLALFRGLAYVLLGDQAVADFPPAYTAFGMDTLGGSFIPLPFVI 177

Query: 186 FIVLAVLFAILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCL 245
            IV A++F +LL +T FGR +YAIG N  AA FSGI V +++  LF+L+G MS +A V  
Sbjct: 178 VIVGAIVFTVLLQSTAFGRSLYAIGANPTAAAFSGIEVAKIRLRLFVLSGAMSALAGVVY 237

Query: 246 TSRLGSTRPSIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNL 305
           T R  S R    +G+EL V+  V+ GG+SI GG     GV +++  ++G++   L L ++
Sbjct: 238 TLRFTSARGDNGEGFELSVIAAVLFGGVSIFGGRGSMIGV-LLSLLIIGVLKNALTLDDV 296

Query: 306 PGIVMSIFIGLLIIVTIAIPIIARRIKLMSSR 337
               ++I  G+L++ ++ IP +  R +    R
Sbjct: 297 SSETLTIVTGVLLLASVLIPNLVARWRAARDR 328


Lambda     K      H
   0.330    0.145    0.423 

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: 304
Number of extensions: 14
Number of successful extensions: 2
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: 337
Length of database: 338
Length adjustment: 28
Effective length of query: 309
Effective length of database: 310
Effective search space:    95790
Effective search space used:    95790
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 (21.8 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