GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Phaeobacter inhibens BS107

Align Histidine transport system permease protein HisM (characterized)
to candidate GFF1140 PGA1_c11550 putative histidine transport system permease protein

Query= SwissProt::P0A2I7
         (235 letters)



>FitnessBrowser__Phaeo:GFF1140
          Length = 268

 Score =  120 bits (302), Expect = 2e-32
 Identities = 71/218 (32%), Positives = 123/218 (56%), Gaps = 9/218 (4%)

Query: 21  TGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLLVFYS 80
           +G+   ++    +VV+G ++A  +A+ + S++  +R     F +IFRG+PL++Q   F++
Sbjct: 38  SGMLWNIYFGAIAVVVGFVIANGVALAKNSTSTPLRKAAEWFIFIFRGSPLFIQF--FFA 95

Query: 81  GMYTLEIVKGTDLLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYG 140
               L++   + + N    + +   ++ L LNT AY+ EIF GA+RS+P G+IEAA AYG
Sbjct: 96  YFLFLQLKSVSPIFNPLSAAWMGALIV-LILNTAAYSAEIFYGALRSIPKGDIEAADAYG 154

Query: 141 FSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVP------DLLKIARDINS 194
            S +  +R I+ P+ +R+A P+Y+NE I + H+T L F +  P      D L  A     
Sbjct: 155 LSGWPRFRRIMWPTMMRLAWPSYTNEAIFLFHATTLVFFSGFPAWQQRGDALYYASYFAD 214

Query: 195 ATYQPFTAFGIAAVLYLLISYVLISLFRRAERRWLQHV 232
            T+ PF  + I A  ++L++ V+I +F     R   H+
Sbjct: 215 KTFNPFVPYPILAFYFILLTLVVIGIFGIINTRLNAHL 252


Lambda     K      H
   0.330    0.141    0.429 

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: 168
Number of extensions: 8
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: 235
Length of database: 268
Length adjustment: 24
Effective length of query: 211
Effective length of database: 244
Effective search space:    51484
Effective search space used:    51484
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 (21.9 bits)
S2: 46 (22.3 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