GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Herbaspirillum seropedicae SmR1

Align ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS08915 HSERO_RS08915 ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__HerbieS:HSERO_RS08915
          Length = 296

 Score =  172 bits (437), Expect = 7e-48
 Identities = 102/305 (33%), Positives = 175/305 (57%), Gaps = 17/305 (5%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MDILLQ + +G+ LG +YA+IA GY + +     +NF  GE LM+GAL   S +G + G 
Sbjct: 1   MDILLQLVFSGIALGMIYAVIAFGYQLTFATSGTLNFGQGEALMLGALVGLSVVGNIHGG 60

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRP-LRSSPRLAPLITAIGMSILLQTLA 119
            P    W+++     I  V  A     +E +  RP ++       +++ I ++I+ + +A
Sbjct: 61  -PYLNYWLMIP----IVLVFGALQGMFVEWIGVRPAIKIKSEFGWIMSTIALAIIFKNVA 115

Query: 120 MIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNL-GRAMR 178
             IW  +  P+P+ +  +PF+I GA + P Q+L++ V A+ + + V L N  ++ G+A+ 
Sbjct: 116 ENIWGKDDLPFPSPISGAPFQIFGANVQPMQVLVV-VGALLIMAAVELFNRKSIYGKAVV 174

Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238
           AT+ +   A LMG+   MVI+ ++ + +  AA AG++ A    T   TMG   GLKAF  
Sbjct: 175 ATSNDRDAAGLMGINTSMVITFSYALSSATAAFAGVLVAPLTLTGA-TMGAALGLKAFAV 233

Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298
           A+ GG+ +  GA+VGG++LG+ E        TLTG  + + Y ++   ++L+++L ++P+
Sbjct: 234 AIIGGLTSGMGAIVGGLILGVAE--------TLTGFYISTGYKEVPGLVLLLLVLAVKPA 285

Query: 299 GLLGE 303
           GL G+
Sbjct: 286 GLFGK 290


Lambda     K      H
   0.327    0.142    0.419 

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: 209
Number of extensions: 15
Number of successful extensions: 4
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: 309
Length of database: 296
Length adjustment: 27
Effective length of query: 282
Effective length of database: 269
Effective search space:    75858
Effective search space used:    75858
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 (21.7 bits)
S2: 48 (23.1 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