GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Klebsiella michiganensis M5al

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate BWI76_RS17245 BWI76_RS17245 hypothetical protein

Query= TCDB::Q8J305
         (216 letters)



>FitnessBrowser__Koxy:BWI76_RS17245
          Length = 215

 Score =  132 bits (333), Expect = 4e-36
 Identities = 74/214 (34%), Positives = 120/214 (56%), Gaps = 8/214 (3%)

Query: 1   MLEVVEFLKYLILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVV 60
           M +   + K+ I    GLFA+ NPVG +PVF+S+T   +   R +      +SV   L+ 
Sbjct: 5   MFDFSAYFKFFI----GLFALVNPVGIIPVFISMTSYQTAAVRNKTNLTANLSVAIILLT 60

Query: 61  FALLGQWIFKFFGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVTLE 120
              LG  I + FG S D+F IAGGIL+  +A+ M+SGKL   K + +E      E    E
Sbjct: 61  SLFLGDAILQVFGISIDSFRIAGGILVVTIAMSMISGKLGEDKQNKQE----KSETAIRE 116

Query: 121 EVAIIPLAIPLISGPGAITTVMLYMAKSTTNLQRLAVILTIILIGITVWFVLCSANRIKA 180
            + ++PLA+PL++GPGAI++ +++  +  +    +   + I L  +  W +   A  +  
Sbjct: 117 SIGVVPLALPLMAGPGAISSTIVWGTRYHSVAHFVGFSVAIALFALCCWGIFRMAPWLVR 176

Query: 181 RLGRVGIKVMTRMMGLILTSMAVQMIINGIKGAF 214
            LG+ GI V+TR+MGL+L ++ ++ I+ GIK  F
Sbjct: 177 LLGQTGINVITRIMGLLLMALGIEFIVTGIKALF 210


Lambda     K      H
   0.327    0.141    0.396 

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: 130
Number of extensions: 5
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: 216
Length of database: 215
Length adjustment: 22
Effective length of query: 194
Effective length of database: 193
Effective search space:    37442
Effective search space used:    37442
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: 45 (21.9 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