GapMind for catabolism of small carbon sources

 

Alignments for a candidate for snatA in Azospirillum brasilense Sp245

Align The SnatA carrier. Transports glycine, L-alanine, L-serine, L-threonine and a variety of neutral L-amino acids (characterized)
to candidate AZOBR_RS31980 AZOBR_RS31980 membrane protein

Query= TCDB::Q8J305
         (216 letters)



>FitnessBrowser__azobra:AZOBR_RS31980
          Length = 221

 Score = 92.4 bits (228), Expect = 6e-24
 Identities = 59/209 (28%), Positives = 102/209 (48%), Gaps = 6/209 (2%)

Query: 12  ILLYGGLFAITNPVGAVPVFLSVTHDLSWRERREIASKTAISVVATLVVFALLGQWIFKF 71
           +L +  LF+I NP+    +F  VT + S +ER ++A++ A+     ++     G ++  F
Sbjct: 6   LLAFTALFSIVNPIAMALIFSQVTAERSPKERVQLAARVAVYSAIVMLAALWAGSYVLNF 65

Query: 72  FGSSTDAFAIAGGILLFRMALDMLSGKLSSVKISNEETEEFSEEVVT-LEEVAIIPLAIP 130
           FG S  A  IAGG ++   A  +LS   +      ++     E   + + E A  PL IP
Sbjct: 66  FGISLAALRIAGGFVVAERAWALLSAPEAHEARKQKQAAPAEEAGDSDVGESAFFPLTIP 125

Query: 131 LISGPGAITTVMLYMA---KSTTNLQR--LAVILTIILIGITVWFVLCSANRIKARLGRV 185
             +GPG I+  +   A   + T  L    + V    + I + +W    SA+R+ A LG  
Sbjct: 126 FTTGPGTISVAIALGATRPRGTEGLTEFFIGVSAAALAIALLIWLSYRSADRLVALLGHT 185

Query: 186 GIKVMTRMMGLILTSMAVQMIINGIKGAF 214
             +V+TR+   +L  + VQ+++ G+  AF
Sbjct: 186 RARVLTRLFAFLLFCVGVQILLTGLLDAF 214


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: 86
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: 221
Length adjustment: 22
Effective length of query: 194
Effective length of database: 199
Effective search space:    38606
Effective search space used:    38606
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