GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_17115 AO353_17115 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17115
          Length = 418

 Score =  268 bits (684), Expect = 3e-76
 Identities = 162/351 (46%), Positives = 215/351 (61%), Gaps = 47/351 (13%)

Query: 8   WIIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66
           W+I  + L+V+ L+   FG+   V IA L L+YVLL LGLNIVVG AGLLDLGYV FYAV
Sbjct: 93  WVI--MGLIVIALVWPFFGSRGAVDIATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAV 150

Query: 67  GAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGD 126
           GAY +AL++  +              GL  S WI +P+A L+AA FG +LG P L+LRGD
Sbjct: 151 GAYSYALLSHYY--------------GL--SFWICLPIAGLMAATFGFLLGFPVLRLRGD 194

Query: 127 YLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EV 178
           YLAIVTLGFGEIIR+FL NL     LT GP G+  I    +FGL   +          E 
Sbjct: 195 YLAIVTLGFGEIIRLFLRNL---TGLTGGPNGISNIPKPSLFGLSFERTAAEGMQTFHEF 251

Query: 179 FGFDINSVTLYYYLFLV---LVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRN 235
           FG   N V+   +L+LV   L + ++ +  RL    IGRAW A+REDEIA +A+G+N   
Sbjct: 252 FGLTYNPVSKVVFLYLVALLLALFALFVINRLLRMPIGRAWEALREDEIACRALGLNPTV 311

Query: 236 MKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAV 295
           +KL AF +GA F G +G+ F A QG V+PESF+ +ES  I+A+VVLGG+G   GV+L AV
Sbjct: 312 IKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESATILAIVVLGGMGSQLGVVLAAV 371

Query: 296 LLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
           ++  LPE++R              D +  R L+    M+++M+ RP+GL P
Sbjct: 372 VMILLPELMR--------------DFSEYRMLMFGALMVLMMIWRPQGLLP 408


Lambda     K      H
   0.328    0.144    0.430 

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: 400
Number of extensions: 20
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: 358
Length of database: 418
Length adjustment: 30
Effective length of query: 328
Effective length of database: 388
Effective search space:   127264
Effective search space used:   127264
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: 50 (23.9 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