GapMind for catabolism of small carbon sources

 

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

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate AO353_12325 AO353_12325 ABC transporter permease

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12325
          Length = 319

 Score =  132 bits (331), Expect = 2e-35
 Identities = 85/207 (41%), Positives = 120/207 (57%), Gaps = 10/207 (4%)

Query: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLA 233
           LW GL  TL ++ +S VL   IG+   L R SN P +R  S +YIE+VRG PL     L 
Sbjct: 118 LW-GLWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPL-----LV 171

Query: 234 QVMLPLFFAADV-RLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTF 292
           Q+ +  FF   V  L R    IA L LF+ AY+AE +R G+Q+++RGQ EAA++LGL+  
Sbjct: 172 QIFIFYFFIGTVLNLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARSLGLSAG 231

Query: 293 FVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAE 352
             +  +VLPQA + V+P L GQFI L KDTSL+S++ + EL    R ++          E
Sbjct: 232 QSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTS---FSPFE 288

Query: 353 VYLFIGLIYWLFCYSMSLASRRLERQL 379
           +   +  +Y L    +S  + RLER+L
Sbjct: 289 ILFCVAGLYLLINLPLSKIASRLERRL 315


Lambda     K      H
   0.332    0.145    0.452 

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: 331
Number of extensions: 19
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: 381
Length of database: 319
Length adjustment: 29
Effective length of query: 352
Effective length of database: 290
Effective search space:   102080
Effective search space used:   102080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 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