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_16280 AO353_16280 amino acid ABC transporter permease

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16280
          Length = 223

 Score =  120 bits (301), Expect = 4e-32
 Identities = 70/209 (33%), Positives = 115/209 (55%), Gaps = 7/209 (3%)

Query: 174 LWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLA 233
           +WNG+++TL +  + +V    +G LLAL R S+  ++   +  Y+   R +PL+ ++   
Sbjct: 15  MWNGMVMTLQLTVLGVVGGIILGTLLALMRLSHSKLLSNIAGAYVNYFRSIPLLLVITWF 74

Query: 234 QVMLPLFF----AADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGL 289
            + +P         D  +      I   ++F AAY  E VR G+Q++ +GQ+ AAKALG+
Sbjct: 75  YLAVPFVLRWITGEDTPIGAFTSCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAKALGM 134

Query: 290 NTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGR 349
               ++ LI+LPQA R + P L+ Q I LF+DTSL+  VGLV+     R   A    IGR
Sbjct: 135 GYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNATR---ASGDIIGR 191

Query: 350 YAEVYLFIGLIYWLFCYSMSLASRRLERQ 378
             E  +  GL+Y+   ++ S   +RL+++
Sbjct: 192 ANEFLIIAGLVYFTISFAASRLVKRLQKR 220


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: 235
Number of extensions: 12
Number of successful extensions: 3
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: 223
Length adjustment: 26
Effective length of query: 355
Effective length of database: 197
Effective search space:    69935
Effective search space used:    69935
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: 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