GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudomonas fluorescens GW456-L13

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PfGW456L13_85 Urea ABC transporter, ATPase protein UrtE

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_85
          Length = 232

 Score =  149 bits (376), Expect = 5e-41
 Identities = 86/212 (40%), Positives = 125/212 (58%), Gaps = 2/212 (0%)

Query: 14  YVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG 73
           Y     IL+G+ F +  GE+  ++G NG GK+TL K + GLL   +G + ++G+ IT   
Sbjct: 10  YYGGSHILRGLTFDVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAKEGAVNWEGKPITAFK 69

Query: 74  SDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQG-PTQTLKDRIYTMFPKLAQRRNQ 132
             Q V  G+ YVPQ   +FG LTV ENL MG     G   + +   IY +FP L Q + +
Sbjct: 70  PHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFPGSEAKEVPAFIYELFPVLLQMKQR 129

Query: 133 RAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATG-KAIIL 191
           R G LSGG++Q LA+GRAL   P LL+LDEP+  + P ++K++ A IK + A G  AI+L
Sbjct: 130 RGGDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAVIKKLAARGDMAILL 189

Query: 192 VEQNAKQALMMADRGYVLENGRDKLEGSGQSL 223
           VEQ    A  +AD+  V+  G    +G G+++
Sbjct: 190 VEQFYDFAAELADQYLVMSRGEIVQQGRGENM 221


Lambda     K      H
   0.320    0.139    0.393 

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: 143
Number of extensions: 8
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: 240
Length of database: 232
Length adjustment: 23
Effective length of query: 217
Effective length of database: 209
Effective search space:    45353
Effective search space used:    45353
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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