GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Pseudomonas stutzeri RCH2

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF558 Psest_0563 urea ABC transporter, ATP-binding protein UrtE

Query= TCDB::P73650
         (240 letters)



>lcl|FitnessBrowser__psRCH2:GFF558 Psest_0563 urea ABC transporter,
           ATP-binding protein UrtE
          Length = 232

 Score =  148 bits (374), Expect = 8e-41
 Identities = 84/215 (39%), Positives = 129/215 (60%), Gaps = 2/215 (0%)

Query: 14  YVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLG 73
           Y     IL+G++F    GE+  ++G NG GK+TL K + GL+   +G + ++G+ ITG  
Sbjct: 10  YYGGSHILRGLSFEAKVGEVTCLLGRNGVGKTTLLKCLMGLIPAKEGAVNWEGKPITGFK 69

Query: 74  SDQIVRRGMCYVPQVCNVFGSLTVAENLDMG-AFLHQGPTQTLKDRIYTMFPKLAQRRNQ 132
             Q V  G+ YVPQ   +FG LTV ENL MG +       + + + IY +FP L + +++
Sbjct: 70  PHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFSAREAKEVPEFIYELFPVLKEMKHR 129

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

Query: 192 VEQNAKQALMMADRGYVLENGRDKLEGSGQSLLND 226
           VEQ    A  +AD+  V+  G    +G G+++  D
Sbjct: 190 VEQFYDFAAELADQYLVMSRGEIIQQGRGENMAAD 224


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: 129
Number of extensions: 6
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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