GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF in Pseudomonas stutzeri RCH2

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate GFF558 Psest_0563 urea ABC transporter, ATP-binding protein UrtE

Query= uniprot:A0A159ZWL6
         (233 letters)



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

 Score =  172 bits (435), Expect = 7e-48
 Identities = 93/224 (41%), Positives = 136/224 (60%), Gaps = 1/224 (0%)

Query: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60
           MLQ + +  +YG    L  ++ E + GE+  L+G NG GK+TLL  L G   A  G++ +
Sbjct: 1   MLQVQQLHQYYGGSHILRGLSFEAKVGEVTCLLGRNGVGKTTLLKCLMGLIPAKEGAVNW 60

Query: 61  MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120
            G+ + G      +   IA VP+GR +F RLTVEENL MG       + +E  + +  LF
Sbjct: 61  EGKPITGFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFSAREAKEVPEFIYELF 120

Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180
           P LKE   +RGG +SGG+QQ LAIGRAL SKP+LL+LDEP+ G+ P +I++I  +I +L 
Sbjct: 121 PVLKEMKHRRGGDLSGGQQQQLAIGRALASKPRLLILDEPTEGIQPSVIKEIGAVIRKLA 180

Query: 181 KDG-VTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTD 223
             G + + LVEQ  + A ++AD+  V+  G ++ QG GE +  D
Sbjct: 181 ARGDMAILLVEQFYDFAAELADQYLVMSRGEIIQQGRGENMAAD 224


Lambda     K      H
   0.320    0.137    0.381 

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: 174
Number of extensions: 9
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: 233
Length of database: 232
Length adjustment: 23
Effective length of query: 210
Effective length of database: 209
Effective search space:    43890
Effective search space used:    43890
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