GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livF in Pseudomonas fluorescens FW300-N1B4

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate Pf1N1B4_1347 Urea ABC transporter, ATPase protein UrtE

Query= CharProtDB::CH_003736
         (237 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1347 Urea ABC transporter,
           ATPase protein UrtE
          Length = 232

 Score =  164 bits (415), Expect = 1e-45
 Identities = 96/228 (42%), Positives = 138/228 (60%), Gaps = 2/228 (0%)

Query: 5   MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64
           ML  D +  +YG    L  ++  +  GE+  L+G NG GKTTLL  L G   A  G + +
Sbjct: 1   MLQVDTLHQYYGGSHILRGLTFEVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAKEGAVNW 60

Query: 65  DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYELF 124
           + K IT ++  + +   +A VP+GR +F R+TVEENL MG       + +E   ++YELF
Sbjct: 61  EGKPITTFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFPGSEAKEVPAFIYELF 120

Query: 125 PRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLR 184
           P L + + +R G +SGG+QQ LAIGRAL S PRLL+LDEP+ G+ P +I++I   I+QL 
Sbjct: 121 PVLLQMKQRRGGDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAVIKQLA 180

Query: 185 EQG-MTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVR 231
            +G M I LVEQ  + A +LAD+  V+  G +V    G+ + A E VR
Sbjct: 181 ARGDMAILLVEQFYDFAAELADQYLVMSRGEIVQQGRGENMEA-EGVR 227


Lambda     K      H
   0.321    0.137    0.390 

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: 154
Number of extensions: 5
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: 237
Length of database: 232
Length adjustment: 23
Effective length of query: 214
Effective length of database: 209
Effective search space:    44726
Effective search space used:    44726
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.

Links

Downloads

Related tools

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, 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