GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudomonas baetica a390

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_008031204.1 C0J26_RS03600 urea ABC transporter ATP-binding subunit UrtE

Query= CharProtDB::CH_003736
         (237 letters)



>NCBI__GCF_003031005.1:WP_008031204.1
          Length = 232

 Score =  164 bits (416), Expect = 1e-45
 Identities = 96/228 (42%), Positives = 139/228 (60%), Gaps = 2/228 (0%)

Query: 5   MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64
           ML  DK+  +YG    L  ++  +  GE+  L+G NG GKTTLL  L G   A  G + +
Sbjct: 1   MLQVDKLHQYYGGSHILRGLTFDVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAKEGAVNW 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++L 
Sbjct: 121 PVLLQMKQRRGGDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAVIKKLA 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: 159
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 24 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