GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Pseudomonas fluorescens GW456-L13

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PfGW456L13_85 Urea ABC transporter, ATPase protein UrtE

Query= uniprot:D8IUY7
         (241 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_85
          Length = 232

 Score =  161 bits (407), Expect = 1e-44
 Identities = 92/226 (40%), Positives = 141/226 (62%), Gaps = 8/226 (3%)

Query: 5   ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64
           +L+V++L   YGG   ++G+  +V  GE+  L+G NG GKTT LK + G LPA   EG +
Sbjct: 1   MLQVEKLHQYYGGSHILRGLTFDVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAK--EGAV 58

Query: 65  EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGA--YTSDDKGQIAADIDK 122
            + G+P+   K  + V   +A VP+GR +F R++++ENLLMG   +   +  ++ A I +
Sbjct: 59  NWEGKPITAFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFPGSEAKEVPAFIYE 118

Query: 123 WFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEV 182
            F V  ++K+R     G LSGG+QQ LA+ RAL S P+LL+LDEP+ G+ P ++++I  V
Sbjct: 119 LFPVLLQMKQRRG---GDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAV 175

Query: 183 IRNVSAQG-ITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQM 227
           I+ ++A+G + ILLVEQ    A E A +  VM  G I  QG+ + M
Sbjct: 176 IKKLAARGDMAILLVEQFYDFAAELADQYLVMSRGEIVQQGRGENM 221


Lambda     K      H
   0.317    0.134    0.365 

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: 162
Number of extensions: 13
Number of successful extensions: 4
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: 241
Length of database: 232
Length adjustment: 23
Effective length of query: 218
Effective length of database: 209
Effective search space:    45562
Effective search space used:    45562
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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