GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00900 in Pseudomonas fluorescens FW300-N2E3

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AO353_13525 AO353_13525 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_13525 AO353_13525 ABC
           transporter ATP-binding protein
          Length = 232

 Score =  161 bits (407), Expect = 1e-44
 Identities = 93/226 (41%), Positives = 139/226 (61%), Gaps = 8/226 (3%)

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

Query: 65  EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGA--YTSDDKGQIAADIDK 122
            + G+P+   K  + V   +A VP+GR +F R++++ENLLMG   +   +  ++ A I +
Sbjct: 59  NWEGKPITSFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFPGSEAREVPAFIYE 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: 166
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.

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, 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