GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Pseudomonas stutzeri RCH2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__psRCH2:GFF3784
          Length = 266

 Score =  157 bits (396), Expect = 3e-43
 Identities = 94/253 (37%), Positives = 145/253 (57%), Gaps = 12/253 (4%)

Query: 8   VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67
           V+L   G+ K FGG  A+++V + ++  QV+ LIGPNGAGKTT FN++T    P AG+  
Sbjct: 20  VMLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLTKFLQPSAGSIR 79

Query: 68  LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGL---FGAVFRT 124
           L       T   +VA+ G+ R+FQ   +F  +T L+NV V   ++   GL   F    R+
Sbjct: 80  LLDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLDNVRVA--LQRPGGLATQFWLPMRS 137

Query: 125 KGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEP 184
                    + +RA +L++ VG+       A  LSYG +R LEIA  LA +P+++ LDEP
Sbjct: 138 LN------RLNERALQLIESVGLADKRHELAADLSYGRKRVLEIATTLALEPKVLLLDEP 191

Query: 185 AAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244
            AGM   +   + E+I  +    R +L++EH++K+V  LC +VTVL  G+ +  G+   V
Sbjct: 192 MAGMGHEDVHVVAEIIREVAT-QRAVLMVEHNLKVVADLCHQVTVLQRGEILTSGDYRTV 250

Query: 245 QKNEKVIEAYLGT 257
            ++E+V  AY+GT
Sbjct: 251 SQDERVRVAYMGT 263


Lambda     K      H
   0.319    0.137    0.384 

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: 196
Number of extensions: 8
Number of successful extensions: 3
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: 260
Length of database: 266
Length adjustment: 25
Effective length of query: 235
Effective length of database: 241
Effective search space:    56635
Effective search space used:    56635
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 (21.7 bits)
S2: 47 (22.7 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