GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Cupriavidus basilensis 4G11

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS16965 RR42_RS16965 ABC transporter

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS16965 RR42_RS16965 ABC
           transporter
          Length = 258

 Score =  382 bits (981), Expect = e-111
 Identities = 192/257 (74%), Positives = 222/257 (86%), Gaps = 1/257 (0%)

Query: 5   SNE-VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63
           SNE ++L V G++KRFGGLQALSDVG+ IK G++YGLIGPNGAGKTTFFNVITGLYTPD+
Sbjct: 2   SNENLLLSVQGVNKRFGGLQALSDVGLQIKPGEIYGLIGPNGAGKTTFFNVITGLYTPDS 61

Query: 64  GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFR 123
           G F L GK Y+PTAVHEVAKAGIARTFQNIRLF EMTALENVMVGRH+RT +GLFGAVFR
Sbjct: 62  GEFVLGGKAYQPTAVHEVAKAGIARTFQNIRLFGEMTALENVMVGRHVRTKAGLFGAVFR 121

Query: 124 TKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDE 183
               + EE ++   A +LL+YVGIGK+A + +R LSYG QRRLEIARALAT+P+L+ALDE
Sbjct: 122 PPSVRREEHSVEDWAHDLLEYVGIGKYAHFTSRNLSYGHQRRLEIARALATEPKLLALDE 181

Query: 184 PAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243
           PAAGMNATEKV+LR L+D+IR+D +TILLIEHDVKLVMGLC+R+TVLDYGK IA+G P E
Sbjct: 182 PAAGMNATEKVELRGLLDKIRSDGKTILLIEHDVKLVMGLCNRLTVLDYGKVIAQGLPHE 241

Query: 244 VQKNEKVIEAYLGTGGH 260
           VQ N  VIEAYLGT  H
Sbjct: 242 VQSNPAVIEAYLGTPAH 258


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: 297
Number of extensions: 5
Number of successful extensions: 1
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: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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 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