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_RS20240 RR42_RS20240 hypothetical protein

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS20240 RR42_RS20240 hypothetical
           protein
          Length = 595

 Score =  209 bits (531), Expect = 1e-58
 Identities = 111/257 (43%), Positives = 158/257 (61%), Gaps = 6/257 (2%)

Query: 4   KSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDA 63
           ++ E++L V    K FGGL A++DV   ++ G++ GLIGPNGAGK+T FN++TG+     
Sbjct: 338 QAGELILDVKAARKEFGGLVAVNDVSFQVRAGEIIGLIGPNGAGKSTTFNLVTGVLPATR 397

Query: 64  GTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTG----SGLFG 119
           G     G+        E+ K GI RTFQ++ L   MT LENV +G H+R       G+  
Sbjct: 398 GEVLYRGEQISGLPSREIVKRGIGRTFQHVHLLPTMTVLENVAIGAHLRGDFAPQGGVTA 457

Query: 120 AVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179
           A+ R    K EEA +   A   L+ VG+      +A +L+ G QR LEIARAL  DP L+
Sbjct: 458 AILRMN--KNEEAKLLHEAARQLERVGLADCMYMEAGSLALGQQRILEIARALCCDPALL 515

Query: 180 ALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEG 239
            LDEPAAG+   EK  L EL+ +++ +  ++LL+EHD+  VM L DR+ V+++G +IAEG
Sbjct: 516 LLDEPAAGLRYKEKQALAELLKKLKGEGMSVLLVEHDMDFVMNLTDRLVVMEFGTRIAEG 575

Query: 240 NPAEVQKNEKVIEAYLG 256
            P +VQK+  V+EAYLG
Sbjct: 576 VPEDVQKDPAVLEAYLG 592


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: 397
Number of extensions: 18
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: 260
Length of database: 595
Length adjustment: 31
Effective length of query: 229
Effective length of database: 564
Effective search space:   129156
Effective search space used:   129156
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: 50 (23.9 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