GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Dyella japonica UNC79MFTsu3.2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_1248 N515DRAFT_1248 ABC-2 type transport system ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1248 N515DRAFT_1248 ABC-2
           type transport system ATP-binding protein
          Length = 315

 Score =  115 bits (288), Expect = 1e-30
 Identities = 78/239 (32%), Positives = 126/239 (52%), Gaps = 22/239 (9%)

Query: 1   MTEKSNEV--VLKVAGISKRF-GGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITG 57
           MTE++      + V GISK + GG QAL  + + I+RG+++ L+GPNGAGKTT  ++I G
Sbjct: 1   MTEQATPTPHAVSVRGISKTYKGGFQALKSIDLDIRRGEIFALLGPNGAGKTTLISIICG 60

Query: 58  LYTPDAGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGL 117
           +  P AGT    G  ++    + + +A I    Q +       A E V     +R   GL
Sbjct: 61  IVKPSAGTVSADG--HDVLRDYRLTRAKIGLVPQEL----STDAFETVWAA--VRFSRGL 112

Query: 118 FGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQ 177
           FG            A   +  +++L  + + +  D K  TLS G +RR+ IA+ALA +P 
Sbjct: 113 FG-----------RARDDRHIEKVLRDLSLWEKKDAKIMTLSGGMKRRVLIAKALAHEPS 161

Query: 178 LIALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQI 236
           ++ LDEP AG++   +  + E++ R+R    T++L  H ++    + DRV V+  G+ I
Sbjct: 162 ILFLDEPTAGVDVELRHDMWEMVRRLRATGVTVILTTHYIEEAEEMADRVGVITRGELI 220


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: 195
Number of extensions: 9
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: 315
Length adjustment: 26
Effective length of query: 234
Effective length of database: 289
Effective search space:    67626
Effective search space used:    67626
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, 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