GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braG in Herbaspirillum seropedicae SmR1

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate HSERO_RS14710 HSERO_RS14710 amino acid ABC transporter ATPase

Query= TCDB::P21630
         (233 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS14710 HSERO_RS14710 amino acid
           ABC transporter ATPase
          Length = 243

 Score =  233 bits (593), Expect = 3e-66
 Identities = 119/234 (50%), Positives = 163/234 (69%), Gaps = 1/234 (0%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           +L  + ++  YG I+A+  +S+ + +GEI  L+GANGAGKST L+ + G  +A  G +  
Sbjct: 10  ILQVEDLAVAYGHIEAVKGISLSLNEGEITALVGANGAGKSTSLLAISGLVKAQRGRVLL 69

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFT-DKDDYQVQMDKVLEL 119
            G++L+ +    I+   +  V EGR   + LTVEENL +G +   DKD     ++ V  L
Sbjct: 70  HGQDLLQMSPHRIVESGVVQVAEGRATLTTLTVEENLGLGAYTRKDKDGVARDLEWVYSL 129

Query: 120 FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179
           FP LK R    AG +SGGEQQMLAIGRALM+KPK+LLLDEPS+GLAP+IIQ+IF I++++
Sbjct: 130 FPVLKNRAAGLAGNLSGGEQQMLAIGRALMAKPKVLLLDEPSMGLAPLIIQEIFRIVQEI 189

Query: 180 RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233
            + G+TV LVEQN  QAL++A R YVLE G+IV+ D+GA LL NPKV +AYLGG
Sbjct: 190 NKTGMTVLLVEQNVRQALRIAQRGYVLETGKIVLEDSGANLLGNPKVVEAYLGG 243


Lambda     K      H
   0.318    0.136    0.374 

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: 158
Number of extensions: 7
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: 233
Length of database: 243
Length adjustment: 23
Effective length of query: 210
Effective length of database: 220
Effective search space:    46200
Effective search space used:    46200
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 (21.7 bits)
S2: 46 (22.3 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