GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braG in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1378 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= TCDB::P21630
         (233 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1378 Branched-chain amino
           acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
          Length = 238

 Score =  255 bits (651), Expect = 6e-73
 Identities = 135/233 (57%), Positives = 167/233 (71%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           +L    +  +YG IQAL  VS+ + +GE V+LIG+NGAGKSTLLM++ G P+AA G I Y
Sbjct: 5   ILELKDLDVFYGPIQALKKVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAADGQIVY 64

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELF 120
           +G ++    S  I    IA  PEGRRVF  +TVEENL MG         +  M ++ ELF
Sbjct: 65  QGVDITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMGTIPIGDKYAKEDMQRMFELF 124

Query: 121 PRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR 180
           PRL+ER  QRA TMSGGEQQMLAI RALMS+PKLLLLDEPSLGLAPI+++QIF  + +L 
Sbjct: 125 PRLEERRTQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFATLRELA 184

Query: 181 REGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233
             G+T+FLVEQNAN ALKL+DRAYV+ NG I +  TG  LL N +VR+AYLGG
Sbjct: 185 STGMTIFLVEQNANHALKLSDRAYVMVNGEIRLSGTGKELLVNDEVRNAYLGG 237


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: 191
Number of extensions: 4
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: 238
Length adjustment: 23
Effective length of query: 210
Effective length of database: 215
Effective search space:    45150
Effective search space used:    45150
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.

Links

Downloads

Related tools

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