GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1692 in Pseudomonas putida KT2440

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_4863 PP_4863 high-affinity branched-chain amino acid transporter, ATP-binding

Query= uniprot:A0A165KC78
         (242 letters)



>lcl|FitnessBrowser__Putida:PP_4863 PP_4863 high-affinity
           branched-chain amino acid transporter, ATP-binding
          Length = 238

 Score =  229 bits (583), Expect = 5e-65
 Identities = 123/233 (52%), Positives = 163/233 (69%), Gaps = 1/233 (0%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L++K L V YG IQA+K V   + EGE VSLIG+NGAGK+T + +I G      G+I Y
Sbjct: 5   ILELKDLDVFYGPIQALKKVSMHINEGETVSLIGANGAGKSTLLMSIFGQPRAASGHIVY 64

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128
            G  I  K +  +   G+   PEGR VF  MT+ ENL MG     DK     D+++M+ +
Sbjct: 65  RGTDITRKSSHYIASNGIAQSPEGRRVFPDMTVEENLMMGTIPIGDKHAD-EDMQRMYEL 123

Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188
           FPRL+ER++Q A TMSGGEQQMLA+ RALMS+PK+LLLDEPS+GL+PI+V +IF  +R++
Sbjct: 124 FPRLKERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFSTLREL 183

Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
              G+TI LVEQNA+ AL ++DR YVM +G I MTG GQ+LL + +VR AYLG
Sbjct: 184 AKTGMTIFLVEQNANHALKLSDRAYVMVNGQIRMTGTGQELLVNEEVRNAYLG 236


Lambda     K      H
   0.317    0.136    0.373 

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: 164
Number of extensions: 6
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: 242
Length of database: 238
Length adjustment: 23
Effective length of query: 219
Effective length of database: 215
Effective search space:    47085
Effective search space used:    47085
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