GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate Pf1N1B4_1643 Amino acid ABC transporter, permease protein

Query= reanno::pseudo5_N2C3_1:AO356_09910
         (229 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1643 Amino acid ABC
           transporter, permease protein
          Length = 229

 Score =  422 bits (1085), Expect = e-123
 Identities = 213/229 (93%), Positives = 221/229 (96%)

Query: 1   MNWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFF 60
           MNW+VIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLW VRA PY YIFFF
Sbjct: 1   MNWEVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWYVRAFPYGYIFFF 60

Query: 61  RGTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQA 120
           RGTPLLVQLFLVYYGLAQFDAVR+S++WPYLR PFWCAT TMTLHTAAYIAEILRGAIQA
Sbjct: 61  RGTPLLVQLFLVYYGLAQFDAVRNSSMWPYLRSPFWCATATMTLHTAAYIAEILRGAIQA 120

Query: 121 IPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTG 180
           IP GEIEAARALGMSR KALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTG
Sbjct: 121 IPPGEIEAARALGMSRTKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTG 180

Query: 181 MARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLERWLRVDACQGR 229
           MARTIIARTYLPVEIFFAAGMFYLLM+++LV+GFK LERWLRVDACQGR
Sbjct: 181 MARTIIARTYLPVEIFFAAGMFYLLMAYVLVRGFKLLERWLRVDACQGR 229


Lambda     K      H
   0.331    0.141    0.434 

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: 310
Number of extensions: 9
Number of successful extensions: 1
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: 229
Length of database: 229
Length adjustment: 23
Effective length of query: 206
Effective length of database: 206
Effective search space:    42436
Effective search space used:    42436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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