GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Pseudomonas putida KT2440

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate PP_4484 PP_4484 histidine / lysine / arginine / ornithine ABC transporter - permease subunit

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



>FitnessBrowser__Putida:PP_4484
          Length = 232

 Score =  219 bits (557), Expect = 5e-62
 Identities = 114/221 (51%), Positives = 156/221 (70%), Gaps = 1/221 (0%)

Query: 2   NWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFR 61
           +++V+ + LP    G   TL+L+AI++  GLL AIPLG+ R SR   V    + Y +  R
Sbjct: 4   DYNVVWEALPMYFGGLLTTLKLLAISLFFGLLAAIPLGLMRVSRQPVVNLAAWLYTYVIR 63

Query: 62  GTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAI 121
           GTP+LVQLFL+YYGLAQF+AVR S  WP L    +CA +   ++T+AY AEI+ G+++A 
Sbjct: 64  GTPMLVQLFLIYYGLAQFEAVRESIFWPLLSSATFCACLAFGINTSAYTAEIIAGSLKAT 123

Query: 122 PKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGM 181
           P GEIEAA+A+GMSR K    I+LP A R  LP YSNEVI+ML+ ++LAS VTL+++TG 
Sbjct: 124 PHGEIEAAKAMGMSRMKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGA 183

Query: 182 ARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLE-RWL 221
           ART+ A+ YLP E +  AG+FYL ++F+LV+ FK  E RWL
Sbjct: 184 ARTVNAQYYLPFEAYITAGVFYLCLTFILVRLFKMAERRWL 224


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: 175
Number of extensions: 4
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: 232
Length adjustment: 23
Effective length of query: 206
Effective length of database: 209
Effective search space:    43054
Effective search space used:    43054
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.

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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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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