GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Pseudomonas putida KT2440

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate PP_0281 PP_0281 Amino acid ABC transporter, permease protein

Query= TCDB::Q9HU30
         (231 letters)



>FitnessBrowser__Putida:PP_0281
          Length = 230

 Score =  318 bits (814), Expect = 7e-92
 Identities = 154/230 (66%), Positives = 190/230 (82%)

Query: 1   MILDLHGFGEQLLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVR 60
           M +DLHGFG  ++AGT MT+KL+L A+ +GL+LGLLGA+AKTS +  L++LGG Y+T+VR
Sbjct: 1   MNIDLHGFGPAMMAGTLMTVKLALCALLLGLVLGLLGALAKTSPFKPLQWLGGFYSTLVR 60

Query: 61  GVPETLWVLMIYFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALL 120
           GVPE LWVL+IYFGTV  +N+LG+    P L LS FAAG +ALGLCFGAYATEVFRGA+L
Sbjct: 61  GVPELLWVLLIYFGTVGLMNSLGEALNMPGLELSAFAAGVIALGLCFGAYATEVFRGAIL 120

Query: 121 SIPRGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIM 180
           +IP+GHREAG ALGLS GRI  RI+LPQ+WR+ALPGLGNL++IL+KDTALVS+I L+EIM
Sbjct: 121 AIPKGHREAGLALGLSKGRILSRIILPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIM 180

Query: 181 RKAQVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRGFVRNE 230
           R +Q+    TKEPFTFYM AA IYL LTV+ M  +HF+E+RA RGF R E
Sbjct: 181 RHSQIGVTVTKEPFTFYMVAACIYLGLTVLAMTGMHFMEKRAARGFARAE 230


Lambda     K      H
   0.327    0.143    0.431 

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: 208
Number of extensions: 7
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: 231
Length of database: 230
Length adjustment: 23
Effective length of query: 208
Effective length of database: 207
Effective search space:    43056
Effective search space used:    43056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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 (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