GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Pseudomonas putida KT2440

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate PP_0618 PP_0618 Branched-chain amino acid ABC transporter, permease protein

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__Putida:PP_0618
          Length = 286

 Score =  157 bits (398), Expect = 2e-43
 Identities = 97/300 (32%), Positives = 161/300 (53%), Gaps = 21/300 (7%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60
           ++ +L QL+NGL LG IY LIA+G T+++G++  +NFAHG  +++GA+   + + A+   
Sbjct: 2   LDLYLFQLLNGLGLGMIYFLIAVGLTIIFGLLNFVNFAHGAFFLLGAY---LCYTAVAVT 58

Query: 61  GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120
           G  W+ L +  ++VA++       W VER+  + +   P    ++  +G+++ +Q    +
Sbjct: 59  GNFWLALLIAPLVVAAL------AWAVERLLIKRIYHLPHTFQILVTLGIALIIQEASVL 112

Query: 121 LQGARSK--PLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQR 178
           + G   K   + P L G L L  G     Y RL  I     +  G   L+ RT  G   R
Sbjct: 113 IWGPVGKNIAVPPELRGVLIL--GDFIYPYYRLFLIGFAALIGIGLWLLLERTRFGALVR 170

Query: 179 ACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTA 238
           A  +  +   LLG N+ R+ SLTF +G  LA VAG++   + G   F    + G+ AF  
Sbjct: 171 AGSESTETVSLLGTNIFRLFSLTFALGVGLAGVAGVLFAPLRGAQPFVGPEILGI-AFVV 229

Query: 239 AVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTI---LVLVLIFRPTGLLGR 295
            V+GG+GS  GA++GG+++G++++     M S W   A+  I   +  V++ RP GL GR
Sbjct: 230 VVIGGMGSFGGALVGGLLVGVVQSM----MTSLWPQGASLMIYGAMAAVILVRPYGLFGR 285


Lambda     K      H
   0.329    0.144    0.425 

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: 325
Number of extensions: 26
Number of successful extensions: 5
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: 301
Length of database: 286
Length adjustment: 26
Effective length of query: 275
Effective length of database: 260
Effective search space:    71500
Effective search space used:    71500
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 (21.8 bits)
S2: 48 (23.1 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 (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