GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Pseudomonas fluorescens FW300-N2E3

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate AO353_11555 AO353_11555 sulfate ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_11555
          Length = 329

 Score =  127 bits (320), Expect = 2e-34
 Identities = 83/223 (37%), Positives = 132/223 (59%), Gaps = 18/223 (8%)

Query: 5   LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64
           +E+R+V K+F A KAL+ ++++I  GE+VALLG +G GK+TL++II+G   PD G +VF 
Sbjct: 3   IEVRNVSKNFNAFKALNSINLDIQSGELVALLGPSGCGKTTLLRIIAGLETPDAGSIVFH 62

Query: 65  GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNI-FLAREVTNKIFLNKKKMMEESKK 123
           G+ V   S +D R   +  ++Q  AL   + ++ N+ F  R        ++ ++  +  +
Sbjct: 63  GEDV---SGHDVRDRNVGFVFQHYALFRHMTVFDNVAFGLRMKPKNQRPSESQIAVKVHE 119

Query: 124 LLDSLQI-----RIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178
           LL+ +Q+     R P      E LSGGQRQ +A+ARA+    K++L+DEP  AL   + R
Sbjct: 120 LLNMVQLDWLSDRYP------EQLSGGQRQRIALARALAVEPKVLLLDEPFGALD-AKVR 172

Query: 179 KVLE--LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI 219
           K L   LAR  +   L  + +TH+  +  EVADRI V+++G I
Sbjct: 173 KELRRWLARLHEDINLTSVFVTHDQEEAMEVADRIVVMNKGVI 215


Lambda     K      H
   0.318    0.137    0.371 

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: 167
Number of extensions: 6
Number of successful extensions: 3
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: 251
Length of database: 329
Length adjustment: 26
Effective length of query: 225
Effective length of database: 303
Effective search space:    68175
Effective search space used:    68175
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: 47 (22.7 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