GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Pseudomonas fluorescens FW300-N2E2

Align galactaro-1,5-lactonase (characterized)
to candidate Pf6N2E2_488 Gluconolactonase (EC 3.1.1.17)

Query= reanno::WCS417:GFF3393
         (291 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_488
          Length = 301

 Score =  469 bits (1206), Expect = e-137
 Identities = 229/293 (78%), Positives = 247/293 (84%), Gaps = 4/293 (1%)

Query: 1   MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIAR 60
           M AELIVDARNAVGE PVWVP ENALYWV+IP GGLQ W+A++G +  W AP+MLACIAR
Sbjct: 1   MQAELIVDARNAVGESPVWVPEENALYWVNIPSGGLQCWNASSGKLQGWEAPEMLACIAR 60

Query: 61  TDAGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVL 120
              G WVAGME+GFF+L P++DGSLD+ L A VEH R DMRLNDGRCDRQGRFWAGSMVL
Sbjct: 61  HQDGGWVAGMESGFFRLHPNDDGSLDSELCANVEHSRTDMRLNDGRCDRQGRFWAGSMVL 120

Query: 121 NMGLNAAEGTLYRYTSG--AAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFD 178
           NMG NA EG +YRY +G  +   AQL GFI  NGL FSPDGRTMY SDSHPLVQQIWAFD
Sbjct: 121 NMGANADEGRMYRYEAGQRSPVEAQLSGFIVPNGLGFSPDGRTMYLSDSHPLVQQIWAFD 180

Query: 179 YDIDTGTPSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTV 238
           YDID+GTPSNRR+FVDM    GRPDGAAVDADGCYWICANDAGLIHRF+PDGRLDRSL V
Sbjct: 181 YDIDSGTPSNRRLFVDMMPLAGRPDGAAVDADGCYWICANDAGLIHRFTPDGRLDRSLQV 240

Query: 239 PVKKPTMCAFGGSRLDTLFVTSIR--DDQSEQSLSGGVFALNPGVVGLPEPTF 289
           PVKKPTMCAFGGSRLDTLFVTSIR  DD   QSL+GGVFALNPGV GL EP F
Sbjct: 241 PVKKPTMCAFGGSRLDTLFVTSIRPGDDNDPQSLAGGVFALNPGVKGLAEPAF 293


Lambda     K      H
   0.321    0.137    0.443 

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: 505
Number of extensions: 22
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: 291
Length of database: 301
Length adjustment: 26
Effective length of query: 265
Effective length of database: 275
Effective search space:    72875
Effective search space used:    72875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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.

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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