GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Pseudomonas simiae WCS417

Align galactaro-1,5-lactonase (characterized)
to candidate GFF1427 PS417_07255 calcium-binding protein

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



>FitnessBrowser__WCS417:GFF1427
          Length = 292

 Score =  169 bits (429), Expect = 5e-47
 Identities = 109/297 (36%), Positives = 154/297 (51%), Gaps = 15/297 (5%)

Query: 1   MNAELIVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIA- 59
           M  E++VD +  +GE PVW   +  LYW+D   G + R +     + AW   Q +  +A 
Sbjct: 1   MRIEVLVDVKTTLGEGPVWDVEQQRLYWIDSADGRILRCTDDGRELRAWEVGQKIGSMAL 60

Query: 60  RTDAGNWVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMV 119
           R D  + +  ++ G   L   +    +  L+A  E    D RLNDG+ DRQGRF  GSM 
Sbjct: 61  RQDGESAIVALQNGVHTLDLKSG---ELNLIADPEPHLPDNRLNDGKVDRQGRFIFGSM- 116

Query: 120 LNMGLNAAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDY 179
            +   + A   LYR  +  + H   +G I  NG  +SP G T Y  D+     +IWA+DY
Sbjct: 117 -DTQEDNASAKLYRLDADLSLHTLDEGIIVSNGPCWSPSGDTFYFCDTWS--GEIWAYDY 173

Query: 180 DIDTGTPSNRRVFVDMH-KHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTV 238
           D+ TG  SNRR F  +  +  G  DG  VDA+GC W     AG + R++P+G +DR + +
Sbjct: 174 DLATGNVSNRRTFAKVDTRGGGAADGCTVDAEGCLWQALVYAGKLVRYTPEGVVDRIIQM 233

Query: 239 PVKKPTMCAFGGSRLDTLFVTSIRDD-----QSEQSLSGGVFALNP-GVVGLPEPTF 289
           PVKK T   FGG  LDTLFVTS+         ++    G +FA+   GV G+ E  F
Sbjct: 234 PVKKVTSLTFGGPNLDTLFVTSMAKPPLPRFPADGQQRGALFAITGLGVQGIAERRF 290


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: 326
Number of extensions: 20
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: 291
Length of database: 292
Length adjustment: 26
Effective length of query: 265
Effective length of database: 266
Effective search space:    70490
Effective search space used:    70490
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