GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pseudomonas fluorescens GW456-L13

Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate PfGW456L13_3458 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= reanno::Phaeo:GFF1301
         (257 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3458
          Length = 251

 Score =  140 bits (353), Expect = 3e-38
 Identities = 94/257 (36%), Positives = 141/257 (54%), Gaps = 12/257 (4%)

Query: 3   RLSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQIGAAAIAVELDVT 62
           +L+GKR ++TG ARGIGAA  +A+  EGA VV   +D   A +     G  A +   D+ 
Sbjct: 2   QLAGKRIIVTGGARGIGAAVVKAFVEEGAHVV--SLDLGEAASITGDGGGWAHSRVCDIA 59

Query: 63  DQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQAA 122
           D  S+D A +   E   GLD+L++ A +   A    +T + +++ F +N  GT F+   A
Sbjct: 60  DSQSVDAAFAWASEQLNGLDVLVHAAGIAPNASADSITLDEWEKVFAVNTRGT-FLTNRA 118

Query: 123 AQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAIA 182
           A +++ +G+GG+IIN AS AG  G+P  + Y A+K AV++ T++        GI VNAIA
Sbjct: 119 AYELL-KGSGGRIINFASAAGVLGQPGKAHYAASKGAVLAWTRTVAREWGPLGITVNAIA 177

Query: 183 PGVVDGEHWDGV-DAFFAKYEGKAPGQKKAEVAQSVPY-GRMG-TAADLTGMAVFLASED 239
           P +     W  + DA  A    +   Q  A +A  VP  G++G  A DL  + VFLA + 
Sbjct: 178 PAM-----WTPMYDATRASMSAEQLQQHDAYMAGQVPIGGKLGEPARDLAPVLVFLAGDG 232

Query: 240 ADYVVAQTYNVDGGQWM 256
           + +V  QT  +DGG  M
Sbjct: 233 SRFVTGQTLVIDGGMMM 249


Lambda     K      H
   0.317    0.130    0.365 

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: 139
Number of extensions: 8
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: 257
Length of database: 251
Length adjustment: 24
Effective length of query: 233
Effective length of database: 227
Effective search space:    52891
Effective search space used:    52891
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.

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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