GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pseudomonas fluorescens FW300-N1B4

Align D-sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Pf1N1B4_5039 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)

Query= reanno::pseudo6_N2E2:Pf6N2E2_1959
         (257 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5039
          Length = 257

 Score =  446 bits (1148), Expect = e-130
 Identities = 228/257 (88%), Positives = 241/257 (93%)

Query: 1   MKRLEGKSALITGSARGIGRSFAQAYIGEGATVAIADINLERAQATASELGPQAYAVEMD 60
           MKRLEGKSALITGSARGIGR+FAQAYI EGATVAIADINLERAQATA+EL P AYAVEMD
Sbjct: 1   MKRLEGKSALITGSARGIGRTFAQAYIREGATVAIADINLERAQATAAELWPNAYAVEMD 60

Query: 61  VTRQASIDAAIAEVVARAGKLDILVNNAALFDLAPITEITRESYDKLFAINVSGTLFTLQ 120
           VT Q SID AIA V+A  GKLDIL+NNAALFDLAPITEI+R+SY++LF+INVSGTLFTLQ
Sbjct: 61  VTDQQSIDGAIAAVIATTGKLDILINNAALFDLAPITEISRDSYERLFSINVSGTLFTLQ 120

Query: 121 AAAKQMISQGHGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIKHKINVNA 180
           AAAKQMI QGHGGKIINMASQAGRRGEALV VYCATKAAVISLTQSAGLNLI H INVNA
Sbjct: 121 AAAKQMIRQGHGGKIINMASQAGRRGEALVAVYCATKAAVISLTQSAGLNLIPHNINVNA 180

Query: 181 IAPGVVDGEHWDGVDALFAKHENRPLGEKKRLVGLEVPYGRMGTAEDLVGMAIFLAGSES 240
           IAPGVVDGEHWDGVDALFAK+ENRPLGEKK+L G EVPYGRMGTA+DLVGMAIFLA +ES
Sbjct: 181 IAPGVVDGEHWDGVDALFAKYENRPLGEKKKLAGQEVPYGRMGTADDLVGMAIFLASAES 240

Query: 241 DYIVAQTYNVDGGNWMS 257
           DYIVAQTYNVDGGNWMS
Sbjct: 241 DYIVAQTYNVDGGNWMS 257


Lambda     K      H
   0.317    0.132    0.368 

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: 314
Number of extensions: 1
Number of successful extensions: 1
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: 257
Length adjustment: 24
Effective length of query: 233
Effective length of database: 233
Effective search space:    54289
Effective search space used:    54289
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 (21.6 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