GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Shewanella loihica PV-4

Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= reanno::BFirm:BPHYT_RS16120
         (260 letters)



>FitnessBrowser__PV4:5210422
          Length = 248

 Score =  130 bits (326), Expect = 3e-35
 Identities = 87/258 (33%), Positives = 135/258 (52%), Gaps = 16/258 (6%)

Query: 1   MAARLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFGDSLRATYGDRVLTV 60
           M +  + KV ++TGAASG G+ +A+R   +GA+ VL D+   D+  D+L +  G+  + +
Sbjct: 1   MQSNFEGKVVLITGAASGFGKLLAQRLAPQGAKLVLGDIN--DTALDALCSELGECAVGL 58

Query: 61  SADVTRRDDIQRIVASTLERFGQIDILFNNAALF-DMRPILEESWDVFDRLFAVNVKGMF 119
             DV+   +   +     E FG++DI  NNA +   M+ +L  +    D  FA+N KG+F
Sbjct: 59  RCDVSIEAEQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGVF 118

Query: 120 FLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKI 179
           F M+A    M +  CG  I+N++S AG  G   ++ Y A K AV+  T++AAL  A   I
Sbjct: 119 FGMKAQIPLMQKHKCGA-ILNVASMAGINGAPKLTPYVAAKHAVVGITRTAALEFAAQGI 177

Query: 180 NVNGIAPGVVDTPMWNE-VDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFL 238
            VN I P    TPM  E VD        R           AVP+ R+  P+++  A L +
Sbjct: 178 QVNAICPFFTPTPMVTEGVDPALIEQLTR-----------AVPMRRLADPNEVVSAMLHM 226

Query: 239 ASADADYITAQTLNVDGG 256
            + D  ++T Q + +DGG
Sbjct: 227 VNPDNGFMTGQAIAIDGG 244


Lambda     K      H
   0.321    0.135    0.393 

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: 142
Number of extensions: 8
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: 260
Length of database: 248
Length adjustment: 24
Effective length of query: 236
Effective length of database: 224
Effective search space:    52864
Effective search space used:    52864
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 (21.9 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