GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Shewanella sp. ANA-3

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 7025539 Shewana3_2690 short chain dehydrogenase (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>FitnessBrowser__ANA3:7025539
          Length = 255

 Score =  138 bits (347), Expect = 1e-37
 Identities = 85/255 (33%), Positives = 138/255 (54%), Gaps = 11/255 (4%)

Query: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKAD 78
           L+ KV ++TGA+ GIG A    FA + A+LV+   +G  +  +      QG + + +  D
Sbjct: 4   LQGKVAIITGASSGIGYATAKRFAREGAKLVLGARRGAILASLVDEIITQGGEAIYLAGD 63

Query: 79  VSRQQDLHAMARLAIELHGRIDVLVNCAGVN--VFRDPLQMTEEDWHRCFAIDLDGAWYG 136
           V+ +     +  LA+E +G +D+  N  G+N  +  D   ++  +W      +L  A+  
Sbjct: 64  VTDEVYASDLVALAVEQYGGLDIAFNNVGINGELGVDSDALSRAEWENTLTTNLTSAFLA 123

Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHI-IPGCFPYPVAKHGLLGLTRALGIEYAPKGIRV 195
            K  LPQM+++G GSII  +S     I  P    Y  +K G++GLT++L +EY  +GIRV
Sbjct: 124 AKYQLPQMLKRGAGSIIFTSSFVGYTIGFPQTAAYAASKAGMIGLTQSLAVEYGARGIRV 183

Query: 196 NAIAPGYIETQLNVDYWNGFADPHAERQRAF--DLHPPRRIGQPIEVAMTAVFLASDEAP 253
           NA+ PG  +T +  ++ N    P A    AF  +LH  +R+  P E+A +A++LASD A 
Sbjct: 184 NALLPGGTDTPMGREFAN---TPEA---MAFVKNLHALKRLADPAEIAQSALYLASDAAS 237

Query: 254 FINASCITIDGGRSV 268
           F     + +DGG S+
Sbjct: 238 FTTGIALLVDGGVSI 252


Lambda     K      H
   0.321    0.138    0.424 

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: 143
Number of extensions: 7
Number of successful extensions: 4
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: 272
Length of database: 255
Length adjustment: 25
Effective length of query: 247
Effective length of database: 230
Effective search space:    56810
Effective search space used:    56810
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.

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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