GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Phaeobacter inhibens BS107

Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate GFF2280 PGA1_c23120 putative sorbitol dehydrogenase

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



>FitnessBrowser__Phaeo:GFF2280
          Length = 269

 Score =  157 bits (398), Expect = 2e-43
 Identities = 97/261 (37%), Positives = 145/261 (55%), Gaps = 8/261 (3%)

Query: 4   RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVK--PADSFGDSLRATYGDRVLTVS 61
           RL+ K  ++TGAA G+G+A A  +  +GA   L D+    A    D++ A      + V 
Sbjct: 5   RLKGKNILITGAARGMGQANAESFAAQGANVCLGDLDGDEAQKVADAINAAGNGMAIAVK 64

Query: 62  ADVTRRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFL 121
            DVT R D    VA+T+E FG I++   NA L   R  ++   D +D +  VN K M+  
Sbjct: 65  MDVTSRADNAAAVAATVEAFGSINVGLFNAGLNKPRFFMDIDEDNWDMIMNVNTKAMWLG 124

Query: 122 MQAVAQKMVEQGCGG----KIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPH 177
           MQ VA++M+ QG       K+IN+ S A ++    V+ YC +K   L+ T+  AL LA H
Sbjct: 125 MQEVARQMIAQGPMEDHPYKLINVGSIASKKPLVDVTVYCTSKYGCLALTECGALGLAEH 184

Query: 178 KINVNGIAPGVVDTPMWNEV--DALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAA 235
            I VNG APGVV TP+W ++  D +   ++ R     + +V  A+ + R+  P D+ G A
Sbjct: 185 NITVNGYAPGVVVTPLWEQLDKDLVDIGFKEREGQAYEDIVDSALVIKRLSYPKDIVGTA 244

Query: 236 LFLASADADYITAQTLNVDGG 256
            FLAS D+DY+T Q +++DGG
Sbjct: 245 SFLASDDSDYMTGQMISIDGG 265


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: 188
Number of extensions: 14
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: 260
Length of database: 269
Length adjustment: 25
Effective length of query: 235
Effective length of database: 244
Effective search space:    57340
Effective search space used:    57340
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