GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Dyella japonica UNC79MFTsu3.2

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate N515DRAFT_1230 N515DRAFT_1230 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family

Query= reanno::BFirm:BPHYT_RS16920
         (266 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1230
          Length = 254

 Score =  330 bits (846), Expect = 2e-95
 Identities = 160/252 (63%), Positives = 185/252 (73%)

Query: 14  SAFARYPSLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKH 73
           S FA YPSL+DR V ++GGATGIGA+FVEHFA QG+RV F DID    EALA  L   +H
Sbjct: 2   SQFATYPSLIDRHVFVSGGATGIGAAFVEHFARQGSRVTFVDIDREHAEALAQSLAGERH 61

Query: 74  KPLFLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNI 133
            P FL CD+TD+DALQ +IA  + A GP+ VLVNNAAND RHT G+ T E FD  IA+N+
Sbjct: 62  APRFLPCDITDLDALQASIAAAREAHGPVAVLVNNAANDVRHTFGDTTGEQFDRSIAINL 121

Query: 134 RHQFFAAQAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGH 193
           RHQ+FA QAV EDM+A   GS+I LGS  WM KN GYP+Y M+KSAV GL  GLAR+LGH
Sbjct: 122 RHQYFATQAVREDMRALGGGSVICLGSTGWMKKNAGYPIYAMAKSAVHGLVNGLARELGH 181

Query: 194 FNIRVNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRM 253
             IR+N LVPGWV+TEKQ+RLWLD AG   IK  QC+   L   DLAR ALFL ADDSRM
Sbjct: 182 DRIRINALVPGWVITEKQRRLWLDAAGEEEIKRVQCLPGYLMAEDLARAALFLGADDSRM 241

Query: 254 ITAQDIVVDGGW 265
            T Q  +VDGGW
Sbjct: 242 CTGQSFLVDGGW 253


Lambda     K      H
   0.320    0.134    0.388 

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: 236
Number of extensions: 4
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: 266
Length of database: 254
Length adjustment: 24
Effective length of query: 242
Effective length of database: 230
Effective search space:    55660
Effective search space used:    55660
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 (21.8 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