GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Gallaecimonas xiamenensis 3-C-1

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

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



>NCBI__GCF_000299915.1:WP_008486155.1
          Length = 249

 Score =  108 bits (271), Expect = 8e-29
 Identities = 87/255 (34%), Positives = 124/255 (48%), Gaps = 21/255 (8%)

Query: 21  SLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADE-------LGDSKH 73
           +L  +  L+TG + G+G +     A  GA V    I AS+ E   D+       LG    
Sbjct: 3   ALNGKRALVTGASRGLGQAMALGLAENGAEV----ICASSREGGCDDTVAKILALGG--- 55

Query: 74  KPLFLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNI 133
           K   L+ DL D  A+Q A+A+   A GP+ VLVNN     R    +   ++FDA I VN+
Sbjct: 56  KARALAADLGDSQAVQ-ALAEQALAAGPVDVLVNNGGCIYREAALDFPLDAFDAVIKVNL 114

Query: 134 RHQFFAAQAVMEDMKAANSGSIINLGSISWMLKNGG--YPVYVMSKSAVQGLTRGLARDL 191
              F  +Q +   M    SG I+N+ S+  +  +GG   P Y  SK A+ GLT+ LA + 
Sbjct: 115 NAAFQLSQLLGRAMVTKGSGKIVNIASM--LSYSGGIRVPAYTASKHAIAGLTKALANEW 172

Query: 192 GHFNIRVNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAEL-EPADLARMALFLAADD 250
           G   I+VN + PG+  T+  + L  DDA R S  E +        P DL    +FLA+  
Sbjct: 173 GQHGIQVNAIAPGYFRTDNTQAL-QDDAERSSEIEKRIPAGRWGNPDDLKGAVVFLASKA 231

Query: 251 SRMITAQDIVVDGGW 265
           S  +    + VDGGW
Sbjct: 232 SDYVNGHILAVDGGW 246


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: 171
Number of extensions: 8
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: 266
Length of database: 249
Length adjustment: 24
Effective length of query: 242
Effective length of database: 225
Effective search space:    54450
Effective search space used:    54450
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 24 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