GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Caulobacter crescentus NA1000

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CCNA_01885 CCNA_01885 short chain dehydrogenase

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



>FitnessBrowser__Caulo:CCNA_01885
          Length = 258

 Score =  129 bits (324), Expect = 6e-35
 Identities = 86/246 (34%), Positives = 126/246 (51%), Gaps = 3/246 (1%)

Query: 22  LVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCD 81
           L  R   +TG + G+G +     AA+GA VA  D+ A   +A ADE+  +  K + L CD
Sbjct: 11  LEGRVAAVTGASRGLGRATAALLAAEGAMVALLDLKAHWAQAAADEIIAAGGKAVGLGCD 70

Query: 82  LTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQ 141
           ++D +AL   +  V  A G   VLVNNA  +    +  +  ES D  ++V      +  Q
Sbjct: 71  VSDREALTATLGAVNDAHGRFDVLVNNAMWNVYEPLAAIRPESLDRMVSVGFSGVIWGMQ 130

Query: 142 AVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTL 201
           A    M A+  GSI+N+ S+S  L       Y   K+ V G+TR  A +LG  NIRVN +
Sbjct: 131 AAAPLMAASGGGSIVNIASVSAQLGIPNGIAYCGVKAGVAGMTRAAAAELGAMNIRVNAV 190

Query: 202 VPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAEL-EPADLARMALFLAADDSRMITAQDIV 260
            P  V TE  +R+  ++  R +++ GQ     L    D+A+   +LA DDS  +T Q + 
Sbjct: 191 APSTVDTEGVRRVVSEE--RIAMRIGQTPLGRLGTTEDIAKAVRYLACDDSDFVTGQMLT 248

Query: 261 VDGGWA 266
           VDGG A
Sbjct: 249 VDGGLA 254


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: 138
Number of extensions: 6
Number of successful extensions: 2
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: 258
Length adjustment: 25
Effective length of query: 241
Effective length of database: 233
Effective search space:    56153
Effective search space used:    56153
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