GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Klebsiella michiganensis M5al

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate BWI76_RS23430 BWI76_RS23430 2-deoxy-D-gluconate 3-dehydrogenase

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



>FitnessBrowser__Koxy:BWI76_RS23430
          Length = 253

 Score =  100 bits (248), Expect = 4e-26
 Identities = 74/246 (30%), Positives = 114/246 (46%), Gaps = 3/246 (1%)

Query: 21  SLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSC 80
           SL  +  +++G  TG+G       A  G  +   +I     E + + +     + L L+ 
Sbjct: 7   SLQGKVAVVSGCDTGLGQGMAVGLAEAGCDIVGINI-VEPTETI-ERVTALGRRFLSLTA 64

Query: 81  DLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAA 140
           DL  ID + + +    A  G I +LVNNA   +R    E + +++D  + +NI+  FF +
Sbjct: 65  DLRQIDGIPQLLERAVAEFGHIDILVNNAGLIRREDAIEFSEKNWDDVMNLNIKSVFFMS 124

Query: 141 QAVMEDMKA-ANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVN 199
           QA  +   A    G IIN+ S+         P Y  SKSAV G+TR LA +     I VN
Sbjct: 125 QAAAKHFIAQGTGGKIINIASMLSFQGGIRVPSYTASKSAVMGVTRLLANEWAKHGINVN 184

Query: 200 TLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDI 259
            L PG++ T   ++L  D+     I +         P+DL    +FLA+  S  I    +
Sbjct: 185 ALAPGYMATNNTQQLRADEQRSSEILDRIPAGRWGLPSDLMGPVVFLASSASDYINGYTV 244

Query: 260 VVDGGW 265
            VDGGW
Sbjct: 245 AVDGGW 250


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: 159
Number of extensions: 13
Number of successful extensions: 3
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: 253
Length adjustment: 24
Effective length of query: 242
Effective length of database: 229
Effective search space:    55418
Effective search space used:    55418
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