GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Jannaschia aquimarina GSW-M26

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_043920347.1 jaqu_RS17725 SDR family oxidoreductase

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



>NCBI__GCF_000877395.1:WP_043920347.1
          Length = 251

 Score =  105 bits (261), Expect = 1e-27
 Identities = 79/250 (31%), Positives = 118/250 (47%), Gaps = 8/250 (3%)

Query: 18  RYPS--LVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKP 75
           R PS  L  R   + GG+ G+G       A  GA V      A A EA A  + ++ H  
Sbjct: 5   RTPSFRLEGRRAFVPGGSRGLGLGCAVALAEAGAEVVIAARSADAVEAAAAAMREAGHAA 64

Query: 76  LFLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRH 135
             ++ D+TD+ A+  A  D +A   P  +L N A   +     E   + FDA  A+N+R 
Sbjct: 65  TGVALDVTDLAAVD-AFLDGEA---PFDILCNAAGVARHGPALETEPDDFDAVAALNLRA 120

Query: 136 QFFAAQAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFN 195
            +F AQ V   M     GSII + S    +      VY  +K  V+G+T+ +A + G  +
Sbjct: 121 AYFLAQRVARGMD--RGGSIIQISSQMGHVGGVDRAVYCATKHGVEGMTKAMAIEWGPRD 178

Query: 196 IRVNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMIT 255
           IRVNT+ P ++ T      + D   R  I E   +    E  D+    +FLA++ S M+T
Sbjct: 179 IRVNTICPTFIRTPLTAATFADPERRAWIDEKIKLPRVGEVEDIMGAVVFLASEASAMVT 238

Query: 256 AQDIVVDGGW 265
              ++VDGGW
Sbjct: 239 GTSLLVDGGW 248


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: 170
Number of extensions: 8
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: 251
Length adjustment: 24
Effective length of query: 242
Effective length of database: 227
Effective search space:    54934
Effective search space used:    54934
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