GapMind for catabolism of small carbon sources

 

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

Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_043920347.1 jaqu_RS17725 SDR family oxidoreductase

Query= SwissProt::Q8P3K4
         (300 letters)



>NCBI__GCF_000877395.1:WP_043920347.1
          Length = 251

 Score =  145 bits (365), Expect = 1e-39
 Identities = 91/257 (35%), Positives = 139/257 (54%), Gaps = 12/257 (4%)

Query: 47  VSIPTTPNTRLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAE---- 102
           + +P TP+ RL+G+R  +     G+G   A+A A AGA V+     A A++A AA     
Sbjct: 1   MDLPRTPSFRLEGRRAFVPGGSRGLGLGCAVALAEAGAEVVIAARSADAVEAAAAAMREA 60

Query: 103 SDAITTQLLDVTDAAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDA 162
             A T   LDVTD AA+ A +    PFD+L N AG    G  L+ +   +    ++N+ A
Sbjct: 61  GHAATGVALDVTDLAAVDAFLDGEAPFDILCNAAGVARHGPALETEPDDFDAVAALNLRA 120

Query: 163 MYYTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQ 222
            Y+  + V  GM +RG GSII +SS    + GV +R VY  TK  V G++KA+A ++  +
Sbjct: 121 AYFLAQRVARGM-DRG-GSIIQISSQMGHVGGV-DRAVYCATKHGVEGMTKAMAIEWGPR 177

Query: 223 GVRCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASD 282
            +R N ICP  I+TP            E+  W    ++  + R+G+  +I   VV+LAS+
Sbjct: 178 DIRVNTICPTFIRTP---LTAATFADPERRAW--IDEKIKLPRVGEVEDIMGAVVFLASE 232

Query: 283 ESSFTTGQTHIIDGGWS 299
            S+  TG + ++DGGW+
Sbjct: 233 ASAMVTGTSLLVDGGWT 249


Lambda     K      H
   0.320    0.133    0.395 

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: 166
Number of extensions: 11
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: 300
Length of database: 251
Length adjustment: 25
Effective length of query: 275
Effective length of database: 226
Effective search space:    62150
Effective search space used:    62150
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