GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Thiothrix lacustris DSM 21227

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_211248857.1 Q394_RS0118475 glucose 1-dehydrogenase

Query= metacyc::MONOMER-16230
         (256 letters)



>NCBI__GCF_000621325.1:WP_211248857.1
          Length = 255

 Score =  147 bits (372), Expect = 2e-40
 Identities = 95/249 (38%), Positives = 136/249 (54%), Gaps = 7/249 (2%)

Query: 3   LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62
           L  K V++TGAS GIG AAA    R+G ++V+G   ++EG A    +A  I A GG A+ 
Sbjct: 9   LAGKVVVITGASSGIGEAAAHAFGREGCKLVLGARRAEEGEA----VAAAIRATGGEAVF 64

Query: 63  VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHS-FLDMPRELYLKTVGTNLNGA 121
           V  D        +LV  A++ FG +DVL NNAG     S F +     Y  T+ TN+   
Sbjct: 65  VCTDVLQEADIARLVQTALDTFGGLDVLFNNAGTEGVSSAFTEQSTAEYDFTMNTNVRSV 124

Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181
            + +Q A R M  Q  GGAII  +SI A VG A    Y+ +KA ++ + +  A+     G
Sbjct: 125 LWGMQHAIRAM--QSAGGAIINNASIVAHVGFANTALYSASKAAVVGMTRVAAVEYFKQG 182

Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241
           IR NAV PG   T +++  L   +++    +  P GR G+P+++A  +VFLAS  A Y++
Sbjct: 183 IRINAVCPGITYTPMSQRLLGGEDEQNAFMATTPAGRTGQPEEIAAAVVFLASGNASYIS 242

Query: 242 GASLLVDGG 250
           G  L VDGG
Sbjct: 243 GQCLNVDGG 251


Lambda     K      H
   0.319    0.136    0.383 

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: 6
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: 256
Length of database: 255
Length adjustment: 24
Effective length of query: 232
Effective length of database: 231
Effective search space:    53592
Effective search space used:    53592
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 Apr 09 2024. 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