GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Caulobacter crescentus NA1000

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate CCNA_00092 CCNA_00092 short chain dehydrogenase

Query= reanno::Korea:Ga0059261_1894
         (259 letters)



>FitnessBrowser__Caulo:CCNA_00092
          Length = 296

 Score =  115 bits (288), Expect = 1e-30
 Identities = 84/256 (32%), Positives = 126/256 (49%), Gaps = 20/256 (7%)

Query: 16  LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75
           L GK  ++TGG SGIG G VE F  +GA V   D+   + ++L +R      +  F R D
Sbjct: 5   LNGKVAVITGGCSGIGLGTVELFVAEGACVVAADLQDEKGRMLEQRFP---DQVRFARCD 61

Query: 76  LTDVASLQAVIARLIKGAGGFDILVNNAANDDRHA-IDEITEAYWDERLSVNLKHIFFCA 134
           +T    L   +A      GG DIL NNA +    A + E+T   WD+  ++ ++      
Sbjct: 62  VTADDDLAKTMALAESSFGGLDILFNNAGHGGTPASVPELTAEAWDKTFALLVRGPAMGM 121

Query: 135 QAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATC 194
              +P M+ RGGG+I+N  SI+        + Y + KAA+  ++R  A +L    IR   
Sbjct: 122 THALPLMQKRGGGSIINTASIAGLQAGFGPLAYSSAKAAVIHMSRCAAAELSPQKIRVNA 181

Query: 195 VIPGNVRT---------PRQLKWYSPEGEAEIVA----AQCLDGRLAPEDVAAMVLFLAS 241
           + PG + T         PR++   + +  A+I +     Q +     PED+AA  L+LAS
Sbjct: 182 ICPGLIATSIFGASMGLPREV---ADQMAAQIASIGPKIQPIPKSGLPEDIAAAALYLAS 238

Query: 242 DDARLVTGHSYFVDAG 257
           DD+R VTG    VD G
Sbjct: 239 DDSRFVTGTHIVVDGG 254


Lambda     K      H
   0.321    0.137    0.409 

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: 179
Number of extensions: 12
Number of successful extensions: 5
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: 259
Length of database: 296
Length adjustment: 25
Effective length of query: 234
Effective length of database: 271
Effective search space:    63414
Effective search space used:    63414
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 (21.9 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