GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Geotalea uraniireducens Rf4

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_011940416.1 GURA_RS18385 3-oxoacyl-ACP reductase FabG

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



>NCBI__GCF_000016745.1:WP_011940416.1
          Length = 246

 Score =  107 bits (267), Expect = 2e-28
 Identities = 89/246 (36%), Positives = 114/246 (46%), Gaps = 10/246 (4%)

Query: 17  KGKRVLVTGGGSGIGAGIVEGFARQGADVT--FFDIAGAESQLLVERLSADGHKACFERV 74
           K K V+VTGG  GIG  I   FAR GA VT  +     A + L+ E     G  +  +  
Sbjct: 4   KDKIVVVTGGTRGIGRAISLHFARLGAQVTAAYLTNDAAAAALMEEAFGLAGTISAVK-- 61

Query: 75  DLTDVASLQAVIARLIKGAG---GFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIF 131
              DVA+ +  +A +   AG     DILVNNA       +  +++  WD  L  NL  +F
Sbjct: 62  --ADVATAEGAMALMEAAAGDGGAIDILVNNAGIIRDGYLPMMSDEDWDAVLRGNLYPLF 119

Query: 132 FCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIR 191
            C +  V  M     G IVNL SIS   G +    Y   K A    TRSLAR++G  GIR
Sbjct: 120 HCCKWGVRKMIGNRRGIIVNLSSISALTGTAGQTNYAASKGAAMSFTRSLAREVGPMGIR 179

Query: 192 ATCVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLVTGHS 251
              V PG + T        PE   +IV +  L      E+VA  V FLAS+ A  +TG  
Sbjct: 180 VNAVAPGLIET-EMTAAMKPEMVDKIVKSASLGRIGRVEEVAEAVAFLASERASYITGQC 238

Query: 252 YFVDAG 257
             VD G
Sbjct: 239 LVVDGG 244


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: 125
Number of extensions: 4
Number of successful extensions: 2
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: 246
Length adjustment: 24
Effective length of query: 235
Effective length of database: 222
Effective search space:    52170
Effective search space used:    52170
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: 46 (22.3 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