GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Lactobacillus oryzae SG293

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_034528539.1 LOSG293_RS06955 glucose 1-dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_000740055.1:WP_034528539.1
          Length = 249

 Score =  103 bits (258), Expect = 3e-27
 Identities = 83/257 (32%), Positives = 126/257 (49%), Gaps = 19/257 (7%)

Query: 8   VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPN-SGGEAQAKKLG-NNCVFAPADV 65
           +KG VA+ITGG +G+GL  AE  V +GA  V+    N  GG+   ++ G  N +F   DV
Sbjct: 5   LKGKVAIITGGVAGIGLGIAECYVREGAKVVITANHNVEGGKQAVERFGAENALFVQQDV 64

Query: 66  TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125
             E D +  +     KFG++DV VN AGI    +       +   L+ + + + VNL G 
Sbjct: 65  AVEADWKKVVDATIEKFGKLDVLVNNAGIGGGGQPI-----EEMPLDAWNKTMSVNLTGN 119

Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185
           F  + + AG     + + G   G IIN +SVA   G      YSA+KGG   +T  +A  
Sbjct: 120 F--LGVKAGINAMKQTNNG--HGSIINVSSVAGLVGLPMAPDYSATKGGTRLLTHAVALS 175

Query: 186 LA--PIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAI--I 241
           LA   I IRV ++ PG   T +   +PE   + +   +P   R G+P +   +   +   
Sbjct: 176 LAQRKIDIRVNSVHPGWIDTNI---IPEAYRDAILQTIPV-GRFGEPKDIGEICVYLGSE 231

Query: 242 ENPFLNGEVIRLDGAIR 258
           E+ + NG    +DG +R
Sbjct: 232 ESKYANGAEFTVDGGVR 248


Lambda     K      H
   0.318    0.135    0.385 

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: 175
Number of extensions: 12
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: 261
Length of database: 249
Length adjustment: 24
Effective length of query: 237
Effective length of database: 225
Effective search space:    53325
Effective search space used:    53325
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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