GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Lactobacillus pobuzihii E100301

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_017867545.1 LACPOB_RS0104010 SDR family oxidoreductase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119
         (272 letters)



>NCBI__GCF_000349725.1:WP_017867545.1
          Length = 254

 Score =  153 bits (386), Expect = 4e-42
 Identities = 89/252 (35%), Positives = 139/252 (55%), Gaps = 5/252 (1%)

Query: 16  GERLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAI 75
           G++L NKV ++TG+  G+G  +   FA++ A ++ +DI  E+  +VA   +  G   +AI
Sbjct: 2   GKKLANKVAIITGSGSGMGAEMATLFAAEGASIVGADINIERANEVAEKIKTNGGQAIAI 61

Query: 76  KADVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAW 134
           K DVS   D+  + + A D  G++D++VN AG+     P+ EMT E W R FA+++D   
Sbjct: 62  KTDVSCLADIKKVFKTAKDKFGQVDIVVNNAGIMDDFSPVGEMTNETWERAFAVNVDSVM 121

Query: 135 YGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194
           Y  +  + + + +  G I+N AS   T+       Y  AKH ++GLT+     Y   G+R
Sbjct: 122 YATREAVKEFLPKKKGVILNTASVGGTNGGRAGAAYTAAKHAVVGLTKNTAFMYEKNGIR 181

Query: 195 VNAIAPGYIETQLNVDYWNGFADPHAERQRA-FDLHPPRRIGQPIEVAMTAVFLASDEAP 253
            NAIAPG I T +     N  ++   ERQ+A   L P   +G    +A TA+FL SD+A 
Sbjct: 182 TNAIAPGGISTNIGESIKNA-SEFGMERQKAGMGLMP--GMGSSSSIAKTALFLVSDDAD 238

Query: 254 FINASCITIDGG 265
           F+N   + +DGG
Sbjct: 239 FVNGVIVPVDGG 250


Lambda     K      H
   0.322    0.138    0.426 

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: 155
Number of extensions: 7
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: 272
Length of database: 254
Length adjustment: 25
Effective length of query: 247
Effective length of database: 229
Effective search space:    56563
Effective search space used:    56563
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 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