GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Maridesulfovibrio zosterae DSM 11974

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>NCBI__GCF_000425265.1:WP_027723082.1
          Length = 240

 Score =  109 bits (273), Expect = 5e-29
 Identities = 79/249 (31%), Positives = 125/249 (50%), Gaps = 17/249 (6%)

Query: 21  NKVVLLTGAAQGIGEAIVATFASQQARLVI---SDIQGEKVEKVAAHWREQGADVVAIKA 77
           +K+ L+TGA++GIG AI    A     + +   SD  G    K A   ++ G     +K 
Sbjct: 2   SKIALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAG--AHKTAEQIKQHGQQCTLLKF 59

Query: 78  DVSRQQDLHAMARLAIELHGRID-VLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYG 136
           DV+ ++ +     L+  L  ++  ++VN AG       + M   DW++   + L G +  
Sbjct: 60  DVTDEKAVEE--NLSSLLEKKVPYIVVNNAGFTRDSIMMMMDSSDWNKVLQVHLTGFFNV 117

Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVN 196
            K V+ +M+ +  G IINIAST     + G   Y  AK GL+G T++L +E A + I VN
Sbjct: 118 TKPVVSRMLRKRTGRIINIASTSGETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVN 177

Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256
           A+ PG+I+T +  +       P  E +      P +R+G P EVA    FL SD+A +I 
Sbjct: 178 AVTPGFIDTDMLSEL------PVDEIKNTI---PLKRLGTPKEVAGVVSFLCSDKASYIT 228

Query: 257 ASCITIDGG 265
              I ++GG
Sbjct: 229 GQTIAVNGG 237


Lambda     K      H
   0.321    0.138    0.424 

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: 118
Number of extensions: 4
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: 272
Length of database: 240
Length adjustment: 24
Effective length of query: 248
Effective length of database: 216
Effective search space:    53568
Effective search space used:    53568
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 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