GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutC in Saccharomonospora marina XMU15

Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate WP_009156708.1 SACMADRAFT_RS25300 lactate utilization protein C

Query= uniprot:A0A0C4YFN9
         (234 letters)



>NCBI__GCF_000244955.1:WP_009156708.1
          Length = 199

 Score = 79.7 bits (195), Expect = 4e-20
 Identities = 78/231 (33%), Positives = 101/231 (43%), Gaps = 43/231 (18%)

Query: 5   SARERMLGRLRAAAPATTADASQLDARIDAHYDARREAATPAELAQAMQAALGASHALAW 64
           SARE +L R+RAA  A +         +   Y   R  A P         AL A     +
Sbjct: 3   SAREEILVRIRAAGAARSVT-------VPREYRRERRVADPV--------ALFAERVADY 47

Query: 65  CASAEAWPAQLAGK-LAAAGVRRLLLDPAAEQGAALMRALPASVAPLSYARPIEAWKAE- 122
            A     P +L G+ L A GVR +              A+PA V P  +  P   W A+ 
Sbjct: 48  RAVVRRGPVELIGECLRARGVRTM--------------AVPADV-PAHWRAPGVRWLADD 92

Query: 123 ------LFDTVDAGFTVARSGIAATGTLVL-APDAQTPRTVSLVPPLHIALVYAETLHPD 175
                 + D VD   T     IA TGT+VL A  AQ  R +SLVP  H+ +V A+ +  +
Sbjct: 93  PPLELAVVDGVDGVLTGCAVAIAETGTIVLDAGQAQGRRLLSLVPDYHLCVVRADQI--E 150

Query: 176 LHCAARAERWSAGMPTNLVLVSGPSKTSDIQQTLAYGAHGPRELWVIIVTG 226
           +  A    R     P  L  VSGPS TSDI+     G HGPR L V++V G
Sbjct: 151 VTVAQALARLDPVRP--LTFVSGPSATSDIELDRVEGVHGPRTLEVLVVAG 199


Lambda     K      H
   0.317    0.127    0.375 

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: 144
Number of extensions: 8
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: 234
Length of database: 199
Length adjustment: 22
Effective length of query: 212
Effective length of database: 177
Effective search space:    37524
Effective search space used:    37524
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: 45 (21.9 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