GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Thiothrix lacustris DSM 21227

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  265 bits (677), Expect = 1e-75
 Identities = 149/351 (42%), Positives = 213/351 (60%), Gaps = 32/351 (9%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M  + ++++   +G +  + +++L+I  GEF+V +G SGCGKSTLL  IAGL  ++ GQ+
Sbjct: 1   MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            +  R++T   P  R + MVFQSYALYP MTVE+N+SF L++AK+ PA I+++VK A++ 
Sbjct: 61  ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           L +   L+R P  LSGGQRQRVAIGR++VR   VFLFDEPLSNLDA LR   RVEI  LH
Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           + L  T +YVTHDQ+EA+TLADR+ V++ G+I+Q+  P+ +Y+ P N FVA FIG P MN
Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240

Query: 241 FFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQ-PGQKVVLGLRPEHVKVDEARDGEPT 299
                                      PA    Q P Q   +G+RPEH+++    DG   
Sbjct: 241 -------------------------VAPASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLA 275

Query: 300 HQAVVDIEEPMGADNLLWL----TFAGQSMSVRIAGQRRYPPGSTVRLSFD 346
            + V  + E +G + L+ +        + + VR+ G+     G  V L +D
Sbjct: 276 GKVV--LVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWD 324


Lambda     K      H
   0.320    0.137    0.392 

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: 356
Number of extensions: 23
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 361
Length of database: 348
Length adjustment: 29
Effective length of query: 332
Effective length of database: 319
Effective search space:   105908
Effective search space used:   105908
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 (21.8 bits)
S2: 49 (23.5 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