GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Skermanella stibiiresistens SB22

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_157619653.1 N825_RS30520 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000576635.1:WP_157619653.1
          Length = 258

 Score =  218 bits (556), Expect = 7e-62
 Identities = 118/258 (45%), Positives = 166/258 (64%), Gaps = 16/258 (6%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           MI  K ++K +G+  VL N++L +   EK+ +IGPSGSGKST +R +  LE   +G + +
Sbjct: 1   MIRFKGISKAFGSLTVLDNLDLDIAPAEKVALIGPSGSGKSTLLRVLMTLERPDTGSIEI 60

Query: 61  NNLVLNH-------KN---------KIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKL 104
           +   L H       KN          +   RK   MVFQ FNL+PHMTVL+N+T AP+ +
Sbjct: 61  DGAPLWHMPGKGGAKNGGLVPADAGHLREMRKNVGMVFQQFNLFPHMTVLRNVTEAPVHV 120

Query: 105 QKKSKKEAEETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTS 164
               K EAE  A   L++VGL DK   YPA LSGGQQQRVAIAR+L  +   +LFDE TS
Sbjct: 121 LGIGKDEAEARARDLLELVGLRDKLGHYPAQLSGGQQQRVAIARALAMRPRVMLFDEVTS 180

Query: 165 ALDPETIQEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFF 224
           ALDPET+ EVL+V+++++ + N TM++VTH+MGFA+E ADR+ F   G I E+  P + F
Sbjct: 181 ALDPETVGEVLNVIRKLAEEHNLTMLMVTHQMGFAREFADRVCFFYQGRICEQGPPDQLF 240

Query: 225 SNPKTERARLFLGKILKN 242
           ++P+ ER + FL  +L++
Sbjct: 241 NHPREERTQAFLRAVLES 258


Lambda     K      H
   0.317    0.133    0.372 

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: 3
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: 242
Length of database: 258
Length adjustment: 24
Effective length of query: 218
Effective length of database: 234
Effective search space:    51012
Effective search space used:    51012
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: 46 (22.3 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