GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Hydrogenovibrio kuenenii DSM 12350

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000526715.1:WP_024851725.1
          Length = 282

 Score =  143 bits (360), Expect = 7e-39
 Identities = 82/208 (39%), Positives = 126/208 (60%), Gaps = 10/208 (4%)

Query: 7   TDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDH 66
           T +TK+ G    ++ + L + + EF+ LVG SGCGKST LR++ GLE  T G + +  + 
Sbjct: 13  TFITKK-GAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVLVDEEI 71

Query: 67  MNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEE-EGYTSAERD-----ERVVEVAE 120
           +N      +D AMVFQDY+LYP +TV++NI+F    +  G  +   D     +R   + +
Sbjct: 72  VN---KPGKDRAMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRSYALLD 128

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            +G+  + D  P++LSGG +QRVA+ RA++  P+V LMDEP   LDA+ R  M   + +L
Sbjct: 129 LMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHDLILHL 188

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVM 208
            +    T V+VTH+  EA+ +ADR+ VM
Sbjct: 189 FEIEKSTIVFVTHDVEEAIYLADRVVVM 216


Lambda     K      H
   0.317    0.135    0.386 

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: 249
Number of extensions: 10
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: 383
Length of database: 282
Length adjustment: 28
Effective length of query: 355
Effective length of database: 254
Effective search space:    90170
Effective search space used:    90170
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 (21.6 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