GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Hydrogenovibrio kuenenii DSM 12350

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_000526715.1:WP_024852149.1
          Length = 263

 Score =  147 bits (371), Expect = 3e-40
 Identities = 87/216 (40%), Positives = 128/216 (59%), Gaps = 4/216 (1%)

Query: 19  LFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADRDLA 78
           L +INL+I  G+    +G SGCGKSTLL+ +AGL   S G + I G+  T V+P+ +   
Sbjct: 25  LTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGK--TVVKPSAK-WN 81

Query: 79  MVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQ 138
           M+FQ  +LYP M+VREN   G+   G     +++R+ E   ++ L ++ D+   +LSGGQ
Sbjct: 82  MMFQKPSLYPWMSVRENAALGLVFAGTYKQ-KQDRVEELLDMVGLSEHKDKNVQELSGGQ 140

Query: 139 RQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAM 198
           +QRVA+ R++   P + L DEP S LDA  R  ++ E+  +  + G TMI VTHD  EA+
Sbjct: 141 QQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGITMIMVTHDIEEAI 200

Query: 199 TMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFI 234
            MADK+V+++    E VG        P  R  A+FI
Sbjct: 201 AMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236


Lambda     K      H
   0.320    0.139    0.396 

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: 196
Number of extensions: 5
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: 338
Length of database: 263
Length adjustment: 26
Effective length of query: 312
Effective length of database: 237
Effective search space:    73944
Effective search space used:    73944
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: 48 (23.1 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