GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Hydrogenovibrio kuenenii DSM 12350

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>NCBI__GCF_000526715.1:WP_024852149.1
          Length = 263

 Score =  142 bits (358), Expect = 9e-39
 Identities = 86/210 (40%), Positives = 127/210 (60%), Gaps = 7/210 (3%)

Query: 18  VIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQIMIDGRDATEMPPAKRGL 77
           V+ +++L+I  G+    +G SGCGKSTLL++IAGL   SDG + I+G+   + P AK   
Sbjct: 24  VLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRINGKTVVK-PSAKWN- 81

Query: 78  AMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKILNLTNYLDRRPGQLSGG 137
            M+FQ  +LYP M+V++N A  L  A    Q+ + RV     ++ L+ + D+   +LSGG
Sbjct: 82  -MMFQKPSLYPWMSVRENAALGLVFAGTYKQK-QDRVEELLDMVGLSEHKDKNVQELSGG 139

Query: 138 QRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELHQSLETTMIYVTHDQVEA 197
           Q+QRVA+ R++  EP   L DEP S LDA  R  ++ E+ ++      TMI VTHD  EA
Sbjct: 140 QQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQGITMIMVTHDIEEA 199

Query: 198 MTMADKIVVLNAGRIEQVGS---PLTLYRN 224
           + MADK+V+++    E VG    PLT  R+
Sbjct: 200 IAMADKVVIMSHNPGEIVGDLDVPLTYPRD 229


Lambda     K      H
   0.320    0.137    0.400 

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: 180
Number of extensions: 7
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: 332
Length of database: 263
Length adjustment: 26
Effective length of query: 306
Effective length of database: 237
Effective search space:    72522
Effective search space used:    72522
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