GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Hydrogenovibrio kuenenii DSM 12350

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_000526715.1:WP_024852149.1
          Length = 263

 Score =  164 bits (416), Expect = 2e-45
 Identities = 99/231 (42%), Positives = 141/231 (61%), Gaps = 6/231 (2%)

Query: 22  IRNLTKSYDGQ--HAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79
           I  L+ SY  Q    + +++L I KG++ A++G SGCGKSTLL+M+AG   PS G + ++
Sbjct: 10  IAELSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVRIN 69

Query: 80  GVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHM 139
           G  +  V P  +  NMMFQ  +L+P M+V +N A GL      K +   RV E+L +V +
Sbjct: 70  GKTV--VKPSAK-WNMMFQKPSLYPWMSVRENAALGLVFAGTYKQK-QDRVEELLDMVGL 125

Query: 140 QEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERV 199
            E   +   +LSGGQ+QRVALARSLA  P++LLLDEP  ALD   R  +Q EV  I    
Sbjct: 126 SEHKDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICHEQ 185

Query: 200 GVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFI 250
           G+T +MVTHD EEA+ MA ++ IM+      +G+ +    +P  R +A+FI
Sbjct: 186 GITMIMVTHDIEEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236


Lambda     K      H
   0.321    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: 220
Number of extensions: 11
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: 377
Length of database: 263
Length adjustment: 27
Effective length of query: 350
Effective length of database: 236
Effective search space:    82600
Effective search space used:    82600
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.

Links

Downloads

Related tools

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