GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Sulfurivirga caldicuralii DSM 17737

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  118 bits (296), Expect = 1e-31
 Identities = 73/208 (35%), Positives = 116/208 (55%), Gaps = 10/208 (4%)

Query: 19  LLEIRNLTKSY-DGQH---AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAG 74
           +LE RNL K+Y DG      +  VSL +++ E  A++G+SG GKSTLL +L G ++P+ G
Sbjct: 5   VLEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDG 64

Query: 75  QIMLDGVDLSQVPPYLRP------INMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIAS 128
           +++L G   S++    R       +  ++Q + L P +T E+N+   L   +  +A    
Sbjct: 65  EVLLLGQPFSKLGEAARGRLRNRHMGFVYQFHHLLPELTAEENVMMPLLIRRESEATARD 124

Query: 129 RVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRM 188
           +   +L  V +      KP +LSGG+RQRVALAR+L   P  +L DEP G LD +  +++
Sbjct: 125 KALALLDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQV 184

Query: 189 QLEVVDILERVGVTCVMVTHDQEEAMTM 216
              + D+ +R G   ++VTHD   A  M
Sbjct: 185 LSLMDDLNQRFGTALLVVTHDVNIAARM 212


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: 209
Number of extensions: 9
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: 377
Length of database: 227
Length adjustment: 26
Effective length of query: 351
Effective length of database: 201
Effective search space:    70551
Effective search space used:    70551
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