GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pseudarthrobacter sulfonivorans Ar51

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_058929181.1 AU252_RS01290 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>NCBI__GCF_001484605.1:WP_058929181.1
          Length = 239

 Score =  167 bits (423), Expect = 2e-46
 Identities = 95/221 (42%), Positives = 133/221 (60%), Gaps = 1/221 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           +L V  +   YG I A+ GV I +  GE V L GANGAGKST +  I GS  A  G +  
Sbjct: 10  LLAVRDLVVNYGPIRAVSGVSIGVHRGETVVLCGANGAGKSTTIKAIMGSVPASSGSVHL 69

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120
           +GQ IT +      R GI  SPEGR++F  M+V EN+++G+   K       +E +   F
Sbjct: 70  DGQPITTVSAALRARRGIRLSPEGRQVFATMTVEENIRIGAHQLKATDRNTRVEELFDTF 129

Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180
           P L ER   RAG +SGG+QQ++A+GRA+ S+PRLLLLDEP LGLAP+ +  +  A++ + 
Sbjct: 130 PLLAERRRSRAGDLSGGQQQIVAMGRAMASRPRLLLLDEPFLGLAPIWIASVSDAIRTV- 188

Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAEL 221
           +     + + EQ A  AL+LA RGYV+ +G +   GT  E+
Sbjct: 189 QAAGTALLISEQMARPALELADRGYVLKHGSIARRGTADEV 229


Lambda     K      H
   0.320    0.136    0.377 

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: 148
Number of extensions: 7
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: 236
Length of database: 239
Length adjustment: 23
Effective length of query: 213
Effective length of database: 216
Effective search space:    46008
Effective search space used:    46008
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: 46 (22.3 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