GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Marivita geojedonensis DPG-138

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_085639218.1 MGEO_RS14460 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_002115805.1:WP_085639218.1
          Length = 276

 Score =  171 bits (433), Expect = 1e-47
 Identities = 88/213 (41%), Positives = 139/213 (65%), Gaps = 2/213 (0%)

Query: 32  VHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPTHEIARLRIAQS 91
           + V +GEI  ++G NGAGKST M  + G    R G V+ +G+DIT +      R  +   
Sbjct: 66  IAVERGEIAVIVGPNGAGKSTAMKAVFGMLDLRQGRVLLDGQDITALTPQARVRNGMGFV 125

Query: 92  PEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFPRLKERHAQRGGTLSGGEQQM 151
           P+   IF  MTV ENL+MGA +     F   +E+++ LFP L+E+  Q  G LSGG++Q 
Sbjct: 126 PQTSNIFTSMTVEENLEMGAFIRE-DDFRSTMEQVYELFPILREKRNQPAGELSGGQRQQ 184

Query: 152 LSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLS 211
           +++GRALM +PK+L+LDEP+ G++P+++  +F+ I ++    G+++ +VEQNA  AL ++
Sbjct: 185 VAVGRALMTQPKVLMLDEPTAGVSPIVMDELFDRIIEVART-GISILMVEQNARQALEIA 243

Query: 212 HRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244
            + YV+V G    SG+GK+LLA+P+VR ++L G
Sbjct: 244 DKGYVLVQGSNGYSGTGKDLLADPDVRRSFLGG 276


Lambda     K      H
   0.320    0.137    0.387 

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: 182
Number of extensions: 8
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: 247
Length of database: 276
Length adjustment: 25
Effective length of query: 222
Effective length of database: 251
Effective search space:    55722
Effective search space used:    55722
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. 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