GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Nocardioides daejeonensis MJ31

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110208105.1 DNK54_RS16590 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_003194585.1:WP_110208105.1
          Length = 263

 Score =  164 bits (414), Expect = 3e-45
 Identities = 101/273 (36%), Positives = 154/273 (56%), Gaps = 23/273 (8%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL+V  + ++FGG+ A+N   F A    IT LIGPNGAGKTT FN ITG  +PT G + F
Sbjct: 3   LLEVNDVVVRFGGVTAVNQARFTADERRITGLIGPNGAGKTTCFNVITGLQRPTSGSVRF 62

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
             +   +  + R           +ARTFQ +  F  LTV +N+ VA     +  +G    
Sbjct: 63  GGRDVTRTAVHR------RARRGMARTFQRLEAFGSLTVRDNVRVA-----LDIAG---- 107

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
              G G   R ++  ++ A   L++  + + A + A  +P G  R LE+AR +   P+LL
Sbjct: 108 ---GFGGLMRSSSARVDEA---LDRVGISEYAAERADSIPTGTARLLELARCLVGDPKLL 161

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEP++GL+  E+     LL ++ +E G +IL++EHDM +VM + D + VL++G+ I  
Sbjct: 162 LLDEPSSGLDESETDAFGELLIALASE-GKAILMVEHDMDLVMTVCDDIHVLDFGEIICS 220

Query: 254 GTPDHVKNDPRVIAAYLGVED-EEVEEVIAAVE 285
           G+P  V+ D RV AAYLG  D +E +  +A ++
Sbjct: 221 GSPAEVRADARVQAAYLGASDTDETQHDLAPLD 253


Lambda     K      H
   0.318    0.136    0.386 

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: 201
Number of extensions: 8
Number of successful extensions: 4
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: 292
Length of database: 263
Length adjustment: 25
Effective length of query: 267
Effective length of database: 238
Effective search space:    63546
Effective search space used:    63546
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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