GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pandoraea thiooxydans ATSB16

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_047214486.1 PATSB16_RS12750 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_001931675.1:WP_047214486.1
          Length = 274

 Score =  199 bits (505), Expect = 7e-56
 Identities = 117/262 (44%), Positives = 161/262 (61%), Gaps = 10/262 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +L +  +S  FGGL  + D + E  +G I  LIGPNGAGKTTVFN ITG   P+ G ITF
Sbjct: 1   MLTLSSVSKSFGGLHVLQDVNIEVPQGTIFGLIGPNGAGKTTVFNLITGLLAPSGGDITF 60

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           +  S    LL   P  RIT+   +ARTFQNIR+F  +++L+N++V  H  L       +L
Sbjct: 61  DGAS----LLGHKP-HRITQRG-IARTFQNIRIFKEMSLLDNVVVGMHRHLDYGPAGLLL 114

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
            L G   Y+R    A E A   L    L  +A + A +L YG QR+LE+ARA+ T P+LL
Sbjct: 115 SLPG---YRRHEKRARERAHELLSWVRLDHKAHETADNLSYGDQRKLELARALATEPKLL 171

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEP AG+N  E   L   +++IRA  G +I +IEHDM  VM + + + VL +G+ I++
Sbjct: 172 LLDEPVAGMNTGEKVDLMGEIENIRAR-GYTIFMIEHDMRFVMGLCERIAVLNFGRIIAE 230

Query: 254 GTPDHVKNDPRVIAAYLGVEDE 275
           G PD +KN+P+VI AYLG +D+
Sbjct: 231 GKPDEIKNNPQVIEAYLGSDDD 252


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: 257
Number of extensions: 15
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: 274
Length adjustment: 26
Effective length of query: 266
Effective length of database: 248
Effective search space:    65968
Effective search space used:    65968
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.

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