GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Nocardiopsis baichengensis YIM 90130

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_017557172.1 C892_RS0110655 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000341205.1:WP_017557172.1
          Length = 281

 Score =  168 bits (425), Expect = 1e-46
 Identities = 98/250 (39%), Positives = 148/250 (59%), Gaps = 5/250 (2%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           +L  + L+ +FGGL A+D     V   S+ GLIGPNGAGKTT+FN +S  +RP  G +  
Sbjct: 7   VLAVEQLTVAFGGLTALDRVTFDVPHRSVVGLIGPNGAGKTTVFNAVSGVVRPRSGTLTR 66

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLL-ADQHQTGEKFLP-RLINFRR 135
           +G  + +  PH +   G  R  Q   + S +TVLEN+++ AD   TG   LP  L    R
Sbjct: 67  HGRPLRRHRPHHLPRLGISRMLQGLGLFSGMTVLENVMVGADPLATGR--LPGMLTGLGR 124

Query: 136 VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAA 195
             ++ER  RE+A + L   G+   A    G L  G +K + +ARA +  P+L+LLDEPA+
Sbjct: 125 APRDERRVRERAESALREFGVAHAAHALPGTLPYGVQKRVALARACVCGPELLLLDEPAS 184

Query: 196 GVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255
           G++   + ++ E +      G + L++EH+MD++M +C  V VL  GR +ADGTP+++++
Sbjct: 185 GLSADEMSELAERVRAMRAYG-SVLLVEHHMDLVMRVCDRVVVLDFGRVIADGTPDEVRA 243

Query: 256 DPRVLEAYLG 265
           DP V  AYLG
Sbjct: 244 DPAVERAYLG 253


Lambda     K      H
   0.319    0.136    0.389 

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: 222
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: 267
Length of database: 281
Length adjustment: 25
Effective length of query: 242
Effective length of database: 256
Effective search space:    61952
Effective search space used:    61952
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 (21.7 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