GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Nocardiopsis baichengensis YIM 90130

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_017540510.1 C892_RS0115135 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_000341205.1:WP_017540510.1
          Length = 268

 Score =  248 bits (634), Expect = 7e-71
 Identities = 126/232 (54%), Positives = 167/232 (71%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEII 63
           LLV  +V AGY+ +V IL G   ++  GE+V VIGPNGAGKSTL KT+FGLL    GE++
Sbjct: 31  LLVADEVKAGYIPEVNILDGCTLTLREGEVVGVIGPNGAGKSTLIKTVFGLLPVRGGELV 90

Query: 64  FKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMF 123
            +G +I  L + ++V RG+ YVPQ  NVF SLTV ENL+MG FL     +     +  +F
Sbjct: 91  LRGSSIANLSAHELVERGVGYVPQTQNVFPSLTVEENLEMGVFLRPKAFRERFAVVAELF 150

Query: 124 PKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAIN 183
           P LA+RR Q+AG LSGGERQM+AMGRALM++P ++LLDEP+A LSPI   +VF +++ IN
Sbjct: 151 PLLAERRRQKAGALSGGERQMVAMGRALMMEPSVVLLDEPTAGLSPIYQDEVFERVRQIN 210

Query: 184 ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
           A G ++I+VEQNA++ L + DRGYVL+ GR+   G+G+ LL DP V ELYLG
Sbjct: 211 AAGVSVIMVEQNARRCLQICDRGYVLDQGRNAYTGTGRELLEDPNVIELYLG 262


Lambda     K      H
   0.320    0.139    0.393 

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: 199
Number of extensions: 4
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: 240
Length of database: 268
Length adjustment: 24
Effective length of query: 216
Effective length of database: 244
Effective search space:    52704
Effective search space used:    52704
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