GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudarthrobacter sulfonivorans Ar51

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_058929181.1 AU252_RS01290 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_001484605.1:WP_058929181.1
          Length = 239

 Score =  157 bits (397), Expect = 2e-43
 Identities = 90/230 (39%), Positives = 133/230 (57%), Gaps = 2/230 (0%)

Query: 3   DLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEI 62
           +LL V+D+   Y   +  + G++  +  GE V + G NGAGKST  K I G +  S G +
Sbjct: 9   ELLAVRDLVVNY-GPIRAVSGVSIGVHRGETVVLCGANGAGKSTTIKAIMGSVPASSGSV 67

Query: 63  IFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAF-LHQGPTQTLKDRIYT 121
              G+ IT + +    RRG+   P+   VF ++TV EN+ +GA  L      T  + ++ 
Sbjct: 68  HLDGQPITTVSAALRARRGIRLSPEGRQVFATMTVEENIRIGAHQLKATDRNTRVEELFD 127

Query: 122 MFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKA 181
            FP LA+RR  RAG LSGG++Q++AMGRA+   P LLLLDEP   L+PI +  V   I+ 
Sbjct: 128 TFPLLAERRRSRAGDLSGGQQQIVAMGRAMASRPRLLLLDEPFLGLAPIWIASVSDAIRT 187

Query: 182 INATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGE 231
           + A G A+++ EQ A+ AL +ADRGYVL++G     G+   + +  L  E
Sbjct: 188 VQAAGTALLISEQMARPALELADRGYVLKHGSIARRGTADEVRSMALAEE 237


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: 125
Number of extensions: 3
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: 239
Length adjustment: 23
Effective length of query: 217
Effective length of database: 216
Effective search space:    46872
Effective search space used:    46872
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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