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_058929664.1 AU252_RS04340 ABC transporter ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>NCBI__GCF_001484605.1:WP_058929664.1
          Length = 257

 Score =  230 bits (586), Expect = 2e-65
 Identities = 114/229 (49%), Positives = 160/229 (69%)

Query: 7   VKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKG 66
           V ++ AGY+  V IL G N     GEL+ +IGPNGAGKSTL K +FGL+    G ++ +G
Sbjct: 22  VTNLVAGYLPGVNILNGCNIEARKGELIGIIGPNGAGKSTLLKAMFGLVKVHSGTVVVRG 81

Query: 67  ENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKL 126
           ++ITGL ++++V  G+ +VPQ  NVF +LT+ EN+ MG F          D + ++FP+L
Sbjct: 82  QDITGLKANKLVTMGVGFVPQNNNVFATLTIEENMQMGMFQRPKDFAERFDFVTSLFPEL 141

Query: 127 AQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATG 186
            +RR QRAG+LSGGERQM+AMGRALM++P +LLLDEPSA LSP+   + F ++  IN  G
Sbjct: 142 GKRRAQRAGSLSGGERQMVAMGRALMMEPAVLLLDEPSAGLSPVKQDETFLRVHEINRAG 201

Query: 187 KAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
            ++I+VEQNA++ L + DR YVL+ GRD   G+G+ L+ DP V +LYLG
Sbjct: 202 VSVIMVEQNARRCLQICDRAYVLDQGRDAYTGTGRELMKDPKVIQLYLG 250


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: 171
Number of extensions: 2
Number of successful extensions: 1
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: 257
Length adjustment: 24
Effective length of query: 216
Effective length of database: 233
Effective search space:    50328
Effective search space used:    50328
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