GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudarthrobacter sulfonivorans Ar51

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_058929664.1 AU252_RS04340 ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWL6
         (233 letters)



>NCBI__GCF_001484605.1:WP_058929664.1
          Length = 257

 Score =  205 bits (522), Expect = 6e-58
 Identities = 103/226 (45%), Positives = 151/226 (66%), Gaps = 1/226 (0%)

Query: 7   VSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYMGEELV 66
           V+ +   +  L+  N+E R+GE++ +IG NGAGKSTLL  + G  + HSG++   G+++ 
Sbjct: 26  VAGYLPGVNILNGCNIEARKGELIGIIGPNGAGKSTLLKAMFGLVKVHSGTVVVRGQDIT 85

Query: 67  GQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLFPRLKER 126
           G  ++ ++   +  VP+   VFA LT+EEN+ MG F   K D+ E+ D V  LFP L +R
Sbjct: 86  GLKANKLVTMGVGFVPQNNNVFATLTIEENMQMGMFQRPK-DFAERFDFVTSLFPELGKR 144

Query: 127 FTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLRKDGVTV 186
             QR G++SGGE+QM+A+GRALM +P +LLLDEPS GL+P+   + F  + ++ + GV+V
Sbjct: 145 RAQRAGSLSGGERQMVAMGRALMMEPAVLLLDEPSAGLSPVKQDETFLRVHEINRAGVSV 204

Query: 187 FLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232
            +VEQNA + L+I DRAYVL+ GR    GTG  L+ DPKV + YLG
Sbjct: 205 IMVEQNARRCLQICDRAYVLDQGRDAYTGTGRELMKDPKVIQLYLG 250


Lambda     K      H
   0.320    0.137    0.381 

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: 151
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: 233
Length of database: 257
Length adjustment: 24
Effective length of query: 209
Effective length of database: 233
Effective search space:    48697
Effective search space used:    48697
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