GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Lutibaculum baratangense AMV1

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate WP_023431213.1 N177_RS05250 amino acid ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771
         (248 letters)



>NCBI__GCF_000496075.1:WP_023431213.1
          Length = 281

 Score = 84.3 bits (207), Expect = 2e-21
 Identities = 64/221 (28%), Positives = 99/221 (44%), Gaps = 17/221 (7%)

Query: 26  VTGLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWY 85
           ++G  + I I++ A  +   +G  LG+M       V  ++    + FRN P LV LF   
Sbjct: 69  LSGFVFNIAISLMAMTLGTVVGLALGLMAVSETMPVRKVSWAVTQFFRNSPWLVLLFFAM 128

Query: 86  FLVPDLLPADLQEWYKQDLNPTTSAF---LSVVVCLGLFTTARVCEQVRTGIQALPKGQE 142
           FLVP          Y+  L   T  F   +  V+   L   A V E VR  I+++P GQ 
Sbjct: 129 FLVP----------YEFRLLGVTVPFPDWIKAVIGFSLPVMANVSEIVRGAIRSIPDGQW 178

Query: 143 SAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTKQTA 202
            +A A+ F   Q  W ++LPQ  R ++PP  + +  V   T +AS++G+ E+L  T Q  
Sbjct: 179 ESAEALAFSRRQTMWMIILPQCLRRMLPPWMNLYSLVTMATVLASVVGVSEMLTLTSQVH 238

Query: 203 EFSAN----LFEAFTLATLIYFTLNMSLMLLMRVVEKKVAV 239
                    L   +  A L +F     +  L R +E +  V
Sbjct: 239 AAEGGRPELLAPLYGFALLCFFVYCYPIDRLTRRLEHRFQV 279


Lambda     K      H
   0.326    0.139    0.432 

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: 164
Number of extensions: 10
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: 248
Length of database: 281
Length adjustment: 25
Effective length of query: 223
Effective length of database: 256
Effective search space:    57088
Effective search space used:    57088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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