GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Skermanella stibiiresistens SB22

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate WP_051511630.1 N825_RS06455 amino acid ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772
         (223 letters)



>NCBI__GCF_000576635.1:WP_051511630.1
          Length = 383

 Score =  117 bits (293), Expect = 3e-31
 Identities = 75/207 (36%), Positives = 113/207 (54%), Gaps = 7/207 (3%)

Query: 15  LWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPLLLVITWF 74
           LW G+ +TL L  +G++    L  +LAL R S   ++ ++   Y+   R +PL+ V+  F
Sbjct: 172 LWGGLPLTLILSVVGLVVAFPLSILLALGRRSDLPIVKSLCVTYIELIRGVPLITVL--F 229

Query: 75  YLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQALGM 134
             +V F L   TG    I       +  ++F +AY  E++R G+Q+IPKGQ  AA +LG+
Sbjct: 230 MASVMFPLFLPTG--VTIDKLLRAQIGLILFASAYLAEVIRGGLQAIPKGQYEAADSLGL 287

Query: 135 SYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRAS-GDIIGRS- 192
           +Y Q  R IILPQA     P L+   I  F+DTSLV  +GL D ++AS+A+  D   R  
Sbjct: 288 TYWQKTRKIILPQALSITIPPLVNTFIGFFKDTSLVIIIGLFDLMSASKAALTDPAWRGF 347

Query: 193 -NEFLIFAGLVYFIISFAASQLVKRLQ 218
             E  +F  +VYF   F  S+  + L+
Sbjct: 348 YKESYLFVAVVYFAFCFFMSKYSQWLE 374


Lambda     K      H
   0.332    0.144    0.428 

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: 210
Number of extensions: 9
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: 223
Length of database: 383
Length adjustment: 26
Effective length of query: 197
Effective length of database: 357
Effective search space:    70329
Effective search space used:    70329
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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