GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Halopiger salifodinae KCY07-B2

Align ABC transporter permease (characterized, see rationale)
to candidate WP_049991587.1 LT39_RS16410 sugar ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>NCBI__GCF_000784335.1:WP_049991587.1
          Length = 319

 Score =  178 bits (452), Expect = 1e-49
 Identities = 104/282 (36%), Positives = 151/282 (53%), Gaps = 20/282 (7%)

Query: 17  PAFVLGFAFIYGLMVWNGVLSLTVSRML--PNYEWAGLAQYERLWEMDRWWVALKNLGIF 74
           P  +L   F+YG + WN V+SLT    L  P Y    L  Y +L     +  AL+N    
Sbjct: 49  PPTLLVLLFVYGAIGWNVVISLTGWSGLGQPEYTNFSLEMYRQLPADQNFRAALRNTVAL 108

Query: 75  GVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKW------LLNP 128
            VG+ G SLL+G+ LA+L+D+KIR E   RTIYL PMALSFVVT   W W      L+N 
Sbjct: 109 LVGFTGVSLLVGLGLALLVDRKIRFENTFRTIYLLPMALSFVVTAIFWSWMYASNGLINA 168

Query: 129 GLGIEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIK 188
            L I               WL +  + +  V+ A +WQ +G+ M ++LAGLR I D   +
Sbjct: 169 VLPISP------------DWLGNPRLKLAAVIFALVWQFSGYCMIVYLAGLRSIPDDHYE 216

Query: 189 AAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPAT 248
           AA++DGAS  ++YWR+++P LR       +VL   A+K+FD +  +    PG + D+ A 
Sbjct: 217 AARIDGASTLKLYWRVIIPQLRSSTVGATVVLMVFALKAFDFIYVMFGTNPGRSVDILAV 276

Query: 249 FMYTMSFSRGQIGLGAASATMMLATVAALVIPYLYSELRTKA 290
            MY  +FS  +   GAA A ++      ++ PY Y++ +  A
Sbjct: 277 MMYREAFSAAEWAYGAAVAVVLFLLALTIIGPYAYTQYKRGA 318


Lambda     K      H
   0.327    0.141    0.451 

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: 301
Number of extensions: 13
Number of successful extensions: 3
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: 293
Length of database: 319
Length adjustment: 27
Effective length of query: 266
Effective length of database: 292
Effective search space:    77672
Effective search space used:    77672
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: 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