GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Acidovorax caeni R-24608

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_054254746.1 BN2503_RS00885 amino acid ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_05500
         (242 letters)



>NCBI__GCF_001298675.1:WP_054254746.1
          Length = 217

 Score =  131 bits (330), Expect = 9e-36
 Identities = 84/221 (38%), Positives = 126/221 (57%), Gaps = 10/221 (4%)

Query: 14  FSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIPAQLYTTLIRGV 73
           ++L   GPL  QG  +T+KL  ++L+L+V LGL+ A A+LSR+KLL      Y  L+RG 
Sbjct: 3   YALSLLGPL-GQGALVTLKLFVITLVLAVPLGLVLALARLSRLKLLSAGVNGYIWLMRGT 61

Query: 74  PDLVLMLLIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILAV 133
           P ++ ML I+++L         F+    + +  F A V      Y AYF E FR  I +V
Sbjct: 62  PLMLQMLFIYFALP--------FVPVIGVRLPDFPAAVAAFALNYAAYFAEIFRAGIQSV 113

Query: 134 PRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKA 193
            RGQ EAA   G+  GQ  R VV PQM+R  LP + N  + ++K T+L+ ++ L DL++A
Sbjct: 114 DRGQYEAAKVLGMNYGQTMRRVVLPQMVRNILPPMSNETITLVKDTSLIYVLALNDLLRA 173

Query: 194 AQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYA 234
           A+   +  +    F+V AA  YL++T    +  + LE+RYA
Sbjct: 174 ARGIVQRDFTTTPFIV-AAAFYLVMTLVLTWAFQRLEQRYA 213


Lambda     K      H
   0.329    0.142    0.423 

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: 172
Number of extensions: 12
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: 242
Length of database: 217
Length adjustment: 23
Effective length of query: 219
Effective length of database: 194
Effective search space:    42486
Effective search space used:    42486
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 (21.8 bits)
S2: 46 (22.3 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