GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Luteipulveratus mongoliensis MN07-A0370

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate WP_052591108.1 VV02_RS09195 sugar ABC transporter permease

Query= reanno::BFirm:BPHYT_RS16110
         (311 letters)



>NCBI__GCF_001190945.1:WP_052591108.1
          Length = 297

 Score =  122 bits (306), Expect = 1e-32
 Identities = 89/273 (32%), Positives = 130/273 (47%), Gaps = 9/273 (3%)

Query: 33  PSVAVLVLWMAIPLAMTIWFSFSRYNLLNPDLKGFAGFDNYKYLASDPSFGPSIGHTLEL 92
           P+ AV   +   PL   ++ SF  ++ L   L  + G  NY  +  D     S GH L L
Sbjct: 23  PAFAVYAAFALYPLLKAVYLSFWDWDGLT--LATWVGLGNYADVFGDERLRASFGHALVL 80

Query: 93  IISVLVITV-VGGVLMAILFDRKFYGQGIARLLAIAPFFVMPTVSALIWKNMILHPVYGL 151
           +    V+ + VG VL A+L   K  G    R +   P  V   V A+ W+   L+   G 
Sbjct: 81  MAFFAVLPLLVGLVLAAVLHRAKVRGLSFFRTVVFLPQVVAMVVIAVAWRR--LYSPDGS 138

Query: 152 IAQGMRAMGMQPID--WFAEYP--LTAVIMIVAWQWLPFAFLILFTAIQSLDQEQKEAAR 207
           +   + A+G+      W  +Y   L AV +I  W       ++L   +  + +E  EAAR
Sbjct: 139 LNSVLSAIGLDSWTRGWLGDYTFALPAVGVIGTWFESGLVTVLLLAGMSRIPRELYEAAR 198

Query: 208 IDGAGPFSMFFYITLPHLKRAIAVVVMMETIFLLSIFAEIYTTTGGGPGTATTNLSYLIY 267
           IDGAGP   FF +TLP ++  IAV + +  I  L  F  IY TT GGPG  TT  SY +Y
Sbjct: 199 IDGAGPVREFFAVTLPSVRGEIAVALTLTVIAALKTFDLIYMTTSGGPGHETTVPSYEVY 258

Query: 268 SLGLQQFDVGLASAGGILAVVLANIVSFFLVRM 300
               +   VGLAS  G++   +  ++SF + R+
Sbjct: 259 RQAFELGHVGLASTIGVVLTAIIFVISFAITRI 291


Lambda     K      H
   0.328    0.141    0.431 

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: 223
Number of extensions: 12
Number of successful extensions: 4
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: 311
Length of database: 297
Length adjustment: 27
Effective length of query: 284
Effective length of database: 270
Effective search space:    76680
Effective search space used:    76680
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