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_052592205.1 VV02_RS13505 sugar ABC transporter permease

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



>NCBI__GCF_001190945.1:WP_052592205.1
          Length = 304

 Score =  194 bits (493), Expect = 2e-54
 Identities = 102/271 (37%), Positives = 162/271 (59%), Gaps = 7/271 (2%)

Query: 33  PSVAVLVLWMAIPLAMTIWFSFSRYNLLNPDLKGFAGFDNYKYLASDPSFGPSIGHTLEL 92
           P++  +++   +P  +T+  SF  +N   PD +GFAG DN+  + +D +   +I  T+ L
Sbjct: 26  PALIFMIIVTQLPFLVTLVVSFMNWNAYYPDDRGFAGVDNFVSVLTDVNARKAIFVTVLL 85

Query: 93  IISVLVITVVGGVLMAILFDRKFYGQGIARLLAIAPFFVMPTVSALIWKNMILHPVYGLI 152
            + V++I+++ G+ +A+L DRKF G+G+AR L I PF V+P  +AL+WK+ + +P YGL+
Sbjct: 86  TVGVVLISLIVGLCIALLLDRKFRGRGVARTLMITPFLVVPVAAALMWKHALFNPEYGLL 145

Query: 153 AQGMRAM----GMQPIDWFAEYPLTAVIMIVAWQWLPFAFLILFTAIQSLDQEQKEAARI 208
             GM  M         DW  + PL ++++ + WQW PF  LIL   +QS   +  EAARI
Sbjct: 146 -NGMLKMVFGDNAPQRDWITDNPLISIVVALVWQWTPFMMLILLAGLQSRPMDVVEAARI 204

Query: 209 DGAGPFSMFFYITLPHLKRAIAVVVMMETIFLLSIFAEIYTTTGGGPGTATTNLSYLIYS 268
           DGA P+ +F  +TLPHL+  I +  ++  I+++  F  ++T T GG GTA  NL Y IY 
Sbjct: 205 DGASPWQIFRSMTLPHLRPYIELSGLLGAIYVVQNFDAVFTITSGGLGTA--NLPYFIYQ 262

Query: 269 LGLQQFDVGLASAGGILAVVLANIVSFFLVR 299
                 D G ASA G++ V+   I++ F +R
Sbjct: 263 TFYTAHDYGRASAAGVVVVIGTIIIATFALR 293


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: 240
Number of extensions: 8
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: 311
Length of database: 304
Length adjustment: 27
Effective length of query: 284
Effective length of database: 277
Effective search space:    78668
Effective search space used:    78668
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