GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21105 in Thiothrix lacustris DSM 21227

Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate WP_084260334.1 Q394_RS0103655 carbohydrate ABC transporter permease

Query= reanno::Smeli:SM_b21105
         (288 letters)



>NCBI__GCF_000621325.1:WP_084260334.1
          Length = 281

 Score =  138 bits (347), Expect = 2e-37
 Identities = 79/260 (30%), Positives = 142/260 (54%), Gaps = 7/260 (2%)

Query: 28  VICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQGGVPVWDYFRNSLI 87
           +I  P L++ +++ +  ++ +A P VW+  T + + +  +   +G      +DY  NS+I
Sbjct: 29  IIFFPLLFMFVTAFKTELQAIAVPSVWV-FTPTWENFALVQERSGY-----FDYAWNSVI 82

Query: 88  VSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIALSLPLFMLYARTGII 147
            SV ST++ L I +   Y+ A    K    I +  + T+ +P +   LP+++L    G++
Sbjct: 83  TSVGSTILGLLIAVPAAYSMAFSPTKRTKDILMWMLSTKMMPAVGALLPIYVLCQTFGLL 142

Query: 148 DTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQAFWQVEFPLAGPGI 207
           D   SLI+ +  +N+P  +W++   F+ +P ++ EAA++DG +  + F  V  PLA  G+
Sbjct: 143 DNVISLIIIFTMMNLPIMVWMLYSNFKDIPIEILEAARMDGASLSEEFRHVLLPLAMGGM 202

Query: 208 ASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAEFTIDWRGMCALAVVMIVPAL 267
           AS G+   + SWNE      +T + N+ TL   +  Y++   + W  + A++V+ I P +
Sbjct: 203 ASTGLLCLVLSWNEAFWVLNLT-AANAGTLASLVASYSSPEGLFWAKLSAVSVLAIAPIV 261

Query: 268 TLTFIIQKHLVSGLTFGAVK 287
              +  QK LV GLTFGAVK
Sbjct: 262 VFGWFSQKQLVQGLTFGAVK 281


Lambda     K      H
   0.328    0.141    0.442 

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: 235
Number of extensions: 11
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: 288
Length of database: 281
Length adjustment: 26
Effective length of query: 262
Effective length of database: 255
Effective search space:    66810
Effective search space used:    66810
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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