GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21220 in Phyllobacterium brassicacearum STM 196

Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate WP_106711243.1 CU102_RS11575 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21220
         (293 letters)



>NCBI__GCF_003010955.1:WP_106711243.1
          Length = 309

 Score =  182 bits (461), Expect = 1e-50
 Identities = 92/278 (33%), Positives = 169/278 (60%), Gaps = 3/278 (1%)

Query: 11  WLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVT 70
           W  ++P LV++ AVI +P V T+ +S  +  L G E  FVG AN+I++ G   F  ++  
Sbjct: 30  WPFVIPALVIVGAVIIFPWVFTLWMSVNEWHL-GGEKSFVGLANFIRLAGDQRFWESMSH 88

Query: 71  TTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEY 130
           T  + V+SV A + LG +AAL+ + +   R  LR + ++P     V  A +W ++++P+ 
Sbjct: 89  TVLYTVLSVVAPLFLGTIAALVFDSKLPMRGLLRGIFVMPMMATPVAIALVWTMMFHPQL 148

Query: 131 GALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAA 190
           G LN  L+ +G+    + W+    T + +L++ + W+  PLV LI L  L A+PRD   +
Sbjct: 149 GVLNYLLSLIGI--GPQEWIFNQNTVIPSLVLVETWQWTPLVMLIVLGGLAAMPRDPFES 206

Query: 191 SLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSIL 250
           + +DGA  + +FR++ +P +   ++VA+++R+I+A K FDII+ MT+GGP  ++ T++I 
Sbjct: 207 AEIDGANGWQKFRYITLPMILPFMMVAVIIRSIDALKSFDIIFAMTQGGPGTASETINIY 266

Query: 251 VYQEAFSFQRAGSGASLALIVTLLVTILAAAYAALLRK 288
           +Y  AF++   G G++LA++  +++  ++ A   L ++
Sbjct: 267 LYNVAFAYYDIGYGSALAVVFFIVIITMSLALLYLRQR 304


Lambda     K      H
   0.326    0.138    0.417 

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: 267
Number of extensions: 14
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: 293
Length of database: 309
Length adjustment: 27
Effective length of query: 266
Effective length of database: 282
Effective search space:    75012
Effective search space used:    75012
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