GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Acidovorax sp. GW101-3H11

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_608 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_608
          Length = 409

 Score =  505 bits (1301), Expect = e-148
 Identities = 247/397 (62%), Positives = 318/397 (80%)

Query: 1   MSSANTTNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQ 60
           ++  N T    +  S+  +++ N+REYGMLI LVAIM FFQ+ T G L +P+NLTNL+LQ
Sbjct: 12  LADGNPTTAARHDKSLLQHLQHNLREYGMLITLVAIMGFFQYMTEGTLMQPLNLTNLVLQ 71

Query: 61  NSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGII 120
           NS+IVIMALGMLLVIVAGHIDLSVGS+  F+GA+AA+L V++  +   A L+CL+ GG+I
Sbjct: 72  NSYIVIMALGMLLVIVAGHIDLSVGSVCGFIGALAAVLMVEYNWHFVPATLVCLLCGGLI 131

Query: 121 GAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGI 180
           GA QG ++A+ RIPSFIVTLAGMLVF+GL L +L G+++GPFP+ FQ++S+GF+PD+  +
Sbjct: 132 GAIQGSFVAFSRIPSFIVTLAGMLVFKGLALALLAGQSVGPFPSAFQMLSSGFIPDLFSV 191

Query: 181 EGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQL 240
           EGL  TS++L   +  AL     R+R   ++HG+  EP G FI + ++  G +++  Y L
Sbjct: 192 EGLRMTSLLLGAAVAAALAVGGLRQRANRLRHGVQTEPAGLFIARTVVFGGLLVYFSYLL 251

Query: 241 STYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVN 300
           ++Y+GLPNVLIVM +LI L+ FVT RTTIGRR+YAMGGNEKA KLSGI TERL+   F+N
Sbjct: 252 ASYKGLPNVLIVMALLIVLFDFVTSRTTIGRRIYAMGGNEKAAKLSGIKTERLTLYAFIN 311

Query: 301 MGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG 360
           MGVLA LAG++ A RLN+ATPKAG+GFELDVIAACFIGGASASGGVGK+ GAVIGAF+MG
Sbjct: 312 MGVLAALAGLVFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGAVIGAFVMG 371

Query: 361 VMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNK 397
           VMNNGMSI+G+GID+QQ++KG+VLLAAV  DVYNKNK
Sbjct: 372 VMNNGMSILGIGIDYQQVIKGVVLLAAVLVDVYNKNK 408


Lambda     K      H
   0.329    0.145    0.422 

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: 629
Number of extensions: 29
Number of successful extensions: 1
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: 398
Length of database: 409
Length adjustment: 31
Effective length of query: 367
Effective length of database: 378
Effective search space:   138726
Effective search space used:   138726
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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