GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Herbaspirillum seropedicae SmR1

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS22470 HSERO_RS22470 D-xylose ABC transporter permease

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__HerbieS:HSERO_RS22470
          Length = 377

 Score =  263 bits (672), Expect = 6e-75
 Identities = 148/368 (40%), Positives = 219/368 (59%), Gaps = 8/368 (2%)

Query: 29  MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88
           +LIA+  I  FF F T G    P NL+NL+ Q S   I+A GM+LVI+AG IDLSVGS++
Sbjct: 16  LLIAIAIIWGFFSFMTDGGFVTPRNLSNLLRQMSVTGILACGMVLVIIAGEIDLSVGSLL 75

Query: 89  AFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRG 148
             +G +AA+L V   +   L  ++ L  G  +G   GY  AY  IPSFIV L GML FRG
Sbjct: 76  GLLGGLAALLDVSHHLPLALNLVLALGFGLALGLLNGYLTAYLGIPSFIVGLGGMLAFRG 135

Query: 149 LTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVV 208
           + L + GG  I P   +   +  G+LP   G+  L     +L V +T       W  RV 
Sbjct: 136 ILLGITGGLTIAPVSDNMVYLGQGYLPPQMGV-ALGIALFVLAVALT-------WMSRVN 187

Query: 209 NVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTT 268
             +HG+ +       ++ ++I   +L     L++Y G+P  ++++L L+ L+S+V+ +T 
Sbjct: 188 RSRHGLPLAALWRDALKVVVIGAVLLAFVRTLNSYDGIPVPVLLLLALLGLFSYVSTQTV 247

Query: 269 IGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFE 328
            GRR+Y++G N +AT+LSG+N + +    F  MGV+  LAG++   RL + +P AG   E
Sbjct: 248 FGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARLAAGSPSAGNMGE 307

Query: 329 LDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAV 388
           LD IAACFIGG S  GG G I GA+IGA +M  ++NGMS++ +G  +Q +VKG +L+ AV
Sbjct: 308 LDAIAACFIGGTSMRGGSGTIYGALIGALVMASLDNGMSMLDVGTYWQMIVKGSILVLAV 367

Query: 389 FFDVYNKN 396
           + DV  ++
Sbjct: 368 WVDVSTRS 375


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: 548
Number of extensions: 38
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: 398
Length of database: 377
Length adjustment: 30
Effective length of query: 368
Effective length of database: 347
Effective search space:   127696
Effective search space used:   127696
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.

Links

Downloads

Related tools

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