GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluP in Pedobacter sp. GW460-11-11-14-LB5

Align The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized)
to candidate CA265_RS04675 CA265_RS04675 L-fucose:H+ symporter permease

Query= TCDB::O25788
         (407 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS04675 CA265_RS04675 L-fucose:H+
           symporter permease
          Length = 436

 Score =  270 bits (691), Expect = 5e-77
 Identities = 164/407 (40%), Positives = 233/407 (57%), Gaps = 27/407 (6%)

Query: 13  LTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGGVFGNVISKIGY 72
           +T+LFF  GF+  L+ +LIPHL+  F L  FE++L+    F AYF++    G ++ K GY
Sbjct: 28  VTSLFFFWGFVHNLDPVLIPHLRKAFQLNVFESTLVDSSVFIAYFLLALPAGYIMRKYGY 87

Query: 73  PFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVTLLSKGKE 132
             G++LG V+ A GC LF PAA+   Y FFLGALFI+A G+  L+TA NP+VT+L   + 
Sbjct: 88  KSGIILGLVLFAIGCLLFIPAANTAQYIFFLGALFIIACGLTFLETAANPYVTVLGPPET 147

Query: 133 A-RNLVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDN--ASLID------KLADAKSVQMP 183
           A + L   Q+FN L   L P+ G   IF+  K  D   A ++        L +A +V+ P
Sbjct: 148 ATQRLNFSQSFNGLAAFLAPVLGGKFIFTEVKYTDAQLAKMLPLEKQAYMLEEASTVKAP 207

Query: 184 YLGLAVFSLLLALIMYLLKLPDVEKEMPKETTQKSLFS----HKHFVFGALGIFFYVGGE 239
           YL L +  +++A++    KLPD+++E  +   +KS FS    H H  +  +G FFYVG +
Sbjct: 208 YLILGILIIVVAILFIFTKLPDIKEE--ENAQEKSSFSHVLGHSHLRWAIIGQFFYVGAQ 265

Query: 240 VAIGSFLVLSFEKLLNLDSQSSAHYLVYYWGGA----MVGRFLGSVLMNKIAPNKYLAFN 295
           V + S L +SF       SQ +A    +Y G A    MVGRF G+  M  +A +K L   
Sbjct: 266 VCVLS-LFISFVTSSAGISQDAAK---WYAGAAGLAFMVGRFAGTFFMRYVAAHKLLMLY 321

Query: 296 ALSSIVLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGHLTSKASGVISMAI 355
           AL S VL  ++I   G I ++AL  V FF SIMFPTIFSL    LG  T   S +I M+I
Sbjct: 322 ALISAVLTLVSIFASGMITVYALIGVSFFMSIMFPTIFSLGIAGLGKDTKLGSSLIVMSI 381

Query: 356 VGGALIPPIQGAVTDMLTATESNLLYAYGVPLLCYFYILFFALKGYK 402
           VGGA +PP+ G ++D       N+ Y Y VP +C+  + +F  KG+K
Sbjct: 382 VGGAFLPPVLGLISD----ATHNIQYGYLVPFVCFLVVFYFGWKGWK 424


Lambda     K      H
   0.328    0.144    0.423 

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: 523
Number of extensions: 30
Number of successful extensions: 6
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: 407
Length of database: 436
Length adjustment: 32
Effective length of query: 375
Effective length of database: 404
Effective search space:   151500
Effective search space used:   151500
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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