GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Phaeobacter inhibens BS107

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__Phaeo:GFF2762
          Length = 353

 Score =  120 bits (300), Expect = 7e-32
 Identities = 100/326 (30%), Positives = 161/326 (49%), Gaps = 42/326 (12%)

Query: 19  PTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPID---ILNRAAPVALLAIGMTL 75
           P+ +P +V +L V++   L+           G  F SP     IL +   V ++A   +L
Sbjct: 40  PSLVPLIVLVLSVIVFGLLL-----------GSKFFSPFALTLILQQVGIVGIVACAQSL 88

Query: 76  VIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGT--GILAGLWNGILVAILK 133
           VI T GIDLSVGA+M ++       T   + LP  +  A G   G + G  NG LVA +K
Sbjct: 89  VILTAGIDLSVGAIMVLSSVVMGQFTFR-YGLPPEVAVACGLICGTICGFINGWLVARMK 147

Query: 134 IQPFVATLILMVAGRGVAQLITAG------------QIVTFNSPDLSWFGS----GSLLF 177
           + PF+ TL       G+ Q++ A             Q +   +P L  FG     G  +F
Sbjct: 148 LPPFIVTL-------GMWQIVLASNFLYSANETIRSQTIAAEAPLLQLFGEKIKIGGAVF 200

Query: 178 LPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCA 237
               + + +L ++L ++L R TA G  + AVG +  AA+ +GV    +++  Y+LSGL  
Sbjct: 201 TYGVIFMVILVVLLAYVL-RHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLIC 259

Query: 238 AIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNT 297
           A AG  +   I G+ +  +G    +++I AVVIGG SL GGR ++L +  GALI+     
Sbjct: 260 AFAGWAMIGRI-GSVSPTSGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTL 318

Query: 298 GILLSGFPPEMNQVVKAVVVLCVLIV 323
           G+ L G   +   ++  ++++  + V
Sbjct: 319 GLRLLGADAQWTYLLIGLLIIAAVAV 344


Lambda     K      H
   0.327    0.142    0.416 

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: 271
Number of extensions: 17
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: 341
Length of database: 353
Length adjustment: 29
Effective length of query: 312
Effective length of database: 324
Effective search space:   101088
Effective search space used:   101088
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: 49 (23.5 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