Align Glucose/galactose porter (characterized)
to candidate 6936374 Sama_0562 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__SB2B:6936374 Length = 413 Score = 417 bits (1072), Expect = e-121 Identities = 215/405 (53%), Positives = 287/405 (70%), Gaps = 9/405 (2%) Query: 1 MATSIPTNNPLHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQS 60 ++++ P N S Q+ A+TSL FF+WGFIT LNDILIPHLK +F L+YTQ+ Sbjct: 4 VSSTTPQNGSAAPAQSHQQLLFGAMTSL---FFIWGFITALNDILIPHLKGIFDLSYTQA 60 Query: 61 MLIQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGA 120 ML+QFCFFGAYF+VS AG L+ RI Y RGI+ GL A GC LF PA+S YALFL A Sbjct: 61 MLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLA 120 Query: 121 LFVLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATD 180 LFVLASG+TILQV+ANP+V LG TAASRL L QA NSLG T+ P+FG++LI AA Sbjct: 121 LFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAG 180 Query: 181 ATVNAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLG 240 +AV+ PYLLLA ++A+ F L V+ + + + +GS ++ L+LG Sbjct: 181 TH-----EAVQLPYLLLAAVIGIIAVGFIFLGGK-VKHADMGVDHRHKGSLLSHKRLLLG 234 Query: 241 AIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYI 300 A+ IF+YVGAEVS+GSFLVN+ ++P++ GL E AA V+++WGGAM+GRF G+A R Sbjct: 235 ALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRF 294 Query: 301 DDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQ 360 + LA NA A +LL +T+ ++G +A+ +VLA+G FNSIMFPTIF+LA+ GLG TS+ Sbjct: 295 NPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSR 354 Query: 361 GSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFY 405 GSG+LC AIVGGA++P+IQG +AD +G+ L+F++P CY YI +Y Sbjct: 355 GSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWY 399 Lambda K H 0.328 0.141 0.420 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: 577 Number of extensions: 24 Number of successful extensions: 3 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: 412 Length of database: 413 Length adjustment: 31 Effective length of query: 381 Effective length of database: 382 Effective search space: 145542 Effective search space used: 145542 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.
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:
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