Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 184 bits (467), Expect = 3e-51 Identities = 113/338 (33%), Positives = 181/338 (53%), Gaps = 23/338 (6%) Query: 3 PQSLPDTTTPKR-------RFRWP-----TGMPQLVALLLVLLVDSLVAPHFWQVVLQDG 50 P S P T+T RF W T + LL+V +V V D Sbjct: 6 PSSSPKTSTVNSDTPGAPVRFTWAALKRSTLFYPFIGLLVVCIV---------MVFASDS 56 Query: 51 RLFGSPID-ILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPI 109 L G+ I+ +L + + A++A+GMT VI TGGIDLSVG+VMA+AG A + VAG + Sbjct: 57 FLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALAGTLAAGLMVAGMNAVA 116 Query: 110 VLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSW 169 L + G+ G NG VA + P + TL M RG+A + T G + +S+ Sbjct: 117 ALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALIYTGGYPIDGLPDWVSF 176 Query: 170 FGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLT 229 FGSG +L + PV+I + ++ W+L + G ++ A+G N +A + +GV + ++ Sbjct: 177 FGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQATRLSGVRVARVKLIV 236 Query: 230 YVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGA 289 Y ++GL +A A I++ A + NAG+ ELDAI AVV+GG S+ GGR +++ +++GA Sbjct: 237 YTIAGLTSAFAAIVLTARLMSGQP-NAGVGFELDAIAAVVMGGTSISGGRGSIIGTLIGA 295 Query: 290 LIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQR 327 L++ +N G+ + G P + V+K ++L + + R Sbjct: 296 LLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDR 333 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: 316 Number of extensions: 16 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: 341 Length of database: 335 Length adjustment: 28 Effective length of query: 313 Effective length of database: 307 Effective search space: 96091 Effective search space used: 96091 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.
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