Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate 6937233 Sama_1403 glucose/galactose transporter (RefSeq)
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__SB2B:6937233 Length = 415 Score = 244 bits (622), Expect = 5e-69 Identities = 143/412 (34%), Positives = 218/412 (52%), Gaps = 23/412 (5%) Query: 18 AGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFII 77 A + +Y L +LFF+W LNDIL+P + F+L QA LIQ F+ YF++ Sbjct: 14 AAGAENYRFALGSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLV 73 Query: 78 PIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETA 137 +PAG+L+K+L Y+ GI+ GL ALG LF+PAA Y +FL LF++A+G+ L+ A Sbjct: 74 SVPAGVLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVA 133 Query: 138 ANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQL 197 ANP+VT LGP + RL L Q FNS G IA FG LILS + Sbjct: 134 ANPYVTALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILS---------------VAV 178 Query: 198 SAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARI 257 A + +V+ PY+++ +++++A++ L K P + A G S LA Sbjct: 179 GASAEAEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ-----SALAH- 232 Query: 258 RHWRWAVLAQFCYVGAQTACWSYLIRYAVE-EIPGMTAGFAANYLTGTMVCFFIGRFTGT 316 RH + F YVG + A S+L+ + E + GM AA+Y+ +GRF G Sbjct: 233 RHLVLGAIGIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGA 292 Query: 317 WLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNL 376 ++ + KVL A +A L L++ + G + + A+ F SI +PTIFSL +KNL Sbjct: 293 AVMQKVDAGKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNL 352 Query: 377 GQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428 G T GS + + I+GG +V + G ++D+ G + + ++P LC+ I + Sbjct: 353 GPATAQGSGILCLAIVGGALVPLLQGLLADSVG-LSASFILPVLCYGYILFY 403 Lambda K H 0.329 0.140 0.425 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: 471 Number of extensions: 33 Number of successful extensions: 5 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: 438 Length of database: 415 Length adjustment: 32 Effective length of query: 406 Effective length of database: 383 Effective search space: 155498 Effective search space used: 155498 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: 51 (24.3 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