Align Glucose/galactose porter (characterized)
to candidate 5208608 Shew_1119 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__PV4:5208608 Length = 418 Score = 191 bits (485), Expect = 3e-53 Identities = 131/416 (31%), Positives = 215/416 (51%), Gaps = 44/416 (10%) Query: 31 LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90 LFF+ GF T LN L+P+LK + QL Q+ LI F F+ A +LP+ +++++ YK G Sbjct: 7 LFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRKVGYKTG 66 Query: 91 IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150 + +G+ + I LFIPAA +V+ALFL A V+ +G T+LQ A NPYV +G E+AA+ Sbjct: 67 MAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGPEESAAA 126 Query: 151 RLTLTQAFNSLGTTVAPVFGAVLILSA--------ATDATVNAEADAVRFPYLLLALAFT 202 R+++ N +AP+ LIL + T A ++ A+ + FPYL +A+ Sbjct: 127 RVSVMGILNKGAGVIAPLVFTALILDSFKDRVGVELTQAQIDEMANGLVFPYLGMAIFIG 186 Query: 203 VLAIIFAILKPPDVQEDEPALSDKKEGS------AWQYRHLVLGAIGIFVYVGAEVSVGS 256 VLA++ P+++ ++ +++EG+ A + +L LG + +F YV EV G Sbjct: 187 VLALLVKKSPLPELENED----EQEEGTKGHTREALSHPNLALGVVALFFYVAVEVIAGD 242 Query: 257 FLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM-RYIDDGKALAFNAFVAII 315 + F L + +Y ++G +G + R+I KAL +A + ++ Sbjct: 243 TIGTF-----ALSLGVENYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISAILGLM 297 Query: 316 L-LFITVATTGHIAMWSVLAI-----------------GLFNSIMFPTIFSLALHGLGSH 357 L L I A+ + L + GL N+I++P ++ LAL G+G Sbjct: 298 LTLGILFGDNESYAIANALLVPFGGAMLPDTLLMIAFLGLANAIVWPAVWPLALSGMGKL 357 Query: 358 TSQGSGILCLAIVGGAIVPLIQG--ALADAIGIHLAFLMPIICYAYIAFYGLIGSK 411 TS GS +L + I GGA PL G + A ++G +++ + CY +I FY + G K Sbjct: 358 TSTGSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYAVKGYK 413 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: 493 Number of extensions: 28 Number of successful extensions: 4 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: 418 Length adjustment: 31 Effective length of query: 381 Effective length of database: 387 Effective search space: 147447 Effective search space used: 147447 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