Align Glucose/galactose porter (characterized)
to candidate 7025962 Shewana3_3110 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__ANA3:7025962 Length = 432 Score = 195 bits (495), Expect = 2e-54 Identities = 131/425 (30%), Positives = 216/425 (50%), Gaps = 27/425 (6%) Query: 14 ETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFI 73 + S QK+ + + LFF+ GF T LN L+P+LK + QLN Q+ LI F F+ A Sbjct: 4 DKSQQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTF 63 Query: 74 VSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQV 133 +LP+ +++++ YK G+ +G+ + + LFIPAA +++ LFL A V+ +G T+LQ Sbjct: 64 TALPSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQT 123 Query: 134 AANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLIL--------SAATDATVNA 185 A NPYV LG E+AA+R+++ N +AP+ + LIL + T ++ Sbjct: 124 AVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDE 183 Query: 186 EADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKEG---SAWQYRHLVLGAI 242 A+++ FPYL +A+ VLA+ P++ ++ +G +A + +L G I Sbjct: 184 MANSLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVI 243 Query: 243 GIFVYVGAEV----SVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMR 298 +FVYV EV ++G+F ++ + S T + Y G ++ RFI Sbjct: 244 ALFVYVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTAL 303 Query: 299 YIDD------GKALAFNAFVAIILLFITVATTGHIAMWSVLA----IGLFNSIMFPTIFS 348 I A+ F + + + G +A+ L +GL N+I++P ++ Sbjct: 304 MISAILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWP 363 Query: 349 LALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADA--IGIHLAFLMPIICYAYIAFYG 406 LAL GLG TS GS +L + I GGA PL G + A +G +++ + CY +I FY Sbjct: 364 LALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYA 423 Query: 407 LIGSK 411 + G K Sbjct: 424 VKGHK 428 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: 515 Number of extensions: 41 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: 412 Length of database: 432 Length adjustment: 32 Effective length of query: 380 Effective length of database: 400 Effective search space: 152000 Effective search space used: 152000 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