Align Glucose/galactose porter (characterized)
to candidate 202604 SO3503 glucose/galactose transporter (NCBI ptt file)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__MR1:202604 Length = 435 Score = 194 bits (492), Expect = 6e-54 Identities = 137/433 (31%), Positives = 223/433 (51%), Gaps = 43/433 (9%) 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+ V I LFIPAA +V+ALFL A V+ +G T+LQ Sbjct: 64 TALPSAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQT 123 Query: 134 AANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLIL--------SAATDATVNA 185 A NPYV LG E+AA+R+++ N +AP+ + LIL + T ++ Sbjct: 124 AVNPYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDE 183 Query: 186 EADAVRFPYLLLALAFTVLAIIFAILKPPDV-QEDEPA-LSDKKE-GSAWQYRHLVLGAI 242 A+ + PYL +A+ +LA+ P++ EDE A +DK + +A + +L LG + Sbjct: 184 MANGLVLPYLGMAVFIGILALAVKKSPLPELSNEDEVADHTDKSQIKAALSHPNLALGVL 243 Query: 243 GIFVYVGAEV----SVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMR 298 +FVYV EV ++G+F ++ D S T + Y G ++ R I Sbjct: 244 ALFVYVAVEVIAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPT-- 301 Query: 299 YIDDGKALAFNAFVAIILLF--------------ITVATTGHIAMWSVLA----IGLFNS 340 AL +A + ++L + + G +A+ L +GL N+ Sbjct: 302 ------ALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANA 355 Query: 341 IMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADA--IGIHLAFLMPIIC 398 I++P ++ LAL G+G TS GS +L + I GGA P+ G ++ A +G +++ + C Sbjct: 356 IVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPC 415 Query: 399 YAYIAFYGLIGSK 411 Y +I FY + G K Sbjct: 416 YLFILFYAVKGHK 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: 500 Number of extensions: 35 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: 435 Length adjustment: 32 Effective length of query: 380 Effective length of database: 403 Effective search space: 153140 Effective search space used: 153140 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: 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