Align gluconate:H+ symporter (gntT) (characterized)
to candidate BPHYT_RS34710 BPHYT_RS34710 gluconate transporter
Query= reanno::BFirm:BPHYT_RS16725 (465 letters) >FitnessBrowser__BFirm:BPHYT_RS34710 Length = 458 Score = 367 bits (942), Expect = e-106 Identities = 188/458 (41%), Positives = 287/458 (62%), Gaps = 18/458 (3%) Query: 5 HGSTLLVFAVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGNT 64 H + L++ V+ +AL+I+ I+ K+ PFL +++ + G A+G+P+ + +F G G Sbjct: 13 HDTQLILSCVLGLALIIVFISVLKLAPFLSILVGTFAAGFAAGLPLEAVASAFTKGAGAL 72 Query: 65 LGHIAIVVGLGTMLGKMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVFFEVG 124 LG + I++ LG MLG +MAESG A+R+ +T++ + + W M +VA+I+GLP+FFEVG Sbjct: 73 LGDVGIIIALGAMLGALMAESGAADRLVSTILKHSTPRTLPWMMAVVALIIGLPLFFEVG 132 Query: 125 FVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRTIAY 184 V+++PI F +A+R+ + +L + +P +AG++ +H LLPPHP ++AV A HAD+G T+ Sbjct: 133 LVMMVPIIFVMARRSQQPILRIAIPALAGMTTLHALLPPHPGPLIAVSALHADLGLTLGL 192 Query: 185 GLIVGVPTAIVAGPLFALMISRYIKLPKENALAAQFLGHGDETKNGAQTAAQNVAPKREL 244 GLIV +P I+AGPL+ + +S+ + + + + F +A Q+ E Sbjct: 193 GLIVAIPAVILAGPLYGIWLSKRMHVVEPEEMGKLF------------SAKQDTG---EP 237 Query: 245 PSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVLVSFWTFGA 304 P F I+L+TILLPV+LML + A L P++ + L+F G VAL + VL + G Sbjct: 238 PGFAISLITILLPVVLMLGRTVAKLLLQPESFLFNTLNFLGEPLVALGLTVLFAVVALGW 297 Query: 305 SRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATAMHLSPLLF 364 SRG RE++ L PIA + L +GAGGG + L+ +GIS I +A H+ +L Sbjct: 298 SRGMARERVGGILRKSLPPIAALLLTIGAGGGLKQALVVAGISSTIGKIAVGAHMPLILL 357 Query: 365 GWLVAALIRLATGSATVAMTTACGIVAP-IASASGVHVEPELLVLATGSGSLIFSHVNDG 423 WL+A +R ATGSATVA TT GIVAP +A S H L+ LA G+GS+ F HVND Sbjct: 358 AWLIAVALRQATGSATVATTTTAGIVAPVVAGLSATH--NSLMALAIGAGSVFFCHVNDA 415 Query: 424 GFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFAL 461 GFW+++EYFG+ + QT WS+L+TI+S++GL LT L Sbjct: 416 GFWMVREYFGLQLKQTVLVWSVLQTIVSVVGLALTLVL 453 Lambda K H 0.326 0.141 0.417 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: 656 Number of extensions: 52 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: 465 Length of database: 458 Length adjustment: 33 Effective length of query: 432 Effective length of database: 425 Effective search space: 183600 Effective search space used: 183600 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 (21.6 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