Align gluconate:H+ symporter (gntT) (characterized)
to candidate GFF658 PS417_03340 gluconate transporter
Query= reanno::BFirm:BPHYT_RS16725 (465 letters) >FitnessBrowser__WCS417:GFF658 Length = 456 Score = 355 bits (910), Expect = e-102 Identities = 190/459 (41%), Positives = 287/459 (62%), Gaps = 18/459 (3%) Query: 4 VHGSTLLVFAVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGN 63 VH + L+ ++AIA +I+LI+ K+ PFL ++I + + G+ +G+P + K+F G G Sbjct: 10 VHDTRLMFCVLLAIASIIVLISATKLPPFLSILIGTFIAGVGAGLPPEEVAKAFSKGAGA 69 Query: 64 TLGHIAIVVGLGTMLGKMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVFFEV 123 LG I++ LG+MLG +MAESG A+RIATTL+ K + W M +VA+++GLP+FFEV Sbjct: 70 ILGEAGIIIALGSMLGALMAESGAADRIATTLLGLGKGKALPWVMALVAMVIGLPLFFEV 129 Query: 124 GFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRTIA 183 G V+++PI +AKR+N+ LL + +P +AG++ +H L+PPHP ++AV A HAD+G T+ Sbjct: 130 GLVMMVPIILVMAKRSNQPLLKIAIPALAGMTTLHALMPPHPGPLIAVSALHADLGLTML 189 Query: 184 YGLIVGVPTAIVAGPLFALMISRYIKLPKENALAAQFLGHGDETKN-GAQTAAQNVAPKR 242 G + VP I+AGP++ +S+ + H DE + GA +A AP++ Sbjct: 190 LGFCLAVPAVILAGPIYGNWLSKRL--------------HVDEPADIGALFSAPPKAPRQ 235 Query: 243 ELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVLVSFWTF 302 PSF ++LL ILLPVILML + A + ++ L F G +AL +AV+ + Sbjct: 236 --PSFTVSLLIILLPVILMLGSTLAKVALPAESAIGLTLKFLGEPLIALGLAVVAAVICL 293 Query: 303 GASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATAMHLSPL 362 G + G R ++ LAPIA + L +GAGGG + L+D+G+S+ I VA H+ L Sbjct: 294 GWAAGMPRAEVGNTLRKALAPIAVLLLTIGAGGGLKQTLLDAGVSQTISKVAEGAHMPYL 353 Query: 363 LFGWLVAALIRLATGSATVAMTTACGIVAPIASASGVHVEPELLVLATGSGSLIFSHVND 422 L WL+A +R ATGSATVA TT GI+AP+ + + L+ LA G+GS+ F HVND Sbjct: 354 LLAWLIAVALRQATGSATVATTTTAGILAPMMAGLAA-PQSSLVALAIGAGSVFFCHVND 412 Query: 423 GGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFAL 461 GFW+++EYFG+ + QT WS+L+TI+S++GL T L Sbjct: 413 AGFWMVREYFGLQLKQTIWVWSVLQTIVSVVGLVGTLLL 451 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: 673 Number of extensions: 47 Number of successful extensions: 3 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: 456 Length adjustment: 33 Effective length of query: 432 Effective length of database: 423 Effective search space: 182736 Effective search space used: 182736 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