Align gluconate:H+ symporter (gntT) (characterized)
to candidate HSERO_RS10490 HSERO_RS10490 gluconate transporter
Query= reanno::BFirm:BPHYT_RS16725 (465 letters) >FitnessBrowser__HerbieS:HSERO_RS10490 Length = 456 Score = 364 bits (934), Expect = e-105 Identities = 185/460 (40%), Positives = 284/460 (61%), Gaps = 19/460 (4%) Query: 3 AVHGSTLLVFAVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNG 62 A + LL+ + A+ +++LI+ + PFL ++I + + G+ +G+P+ I K+F G G Sbjct: 10 AAQDTQLLLVTLTALVTIVVLISFLSIAPFLSILIGTFVAGIGAGLPLEDIAKAFSKGAG 69 Query: 63 NTLGHIAIVVGLGTMLGKMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVFFE 122 + LG I++ LG MLG +MAESG A+RI TL+ + I W M +VA++VGLP+FFE Sbjct: 70 SLLGEAGIIIALGAMLGALMAESGAADRIVNTLLRYARGSFIPWMMALVALVVGLPLFFE 129 Query: 123 VGFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRTI 182 VG V++ PI F +A+R+ ++ V +P +AG++ +H LLPPHP ++AV A HAD+G T+ Sbjct: 130 VGLVMMAPIIFVMARRSELPIMRVAIPALAGMTTLHALLPPHPGPLIAVSALHADLGTTM 189 Query: 183 AYGLIVGVPTAIVAGPLFALMISRYIKLPKENALAAQFLGHGDETKNGAQTAAQNVAPKR 242 G IV +P I+AGPL+ I+ + L + + + F +++ Sbjct: 190 LLGFIVAIPAVIIAGPLYGNFIAPRLNLAEPDQIGKLFSAREGQSQ-------------- 235 Query: 243 ELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVLVSFWTF 302 PSF + L+TILLPV+LML + A ++ TPKT ++L+F G +AL + VL + Sbjct: 236 --PSFLVALVTILLPVVLMLGRTVARIWVTPKTELFEMLNFFGEPIIALTVTVLFAVVVL 293 Query: 303 GASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATAMHLSPL 362 G +G +R ++ L PIAG+ L +GAGGG + L+ +GIS I +A H+ + Sbjct: 294 GWGQGSSRFEVGATLRRALPPIAGLLLTIGAGGGLKQTLLSAGISDTITKIADGTHMPLI 353 Query: 363 LFGWLVAALIRLATGSATVAMTTACGIVAP-IASASGVHVEPELLVLATGSGSLIFSHVN 421 L W++A +R ATGSATVA T GIVAP +A S H L+ LA G+GS+ F HVN Sbjct: 354 LLAWIIAVALRQATGSATVATTATAGIVAPLVAGLSATH--NSLMALAIGAGSVFFCHVN 411 Query: 422 DGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFAL 461 D GFW++KEYFG+ + QT TWS+++T++S++GLG+T L Sbjct: 412 DAGFWMVKEYFGLNLKQTLATWSVIQTLVSVIGLGMTLVL 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: 651 Number of extensions: 49 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: 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