Align gluconate:H+ symporter (gntT) (characterized)
to candidate Pf1N1B4_5074 Gluconate permease
Query= reanno::BFirm:BPHYT_RS16725 (465 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5074 Length = 470 Score = 295 bits (756), Expect = 2e-84 Identities = 165/466 (35%), Positives = 253/466 (54%), Gaps = 24/466 (5%) Query: 20 LILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGNTLGHIAIVVGLGTMLG 79 L+ L+ +YK PF+ L++VS+L+ L +G+ A +V + E G G TLGHIAI++ LG M+G Sbjct: 1 LLFLVLKYKFQPFVALMLVSILVALVAGVKPADLVATIEGGMGKTLGHIAIIIALGAMIG 60 Query: 80 KMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVFFEVGFVLLIPIAFNVAKRT 139 +++ SGGAE +A TLI FG + A+ I +VG+PVFFEVG ++L+P+A+ VA+ Sbjct: 61 RIIELSGGAEALAKTLITRFGNRRTPLALTIAGFMVGVPVFFEVGVIILMPLAYGVARSA 120 Query: 140 NKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGRTIAYGLIVGVPTAIVAGPL 199 K LL+ LPM A L VH LPPHP A+ A AD+GR + +GL + V + Sbjct: 121 RKPLLVFALPMCAALLTVHAFLPPHPGAVAAASQLGADLGRVLMFGLPITAFLCYVGYRV 180 Query: 200 FALMISRYIKLPKE-----------NALAAQFLGHGDETKNGAQTAAQNVA--------- 239 M R + + N A + D++ A AA ++ Sbjct: 181 AGRMTRRVYPMTDDIRAEVYGPHVTNEDLAAWSNGNDKSPERAAVAASHMGLEEATSSIV 240 Query: 240 ---PKRELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVL 296 P P FG+ + I+LP+IL+L+G+ + ++ ++ G VALLI L Sbjct: 241 SKLPPAPPPGFGLIVSLIVLPIILILLGTLSTSLLPADSVLRGIMTVLGAPLVALLIDTL 300 Query: 297 VSFWTFGASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATA 356 + W G+ RG++R Q+ G L +A + LI GAGG FG+VL+D+GI + ++ Sbjct: 301 LCAWLLGSRRGWSRTQVSDVIGSALPGVAMVILIAGAGGVFGKVLVDTGIGAVVSDMLRT 360 Query: 357 MHLSPLLFGWLVAALIRLATGSATVAMTTACGIVAP-IASASGVHVEPELLVLATGSGSL 415 L L G+L+ L+R GS TVA+ T GI++P I + LL LA G G L Sbjct: 361 TGLPVLALGFLLTMLLRAVQGSTTVALVTTAGIISPLIVTLDLTANHMALLCLAMGGGGL 420 Query: 416 IFSHVNDGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFAL 461 SH+ND G+W+ + G+ V +TW++L T++ +G G+T + Sbjct: 421 AMSHINDAGYWIFTKLSGLNVADGLRTWTVLTTLLGTLGFGITLLI 466 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: 616 Number of extensions: 32 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: 470 Length adjustment: 33 Effective length of query: 432 Effective length of database: 437 Effective search space: 188784 Effective search space used: 188784 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