Align gluconate:H+ symporter (gntT) (characterized)
to candidate H281DRAFT_04276 H281DRAFT_04276 gluconate permease GntT
Query= reanno::BFirm:BPHYT_RS16725 (465 letters) >FitnessBrowser__Burk376:H281DRAFT_04276 Length = 461 Score = 835 bits (2158), Expect = 0.0 Identities = 429/465 (92%), Positives = 445/465 (95%), Gaps = 4/465 (0%) Query: 1 MEAVHGSTLLVFAVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETG 60 MEAVHGSTLLVF VIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETG Sbjct: 1 MEAVHGSTLLVFGVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETG 60 Query: 61 NGNTLGHIAIVVGLGTMLGKMMAESGGAERIATTLIDFFGEKNIHWAMMIVAIIVGLPVF 120 NGNTLGHIA+VVGLGTMLGKMMAESGGAERIATTLI++FGEKNIHWAMM+VAIIVGLPVF Sbjct: 61 NGNTLGHIAVVVGLGTMLGKMMAESGGAERIATTLINWFGEKNIHWAMMVVAIIVGLPVF 120 Query: 121 FEVGFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLLPPHPAAMLAVQAYHADIGR 180 FEVGFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGL+PPHPAAMLAVQ YHADIG+ Sbjct: 121 FEVGFVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLIPPHPAAMLAVQQYHADIGK 180 Query: 181 TIAYGLIVGVPTAIVAGPLFALMISRYIKLPKENALAAQFLGHGDETKNGAQTAAQNVAP 240 TIAYGLI+GVPTAIVAGPLFAL+ISRY+KLP+ENALAAQFLGH D KNG A N AP Sbjct: 181 TIAYGLIIGVPTAIVAGPLFALLISRYVKLPQENALAAQFLGHDDAAKNG----ATNTAP 236 Query: 241 KRELPSFGITLLTILLPVILMLVGSWADLFTTPKTLPNDLLHFAGNSDVALLIAVLVSFW 300 KRELPSFGITL T+LLPVILMLVGSWADL TPKTLPNDLLHF GNSDVALLIAVLVSFW Sbjct: 237 KRELPSFGITLFTVLLPVILMLVGSWADLVFTPKTLPNDLLHFVGNSDVALLIAVLVSFW 296 Query: 301 TFGASRGFTREQIQKFCGDCLAPIAGITLIVGAGGGFGRVLMDSGISKEIVNVATAMHLS 360 TFGASRGF R+QIQKFCG+CLAPIAGITLIVGAGGGFGRVLMDSGISKEIV ATA HLS Sbjct: 297 TFGASRGFNRDQIQKFCGECLAPIAGITLIVGAGGGFGRVLMDSGISKEIVAAATAAHLS 356 Query: 361 PLLFGWLVAALIRLATGSATVAMTTACGIVAPIASASGVHVEPELLVLATGSGSLIFSHV 420 PLLFGWLVAALIRLATGSATVAMTTACGIVAPIA+ASGV V+PELLVLATGSGSLIFSHV Sbjct: 357 PLLFGWLVAALIRLATGSATVAMTTACGIVAPIAAASGVQVKPELLVLATGSGSLIFSHV 416 Query: 421 NDGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFALAAVV 465 NDGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFALAAV+ Sbjct: 417 NDGGFWLIKEYFGMTVGQTFKTWSLLETIISLMGLGLTFALAAVL 461 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: 920 Number of extensions: 37 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: 461 Length adjustment: 33 Effective length of query: 432 Effective length of database: 428 Effective search space: 184896 Effective search space used: 184896 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