Align Fructose:H+ symporter, Frt1 (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= TCDB::Q8NJ22 (566 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 184 bits (468), Expect = 5e-51 Identities = 139/460 (30%), Positives = 230/460 (50%), Gaps = 29/460 (6%) Query: 86 SNKTYMVIMLGFFASFAGILSGVDQSTISGASYGMKASLKLTSDEDSLISSLMPLGAVGG 145 SNK M + F A+ AG+L G+D I+GA + ++TS + S M GA G Sbjct: 10 SNKA-MTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVG 68 Query: 146 SILLTPLSEYFGRKVALVISCIFYTIGGILCAAAQDVHTMYAGRFLIGVGVGIEGGGVGV 205 ++ LS GRK +L+I I + G + AAA +V + R L+G+ VG+ + Sbjct: 69 AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPL 128 Query: 206 YIAESVPSTVRGSLVSLYQFNIALGELVGYVIGVIFFDVKGGWRYMLGSSLVFSTILFVG 265 Y++E P +RGS++S+YQ I +G ++G + F G WR+MLG ++ + +L +G Sbjct: 129 YLSEIAPEKIRGSMISMYQLMITIG-ILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIG 187 Query: 266 LFFLPESPRWLIHKGYDVEAYKVWRRLRDTS-----DLGNKREFLEMKHAAEQDRQLKEQ 320 +FFLP+SPRW K V+A +V RLRDTS +L RE L++K + L ++ Sbjct: 188 VFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVK---QSGWALFKE 244 Query: 321 ESRFKSMFDLILIPRNRRALLYSIMMVSLGQLTGINAIMYYMSTLMGQIGF-SPKQAVAM 379 S F RRA+ +++ + Q TG+N IMYY + G+ + + + Sbjct: 245 NSNF------------RRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWG 292 Query: 380 SMVGGAALLIGTIPAILYMDKFGRRPWSMTIIGFSVGLVLVGV-GYQIDLNTNLAAAEGV 438 +++ G ++ T AI +D++GR+P +GF V +GV G + + + +A+ Sbjct: 293 TVIVGLTNVLATFIAIGLVDRWGRKP--TLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYF 350 Query: 439 YLTGQILYNIFFGTYA-TLTWVVPSESFSLATRSIGMTICSAFLYLWAFTVTYNFNKMKD 497 + +++ + F A L WV+ SE L R G+T +A ++ V F M + Sbjct: 351 AIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLN 410 Query: 498 AFTYTGLTLGFYGGIAIVIGIPYQLLFMPETKDKTLEEID 537 T Y + ++ I L +PETK +LE I+ Sbjct: 411 TLGNAN-TFWVYAALNVLF-ILLTLWLVPETKHVSLEHIE 448 Lambda K H 0.323 0.139 0.404 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: 588 Number of extensions: 28 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: 566 Length of database: 464 Length adjustment: 35 Effective length of query: 531 Effective length of database: 429 Effective search space: 227799 Effective search space used: 227799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 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