Align glycerol permease (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= CharProtDB::CH_122745 (546 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 170 bits (431), Expect = 9e-47 Identities = 138/470 (29%), Positives = 224/470 (47%), Gaps = 34/470 (7%) Query: 12 TTTAGLTGRKLRAAVTITATLGFSLFGYDQGLMAGLISAEQFNWEFPATKDNSVIQGAVT 71 T TA + G + V A L +FG D G+++G A QF A D+++ + Sbjct: 8 TPTAHVKGTVIYTCVL--AALAGLMFGLDIGVISG---ASQFIKAEFAISDHTIEW--IV 60 Query: 72 ASYELGCFFGAIFALLRGDALGRKPIIFFGATIIILGTIISVTPFRPHWPLGQFVVGRVI 131 +S G GA+ A LGRK + GA + ++G+++ + P + RVI Sbjct: 61 SSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPE----TLIAARVI 116 Query: 132 TGIGNGMNTATIPVWQSEMSKPENRGKLVNLEGAVVAFGTFIAYWLDFGLSYVDSSVSWR 191 G+ G+ T T P++ +E++ RG +++ ++ G +A+ D LSY + WR Sbjct: 117 LGLAIGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGA---WR 173 Query: 192 FPVAFQIFFALWVIFGIIQLPESPRWLISKDRKPEAFEVLAALNDTTPDDDAIVAEASVI 251 + + + G++ LP+SPRWL+ + R+ EA +VL L D+ +VA + Sbjct: 174 WMLGVIAIPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRG----DEVVVAREAAD 229 Query: 252 IDAVRRNAKVQAGFKDLFTGGKTAHFQR-MLIGSSTQFFQQFTGCNAAIYYSTLLFYETV 310 I+ + Q G+ DLF + +F+R + +G+ Q QQFTG N +YY+ +F E Sbjct: 230 IEEQLKTP--QRGW-DLFA--ENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMG 284 Query: 311 FHHTKYRLSMILGGVFATIYALATLPSFFLIDTLGRRNL----FLIGAIGQGISFLISFA 366 + L G+ LAT + LID GR+ + F + A+G G+ + Sbjct: 285 YDTAAQMWFTALVGL---TNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNG 341 Query: 367 CLINPTEQNAKGAAVGIYLFIVFFAFTILPLPWIYPPEINPLRTRTTASAVSTCTNWLTN 426 + TEQ A + FIV FA + PL W EI PL+ R VST TNW+TN Sbjct: 342 GINGQTEQYTCVAM--LLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITN 399 Query: 427 FAV-VMFTPPFISASGWGCYLYFAVMNFLFVPIIFFFYPETAGRSLEEID 475 V F + + +A +N +F+ + F+ PET G +LE+I+ Sbjct: 400 MVVGFTFLSLLNTIGNASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIE 449 Lambda K H 0.325 0.141 0.434 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: 717 Number of extensions: 45 Number of successful extensions: 8 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: 546 Length of database: 463 Length adjustment: 34 Effective length of query: 512 Effective length of database: 429 Effective search space: 219648 Effective search space used: 219648 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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