Align polyol transporter 5 (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= CharProtDB::CH_091483 (539 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 227 bits (579), Expect = 6e-64 Identities = 142/468 (30%), Positives = 235/468 (50%), Gaps = 32/468 (6%) Query: 41 ILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDWI 100 +LA++ ++ G DIGV+SGA +IK + I+D I + S+ + +G+ AG S + Sbjct: 22 VLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEWIVSSMMFGAAVGALGAGWLSSHL 81 Query: 101 GRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSPASSR 160 GR+ +++L +F G++L GL+ + L+ R I G+ +G A AP+Y AEV+P R Sbjct: 82 GRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLAEVAPEHIR 141 Query: 161 GFLNSFPEVFINAGIMLGYVSNLAFSNLPLKVGWRLMLGIGAVPSVILAIGVLAMPESPR 220 G + S ++ I GI++ ++S+ A S WR MLG+ A+P + +GVL +P+SPR Sbjct: 142 GAMISTYQLMITIGILVAFLSDTALS---YHGAWRWMLGVIAIPGALFLLGVLGLPDSPR 198 Query: 221 WLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNSHGEGVW 280 WL+M+GR +A VL + DI+ P D Sbjct: 199 WLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQRGWD---------------- 242 Query: 281 RELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLATVAVG 340 L P RR + + QQ +G++ V+ ++PRIF+ G T Q+ T VG Sbjct: 243 ---LFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDT-AAQMWFTALVG 298 Query: 341 VVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLT--IIDQSEKKVMWAVVVA 398 + +A L+DR GR+P+L T M + L +G + I Q+E+ Sbjct: 299 LTNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTEQ------YTC 352 Query: 399 IATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMSKA 458 +A ++ ++ F++ AGP+ W SEI PL+ R G + N +T+ V+ +FL + Sbjct: 353 VAMLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNT 412 Query: 459 MTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMD-ELFSGFRWRD 505 + F+L+ + V V + +PET+G LE ++ L +G R RD Sbjct: 413 IGNASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIERNLMAGKRLRD 460 Lambda K H 0.322 0.137 0.410 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: 748 Number of extensions: 55 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: 539 Length of database: 463 Length adjustment: 34 Effective length of query: 505 Effective length of database: 429 Effective search space: 216645 Effective search space used: 216645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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