Align polyol transporter 5 (characterized)
to candidate WP_009122015.1 BUB52_RS10060 sugar porter family MFS transporter
Query= CharProtDB::CH_091483 (539 letters) >NCBI__GCF_900129655.1:WP_009122015.1 Length = 479 Score = 262 bits (670), Expect = 2e-74 Identities = 154/475 (32%), Positives = 260/475 (54%), Gaps = 36/475 (7%) Query: 37 FACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRT 96 + AI+A+ +L G+D GV+SGA+ ++++D I+D I ++ + + ++ G+ G+ Sbjct: 14 YVIAIIAATGGLLFGFDTGVISGAIPFLQKDFGIDDGVIELITTAGLVGAIAGALFCGKV 73 Query: 97 SDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSP 156 +D++GR+ I+ + IF GA+ G++P+ L+ R GI +G + P+Y AE+SP Sbjct: 74 TDYLGRKKVILASAVIFAIGAVWSGIAPDSTNLILARLFLGIAIGVSSFAVPLYIAEISP 133 Query: 157 ASSRGFLNSFPEVFINAGIMLGYVSNLAFSNLPLKVGWRLMLGIGAVPSVILAIGVLAMP 216 + RG L S ++ + G+++ Y+S+L F++ WR M G +P++IL IG+ MP Sbjct: 134 TNIRGTLVSMFQLMVTLGVLVSYLSDLFFADEVDVTCWRPMFYAGILPALILLIGMFCMP 193 Query: 217 ESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNSHG 276 ESPRWL+ +GR A +L+K E E++ H+ I + ++S+ Sbjct: 194 ESPRWLMSKGRKQKAMLILNK-----IEGHGAAEEVAHS--INEEIEKSKNEISK----- 241 Query: 277 EGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLAT 336 W EL+ P +R + AIGI FFQQ GI+ V+ +SP+IF AG + A Sbjct: 242 ---WSELI---KPTLRTPLFIAIGIMFFQQFVGINTVIYYSPKIFFMAGFDGAVSAIWAA 295 Query: 337 VAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVMWAVV 396 V VGVV LV+ + +DR+GRR L T + G++LSL L S +++ W V Sbjct: 296 VGVGVVNVVATLVSIYFVDRLGRRKLYFTGLTGIILSLITLSLSFVFVNELGNAGQWLTV 355 Query: 397 VAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMS 456 + + YVA F+I GP+ W+ SE+FP ++R G+S+G + V + ++S +F + Sbjct: 356 I---FMFLYVAFFAISIGPLGWLIISEVFPQKVRGLGASVGSLSVWVFNSIVSFTFFKIV 412 Query: 457 KAMT---------------TGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDE 496 A+T GAF +G IA +A ++ Y ++PET+G LE +++ Sbjct: 413 NALTIPGTEIMVDGEQVGNPAGAFGFYGLIALLALIWGYFYVPETKGISLEKIED 467 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: 746 Number of extensions: 43 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: 539 Length of database: 479 Length adjustment: 34 Effective length of query: 505 Effective length of database: 445 Effective search space: 224725 Effective search space used: 224725 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 24 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