Align polyol transporter 5 (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter
Query= CharProtDB::CH_091483 (539 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 231 bits (590), Expect = 3e-65 Identities = 141/465 (30%), Positives = 247/465 (53%), Gaps = 37/465 (7%) Query: 35 YAFACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAG 94 Y ++LA+ L G+D V+SG++ ++++ ++ G GSL + +++G AG Sbjct: 10 YITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGAMVGCLIAG 69 Query: 95 RTSDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEV 154 SD GR+ +++A +F A ++ M ++PN F + RF +GIGVG A M++P+Y AE+ Sbjct: 70 YVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASMLSPMYIAEL 129 Query: 155 SPASSRGFLNSFPEVFINAGIMLGYVSNLAFSNLPLKVGWRLMLGIGAVPSVILAIGVLA 214 +P RG L + ++ I GI++ + N N + WR M G+GA+PS I IG+ Sbjct: 130 APPKFRGRLVAINQLTIVLGILITNLINYTLRNTG-EDAWRWMFGLGAIPSGIFLIGISI 188 Query: 215 MPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNS 274 +PESPRWLV +G+ A +VL+K + AD ++ Q +R S Sbjct: 189 LPESPRWLVQKGKNEKALKVLNKIGNHE---------------FAADALKNIEQTLQRKS 233 Query: 275 H--GEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQ 332 + E ++ ++ PAV + IG+ FQQ GI+ V ++P++F++ G D Q Sbjct: 234 NVEHESIFNKMYF---PAV----MIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQD-DQ 285 Query: 333 LLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVM 392 LL TV +G V F + A FL+D+IGR+PL+L GG+ + + ++ V Sbjct: 286 LLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAVLYVLIS---QLLASGSTMVS 342 Query: 393 WAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISF 452 W ++ AI +++ P+TWV SEIFP ++R + ++ ++ V+ +F Sbjct: 343 WFLLSAI-------GVYAVSLAPVTWVLISEIFPNKVRVKATTWAILCLWGAYFVLVFTF 395 Query: 453 LPMSKAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDEL 497 P+ FY++ I T+ + + F+ ET+G+ LE+++++ Sbjct: 396 -PILFDWLKESIFYIYAAICTLGCIGIWKFVKETKGKTLEEIEDI 439 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: 650 Number of extensions: 33 Number of successful extensions: 6 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: 443 Length adjustment: 34 Effective length of query: 505 Effective length of database: 409 Effective search space: 206545 Effective search space used: 206545 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