Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate BWI76_RS19960 BWI76_RS19960 MFS transporter
Query= TCDB::Q9Z7N9 (455 letters) >FitnessBrowser__Koxy:BWI76_RS19960 Length = 448 Score = 337 bits (865), Expect = 4e-97 Identities = 178/443 (40%), Positives = 262/443 (59%), Gaps = 24/443 (5%) Query: 8 FQPPKHIKEIEDQEVVKKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDK 67 F+P H + E+ Y+ R +IF +F GY YY RK+F AMP LI + GF + Sbjct: 5 FKPAAHKARLPTAEI-DPLYRRLRWQIFIGIFFGYAAYYLVRKNFALAMPYLI-EQGFSR 62 Query: 68 AQLGIIGSTLYFSYGISKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGM-----SSSIV 122 LG S + +YG SKF+ G +SD+SNPR F+ GL++ L + G SS +V Sbjct: 63 GDLGFALSGISIAYGFSKFIMGSVSDRSNPRIFLPAGLILAALVMLVMGFVPWATSSIMV 122 Query: 123 LFALWWGLNGWFQGWGWPPCARLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIID 182 +F L + L GWFQG GWPPC R + HW+++ ERG SVW+ +HN+GG + P+L F++ Sbjct: 123 MFVLLF-LCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLL--FLLG 179 Query: 183 ---YSGWRGAMYVPGILCIGMGLVLINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASE 239 ++ W A+Y+P I + + +RDTPQS GLPPIE+YK D + Sbjct: 180 MAWFNDWHAALYMPAFGAILLAIFAFAMMRDTPQSCGLPPIEEYKND---------YPDD 230 Query: 240 GTEEIERELSTREILFTYVLTNQWLWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVK 299 +E+ E EL+ ++I Y+L N+ LW++A A+ F+Y++R + DWS +L E KH+A K Sbjct: 231 YSEKHEEELTAKQIFMQYILPNKLLWYIAVANVFVYLLRYGILDWSPTYLKEVKHFALDK 290 Query: 300 ANFCVSLFEIGGLFGMLVAGWLSDKISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWV 359 +++ L+E G+ G L+ GW+SDK+ KGNRG V F + A + W + N V Sbjct: 291 SSWAYFLYEYAGIPGTLLCGWMSDKVFKGNRGATGVFFMTLVTIATVVYWLNPPGNP-GV 349 Query: 360 DGTLLFVIGFFLYGPQMMIGLAAAELSHKKAAGTASGFTGWFAYFGATFAGYPL-GKVTD 418 D + +IGF +YGP M+IGL A EL+ KKAAGTA+GFTG F Y G + A + G D Sbjct: 350 DMACMIIIGFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYTVD 409 Query: 419 VWGWKGFFIALLACASIALLLFL 441 +GW G F+ ++ + +A+LL + Sbjct: 410 FFGWDGGFMVMIGGSVLAVLLLI 432 Lambda K H 0.327 0.141 0.476 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: 809 Number of extensions: 60 Number of successful extensions: 7 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: 455 Length of database: 448 Length adjustment: 33 Effective length of query: 422 Effective length of database: 415 Effective search space: 175130 Effective search space used: 175130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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