Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate 354254 BT4728 putative hexose phosphate transport protein (NCBI ptt file)
Query= TCDB::Q9Z7N9 (455 letters) >FitnessBrowser__Btheta:354254 Length = 452 Score = 221 bits (562), Expect = 5e-62 Identities = 143/456 (31%), Positives = 221/456 (48%), Gaps = 33/456 (7%) Query: 10 PPKHIKEIEDQEVVKKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDKAQ 69 PP E + + V+ K W F S GY YY R S ++ D F + Q Sbjct: 13 PPVSGGETDSERSVRFKRIRWAT--FLSATTGYGIYYVCRLSMNVIRKPIVEDGVFTETQ 70 Query: 70 LGIIGSTLYFSYGISKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGMSSSIVLFALWWG 129 LGIIGS L+F Y + K +G ++D+SN + FM+ GL+ + L N+ G ++S F L WG Sbjct: 71 LGIIGSCLFFVYAVGKLTNGFLADRSNVKRFMSTGLLCSALINLCLGFTNSFFAFVLLWG 130 Query: 130 LNGWFQGWGWPPCARLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIIDYSGWRGA 189 LNGWFQ G LT WY+ ERGT++ WS SHN+G AL I ++ + GWR Sbjct: 131 LNGWFQSMGAASGVVSLTRWYSSKERGTFYGFWSASHNLGEALTFISIALLVSWMGWRYG 190 Query: 190 MYVPGILCIGMGLVLINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASEGTEEIERELS 249 M G++ + L+++ +RDTPQS G + D H + + TEE + Sbjct: 191 MIGAGVIGLLGFLMMLAFMRDTPQSQGFLLDRRGTSDAHSV------SGKQTEEFNKAQK 244 Query: 250 TREILFTYVLTNQWLWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVKANFCVSLFEI 309 VL N +W LA +S F+YI R AVN W +L K Y+ + A+F +S+ + Sbjct: 245 A-------VLKNPAIWILALSSAFMYISRYAVNSWGVFYLEAQKGYSTLDASFIISISSV 297 Query: 310 GGLFGMLVAGWLSDKISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWVDGTLLFVIGF 369 G+ G + +G +SDK G+R ++F L + + L ++ +WVD + + G Sbjct: 298 CGIVGTVFSGIISDKFFAGSRNVPALIFGL-MNVSALCLFLLVPGVHFWVDALAMVLFGL 356 Query: 370 FLYGPQMMI----GLAAAELSHKKAAGTASGFTGWFAYFGATFAGYPLGKV--------- 416 G ++I GL A +++ A+G A G G +Y GA G + Sbjct: 357 ---GIGVLICFLGGLMAVDIAPCNASGAALGVVGIASYIGAGLQDVMSGILIEGQKTVQN 413 Query: 417 -TDVWGWKGFFIALLACASIALLLFLPTWNATEKNT 451 +V+ + + A ++++ L WNA EK + Sbjct: 414 GVEVYDFTYINWFWIGAALLSVVFALLVWNAGEKRS 449 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: 750 Number of extensions: 48 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: 455 Length of database: 452 Length adjustment: 33 Effective length of query: 422 Effective length of database: 419 Effective search space: 176818 Effective search space used: 176818 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