Align Glucose-6-P:Pi antiporter, Hpt (may also transport other organophosphates including C3 organophosphates) (characterized)
to candidate WP_046156002.1 VL52_RS04955 glycerol-3-phosphate transporter
Query= TCDB::Q9Z7N9 (455 letters) >NCBI__GCF_000971335.1:WP_046156002.1 Length = 447 Score = 337 bits (864), Expect = 5e-97 Identities = 183/458 (39%), Positives = 271/458 (59%), Gaps = 25/458 (5%) Query: 8 FQPPKHIKEIEDQEVVKKKYKYWRIRIFYSMFIGYIFYYFTRKSFTFAMPTLIADLGFDK 67 F+P H+ + D + Y+ R +IF +F+GY YY RK+F+ AMP L+ + GF + Sbjct: 5 FKPAPHLPPLPDAQQ-HGLYRRLRWQIFLGIFLGYAGYYLVRKNFSLAMPYLV-EQGFSR 62 Query: 68 AQLGIIGSTLYFSYGISKFVSGVMSDQSNPRYFMAIGLMITGLTNIFFGM-----SSSIV 122 LG S + +YG+SKF+ G +SD+SNPR F++ GL+++ + G SS V Sbjct: 63 GDLGFAMSGVAIAYGLSKFLMGAVSDRSNPRVFLSAGLVLSAAVFLLMGFAPWATSSVGV 122 Query: 123 LFALWWGLNGWFQGWGWPPCARLLTHWYAKSERGTWWSVWSTSHNIGGALIPILTGFIID 182 +F L + LNGWFQG GWP C R + HW+++ ERG S+W+ +HN+GG LI L FI+ Sbjct: 123 MFVLLF-LNGWFQGMGWPACGRTMVHWWSQKERGGVVSIWNCAHNVGGGLIGPL--FILG 179 Query: 183 ---YSGWRGAMYVPGILCIGMGLVLINRLRDTPQSLGLPPIEKYKRDPHHAHHEGKSASE 239 ++ WR A YVP IG+ + +RDTPQS GLPP+E Y+ D + Sbjct: 180 MGWFNDWRAAFYVPAAAAIGVAVFAWLTMRDTPQSCGLPPVEAYRND---------YPED 230 Query: 240 GTEEIERELSTREILFTYVLTNQWLWFLAAASFFIYIVRMAVNDWSALFLIETKHYAAVK 299 ++ E+EL+ REI Y+L N+ LW++A A+ FIY++R V DW+ +L E KH++ K Sbjct: 231 YSDTHEQELTAREIFRKYILPNKLLWYIALANVFIYLLRYGVLDWAPTYLKEVKHFSVDK 290 Query: 300 ANFCVSLFEIGGLFGMLVAGWLSDKISKGNRGPMNVLFSLGLLFAILGMWFSRSHNQWWV 359 +++ L+E G+ G L+ GW+SDK+ +GNRG V F + A + W + + N V Sbjct: 291 SSWAYFLYEWAGIPGTLLCGWMSDKLFRGNRGATGVFFMALVTLATVVYWLNPAGNP-TV 349 Query: 360 DGTLLFVIGFFLYGPQMMIGLAAAELSHKKAAGTASGFTGWFAYFGATF-AGYPLGKVTD 418 D L IGF +YGP M++GL A EL+ KKAAGTA+GFTG F Y G + A +G D Sbjct: 350 DMLALIAIGFLIYGPVMLVGLHALELAPKKAAGTAAGFTGLFGYLGGSVAANAAVGYTVD 409 Query: 419 VWGWKGFFIALL-ACASIALLLFLPTWNATEKNTRSKA 455 +GW G F L+ +C + +LL L TW+ ++ + A Sbjct: 410 HFGWDGGFALLIGSCVAAIVLLALTTWHGHQQGKLASA 447 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: 825 Number of extensions: 48 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: 455 Length of database: 447 Length adjustment: 33 Effective length of query: 422 Effective length of database: 414 Effective search space: 174708 Effective search space used: 174708 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 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