Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate PfGW456L13_439 High-affinity choline uptake protein BetT
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_439 Length = 664 Score = 362 bits (929), Expect = e-104 Identities = 190/515 (36%), Positives = 292/515 (56%), Gaps = 26/515 (5%) Query: 31 ALKVGPFGLDIHNR-VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLAS 89 A + P GL N VF S I+LF V + +Q + + W + + W++L + Sbjct: 3 ASSIPPSGLIRMNPPVFWFSASFILLFGVVVIAMPEQAGAWLLAAQNWAANTVGWYYLLA 62 Query: 90 GNVFVIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHF 149 ++++ +V ++ G++++G P++SY W MLFAAG+ I L FF VSEP++H Sbjct: 63 MTLYLVFVVVTALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHM 122 Query: 150 SSALGGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIF 209 P G G DAA M HW LH W ++A + + LA F Sbjct: 123 LQ----------------PPQGEAGTADAARQ-AMQILFLHWGLHGWGVFAFVGMALAYF 165 Query: 210 SFNKGLPLTMRSIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFL 269 ++ LPL +RS YPL G+R+ G +G+ +D ++ATVFGL +G+G +GL++L Sbjct: 166 AYRHNLPLALRSALYPLIGKRINGPIGYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYL 225 Query: 270 FGVPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAI 329 FG+ T QV LI ++ A+I V+G+D GV+ +S+INM+LA LL FV+ GPT + Sbjct: 226 FGIAHTQWVQVGLITLMMGAAIIVAVSGVDKGVRVMSDINMLLACALLLFVLFAGPTQHL 285 Query: 330 LTGFFDNIASYITNIPALSMPFERED--VNYSQGWTAFYWAWWISWSPFVGMFIARVSRG 387 L N+ Y+ +P S D ++ GWT FYWAWWI+WSPFVG+FIAR+SRG Sbjct: 286 LNTLIQNLGDYLGALPMKSFDLYAYDKPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRG 345 Query: 388 RSVREFIICVILIPSTVCVLWMTAFGGTAISQYVNDGYEAVFNAEL---PLKLFAMLDVM 444 R++REF+ V+LIP + WM+ FG +AI Q +N G A+ + + + L+ +L+ Sbjct: 346 RTIREFVFGVLLIPLGFTLAWMSIFGNSAIDQVLNHGMSALGMSAIDNPSMTLYLLLETY 405 Query: 445 PFAEITSVVGIILVVVFFITSSDSGSLVIDTIAA-GGKVDAPTPQ--RVFWCTFEGLVAI 501 P+++ V + + VFF+TS+DSG++V+ T++A GG D P+ RVFW LV Sbjct: 406 PWSKTVIAVTVFISFVFFVTSADSGTVVLSTLSAKGGNPDEDGPKWLRVFWGAMTALVTS 465 Query: 502 ALMLGGGLAAAQAMAVTTGLPFTIVLLVATVSLIK 536 AL+ G + A ++ V T LPF+++LL+ L K Sbjct: 466 ALLFSGSIDALKSAVVLTSLPFSLILLLMMWGLHK 500 Lambda K H 0.327 0.141 0.435 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: 1032 Number of extensions: 77 Number of successful extensions: 5 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: 553 Length of database: 664 Length adjustment: 37 Effective length of query: 516 Effective length of database: 627 Effective search space: 323532 Effective search space used: 323532 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: 53 (25.0 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