Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate Pf6N2E2_3917 High-affinity choline uptake protein BetT
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3917 Length = 667 Score = 363 bits (932), Expect = e-104 Identities = 185/500 (37%), Positives = 286/500 (57%), Gaps = 24/500 (4%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF + I+LF + + Q + + W + + W+++ + ++++ +V ++ Sbjct: 18 VFYFAATFILLFGLVVIAMPAQAGAWLLAAQNWAANTVGWYYMLAMTLYLVFVVVTALSG 77 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 G++++G P++SY W MLFAAG+ I L FF VSEP++H Sbjct: 78 YGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMVQ------------- 124 Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224 P G G T A+ M HW LH W ++A + + LA F++ LPL +RS Y Sbjct: 125 ---PPQGEAGGTAEAARQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALY 181 Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIV 284 PL G+R+ G +G+ +D ++ATVFGL +G+G +GL++LFG+ T QV LIV Sbjct: 182 PLIGKRINGPIGYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLIV 241 Query: 285 VITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNI 344 ++ A+I VAG+D GV+ +S+INM+LA LL FV+ GPT +L NI Y+ + Sbjct: 242 LMMGAAIIVAVAGVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNIGDYLGAL 301 Query: 345 PALSMPFERED--VNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPS 402 P S D ++ GWT FYWAWWI+WSPFVG+FIAR+SRGR++REF+ V+LIP Sbjct: 302 PMKSFDLYAYDKPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPL 361 Query: 403 TVCVLWMTAFGGTAISQYVNDGYEAVFNAEL---PLKLFAMLDVMPFAEITSVVGIILVV 459 + WM+ FG +AI Q +N G A+ + L + L+ +L+ P+++ V + + Sbjct: 362 GFTLAWMSIFGNSAIDQVLNHGMSALGMSALENPSMSLYLLLETYPWSKTVIAVTVFISF 421 Query: 460 VFFITSSDSGSLVIDTIAA-GGKVDAPTPQ--RVFWCTFEGLVAIALMLGGGLAAAQAMA 516 VFF+TS+DSG++V+ T++A GG D P+ RVFW LV AL+ G + A ++ Sbjct: 422 VFFVTSADSGTVVLSTLSAKGGNPDEDGPKWLRVFWGAMTALVTSALLFSGSIDALKSAV 481 Query: 517 VTTGLPFTIVLLVATVSLIK 536 V T LPF+++LL+ L K Sbjct: 482 VLTSLPFSLILLLMMWGLHK 501 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: 1042 Number of extensions: 80 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: 667 Length adjustment: 37 Effective length of query: 516 Effective length of database: 630 Effective search space: 325080 Effective search space used: 325080 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