Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_050655916.1 C1M55_RS03105 BCCT family transporter
Query= SwissProt::Q87PP5 (562 letters) >NCBI__GCF_002893965.1:WP_050655916.1 Length = 617 Score = 390 bits (1002), Expect = e-113 Identities = 204/504 (40%), Positives = 322/504 (63%), Gaps = 13/504 (2%) Query: 64 DIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFAV 123 ++ PVF I A +V+F LI+ ++ TA DA + N I + +++ S F++FA+ Sbjct: 10 ELRKPVF-IPASIVIFALIAFAVIYAGTAADAFETLNNVISDGVGWWYILSATGFVIFAL 68 Query: 124 GLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTPLN 183 S +G IRLG + P+ +SW +MLF+AGMGIGL+F+ VAEP +++ + P+ Sbjct: 69 YCGISRIGNIRLGRDDEQPEFGMLSWFAMLFSAGMGIGLVFYGVAEPLSHYVN---PPVA 125 Query: 184 AE-AYSADAKS-LAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFGD 241 + A S DA + AM T+FHWG+H W+IY +V L LA+ + KG PLS+R P+ G Sbjct: 126 GQIAGSTDAAANQAMELTLFHWGLHAWAIYVVVGLGLAYMTYRKGRPLSIRWLLEPLLGR 185 Query: 242 -RAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGGIGTQMVVIAFVTF 300 R G +GH ID++A++ TLFG+ATSLG G QQ ++G++++ + + +I VT Sbjct: 186 ARIEGKIGHAIDVVAIVGTLFGVATSLGFGVQQISAGLDYLGWVETDNWLVITIIVIVTG 245 Query: 301 IAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFITFDT-AMGSLVDTTMAYIQNIIPL- 358 +A SVV G+ G+K LSN+NM++A AL +F+ + M S V Y+Q + L Sbjct: 246 MATFSVVSGVTKGLKWLSNINMMLAAALALFVLILGPTLFLMQSWVQNLGGYVQALPELM 305 Query: 359 --SNPHGREDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVT 416 ++P ++ W WT+FYW WW+SW+PFVGMFIAR+S+GRT+REF+F V++ PTLV Sbjct: 306 LRTSPFA--EDGWQGAWTIFYWGWWMSWAPFVGMFIARISRGRTIREFVFGVLLAPTLVG 363 Query: 417 LVWMSVFGGIALDQVVNKVGELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFI 476 +W ++FG + + N+ L A+G D + +LF + D LP ++ S+L+IV+I+ FF+ Sbjct: 364 SLWFTIFGNSGILRQRNEGTMLDASGAVDTNTSLFTLLDGLPLGTISSVLAIVVIVFFFV 423 Query: 477 TSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEALQALQSGVVATG 536 TS+DSGS+VID + GG ++ R++W + G+ AAV+L VGG +L ALQ+ +AT Sbjct: 424 TSADSGSIVIDILATGGSLETSKITRVYWTFLSGAAAAVLLIVGGSGSLTALQTVAIATA 483 Query: 537 LPFTFVLLLMCVSLVKGLRTELSA 560 +PF+ +++L C+S++K R E+++ Sbjct: 484 VPFSVIMVLACLSMLKAFRYEVAS 507 Lambda K H 0.327 0.141 0.445 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: 985 Number of extensions: 52 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: 562 Length of database: 617 Length adjustment: 37 Effective length of query: 525 Effective length of database: 580 Effective search space: 304500 Effective search space used: 304500 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 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