Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate GFF2851 HP15_2795 transporter, BCCT family protein
Query= SwissProt::Q87PP5 (562 letters) >FitnessBrowser__Marino:GFF2851 Length = 531 Score = 634 bits (1634), Expect = 0.0 Identities = 305/511 (59%), Positives = 397/511 (77%), Gaps = 3/511 (0%) Query: 49 TDYQVGQDNVQKWGFDIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFD 108 TDY GQDN++K+GFDIHN VF ++A L+V ++ L+ P A++ L+ KNG I FD Sbjct: 11 TDYVAGQDNIEKFGFDIHNIVFPLTAILIVAFVVGTLIF-PAGAKELLDSAKNGAIAVFD 69 Query: 109 AFFMWSTNFFLLFAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVA 168 F+ S N F++F + L+F P+GKIR+GG +A P+ S +SW +MLFAAGMG GL+FWSVA Sbjct: 70 WGFLLSANLFVVFCLALIFMPVGKIRIGGLDAKPEFSLLSWFAMLFAAGMGTGLMFWSVA 129 Query: 169 EPTAYFTDWWGTPLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLP 228 EP AY+TDW+GTPL E +A+ LAMGATM+HWG+H W+IYA+V L+L+FFAFNKGLP Sbjct: 130 EPVAYYTDWYGTPLGVEPNTAEGARLAMGATMYHWGLHPWAIYAIVGLSLSFFAFNKGLP 189 Query: 229 LSLRAAFYPIFGDRAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGGI 288 L++R+AF+PI GD+ WGW G+VID ++VL+T+FGLATSLG GAQQA SGI+++F + GG+ Sbjct: 190 LTIRSAFFPILGDKVWGWPGNVIDTVSVLATIFGLATSLGFGAQQAASGISYLFDIEGGL 249 Query: 289 GTQMVVIAFVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFITFDTAMGS-LVDT 347 Q+ VIA VT +A LSV+RGI GGV++LSN NMI+A LL+F+ F A+ L DT Sbjct: 250 NIQVGVIAGVTAVATLSVIRGIHGGVRILSNANMIMAGLLLLFVIFAGPTLAVFQWLWDT 309 Query: 348 TMAYIQNIIPLSNPHGR-EDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLF 406 +++Y N+ LSNP GR ED TW HGWTVFYWAWW+SWSPFVGMFIARVS GRTVREF+ Sbjct: 310 SVSYASNMFSLSNPFGREEDTTWFHGWTVFYWAWWISWSPFVGMFIARVSHGRTVREFVT 369 Query: 407 AVIVIPTLVTLVWMSVFGGIALDQVVNKVGELGANGLTDISLTLFHVYDVLPYSSVISIL 466 AV++IPT++TL WMS FGG AL+QV N++G LG+ GLT++SL +F + + + S + S + Sbjct: 370 AVLIIPTIITLFWMSAFGGGALNQVQNEIGVLGSEGLTEVSLAMFQMLENISLSGITSFI 429 Query: 467 SIVLILVFFITSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEALQ 526 I L+L FF+TSSDSGSLVIDSIT+GGK DAP QRIFWA EG+IA V+L+VGG++AL Sbjct: 430 GITLVLTFFVTSSDSGSLVIDSITSGGKTDAPKAQRIFWAVTEGTIAGVLLFVGGEQALN 489 Query: 527 ALQSGVVATGLPFTFVLLLMCVSLVKGLRTE 557 ALQ+G ++ GLPFT VLL+M SL KGL E Sbjct: 490 ALQAGALSVGLPFTLVLLVMTYSLFKGLHHE 520 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: 1040 Number of extensions: 56 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: 562 Length of database: 531 Length adjustment: 36 Effective length of query: 526 Effective length of database: 495 Effective search space: 260370 Effective search space used: 260370 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: 52 (24.6 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