Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate GFF2585 Psest_2635 choline/carnitine/betaine transport
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__psRCH2:GFF2585 Length = 688 Score = 384 bits (986), Expect = e-111 Identities = 199/503 (39%), Positives = 297/503 (59%), Gaps = 28/503 (5%) Query: 45 VFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVLIVTP 104 VF S +AIVLF V T+ F + + W+ + WF+ + ++++ +V+ + Sbjct: 22 VFYGSAIAIVLFAVWTMFFTDRSLAVINTVLGWISNTFGWFYFLAVLLYLLFVVVVATSR 81 Query: 105 LGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIENGVRT 164 G++R+G + P+++ W AMLF+AG+GI L+FF ++EP++ F Sbjct: 82 YGKIRLGPDHSKPEFNVVTWAAMLFSAGIGIDLLFFCIAEPITQFLE------------- 128 Query: 165 DWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMRSIFY 224 P G G T AA M T HW L W +Y L+ + LA FSF +GLPL++RS Y Sbjct: 129 ---PPVGEGGSTQAARH-AMELTFLHWGLSGWGVYTLVGMSLAYFSFRQGLPLSIRSSLY 184 Query: 225 PLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQVVLIV 284 P+FG+R++G +GH +D AV+ T+FG+ATSLG G Q GLN++FG+P TQ VL+V Sbjct: 185 PIFGKRIYGPIGHTVDTAAVLGTIFGIATSLGIGIIQLNFGLNYIFGIPEGTLTQAVLVV 244 Query: 285 VITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASYITNI 344 +I + IS G++ G++RLSE NM+LA +LL FV++VG T+ +L N+ Y +N Sbjct: 245 LIVVFSAISAATGVERGIRRLSEFNMLLAVLLLLFVLVVGDTVFLLNALVMNVGDYFSNF 304 Query: 345 PALSMP--FEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICVILIPS 402 +LS+ R ++ WT F+WAWWI+W PFVG+F+AR+SRGR++REF+I +L+P Sbjct: 305 ISLSLDTYAYRRPTDWLNAWTVFFWAWWIAWGPFVGLFLARISRGRTIREFVIGTLLLPL 364 Query: 403 TVCVLWMTAFGGTAISQYVND----GYEAVFNAELPLKLFAMLDVMPFAEITSVVGIILV 458 + WM+ G +AI + G +AV N + LF L +P+A +T++V IL Sbjct: 365 AFMMAWMSIMGNSAIEMVMGGALEFGQQAVSNPGSSIYLF--LQSLPWAGLTTIVVTILA 422 Query: 459 VVFFITSSDSGSLVID---TIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAM 515 +VFF+TS DSGSLV+ +I DAP R+ W G++ +AL++ GGL A Q Sbjct: 423 IVFFVTSGDSGSLVLSNFTSILKDVNSDAPVWMRILWAAIIGVLTLALLIAGGLTALQGT 482 Query: 516 AVTTGLPFTIVLLVATVSLIKGL 538 V GLPF+IVLL L K L Sbjct: 483 VVIMGLPFSIVLLFMMYGLFKAL 505 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: 1031 Number of extensions: 56 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: 688 Length adjustment: 37 Effective length of query: 516 Effective length of database: 651 Effective search space: 335916 Effective search space used: 335916 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