Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate Echvi_0794 Echvi_0794 choline/carnitine/betaine transport
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Cola:Echvi_0794 Length = 529 Score = 518 bits (1333), Expect = e-151 Identities = 249/496 (50%), Positives = 347/496 (69%) Query: 51 FKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSML 110 F V+ PVF + +I +F+ I +I + E F ++ I GWL+++++ +F+ Sbjct: 6 FDVHAPVFWPASVLIIIFIAITLIVGEPMEKAFDAIKFFITDKTGWLFIIAINIFIVFCF 65 Query: 111 FLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPL 170 +LAFS+YG ++LG D+E EF +W AMLF+AGMGIGL+++ V EP++H+A PP EP Sbjct: 66 YLAFSKYGTIRLGGKDAETEFSTSAWFAMLFSAGMGIGLLFWGVAEPVSHYAKPPYGEPF 125 Query: 171 TIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPI 230 +I + + M++TF HWG HAWAIY+VV L+LA+F + LPLT+RS YP+L + IHG I Sbjct: 126 SIGSAQRGMNLTFLHWGFHAWAIYAVVALALAFFTFNRKLPLTIRSIFYPILGDRIHGWI 185 Query: 231 GHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVV 290 G V+D+ A+ T+FGLATSLGFG+ QIN GLNYL + S+ VQ+LL++ +T +AT SV Sbjct: 186 GDVIDVMAVLATLFGLATSLGFGVRQINGGLNYLFDVDISVTVQVLLISGITLMATASVF 245 Query: 291 TGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYE 350 +G++KGVR+LSE N+ +A L++FV++ GPT + R FVQN+G YL+ + + AY Sbjct: 246 SGLDKGVRVLSEWNVRIAAALLIFVILAGPTVFIFRGFVQNLGNYLNQFIAVSTWTEAYR 305 Query: 351 PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGN 410 W +WT+FYWAWW+SWSPFVGMFIARIS+GRT+REF+ VL VPA+ TF W+T G Sbjct: 306 DNEWQGTWTIFYWAWWVSWSPFVGMFIARISKGRTIREFILGVLLVPALLTFFWLTAMGG 365 Query: 411 TAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSL 470 +AI++D + A+D+ D S ALF F P + S + VLLV FFVTSSDSGSL Sbjct: 366 SAIFMDMQNETHQFAKDIIKDESTALFVFLHEFPLSTLGSGIGVLLVMSFFVTSSDSGSL 425 Query: 471 VIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILV 530 VID+I +GG+ P QRIFW G VAAVLL GGLTALQ+ATI+T LPF +V+LI+ Sbjct: 426 VIDSITAGGKLDAPVGQRIFWALAEGTVAAVLLIGGGLTALQTATITTGLPFLIVLLIMC 485 Query: 531 WSLFVGMRADLARTQS 546 +SLF G++ + AR ++ Sbjct: 486 FSLFRGLQKEHARKEA 501 Lambda K H 0.326 0.139 0.422 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: 1053 Number of extensions: 52 Number of successful extensions: 2 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: 706 Length of database: 529 Length adjustment: 37 Effective length of query: 669 Effective length of database: 492 Effective search space: 329148 Effective search space used: 329148 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