Align Ectoine/proline transporter ProP (characterized)
to candidate WP_004684138.1 BMI_RS07815 MFS transporter
Query= SwissProt::Q79VC4 (504 letters) >NCBI__GCF_000022745.1:WP_004684138.1 Length = 450 Score = 187 bits (474), Expect = 9e-52 Identities = 134/425 (31%), Positives = 213/425 (50%), Gaps = 25/425 (5%) Query: 36 TVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFG-FAVSYLVRPLGGLVLGP 94 + +G +E+YDF I+ + + +F +W +L FG FA YLVRP+GG+VL Sbjct: 26 SALGGALEFYDFIIFVFFASVIGHLFFPPDMPDWLVLIQTFGIFAAGYLVRPVGGIVLAH 85 Query: 95 LGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEYAGA 154 GDK GR++V ++ +M++ST + LPT A++G A +LL + +M+QG + GGE GA Sbjct: 86 FGDKFGRKRVFAFSVFLMSISTLAMAALPTYATLGVGAPILLIVFRMLQGAAIGGEVPGA 145 Query: 155 TTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTWVTTHFYGATAMEDFGWRIPF 214 T+VAE P R G FL G LG G+ + W+ T + + WRIPF Sbjct: 146 WTFVAEHVPANRVGMACGFLCSGLTLGIMIGSLIATAINWIFT----PEELSAYAWRIPF 201 Query: 215 LTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWRPLLI 274 G++AVYLR + ETP F + N+ + KD +L L V+R+H ++I Sbjct: 202 FIGGIFGLLAVYLRRWLAETPIF---TEMKNSRLLKD------KLPLGTVLRNHMHGVVI 252 Query: 275 GIAIVAATNTAGYALTSYM-PVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWSDRV 333 + ++ +AG +T+ M +L++ G + A T + + G DR+ Sbjct: 253 SV-LLTWILSAGIVVTTLMTATFLQKLYGYTPLQSLAATSFGTLFLMFGTVSAGAIVDRI 311 Query: 334 GRKPVYATAVAATLILMVPAFLIMNTGTIG-AVLIAL-SMVAIPTGLYVALSASALPALF 391 G +A A + V F+ + VL AL +++ + G+ V + + F Sbjct: 312 GSGRFFA---VAGIFFGVATFVFYTYAAVSLPVLFALYAVMGLSVGM-VGAAPYVMVRAF 367 Query: 392 PTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAI-AGVALLFM 450 P RFSG+ SYN+S ++FGG TP+I LL + A Y++F + + G+ L M Sbjct: 368 PAPVRFSGLSFSYNVSYAVFGGLTPVIVTSLLAVN--PMAHAWYLVFIAVLTCGLGLYLM 425 Query: 451 TESSQ 455 S Q Sbjct: 426 ARSDQ 430 Lambda K H 0.322 0.138 0.407 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: 629 Number of extensions: 51 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: 504 Length of database: 450 Length adjustment: 33 Effective length of query: 471 Effective length of database: 417 Effective search space: 196407 Effective search space used: 196407 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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