Align Ectoine/proline transporter ProP (characterized)
to candidate WP_057507085.1 ABB28_RS02395 MFS transporter
Query= SwissProt::Q79VC4 (504 letters) >NCBI__GCF_001431535.1:WP_057507085.1 Length = 549 Score = 172 bits (435), Expect = 4e-47 Identities = 101/325 (31%), Positives = 162/325 (49%), Gaps = 12/325 (3%) Query: 30 RPAIKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGG 89 + I + +G EWYDF +YG L + F G+ + ++ + FA + VRP G Sbjct: 15 KKVIFASSLGTVFEWYDFFLYGSLAAIIAKQFFSGVNETTGMIFALLAFAAGFFVRPFGA 74 Query: 90 LVLGPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGG 149 G LGD++GR+ VT+ +M +ST L+G+LP ASIG A V+L +L++ QG + GG Sbjct: 75 AFFGSLGDRIGRKYTFLVTILIMGISTFLVGVLPNYASIGFAAPVILIILRLAQGLAMGG 134 Query: 150 EYAGATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTWVTTHFYGATAMEDFG 209 EY GA TYVAE AP +RG + +F+ + LG ++ +F G A E +G Sbjct: 135 EYGGAATYVAEHAPANKRGLYTSFIQCTATLGLFMSLLIIL----ACRYFLGNEAFEAWG 190 Query: 210 WRIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHW 269 WRIPFL +I L I+V++R ++ E+P F+ + E K ++ P+ G ++ Sbjct: 191 WRIPFLVSIVLLGISVWIRLQLSESPLFQQMKAE-----GKGSKTPFRDSLKDGNLK--- 242 Query: 270 RPLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMW 329 LL+ + A Y Y +L + + + ++ + L + F G Sbjct: 243 LMLLVLLGAAAGQAVVWYGGQFYALFFLSSMLKVDATTSYLLIAAALALGVPFFIFFGWL 302 Query: 330 SDRVGRKPVYATAVAATLILMVPAF 354 SDR+GRK + + +P F Sbjct: 303 SDRIGRKWIILAGCLLAAVTYIPVF 327 Score = 36.2 bits (82), Expect = 3e-06 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 1/65 (1%) Query: 363 GAVLIALSMVAIPTGLYVALSASALPALFPTASRFSGMGISYNISVSLFGGTTPLITQFL 422 G + + +V T +Y ++A L LFPT R++ M + Y+I FGG P I+ L Sbjct: 452 GTIFMLWILVLYVTMVYGPIAAY-LVELFPTRIRYTSMSLPYHIGNGWFGGFLPAISFAL 510 Query: 423 LQKTG 427 + TG Sbjct: 511 VAGTG 515 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: 706 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 504 Length of database: 549 Length adjustment: 35 Effective length of query: 469 Effective length of database: 514 Effective search space: 241066 Effective search space used: 241066 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: 52 (24.6 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