Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate 16092 b1981 shikimate transporter (NCBI)
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Keio:16092 Length = 438 Score = 231 bits (589), Expect = 4e-65 Identities = 138/426 (32%), Positives = 224/426 (52%), Gaps = 15/426 (3%) Query: 23 RLRKAITAAALGNAMEWFDFGVYGFVA-YALGQVFFPGADPGVQMIAALATFSVPFLIRP 81 R R+A + G ++W+DF +YG A + FFP P + +AA ATF V FL RP Sbjct: 19 RARRAALGSFAGAVVDWYDFLLYGITAALVFNREFFPQVSPAMGTLAAFATFGVGFLFRP 78 Query: 82 LGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFS 141 LGGV FG GD+ GR+++L +T+ +M I+T IG++PS+ IG WAPILL+ + QGF+ Sbjct: 79 LGGVIFGHFGDRLGRKRMLMLTVWMMGIATALIGILPSFSTIGWWAPILLVTLRAIQGFA 138 Query: 142 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGW 201 VGGE+ GA++ E +P K+ F S + G G +L G+V LIS + ++ FL+WGW Sbjct: 139 VGGEWGGAALLSVESAPKNKKAFYSSGVQVGYGVGLLLSTGLVSLISMMTTDEQFLSWGW 198 Query: 202 RLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKS 261 R+PF ++ L L L++R+ +EE+ F EQ A + E H + Sbjct: 199 RIPFLFSIVLVLGALWVRNGMEESAEF-------EQQQHYQAAAKKRIPVIEALLRHPGA 251 Query: 262 LLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGML--FVQPVMGLL 319 L I L + +T Y++ + +Y + ++ + + I +++G L P L Sbjct: 252 FLKIIALRLCELLTMYIVTAFALNYSTQNMGLPRE--LFLNIGLLVGGLSCLTIPCFAWL 309 Query: 320 SDRFGRKPFVVIGSVAMFFLAVPSFMLINS-DIIGLIFLGLLMLAVILNAFTGVMASTLP 378 +DRFGR+ + G++ A P FM + + I ++F +++ + + V Sbjct: 310 ADRFGRRRVYITGTLIGTLSAFPFFMALEAQSIFWIVFFSIMLANIAHDMVVCVQQPMFT 369 Query: 379 ALFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVE-SSQNLYMPAYYLMVIAVIGLLTG 436 +F RYS + + SV+ G TP +AA L+ + N + A YL+ +I +T Sbjct: 370 EMFGASYRYSGAGVGYQVASVVGGGFTPFIAAALITYFAGNWHSVAIYLLAGCLISAMTA 429 Query: 437 LFMKET 442 L MK++ Sbjct: 430 LLMKDS 435 Lambda K H 0.327 0.142 0.427 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: 521 Number of extensions: 28 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: 501 Length of database: 438 Length adjustment: 33 Effective length of query: 468 Effective length of database: 405 Effective search space: 189540 Effective search space used: 189540 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: 51 (24.3 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