Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate RR42_RS19610 RR42_RS19610 MFS transporter
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Cup4G11:RR42_RS19610 Length = 432 Score = 287 bits (735), Expect = 5e-82 Identities = 162/436 (37%), Positives = 243/436 (55%), Gaps = 16/436 (3%) Query: 19 IDDGRLRKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFL 78 I + RKAI AA +GN +EWFDF VY F A + ++FFP + + +ATF V F Sbjct: 7 ISKAQRRKAILAATIGNGLEWFDFTVYSFFALIIAKLFFPTGNDLTSFLLTVATFGVGFF 66 Query: 79 IRPLGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQ 138 +RP+G + G D+ GR+ L +TI++M++ T IGL P+Y IG+WAP L++LA++ Q Sbjct: 67 MRPVGAIVLGVYADRVGRKAALTLTILMMALGTAIIGLAPTYSSIGLWAPALIVLARLIQ 126 Query: 139 GFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLA 198 GFS GGE GA+ F+ E++PD +RG SW F+LGA + L+ + + A Sbjct: 127 GFSAGGEVGGATAFLIEHAPDEERGAYASWQQASQGISFMLGAAMGALVINGLEPEQIDA 186 Query: 199 WGWRLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHH 258 WGWR+PF L +G +G+Y+R LEE PAF + + +K P ++ H Sbjct: 187 WGWRIPFLFGLLIGPVGMYIRSHLEEPPAFE---ARRAERAASKVKFSP---LTQVLRDH 240 Query: 259 WKSLLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIG--MLFVQPVM 316 + +L +G+ I V Y+L+ YMPSY L G + G +L + P+M Sbjct: 241 PREVLAGLGVTILWTVCTYVLVFYMPSYAKQQLGLP--LGATFQSTALCGAIILVLCPLM 298 Query: 317 GLLSDRFGRKPFVVIGSVAMFF--LAVPSFMLIN-SDIIGLIFLGLLMLAVILNAFTGVM 373 G+LSDR GRK ++G+VA+ LA P F +N S + + ++L ++L AFTG Sbjct: 299 GMLSDRVGRKR--MLGTVALIIGVLAYPLFHWLNVSPTTQTLLMVQVILGILLAAFTGPA 356 Query: 374 ASTLPALFPTHIRYSALASAFNISVLI-AGLTPTVAAWLVESSQNLYMPAYYLMVIAVIG 432 + L FPT +R + L+ A+N +V I G P + WL+ SS + PAYY++ A I Sbjct: 357 PAVLAEQFPTEVRSTGLSLAYNFAVTIFGGFAPLIVTWLIASSGSKLAPAYYVIAAAAIS 416 Query: 433 LLTGLFMKETANKPLK 448 + LFM + KPL+ Sbjct: 417 FVALLFMHDRTGKPLQ 432 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: 507 Number of extensions: 26 Number of successful extensions: 6 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: 432 Length adjustment: 33 Effective length of query: 468 Effective length of database: 399 Effective search space: 186732 Effective search space used: 186732 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