Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate SMa1328 SMa1328 MtbA protein
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__Smeli:SMa1328 Length = 440 Score = 200 bits (508), Expect = 1e-55 Identities = 136/430 (31%), Positives = 217/430 (50%), Gaps = 24/430 (5%) Query: 25 RKAITAAALGNAMEWFDFGVYGFVAYALGQVFFPGADPGVQMIAALATFSVPFLIRPLGG 84 R+ I AA++GN +EW+DF ++G +A L FF + P +++ +A F+ FLIRPLG Sbjct: 10 RRVIVAASVGNIIEWYDFYIFGSLAAVLSVKFFEQSHPVAALLSTIALFTAGFLIRPLGA 69 Query: 85 VFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSVGG 144 FG +GD+ GR+ IT+ M + T IGLIP+YE IG+ A LL +M QG +GG Sbjct: 70 FLFGWMGDRVGRKYTFLITLTGMGLGTGAIGLIPTYESIGLTAAFLLFSLRMIQGLCLGG 129 Query: 145 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWRLP 204 EY GA +VAE+ PD +RG+ WL G V+ V++ T G +AF AW WR+P Sbjct: 130 EYGGAITYVAEHVPDERRGYYTGWLQTSPTLGIVVSLAVIIAARTYFGSEAFDAWAWRVP 189 Query: 205 FFLALPLGLIGLYLRHALEETPAFRQHVEK--LEQNDRDGLKAGPGVSFREIATHHWKSL 262 F ++ L I +Y+R L+ETP F++ K + QN + + IAT Sbjct: 190 FLVSFLLVGIAIYIRLQLQETPIFQEIKAKGQMTQNPWREAFLSSNIKYVGIAT------ 243 Query: 263 LVCIGLVIATNVTYYMLLTYMPSYLS-HSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSD 321 +V IG + + L ++ L+ + G +++A +LF G LSD Sbjct: 244 IVLIGQGVVWYSGQFWALYFLQQVSKVDPLNSAYIVGAALLLATPSLILF-----GWLSD 298 Query: 322 RFGRKPFVVIGSVAMFFLAVPSFMLI-------NSDIIGLIFLGLLMLAVILNAFTGVMA 374 GRKP ++ G + P ++ + N + IF+ + +L + G + Sbjct: 299 IIGRKPVILGGMLLAALTYYPLYLWLGAVTQPDNINYPIAIFI-IFILVCYVGMVYGPVG 357 Query: 375 STLPALFPTHIRYSALASAFNI-SVLIAGLTPTVAAWLVESSQNL-YMPAYYLMVIAVIG 432 + L FP IRY++++ ++I + GL P + + ++ ++ Y Y + V AV Sbjct: 358 AFLAEYFPGRIRYTSVSVPYHIGNGWGGGLVPFITSAAFAATGSIGYALIYPIAVPAVCF 417 Query: 433 LLTGLFMKET 442 +L M ET Sbjct: 418 VLAIFLMPET 427 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: 603 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 440 Length adjustment: 33 Effective length of query: 468 Effective length of database: 407 Effective search space: 190476 Effective search space used: 190476 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