Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate WP_099093393.1 AU252_RS13810 MFS transporter
Query= SwissProt::Q47421 (501 letters) >NCBI__GCF_001484605.1:WP_099093393.1 Length = 436 Score = 252 bits (644), Expect = 2e-71 Identities = 143/442 (32%), Positives = 245/442 (55%), Gaps = 11/442 (2%) Query: 24 LRKAITAAALGNAMEWFDFGVYGFV-AYALGQVFFPGADPGVQMIAALATFSVPFLIRPL 82 +RK A+ +G +EW+D ++ A ++FFP D V + A TF+ ++ R Sbjct: 1 MRKIAVASVIGTTVEWYDLFLFATASALVFNKIFFPSFDALVGTMLAFGTFAAAYVARMA 60 Query: 83 GGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFSV 142 G FG GD+ GR+ +L +++ M +TF IGL+P Y IGI APILLL+ ++ QG ++ Sbjct: 61 GAALFGHFGDRMGRKSMLLTSLLTMGAATFAIGLLPDYATIGIAAPILLLVLRVIQGLAL 120 Query: 143 GGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGWR 202 GGE+ GA + V E+SP KRGF GS + G G ++ V ++I+ ++ E+A LAWGWR Sbjct: 121 GGEWGGAVLMVVEHSPKDKRGFYGSLVQVGVPGGTLIANLVFLIIAGIMPEEALLAWGWR 180 Query: 203 LPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKSL 262 +PF ++ L +GLY+R LEETP+F+ + G KA + E+ +WK + Sbjct: 181 IPFLASVILVAVGLYIRLTLEETPSFQAVKDA-------GAKA--KMPLAELLRKYWKQV 231 Query: 263 LVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSDR 322 L+ I+T + +L+ + +Y L +S N ++ ++A + + PV G LSD+ Sbjct: 232 LLGALATISTGTAFNILVAFGLTYGKTKLGFSTNDMLIAVLAACAVGIIMLPVFGKLSDK 291 Query: 323 FGRKPFVVIGSVAMFFLAVPSFMLINSDIIGLIFLGLLMLAVILNAFTGVMASTLPALFP 382 FGRKP +V G +A +A P F L+++ + + G ++L A G +A+ L LF Sbjct: 292 FGRKPIIVGGIIAEIVVAFPLFWLMDTRSLAGVVFGYILLMTAFCANYGPIATFLAELFG 351 Query: 383 THIRYSALASAFNISVLI-AGLTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTGLFMKE 441 + +RYS L+ A+ ++ L+ + +TP V L+ ++ A++++ A + L+ L + E Sbjct: 352 SRVRYSGLSVAYMLAGLLGSAITPVVTTALLNATGQGSSVAWFMIGSAAVSLVALLLLTE 411 Query: 442 TANKPLKGATPAASDLSEAKEI 463 T + A ++ ++ E+ Sbjct: 412 TLRSNIDAIHEAPAEAADRDEL 433 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: 519 Number of extensions: 30 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: 501 Length of database: 436 Length adjustment: 33 Effective length of query: 468 Effective length of database: 403 Effective search space: 188604 Effective search space used: 188604 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 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