Align Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized)
to candidate Pf1N1B4_5977 Transporter, MFS superfamily
Query= SwissProt::Q47421 (501 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5977 Length = 465 Score = 275 bits (702), Expect = 3e-78 Identities = 150/431 (34%), Positives = 257/431 (59%), Gaps = 17/431 (3%) Query: 24 LRKAITAAALGNAMEWFDFGVYGFV-AYALGQVFFPGADPGVQ-MIAALATFSVPFLIRP 81 L++ + AA G EW++F +YG A GQ+FF D + +IAA A ++V FL RP Sbjct: 16 LKRVVAAAMAGTVAEWYEFFLYGTASALVFGQLFFRQTDSPIDGIIAAFALYAVGFLARP 75 Query: 82 LGGVFFGALGDKYGRQKILAITIIIMSISTFCIGLIPSYERIGIWAPILLLLAKMAQGFS 141 LGG+ FG GDK+GR+++L ++++++ I+TF +G +P +++IG AP+LL+L ++ QGF+ Sbjct: 76 LGGLVFGHYGDKFGRKRLLQLSLVVVGITTFLMGCLPGFDQIGYAAPVLLVLLRLIQGFA 135 Query: 142 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTLIGEQAFLAWGW 201 GGE+ GA + V+E+ PD +RGF SW G AG ++ ++L+S+ + E+ FLAWGW Sbjct: 136 FGGEWGGAILLVSEHCPDNRRGFWASWPQAGVPAGNLVATVALLLLSSNLSEEQFLAWGW 195 Query: 202 RLPFFLALPLGLIGLYLRHALEETPAFRQHVEKLEQNDRDGLKAGPGVSFREIATHHWKS 261 R+ F+ + + LIG ++R ++++ P F++ + Q + L GV E+ HHW++ Sbjct: 196 RVAFWFSAVVVLIGYWIRTSVDDAPIFKEAQARQAQIKQQQL----GVV--EVLRHHWRA 249 Query: 262 LLVCIGLVIATNVTYYMLLTYMPSYLSHSLHYSENHGVLIIIAIMIGMLFVQPVMGLLSD 321 +LV IG A N+ YY ++T+ +YL +H + +L++ + F+ P+MG LSD Sbjct: 250 VLVGIGARFAENILYYTVVTFSITYLKLVVHKDTSEILLLMFGAHLVHFFLIPLMGYLSD 309 Query: 322 RFGRKPFVVIGSVAMFFLAVPSFMLINSD----IIGLIFLGLLMLAVILNAFTGVMASTL 377 GRKP + G+V F F ++++ I+ I LGL + ++ ++ +MA Sbjct: 310 IVGRKPVYLTGAVLTAFWGFVGFPMMDTGNNWLIMAAIILGLGIESMTYAPYSALMAE-- 367 Query: 378 PALFPTHIRYSALASAFNISVLIAG-LTPTVAAWLVESSQNLYMPAYYLMVIAVIGLLTG 436 +FPTH+RY+AL+ + ++ + AG L P +A L+ + A+YL+ A+I ++ Sbjct: 368 --MFPTHVRYTALSLCYQVAPIFAGSLAPLIAITLLNKYHSSTPIAWYLVGAALISIVAV 425 Query: 437 LFMKETANKPL 447 +ET K L Sbjct: 426 GLTRETRGKSL 436 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: 543 Number of extensions: 37 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: 465 Length adjustment: 34 Effective length of query: 467 Effective length of database: 431 Effective search space: 201277 Effective search space used: 201277 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: 52 (24.6 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