Align L-lysine transport protein (characterized)
to candidate Pf1N1B4_614 Arginine/ornithine antiporter ArcD
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_614 Length = 475 Score = 431 bits (1107), Expect = e-125 Identities = 224/483 (46%), Positives = 315/483 (65%), Gaps = 16/483 (3%) Query: 20 VSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRK 79 + + L+AL++GS +G GIFS+PQN+ + A GA+LIGW I VGML++AFVF LA RK Sbjct: 8 LKLGALVALVVGSMIGGGIFSLPQNMAASADVGAVLIGWAITAVGMLTLAFVFQTLANRK 67 Query: 80 PHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFV 139 P LD GVYAYA+ G GDY+GFSSAWGYW+ + + VGY L FSTLG++ P+F + + Sbjct: 68 PDLDGGVYAYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFFPVFGEGNTVA 127 Query: 140 SALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLW 199 + + S L W V +V RGI +AAF+ VTTVAKI+PLL F+ L+A F E FT D+W Sbjct: 128 AVIGASLLLWGVHFLVLRGIKEAAFINLVTTVAKIVPLLLFV-LIAIFAFKLEIFTADIW 186 Query: 200 A-RDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLV 258 ++ +GS+ +QVR +M+ TVWVFIGIEGAS++S +A RSDV +ATVIGF+ VLL LV Sbjct: 187 GLKNPDLGSVMNQVRKMMLVTVWVFIGIEGASIFSARAEKRSDVGKATVIGFITVLLFLV 246 Query: 259 SISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAE 318 ++ LS G++TQ ELA L + SMA+VLE VVG WGA LIS+GL +S+LGA +SW +LCAE Sbjct: 247 LVNVLSLGIMTQPELAKLQNPSMAAVLEHVVGHWGAVLISVGLIISLLGALLSWVLLCAE 306 Query: 319 PLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNLY 378 + A D +P+ + N+ A ++ ++Q+F+II + +TY+S++ LAT++ Sbjct: 307 IMFAAAKDHTMPAFLRRENANHVPVNALWLTNAMVQLFLIITLFSASTYLSLIYLATSMI 366 Query: 379 LVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLF 438 LVPYL+SA Y ++LA RG+ E + E RK L +G VA Y+VWL Sbjct: 367 LVPYLWSAAYALLLAVRGESY--------------ENAAAERRKDLFIGAVALTYAVWLI 412 Query: 439 YAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGS 498 YA +++L A+ PG I + ++ + VF E + +VV A GL +G Sbjct: 413 YAGGVKYLLLSALLYAPGAILFAKAKLEVNKSVFTNVEKLIFAAVVVGALVAAYGLYDGF 472 Query: 499 LSL 501 L+L Sbjct: 473 LTL 475 Lambda K H 0.327 0.139 0.421 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: 722 Number of extensions: 35 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: 475 Length adjustment: 34 Effective length of query: 467 Effective length of database: 441 Effective search space: 205947 Effective search space used: 205947 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