Align L-lysine transport protein (characterized)
to candidate AO356_05265 AO356_05265 arginine-ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05265 Length = 475 Score = 426 bits (1094), Expect = e-123 Identities = 219/487 (44%), Positives = 314/487 (64%), Gaps = 16/487 (3%) Query: 16 TSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVL 75 T + + L+AL++GS +G GIFS+PQN+ + A GA+LIGW I VGML++AFVF L Sbjct: 4 TPGKLRLGALVALVVGSMIGGGIFSLPQNMAASADVGAVLIGWAITAVGMLTLAFVFQTL 63 Query: 76 ARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQD 135 A RKP LD GVY YA+ G GDY+GFSSAWGYW+ + + VGY L FSTLG++ P+F + Sbjct: 64 ANRKPDLDGGVYVYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFFPIFGEG 123 Query: 136 HPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFT 195 + + + S L W V +V RGI +AAF+ VTT+AK++PLL F +L+A F + FT Sbjct: 124 NTVAAVIGASVLLWAVHFLVLRGIKEAAFINLVTTIAKVVPLLLF-VLIAVFAFRLDIFT 182 Query: 196 VDLW-ARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVL 254 D+W ++ +GS+ +QVR +M+ TVWVFIGIEGAS++S +A RSDV +ATVIGF+ VL Sbjct: 183 ADIWGVKNPDLGSVMNQVRKMMLVTVWVFIGIEGASIFSARAEKRSDVGKATVIGFITVL 242 Query: 255 LLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQM 314 L LV ++ LS G++TQ ELA L + SMA+VLE VVG WGA LIS+GL +S+LGA +SW + Sbjct: 243 LFLVLVNVLSLGIMTQPELAKLQNPSMAAVLEHVVGHWGAVLISVGLIISLLGALLSWVL 302 Query: 315 LCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLA 374 LCAE + A D +P + N+ A ++ ++Q+F++I + +TY+S++ LA Sbjct: 303 LCAEIMFAAAKDHTMPEFLRRENANHVPANALWLTNAMVQLFLVITLFSASTYLSLIYLA 362 Query: 375 TNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYS 434 T++ LVPYL+SA Y V+LA RG+ E E RK L++G +A +Y+ Sbjct: 363 TSMILVPYLWSAAYAVLLAVRGETY--------------EGFAAERRKDLLIGAIALIYA 408 Query: 435 VWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGL 494 VWL YA +++L A+ PG I + + G+ VF E + ++ A GL Sbjct: 409 VWLLYAGGIKYLLLSALLYAPGAILFAKAKHELGKPVFTSVEKLIFAAVIAGALVAAYGL 468 Query: 495 VNGSLSL 501 +G L+L Sbjct: 469 YDGFLTL 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: 732 Number of extensions: 36 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: 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