Align L-lysine transport protein (characterized)
to candidate PP_1002 PP_1002 arginine/ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__Putida:PP_1002 Length = 475 Score = 422 bits (1086), Expect = e-122 Identities = 220/487 (45%), Positives = 316/487 (64%), Gaps = 16/487 (3%) Query: 16 TSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVL 75 +S + + L+AL++GS +G GIFS+PQN+ + AG GA+LIGW I VGML++AFVF L Sbjct: 4 SSGKLKLGALVALVVGSMIGGGIFSLPQNMAASAGVGAVLIGWAITAVGMLTLAFVFQTL 63 Query: 76 ARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQD 135 A RKP LD GVYAYA+ G GDY+GFSSAWGYW+ + + VGY L FSTLG++ P+F + Sbjct: 64 ANRKPDLDGGVYAYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFFPIFGEG 123 Query: 136 HPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFT 195 + + + S L W V +V RGI +AAF+ VTTVAK++PL+ F ++ F F + FT Sbjct: 124 NTPAAIIGASILLWAVHFLVLRGIKEAAFINLVTTVAKVVPLVLFALICLF-AFRLDIFT 182 Query: 196 VDLWAR-DGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVL 254 D+WA +GS+ +QVR +M+ TVWVFIGIEGAS++S +A R+DV +ATVIGFV VL Sbjct: 183 ADIWAMGTPELGSVMNQVRNMMLVTVWVFIGIEGASIFSARAEKRTDVGKATVIGFVTVL 242 Query: 255 LLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQM 314 L LV ++ LS G++TQ ELA L + SMA+VLE VVG WGA LIS+GL +S+LGA +SW + Sbjct: 243 LFLVLVNVLSLGIMTQPELAKLQNPSMAAVLEHVVGHWGAVLISVGLVISLLGALLSWVL 302 Query: 315 LCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLA 374 LCAE + A D +P + N++ A ++ ++QIF++I + +TY+S++ LA Sbjct: 303 LCAEIMFAAAKDHTMPEFLRRENAKQVPANALWLTNAMVQIFLVITLFSSSTYLSLIYLA 362 Query: 375 TNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYS 434 T++ LVPYL+SA Y +LA R + E + E +K LI+G +A +Y+ Sbjct: 363 TSMILVPYLWSAAYAFLLALRSETY--------------EQALAERKKDLIIGGIALLYA 408 Query: 435 VWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGL 494 +WL YA +++L A+ PG I + + G+ VF E + +V+ A GL Sbjct: 409 IWLLYAGGVKYLLLSALLYAPGAILFAKAKREVGKPVFTNVEKLIFAAVVIGALVAAYGL 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: 726 Number of extensions: 36 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