Align L-lysine transport protein (characterized)
to candidate WP_011778655.1 MVAN_RS07035 arginine-ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >NCBI__GCF_000015305.1:WP_011778655.1 Length = 496 Score = 409 bits (1051), Expect = e-118 Identities = 211/487 (43%), Positives = 306/487 (62%), Gaps = 21/487 (4%) Query: 20 VSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRK 79 + + L AL++GS +G+GIF++P + A PG +LIGW++ GVGML +AFVF LA RK Sbjct: 25 LGLAALTALVVGSMIGSGIFALPSQMAGSAAPGPLLIGWVVTGVGMLMLAFVFQTLATRK 84 Query: 80 PHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFV 139 P +D GVY YAR G G+Y+GF+SA+GYW+ + + V Y L FSTLG++ P F Sbjct: 85 PDVDGGVYGYARAGFGNYIGFTSAFGYWMSAWVGNVAYLVLLFSTLGYFFPSFEGGATVP 144 Query: 140 SALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLW 199 + + S + W+V + RG+ AA + V T+AK++P++ FI L A +GF FT D W Sbjct: 145 AIIGASVVLWIVHAMTLRGVQTAALVNVVVTIAKVVPIVVFIALAA-VGFKAGLFTADFW 203 Query: 200 AR----DGG-VGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVL 254 R DG +G QV+ +M+ TVWVFIGIEGA+VYS++A R+DV RATV+GF AVL Sbjct: 204 GRTTEIDGAPLGDTMTQVKNMMLVTVWVFIGIEGAAVYSQRAARRADVGRATVLGFAAVL 263 Query: 255 LLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQM 314 LL+ ++ LS+G++ Q ELA +PD SMA +LE VG WGAA IS+GL +S+LGA ++W + Sbjct: 264 ALLLLVNLLSYGLVAQAELAGIPDPSMAGLLENEVGSWGAAFISIGLIISLLGALIAWVL 323 Query: 315 LCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLA 374 LC E L L A++ ++P + N+ G+ A ++ + +Q ++ NE+TY +++ LA Sbjct: 324 LCVEILRLPALENVMPKALAKENAHGSPATALWLTNLCVQALLLWTLANESTYTNLIYLA 383 Query: 375 TNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYS 434 T+L L+PYL+SA Y V+LA RG+ H T K L+VG+VA VY+ Sbjct: 384 TSLILLPYLWSAAYQVLLAVRGETYESGHGRT---------------KDLLVGVVALVYA 428 Query: 435 VWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGL 494 VWL YA Q++L A+ L G YVW R G F + E+ V V+VV + A + L Sbjct: 429 VWLLYAGGWQYLLMAAVFYLVGTALYVWARRESGLPAFTKGELVVFAVVVVTSVAAIALL 488 Query: 495 VNGSLSL 501 G+L++ Sbjct: 489 ATGNLAV 495 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: 755 Number of extensions: 31 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: 496 Length adjustment: 34 Effective length of query: 467 Effective length of database: 462 Effective search space: 215754 Effective search space used: 215754 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 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