Align L-lysine transport protein (characterized)
to candidate WP_034526228.1 LOSG293_RS01580 arginine-ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >NCBI__GCF_000740055.1:WP_034526228.1 Length = 490 Score = 323 bits (829), Expect = 7e-93 Identities = 169/474 (35%), Positives = 271/474 (57%), Gaps = 25/474 (5%) Query: 20 VSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRK 79 +S+ LIAL++GS +G G+F++ ++ + AG GA++IGW+I G+GML +A F L ++ Sbjct: 9 LSLLELIALVVGSIIGGGVFNLMHDMAAGAGAGAIIIGWVITGIGMLMLAKTFQNLTMKR 68 Query: 80 PHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFV 139 P L++GVY+YA G G Y+GF+SAWGYWL + + VGYATL S + ++ P+F Sbjct: 69 PDLEAGVYSYAEAGFGKYMGFNSAWGYWLSAWLGNVGYATLMMSAVAYFFPVFKDGQNIW 128 Query: 140 SALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLW 199 S LA S + W ++ RG+ A+F+ T+ T+AK++P+ F++ + + F FT W Sbjct: 129 SILAASVILWACHFMILRGVESASFVNTIITIAKLIPIFIFLVTM-IIAFRLGVFTSGFW 187 Query: 200 ARDGG---VGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLL 256 G ++ QVR M+ TVWVFIGIEGA V+S +AR R DV RATV+G + V+L+ Sbjct: 188 YTPSGDFQFSNVMSQVRNTMLVTVWVFIGIEGAVVFSGRARRRKDVGRATVLGIITVILI 247 Query: 257 LVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLC 316 I+ LS GV+ + LA L +MA++L++VVG WGA L++ GL +SV+GA++SW M Sbjct: 248 YALITLLSLGVMRRAGLAELSQPAMAALLQSVVGKWGAVLVNAGLIISVIGAWLSWTMFA 307 Query: 317 AEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATN 376 + A +G P N GA + + I +++F+ + + Y +A+ Sbjct: 308 GQLPYEAAKEGTFPKIFAKENKNGAPVNSLWFTNICVELFMFSYLITAQAYHFFYSIASA 367 Query: 377 LYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVW 436 L+PY FSAFY + + + G ++ VG+++++Y+VW Sbjct: 368 AILIPYAFSAFYQLKYSLQEDASVAGRTG-----------------NIWVGVISSIYAVW 410 Query: 437 LFYAAEPQFVLFGAMAMLPGLIPYVW---TRIYRGEQVFNRFEIGVVVVLVVAA 487 L YAA ++L ++ G IP W R + E+VF E+ V +++ + A Sbjct: 411 LLYAANLGYILLMSLLFAAG-IPVYWLLQKRDNKAEKVFGPTEMVVAILVALLA 463 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: 683 Number of extensions: 41 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 490 Length adjustment: 34 Effective length of query: 467 Effective length of database: 456 Effective search space: 212952 Effective search space used: 212952 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