Align L-lysine transport protein (characterized)
to candidate AO356_23935 AO356_23935 arginine-ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23935 Length = 497 Score = 389 bits (998), Expect = e-112 Identities = 208/484 (42%), Positives = 306/484 (63%), Gaps = 16/484 (3%) Query: 18 RTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLAR 77 R +S+ LIAL++GS +G+GIFS+PQN+ + AG GA+LIGWLI GVGMLS+A V+ L+ Sbjct: 30 RRLSLSLLIALVVGSMIGSGIFSLPQNMAASAGAGAILIGWLITGVGMLSLALVYQTLSN 89 Query: 78 RKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHP 137 R+P LD+GV+AYAR G+++GF+SAWGYW+ + I V Y + F+ L ++ PLF + + Sbjct: 90 RQPELDNGVFAYARALGGEFLGFNSAWGYWISAWIGNVSYLVILFAALSYFFPLFGEGNN 149 Query: 138 FVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVD 197 + + S + W + ++ RG+ AA +TT+AK++PLL FI LV FS + F VD Sbjct: 150 KAAIIGASVVLWALHWMILRGMRTAAKANALTTIAKVVPLLLFIGLV-IAAFSKDTFMVD 208 Query: 198 LWARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLL 257 W +GS DQV+ M+ TVWVFIGIEGA+V+S +A R+DV RATV+GF+ LLLL Sbjct: 209 FWGTPA-LGSTLDQVKSTMLVTVWVFIGIEGANVFSARAAERADVGRATVMGFILTLLLL 267 Query: 258 VSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCA 317 +++S LS G+L Q ELAAL + SMA VLEAV GPWGA LIS+GL +SV GA ++W +L A Sbjct: 268 IAVSLLSLGILRQPELAALKNPSMAGVLEAVTGPWGAVLISIGLIVSVGGALLAWTLLAA 327 Query: 318 EPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNL 377 E + A + ++P + N GA A I+ IQ+F+++ + +Y++++ LAT++ Sbjct: 328 ESVFTPAKEKVMPRLLATENQHGAPANALWITNGCIQLFLLLTLYSSASYLALISLATSM 387 Query: 378 YLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWL 437 L+PYLFS Y + + +G+ H G + D + + +VAT Y VWL Sbjct: 388 ILLPYLFSGLYALKMTWQGQTYA-GHRGLQLRD-------------MAIAVVATGYCVWL 433 Query: 438 FYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNG 497 YAA P+++L A+ PG + Y+ + R + F G+++V+ VAA L G Sbjct: 434 LYAAGPRYMLLSALLYAPGSLIYLSAQRARTGRALTGFGWGLLIVIWVAAIFAGWMLWAG 493 Query: 498 SLSL 501 LSL Sbjct: 494 QLSL 497 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: 746 Number of extensions: 40 Number of successful extensions: 3 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: 497 Length adjustment: 34 Effective length of query: 467 Effective length of database: 463 Effective search space: 216221 Effective search space used: 216221 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