Align L-lysine transport protein (characterized)
to candidate PfGW456L13_1876 Arginine/ornithine antiporter ArcD
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1876 Length = 475 Score = 431 bits (1107), Expect = e-125 Identities = 227/481 (47%), Positives = 315/481 (65%), Gaps = 16/481 (3%) Query: 22 IRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRKPH 81 + LIAL++GS +G GIFS+PQN+ + A GA+LIGW I VGML++AFVF LA RKP Sbjct: 10 LSALIALVVGSMIGGGIFSLPQNMAARADAGAILIGWAITAVGMLTLAFVFQTLANRKPE 69 Query: 82 LDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFVSA 141 LDSGVYAYA+ G GDY+GFSSAWGYW+ + + VGY L FSTLG++VP+F + + ++ Sbjct: 70 LDSGVYAYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFVPVFGEGNTPIAI 129 Query: 142 LAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLWAR 201 S L W V VV RGI +AAF+ VTTVAKI+PL+ FI++ A + F + FT D+W R Sbjct: 130 ACASVLLWTVHFVVMRGIKEAAFINQVTTVAKIVPLIMFIVIAA-VAFKADIFTADIWGR 188 Query: 202 DG-GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLVSI 260 + GS+ DQVR +M+ TV+VFIGIEGASVYS +A RSDV RATVIGF+ VL LLV + Sbjct: 189 NNPEFGSVMDQVRHMMLVTVFVFIGIEGASVYSARAEKRSDVGRATVIGFIGVLALLVLV 248 Query: 261 SSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAEPL 320 + LS G++TQ +LA L + S+A+VLE +VGPWGA LIS+GL +S+LGA +SW +LCAE L Sbjct: 249 NVLSLGIMTQPQLAKLQNPSLAAVLEHIVGPWGALLISVGLAISLLGALLSWALLCAEIL 308 Query: 321 ALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNLYLV 380 A D +P+ + N+ A ++ +IQ+F++I + TY S++ LA+++ LV Sbjct: 309 FATAKDKTMPAFLTKENANHVPVNAMWLTNSMIQLFLLITLFSAGTYTSLIYLASSMILV 368 Query: 381 PYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLFYA 440 PYL+SA Y V+L RG+ A E K L++G +A Y+VWL YA Sbjct: 369 PYLWSAAYAVLLCARGETYQQAPA--------------ERIKDLLIGGIALGYAVWLLYA 414 Query: 441 AEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGSLS 500 +++L A+ PG+I + R +G+ +F E G+ ++ A GL +G LS Sbjct: 415 GGLKYLLLSALLYAPGVILFAKARNEQGKPLFTVVEKGIFTCVIGGAGLAAYGLYSGLLS 474 Query: 501 L 501 L Sbjct: 475 L 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: 703 Number of extensions: 30 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