Align L-lysine transport protein (characterized)
to candidate Pf1N1B4_4214 Arginine/ornithine antiporter ArcD
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4214 Length = 488 Score = 428 bits (1100), Expect = e-124 Identities = 227/489 (46%), Positives = 315/489 (64%), Gaps = 16/489 (3%) Query: 14 AATSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFH 73 +A+S + LIAL++GS VG GIFS+PQNI A GA LIGWLI GVGML +AFVF Sbjct: 15 SASSDKLKFGALIALVVGSMVGGGIFSLPQNIAKSASAGATLIGWLITGVGMLMLAFVFQ 74 Query: 74 VLARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFS 133 LA RKP LD GVYAYA+ G GDY+GFSSAWGYW+ + I V Y L FSTLG + P+F Sbjct: 75 TLANRKPKLDGGVYAYAKAGFGDYMGFSSAWGYWISAWIGNVSYMVLLFSTLGFFFPMFG 134 Query: 134 QDHPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEK 193 + + + + S L WL+ +V RGI +AAF+ +TT+AK++PL FI+ +A + F + Sbjct: 135 EGNTLPAIICASVLLWLLHFLVLRGIKEAAFINVITTIAKMVPLALFIV-IAGVAFKMDV 193 Query: 194 FTVDLW-ARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVA 252 FT D W A + +G++ +QVR +M+ TVWVFIGIEGAS++S +A RSDV +ATV+GFV Sbjct: 194 FTSDFWGAGNSDLGTVMNQVRNMMLVTVWVFIGIEGASIFSARAEKRSDVGKATVVGFVG 253 Query: 253 VLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSW 312 VLLLLV ++ S G++ Q +LA L + SMA VLE VVG WGA LIS GL +S++GA +SW Sbjct: 254 VLLLLVLVNVFSQGIMAQAQLAGLKNPSMAGVLEHVVGHWGAVLISAGLIVSLVGALLSW 313 Query: 313 QMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQ 372 +LCAE L A D +P + N+ A +S +IQ+F+II N +TY+S++ Sbjct: 314 TLLCAEILFASARDHTMPEFLRKENANQVPANALWLSNGLIQLFLIITLFNSSTYLSLLY 373 Query: 373 LATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATV 432 LAT++ LVPY +SA Y ++LA R + E ++ E K L++G++A + Sbjct: 374 LATSMILVPYFWSAAYALLLAWRNETY--------------EEAQGERTKDLVIGVIAVL 419 Query: 433 YSVWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVI 492 Y+VWL YAA Q++L A+ PG I + + G+ VF E + VV+++ A Sbjct: 420 YAVWLVYAAGAQYLLLSALLYAPGAILFAKAKRELGQPVFTSIEKVIFVVVMIGALIAGY 479 Query: 493 GLVNGSLSL 501 GL +G LSL Sbjct: 480 GLYSGFLSL 488 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: 714 Number of extensions: 35 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: 488 Length adjustment: 34 Effective length of query: 467 Effective length of database: 454 Effective search space: 212018 Effective search space used: 212018 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