Align L-lysine transport protein (characterized)
to candidate Pf1N1B4_613 Arginine/ornithine antiporter ArcD
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_613 Length = 475 Score = 433 bits (1113), Expect = e-126 Identities = 227/486 (46%), Positives = 320/486 (65%), Gaps = 16/486 (3%) Query: 17 SRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLA 76 ++ + + LIAL++GS +G GIFS+PQN+ + A GA+LIGW I VGML++AFVF LA Sbjct: 5 TQKLRLGALIALVVGSMIGGGIFSLPQNMAARADAGAILIGWAITAVGMLTLAFVFQTLA 64 Query: 77 RRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDH 136 RKP LDSGVYAYA+ G GDY+GFSSAWGYW+ + + VGY L FSTLG++ P F Q + Sbjct: 65 NRKPELDSGVYAYAKAGFGDYMGFSSAWGYWISAWLGNVGYFVLLFSTLGYFFPAFGQGN 124 Query: 137 PFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTV 196 ++ S L W V +V RGI +AAF+ +TTVAKI+PL+ FI++ A + F + FT Sbjct: 125 TPIAIGCASVLLWAVHFLVLRGIKEAAFINQLTTVAKIVPLIMFIVIAA-VAFKADIFTR 183 Query: 197 DLWARDG-GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLL 255 D+W R G + DQVR +M+ TV+VFIGIEGASVYS +A+ RSDV RATVIGF+ VL Sbjct: 184 DIWGRSNPNFGGVMDQVRNMMLVTVFVFIGIEGASVYSARAQKRSDVGRATVIGFIGVLA 243 Query: 256 LLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQML 315 LLV ++ LS G+++Q ELA L + S+A+VLE +VGPWGA LIS+GL +S+LGA +SW +L Sbjct: 244 LLVLVNLLSLGIMSQPELATLQNPSLAAVLEHIVGPWGALLISIGLAISLLGALLSWALL 303 Query: 316 CAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLAT 375 CAE L A D +P+ + N+ A ++ ++IQIF++I + TY S++ LA+ Sbjct: 304 CAEILFATAKDKTMPAFLKKENANHVPVNALWLTNVMIQIFLLITLFSAGTYTSLIYLAS 363 Query: 376 NLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSV 435 ++ LVPYL+SA Y V+L+ G+G T+ HA E K L++G +A Y+V Sbjct: 364 SMILVPYLWSAAYAVLLS--GRGETYEHASA------------ERTKDLLIGGIALCYAV 409 Query: 436 WLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLV 495 WL YA +++L A+ PG+I + + +G+ +F E G+ +V A GL Sbjct: 410 WLLYAGGVKYLLLSALLYAPGVILFAQAKREQGKPLFTLMEKGIFSCVVAGAGLAAYGLY 469 Query: 496 NGSLSL 501 +G LSL Sbjct: 470 SGLLSL 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: 702 Number of extensions: 31 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: 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