Align L-lysine transport protein (characterized)
to candidate PP_1003 PP_1003 arginine/ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__Putida:PP_1003 Length = 475 Score = 419 bits (1076), Expect = e-121 Identities = 227/478 (47%), Positives = 315/478 (65%), Gaps = 16/478 (3%) Query: 25 LIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLARRKPHLDS 84 LIAL++GS +G GIFS+PQN+ + A GA+LIGW I VGML++AFVF LA RKP LDS Sbjct: 13 LIALVVGSMIGGGIFSLPQNMAARADVGAVLIGWGITAVGMLALAFVFQTLANRKPELDS 72 Query: 85 GVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDHPFVSALAV 144 GVYAYA+ G G+Y+GFSSAWGYW+ + + VGY L FSTLG Y P+F + + ++ Sbjct: 73 GVYAYAKAGFGEYMGFSSAWGYWISAWLGNVGYFVLLFSTLGFYFPVFGEGNTPIAIGCA 132 Query: 145 SALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTVDLWA-RDG 203 S L W V +V RGI +AAF+ VTTVAK++PLL F+++ AF F + FT D+W + Sbjct: 133 SLLLWSVHFLVLRGIKEAAFINQVTTVAKVVPLLIFVVIAAF-AFRADIFTRDIWGLSNP 191 Query: 204 GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVAVLLLLVSISSL 263 GS+ +QVR +M+ TV+VFIGIEGASVYS +A+ RSDV +ATVIGF+ VL LLV ++ L Sbjct: 192 QFGSVLEQVRNMMLVTVFVFIGIEGASVYSGRAQRRSDVGKATVIGFLGVLALLVLVNVL 251 Query: 264 SFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSWQMLCAEPLALM 323 S G++TQ ELA L + S+ASVLE +VGPWGA LISLGL +S+LGA +SW +LCAE L Sbjct: 252 SLGIMTQPELAGLQNPSLASVLEHIVGPWGALLISLGLAVSLLGALLSWALLCAEILYAT 311 Query: 324 AMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQLATNLYLVPYL 383 A D +P + N+ A ++ +IQ F++I + TY S++ LA+++ LVPYL Sbjct: 312 ARDKTMPRFLAKENANHVPANALWLTNCMIQGFLLITLFSAGTYTSLIYLASSMILVPYL 371 Query: 384 FSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATVYSVWLFYAAEP 443 +SA Y V+LA R + +AG R RK L+V LVA +Y+VWL YA Sbjct: 372 WSAAYAVLLAMRAE----TYAG----------QPRLRRKDLLVALVALLYAVWLLYAGGL 417 Query: 444 QFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVIGLVNGSLSL 501 +++L A+ PG+I + + +G+ +F +E + ++V A+ L +G LSL Sbjct: 418 KYLLLSALLYAPGVILFARAKHEQGQTLFTAWEKLIFAAVLVGAALAAYALYSGLLSL 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: 710 Number of extensions: 35 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