Align L-lysine transport protein (characterized)
to candidate GFF272 Psest_0273 arginine/ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__psRCH2:GFF272 Length = 475 Score = 430 bits (1105), Expect = e-125 Identities = 226/489 (46%), Positives = 317/489 (64%), Gaps = 16/489 (3%) Query: 14 AATSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFH 73 AA S+ + + L+AL++GS +G GIFS+PQN+ + A G +LIGW I VGML++AFVF Sbjct: 2 AANSKQLKLGALVALVVGSMIGGGIFSLPQNMAASASAGGILIGWAITAVGMLTLAFVFQ 61 Query: 74 VLARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFS 133 LA RKP LD+GVYAYA+ G GDY+GFSSAWGYW+ + I V Y L FSTLG++VP+F Sbjct: 62 SLANRKPELDAGVYAYAKAGFGDYMGFSSAWGYWISAWIGNVSYFVLLFSTLGYFVPMFG 121 Query: 134 QDHPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEK 193 + + + + S + W V +V RGI +AAF+ VTT+AKI+PL+ FI++ A + F E Sbjct: 122 EGNTLPAVIGASLVLWGVHFLVLRGIREAAFINLVTTIAKIVPLILFIVITA-VAFRLEV 180 Query: 194 FTVDLWARDG-GVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVA 252 FT D W R +G + QVR +M+ TVWVFIGIEGAS++S +A RSDV RATVIGF + Sbjct: 181 FTADFWGRGNIELGGVMQQVRNMMLVTVWVFIGIEGASIFSARAERRSDVGRATVIGFCS 240 Query: 253 VLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSW 312 VL LLV ++ LS G+++Q ELA L + SMA VLE VVG WGA LIS+GL +S+ GA +SW Sbjct: 241 VLALLVLVNVLSMGIMSQAELAGLKNPSMAGVLEQVVGRWGAVLISVGLVVSLAGALLSW 300 Query: 313 QMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQ 372 +LCAE L A D +P + N++ A +S +IQ+F+II N +TY+S++ Sbjct: 301 TLLCAEILFAAARDHTMPQFLRKENAKHVPVNALWLSNGLIQLFLIITLFNASTYLSLLY 360 Query: 373 LATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATV 432 LAT++ LVPY +SA Y ++L RG+G E + RE RK L+ +AT+ Sbjct: 361 LATSMILVPYFWSAAYGLLLGLRGEGY--------------EGAPRERRKDLLNAAIATL 406 Query: 433 YSVWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVI 492 Y++WL YA Q+VL A+ PG++ + + G+ VF E + +++ A+ Sbjct: 407 YAMWLVYAGGMQYVLLSALLYAPGVLFFAKAKHELGQPVFTAIERLIFAAVLIGAAIAAY 466 Query: 493 GLVNGSLSL 501 GL +G LSL Sbjct: 467 GLYDGFLSL 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: 694 Number of extensions: 32 Number of successful extensions: 5 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