Align L-lysine transport protein (characterized)
to candidate BPHYT_RS27675 BPHYT_RS27675 amino acid APC transporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__BFirm:BPHYT_RS27675 Length = 493 Score = 426 bits (1095), Expect = e-124 Identities = 214/492 (43%), Positives = 316/492 (64%), Gaps = 16/492 (3%) Query: 10 SQGAAATSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVA 69 +Q AA T++ + + L AL+IGS +G+G+FS+PQN+ S AG A+LIGWLI GVGML++A Sbjct: 18 AQTAAQTAKPLRLGLLTALVIGSMIGSGVFSLPQNMASGAGAAAVLIGWLITGVGMLTLA 77 Query: 70 FVFHVLARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYV 129 FV+ L+ RKP LD+G+YAYAR GD+VGF+SAWGYW+ + I VGY + F TLG++ Sbjct: 78 FVYQTLSTRKPELDNGIYAYARASAGDFVGFNSAWGYWVSAWIGNVGYLVIVFGTLGYFF 137 Query: 130 PLFSQDHPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGF 189 P+F + + L S + W++ V+ RG+ AA L +TTVAK++PLL FI+L A F Sbjct: 138 PVFGDGNTRAAVLGASIVLWIMHAVILRGVRSAAVLNAITTVAKVIPLLVFILL-ALAAF 196 Query: 190 SWEKFTVDLWARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIG 249 F D W +G++F QV+ M+ TVWVFIGIEGA+V+S +A+ R D+ RAT++G Sbjct: 197 RSHVFAQDFWG-SSKLGNVFTQVKSTMLITVWVFIGIEGANVFSARAQRRQDIGRATLLG 255 Query: 250 FVAVLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAY 309 F VLLLL+++S LS G++ Q ELAA+ + SMA VL+ VG WGA LIS+GL +SV GA Sbjct: 256 FTVVLLLLMAVSLLSLGIVPQSELAAMKNPSMAGVLDKAVGTWGAVLISIGLLVSVGGAL 315 Query: 310 VSWQMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVS 369 ++W +L AE L A G++P+ + NS G A ++ ++Q+F+II ++ TY + Sbjct: 316 LAWTLLAAETLFTPASGGVMPTFLARQNSHGVPANALWLTNGLVQLFLIITLVSNATYQA 375 Query: 370 MVQLATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLV 429 ++ LAT++ L+PYLFSA Y +A RG G T I+ + ++G + Sbjct: 376 LISLATSMILIPYLFSAVYATRIAMRGDGYT--------------ITDTTRSRDTLIGAM 421 Query: 430 ATVYSVWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASA 489 ATVY WL YAA P+++L A+ PG++ + W + RG +F FE+ ++ L+ A+ Sbjct: 422 ATVYCCWLLYAAGPKYLLLSALLYAPGVLLFGWAKRERGASLFKPFEVAILAALIALAAL 481 Query: 490 GVIGLVNGSLSL 501 L +G+L L Sbjct: 482 AAWLLSSGALGL 493 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: 732 Number of extensions: 32 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: 493 Length adjustment: 34 Effective length of query: 467 Effective length of database: 459 Effective search space: 214353 Effective search space used: 214353 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