Align uncharacterized amino-acid permease C869.11 (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= CharProtDB::CH_091412 (580 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 180 bits (456), Expect = 1e-49 Identities = 121/404 (29%), Positives = 194/404 (48%), Gaps = 23/404 (5%) Query: 73 LKRSLKSRHMQMISIGGAIGTGLYVGSGSSLADGGPASVIINYSLIGIMMFFIVYALGEM 132 L+R L + + MI+IGGAIGTGL++GSG ++ GP SV+++Y++ ++ ++ L EM Sbjct: 18 LQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGP-SVLVSYAIGALIALLLMGCLAEM 76 Query: 133 AVAYPVAGGFNTYATRFIDPAWGFAVSWNYFINYFVTFPLELTTCAITFRYW-TDINSAA 191 VA+P +G F YA +I P GF V + Y+ + E+T A+ +YW + Sbjct: 77 TVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAVPGWY 136 Query: 192 WISIFLVVIIIVNLFGVRAYGEVEFILSTVKVVATFGFIILAIIINCGGVPTDHRGYIGG 251 WI F +I +N V+ +G VE++ S +K+VA GFI+L + G P D Sbjct: 137 WIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYV-VFGAPADSTIGFAN 195 Query: 252 SIIKHKPFRHGFKGFCSVFTTAAFSFSGTEVIGLAAAEVDNPQKALPHAVKQVFWRIAIF 311 F G G + FS+ E+I +AA E +PQKA+ A + +R+ F Sbjct: 196 YTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMFRLVFF 255 Query: 312 YVVSLILIGLLISPDDPNLMGNGSTSVSPFVLAIKEANIKGLPSVFNAVIIISVVSVTNS 371 Y+++L L+ L I P T SPFV + ++ G V N VI+++ +S NS Sbjct: 256 YLLTLALM-LAIVP-----WNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNS 309 Query: 372 STYTAGRTLHGMANLKQAPSFFKYTDRLGRPLLAM-IVVLLFGFFAYINEADKNGNDVSD 430 Y R + ++ AP + G P+ A+ + + +N D Sbjct: 310 QLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVV------YPD 363 Query: 431 TVFNWLLALSGLSNFFTWGSICLCHIIFR-------LAFKKQGH 467 F ++++S FTW I + H FR LAF+ G+ Sbjct: 364 ASFVLMMSVSMFGAMFTWLMIFVTHFFFRHRHQGAPLAFRMWGY 407 Lambda K H 0.325 0.141 0.429 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: 688 Number of extensions: 44 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: 580 Length of database: 466 Length adjustment: 35 Effective length of query: 545 Effective length of database: 431 Effective search space: 234895 Effective search space used: 234895 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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