Align histidine permease (characterized)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 318 bits (815), Expect = 2e-91 Identities = 171/454 (37%), Positives = 268/454 (59%), Gaps = 12/454 (2%) Query: 7 GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEM 66 GL+RGLS + +A+G AIGTGLF GS AI AGP+VL++Y IG ++M L EM Sbjct: 17 GLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALLLMGCLAEM 76 Query: 67 AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWI 126 V +P +GSFG YA Y+ P AGF++ + Y +V +VTA +YM +WFP V W Sbjct: 77 TVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAVPGWY 136 Query: 127 WVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVT-D 185 W++G + + G+N +VKVFG +E+ S+LK+ AIV IL G ++FG AP T Sbjct: 137 WIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLG-AYVVFG---APADSTIG 192 Query: 186 ISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRI 245 +N + GGF P G+ G+ + V +F++ IE+I V AGEA+DPQ + RA A R+ Sbjct: 193 FANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMFRL 252 Query: 246 LLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIF 305 + FY+LT+ ++++I PW G+ SPFV++ + AA ++N V++ AA+SA+NS ++ Sbjct: 253 VFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNSQLY 312 Query: 306 GAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASI 365 RMMF L++ G+AP+ L+ GVP + + ++ + L +LN + P+ F+L+ S+ Sbjct: 313 ITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYPDASFVLMMSV 372 Query: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVL--GY 423 + F ++ WLMI T R Q A L F + W Y +A+ L V ++ + Sbjct: 373 SMFGAMFTWLMIFVTHFFFRH---RHQGAPLAFRM--WGYPGTSALGAGLMVSALVTTWF 427 Query: 424 FPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQAA 457 + + L++GV +IV L++ Y +W + A + A Sbjct: 428 TREFRMTLVIGVPFIVSLLVVYFVWYRKRAVEGA 461 Lambda K H 0.329 0.142 0.441 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: 664 Number of extensions: 37 Number of successful extensions: 2 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: 468 Length of database: 466 Length adjustment: 33 Effective length of query: 435 Effective length of database: 433 Effective search space: 188355 Effective search space used: 188355 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 (21.8 bits) S2: 51 (24.3 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