Align histidine permease (characterized)
to candidate WP_013076931.1 BTUS_RS15100 amino acid permease
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >NCBI__GCF_000092905.1:WP_013076931.1 Length = 462 Score = 427 bits (1098), Expect = e-124 Identities = 205/450 (45%), Positives = 298/450 (66%), Gaps = 2/450 (0%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 L RGL RH++ +ALG AIG GLF GSA AI +AGPA+ ++YL+GG +F++MRALGE+A Sbjct: 7 LVRGLKERHLQLIALGGAIGVGLFLGSARAIHLAGPALTISYLVGGLVIFLIMRALGELA 66 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 ++ PVAGSF YA ++GP AGFI GWTY F + MA++TA G+Y+ +WFP V +W+ Sbjct: 67 LYKPVAGSFSTYAEEFVGPWAGFITGWTYWFMWITTAMAEITAVGVYVRYWFPAVPQWLP 126 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 L + ++ +NL V +GE EFW +L+KV IVAMI+ G I+LFG+ G S Sbjct: 127 ALIALVVMFLVNLIAVGAYGEFEFWFALIKVVTIVAMIVVGLLIILFGVWNQ-GVPVGFS 185 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLW+ GGF P G+GG + + +VMFA+ G+E+IGVTAGEA+DP +P A N + RIL+ Sbjct: 186 NLWSHGGFFPTGIGGALLALQMVMFAYVGVELIGVTAGEARDPSKTIPSATNKIIWRILI 245 Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 FYV ++++MS++PW ++ +Q SPFV F ++G +AA ++N VV+TAA+S+ NS +F Sbjct: 246 FYVGALVIIMSLYPWNELDAQNSPFVLTFQRIGFPAAADVINFVVLTAALSSCNSGVFST 305 Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367 GRM++ LAQ G AP+ LS VP + + +L+GV+LNY++P+ VF + S+ Sbjct: 306 GRMLYSLAQYGQAPRFLRGLSSRRVPAAAIAASAAVMLVGVILNYVVPQQVFTYVTSLGA 365 Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427 A +W W MIL +A RR + A QV +K+ +P P +AF+ V +L + PDT Sbjct: 366 EAAIWTWGMILVAHMAYRRRVAAGQVQAVKYRMPGSPVTNWIGLAFLALVVVLLLFDPDT 425 Query: 428 QAALIVGVVWIVLLVLAYLMWVKPAAGQAA 457 + A V +VW +LV+AY +V+ AG A Sbjct: 426 RVAFYVALVWFAILVIAY-QFVRRRAGHGA 454 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: 693 Number of extensions: 42 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: 462 Length adjustment: 33 Effective length of query: 435 Effective length of database: 429 Effective search space: 186615 Effective search space used: 186615 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 24 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