Align histidine permease (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 511 bits (1317), Expect = e-149 Identities = 241/443 (54%), Positives = 330/443 (74%), Gaps = 1/443 (0%) Query: 6 NGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65 + L+RGL RHIR MALGSAIG GLF GSA+AI++AGPA+LL+YL+GG A+F++MRALGE Sbjct: 5 DSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGE 64 Query: 66 MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRW 125 MAV NPVAGSF +YA YLGP+ G++ GW Y F ++ +A++TA G+YMG WFP+V +W Sbjct: 65 MAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQW 124 Query: 126 IWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTD 185 IW L + +G +NL VK +GE EFW +++KV IV MI+GG +++FG+ G T Sbjct: 125 IWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQ-GVPTG 183 Query: 186 ISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRI 245 ISNLWT GGFMPNG G++ + +VMFA+ G+E+IG+TAGEA +P+ +P AIN+V RI Sbjct: 184 ISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRI 243 Query: 246 LLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIF 305 L+FYV + V+MSI+PW ++G+ GSPFV F++LGI SAA I+N VV+TAA+S+ N I+ Sbjct: 244 LIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGIY 303 Query: 306 GAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASI 365 GRM+F LAQQG AP+ FA S +G+P V+V VALL GVLLNYL+P VF+ + S Sbjct: 304 STGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVTSA 363 Query: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFP 425 ATF +W W ++L TQ+ RR ++ Q +QL F +PF+PYA A+AF++ V G++GYFP Sbjct: 364 ATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGYFP 423 Query: 426 DTQAALIVGVVWIVLLVLAYLMW 448 DT+ ALIVG +W+VLL + Y ++ Sbjct: 424 DTRVALIVGPLWLVLLTVLYYVF 446 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: 737 Number of extensions: 38 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: 454 Length adjustment: 33 Effective length of query: 435 Effective length of database: 421 Effective search space: 183135 Effective search space used: 183135 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