Align histidine permease (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 473 bits (1217), Expect = e-138 Identities = 232/438 (52%), Positives = 302/438 (68%), Gaps = 6/438 (1%) Query: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 L+R L+ RHI FMALG AIG GLF GSA+AI +AGP+VL AYL GGA +F++MRALGEMA Sbjct: 5 LQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMA 64 Query: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 VH+PVAGSF YA YLGP AG++ GW Y MV VGMA+ TA GIYM WFPE+ +WIW Sbjct: 65 VHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQWIW 124 Query: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 V G V+++GGLNL VKV+GEMEFW +L+KV +V MILGG G++ G GQ ++ Sbjct: 125 VFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNG-GQPVGLA 183 Query: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 NLW+ GG+ P+G G++ + VV+FAFGGIE IG+ AGEA P+ +PRA+N+V RIL+ Sbjct: 184 NLWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILI 243 Query: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 FYV + V+M+I+PW Q+G+QGSPFV F KLGI AA ++N VVITAA+S NS F Sbjct: 244 FYVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSG 303 Query: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367 RM++ L+ + AP +S +GVP V+V L+ GV+LNYL+PE +F ++ SI Sbjct: 304 SRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSILA 363 Query: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427 F TVW W+M+L + RR A FP+ WP + + F+ FV +LGY DT Sbjct: 364 FNTVWTWMMVLIAHYSFRRRHGA-----TAFPLRAWPLTSVVCLLFLAFVLFMLGYSADT 418 Query: 428 QAALIVGVVWIVLLVLAY 445 + AL VG W+VLL LAY Sbjct: 419 RVALYVGAGWVVLLSLAY 436 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: 759 Number of extensions: 42 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: 468 Length of database: 453 Length adjustment: 33 Effective length of query: 435 Effective length of database: 420 Effective search space: 182700 Effective search space used: 182700 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