Align histidine permease (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= reanno::pseudo3_N2E3:AO353_12275 (468 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 381 bits (979), Expect = e-110 Identities = 193/453 (42%), Positives = 283/453 (62%), Gaps = 13/453 (2%) Query: 7 GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEM 66 GLKRGL RHI+ +ALG AIGTGLF GSA ++ AGP+++L Y I G F++MR LGEM Sbjct: 10 GLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEM 69 Query: 67 AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWI 126 V PVAGSF +A Y G AGF+ GW Y V+VGMA++TA G Y+ FW+P++ W+ Sbjct: 70 IVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWV 129 Query: 127 WVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDI 186 L V +N NVK FGE EFW +++KV AIV MI+ G ++ G G + Sbjct: 130 SALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTG---GPQASV 186 Query: 187 SNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRIL 246 SNLW+ GGF PNG GL+ S A +MF+FGG+E++G+TA EA +P+ V+P+AIN V RIL Sbjct: 187 SNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRIL 246 Query: 247 LFYVLTMLVLMSIFPWQQI---------GSQGSPFVQIFDKLGISSAATILNIVVITAAI 297 +FYV + VL+S++PW Q+ GSPFVQIF +G +AA ILN VV+TAA+ Sbjct: 247 IFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAAL 306 Query: 298 SAINSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPEN 357 S NS ++ RM+FGLA+QG APK L++ GVP + + ++ +L V++NY+ P++ Sbjct: 307 SVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQS 366 Query: 358 VFLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFV 417 L+ ++ + + W +I T + R++M EQ F ++P++ +AFM+ + Sbjct: 367 ALELLFALVVASLMINWALISITHIKFRKAM-GEQGVTPSFKTFWFPFSNYLCLAFMVMI 425 Query: 418 FGVLGYFPDTQAALIVGVVWIVLLVLAYLMWVK 450 V+ P ++ VW+ ++ +AY + V+ Sbjct: 426 ISVMLAIPGISESVYAMPVWVGIIYVAYRLRVR 458 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: 650 Number of extensions: 36 Number of successful extensions: 4 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: 467 Length adjustment: 33 Effective length of query: 435 Effective length of database: 434 Effective search space: 188790 Effective search space used: 188790 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