Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= uniprot:A0A0C4YP23 (465 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 634 bits (1634), Expect = 0.0 Identities = 310/452 (68%), Positives = 366/452 (80%), Gaps = 9/452 (1%) Query: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 LKRGLKNRHIQLIALGGAIGTGLFLG A +K AGPS++LGYA+AG IAF IMRQLGEM+ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 V+EPVAGSFSHFA+ Y GSFAGF+SGWNYWVLY+LV MAEL+AVG YVQ+WWP +PTW S Sbjct: 71 VEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWVS 130 Query: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVSNLW 192 A FF+L+N IN +VK FGEMEFWF+I+KV+AI+GMI G Y+L SGT GPQASVSNLW Sbjct: 131 AAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGPQASVSNLW 190 Query: 193 QHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIFYV 252 HGGFFPNG +GL+MAMA IMFSFGGLELVGITAAEA EP K IPKA NQV+YR+LIFYV Sbjct: 191 SHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRVLIFYV 250 Query: 253 GALGVLLSLYPWEKVVT---------GGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYN 303 GAL VLLSLYPW++++ GSPFV IF + S+ A +LN VVLTAALSVYN Sbjct: 251 GALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVLTAALSVYN 310 Query: 304 SGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFEL 363 SGVYCNSRML+GLA+QG+APK+L+K+NK+G+PL ALG+SAL T CVV+NY P EA EL Sbjct: 311 SGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYVAPNEALEL 370 Query: 364 LMGLVVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMY 423 L LVV++L+INWAMIS+ HLKFR+ G FK+ P TNY+CLAF+A I+YVM Sbjct: 371 LFALVVASLMINWAMISLTHLKFRKAMGQRGIVPGFKAFWSPYTNYLCLAFMAMIIYVML 430 Query: 424 LTPGLRISVYLIPAWLAVLGLSYRLRQKQKRA 455 L PG+R SVY IP W+ +L + YR+R + RA Sbjct: 431 LIPGVRASVYAIPVWVLILFVFYRIRVARTRA 462 Lambda K H 0.326 0.140 0.426 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: 739 Number of extensions: 29 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: 465 Length of database: 466 Length adjustment: 33 Effective length of query: 432 Effective length of database: 433 Effective search space: 187056 Effective search space used: 187056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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