Align L-tyrosine transporter (characterized)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400 Length = 473 Score = 887 bits (2292), Expect = 0.0 Identities = 439/470 (93%), Positives = 457/470 (97%) Query: 1 MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60 MSGQN SGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF Sbjct: 1 MSGQNPQSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60 Query: 61 MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120 MIMRQLGEMIVE+PVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY Sbjct: 61 MIMRQLGEMIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120 Query: 121 WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180 WAPDIPTW SAAAFF+LINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSG+G Sbjct: 121 WAPDIPTWASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGNG 180 Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 GPQA+V+NLWSHGGFFPNGV+GLVMAMA IMFSFGGLEMLGFTAAEADKPKTVIPKAINQ Sbjct: 181 GPQAAVSNLWSHGGFFPNGVTGLVMAMAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 VIYRILIFYIGALV+LLSLTPWDSLL TLNASGD+YSGSPFVQVFSMLGSNTAAHILNFV Sbjct: 241 VIYRILIFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNFV 300 Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKAL++IDKRGVPVRSILASAAVTL+AVLLN Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLLN 360 Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA 420 YL+P ALELLMSLVVATLVINWAMISYSHFKFRQHMN+T+QTPLFKALWYPYGNYICLA Sbjct: 361 YLIPHSALELLMSLVVATLVINWAMISYSHFKFRQHMNKTKQTPLFKALWYPYGNYICLA 420 Query: 421 FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELAVAAA 470 FV+FILGVMLLIPGIQ SVYAIPVW+VFMWVCY IKNKRSA+ L VA + Sbjct: 421 FVLFILGVMLLIPGIQTSVYAIPVWLVFMWVCYGIKNKRSAQHALQVAGS 470 Lambda K H 0.327 0.139 0.432 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: 882 Number of extensions: 28 Number of successful extensions: 1 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: 471 Length of database: 473 Length adjustment: 33 Effective length of query: 438 Effective length of database: 440 Effective search space: 192720 Effective search space used: 192720 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 (21.7 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