Align L-tyrosine transporter (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 703 bits (1815), Expect = 0.0 Identities = 337/450 (74%), Positives = 392/450 (87%) Query: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAI GFIAF+IMRQLGEMI Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 71 VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWVS 130 VEEPVAGSFSHFAHKYWGG+AGFL+GWN W+LY+LVGM+ELTAVGKYI +W PDIPTWVS Sbjct: 71 VEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVS 130 Query: 131 AAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHGGPQASVTNLW 190 A FF+ +N IN NVK FGE EFWFAIIKVVAIVGMI LG YLL SG GGPQASV+NLW Sbjct: 131 ALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSNLW 190 Query: 191 SHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILIFYI 250 SHGGFFPNG GL+M+MA IMFSFGGLE++G TAAEA +P+ VIPKAINQV+YRILIFY+ Sbjct: 191 SHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRILIFYV 250 Query: 251 GALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAALSVYN 310 GAL VLLSL PWD LL TL ASGDAYSGSPFVQ+FS++G++TAAHILNFVVLTAALSVYN Sbjct: 251 GALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAALSVYN 310 Query: 311 SGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLNYLVPQHALEL 370 SG YCNSRML G+AEQGDAPK+L +++K+GVP+R++ SA VT++ V++NY+ PQ ALEL Sbjct: 311 SGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQSALEL 370 Query: 371 LMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLAFVVFILGVML 430 L +LVVA+L+INWA+IS +H KFR+ M + TP FK W+P+ NY+CLAF+V I+ VML Sbjct: 371 LFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLCLAFMVMIISVML 430 Query: 431 LIPGIQISVYAIPVWVVFMWVCYVIKNKRS 460 IPGI SVYA+PVWV ++V Y ++ +RS Sbjct: 431 AIPGISESVYAMPVWVGIIYVAYRLRVRRS 460 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: 759 Number of extensions: 32 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: 467 Length adjustment: 33 Effective length of query: 438 Effective length of database: 434 Effective search space: 190092 Effective search space used: 190092 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