Align L-tyrosine transporter (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 708 bits (1827), Expect = 0.0 Identities = 341/466 (73%), Positives = 400/466 (85%) Query: 1 MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60 M+ + G LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAI GFIAF Sbjct: 1 MADEQLQQGVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAF 60 Query: 61 MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120 +IMRQLGEMIVEEPVAGSFSHFAH YWG FAGFLSGWN W+LY+LVGM+ELTAVGKY+ + Sbjct: 61 LIMRQLGEMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQF 120 Query: 121 WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180 W P++PTWVSAA FF+L+N IN NVKVFGE EFWFAIIKVVAI+GMIALG Y+LVSG G Sbjct: 121 WWPEVPTWVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTG 180 Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 GPQASV+NLWSHGGFFPNG +GL+MAMA IMFSFGGLE++G TAAEA +P+ VIPKAINQ Sbjct: 181 GPQASVSNLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQ 240 Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 V+YR+LIFY+GAL VLLSL PWD LL TL ASGDAYSGSPFVQ+F+++GSNTAA ILNFV Sbjct: 241 VVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFV 300 Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360 VLTAALSVYNSG YCNSRML G+AEQGDAPK+L +++K+GVP+R++ SA +T++ V++N Sbjct: 301 VLTAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVN 360 Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA 420 Y+ P ALELL +LVVA+L+INWAMIS +H KFR+ M Q P FKA W PY NY+CLA Sbjct: 361 YVAPNEALELLFALVVASLMINWAMISLTHLKFRKAMGQRGIVPGFKAFWSPYTNYLCLA 420 Query: 421 FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELA 466 F+ I+ VMLLIPG++ SVYAIPVWV+ ++V Y I+ R+ +A Sbjct: 421 FMAMIIYVMLLIPGVRASVYAIPVWVLILFVFYRIRVARTRALSVA 466 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: 741 Number of extensions: 30 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: 466 Length adjustment: 33 Effective length of query: 438 Effective length of database: 433 Effective search space: 189654 Effective search space used: 189654 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