Align L-tyrosine transporter (characterized)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__Putida:PP_4495 Length = 472 Score = 806 bits (2082), Expect = 0.0 Identities = 392/467 (83%), Positives = 435/467 (93%) Query: 1 MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60 MSGQN HSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGV+KSAGPSMILGYAICGFIAF Sbjct: 1 MSGQNMHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAF 60 Query: 61 MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120 MIMRQLGEMIVEEPVAGSFSHFAH YWGGFAGFLSGWNCW+LYILVGMSEL+AVGKY+HY Sbjct: 61 MIMRQLGEMIVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHY 120 Query: 121 WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180 W P+IPTWV+AAAFF+LINAINL NVK FGEAEFWFAIIKVVAIV MI LG+YLL SG G Sbjct: 121 WWPEIPTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSG 180 Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 GP+A+V NLW+HGGFFPNGVSGLVMA+A IMFSFGGLEMLGFTAAEADKPKTVIPKAINQ Sbjct: 181 GPEATVANLWTHGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 VIYRILIFY+GALVVLLSLTPWD+L+A+++ASG +Y SPFVQVFS+LGS+ AA++LNFV Sbjct: 241 VIYRILIFYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFV 300 Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360 VLTAALSVYNSGTYCN+RMLLGMAEQGDAP +L+++DKRGVPVRSIL SAAVT VAVLLN Sbjct: 301 VLTAALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLN 360 Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA 420 YL+PQ+ALELLMSLVVATLVINWAMISYSH KFRQH+++T Q PLFKALWYPYGNY+ LA Sbjct: 361 YLMPQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALWYPYGNYVVLA 420 Query: 421 FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELAV 467 FVV ILG+ML+IPGIQ+SVYAIPVW++ M V Y++K++R AV Sbjct: 421 FVVLILGIMLMIPGIQVSVYAIPVWLLAMLVVYMVKSRRQVNAGGAV 467 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: 810 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: 472 Length adjustment: 33 Effective length of query: 438 Effective length of database: 439 Effective search space: 192282 Effective search space used: 192282 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