Align L-tyrosine transporter (characterized)
to candidate GFF344 PS417_01755 proline-specific permease
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 387 bits (995), Expect = e-112 Identities = 203/462 (43%), Positives = 288/462 (62%), Gaps = 14/462 (3%) Query: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 LKRGL RHI+ +ALG AIGTGLF GSA ++ AGP+++L Y I G FM+MR LGEM Sbjct: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 Query: 71 VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWVS 130 V PVAGSF +A Y G AGF+ GW I+V ++++TA G Y+ +W PD+ WV Sbjct: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFPDVARWVW 127 Query: 131 AAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSG---HGGPQAS-V 186 +LI +NL NVKVFGE EFW +++KV AIV MI G +++ G G QAS + Sbjct: 128 VLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAGETQASGL 187 Query: 187 TNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRIL 246 +NLW+HGGF PNG+ GL+ + A++MF+FGG+E++G TA EA P+ VIPKAIN V RIL Sbjct: 188 SNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAINAVPLRIL 247 Query: 247 IFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAAL 306 +FY+ L VL+++ PW + GSPFVQ+FS LG +AA ILN VV++AA+ Sbjct: 248 LFYVLTLFVLMAIYPWPQI---------GSQGSPFVQIFSNLGIGSAATILNIVVISAAV 298 Query: 307 SVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLNYLVPQH 366 S NS + RM+ G+A+QG APK +++ K+GVP +++ A L V+LNYL+P++ Sbjct: 299 SAINSDIFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPEN 358 Query: 367 ALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPL-FKALWYPYGNYICLAFVVFI 425 ++ S+ V W MI ++ R+ M + Q L F ++PY + F++F+ Sbjct: 359 VFLVIASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFV 418 Query: 426 LGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSARQELAV 467 GV+ P Q ++ VW+V + V Y++ K SA Q V Sbjct: 419 FGVLGYFPDTQAALLVGAVWIVLLVVAYLLWVKPSAGQAAKV 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: 689 Number of extensions: 41 Number of successful extensions: 5 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: 469 Length adjustment: 33 Effective length of query: 438 Effective length of database: 436 Effective search space: 190968 Effective search space used: 190968 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