Align L-tyrosine transporter (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 708 bits (1827), Expect = 0.0 Identities = 341/462 (73%), Positives = 401/462 (86%) Query: 1 MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60 M+ + H+G L+RGLKNRHIQLIALGGAIGTGLFLGSAGVL+SAGPSMILGYAI GFIAF Sbjct: 1 MTAETLHTGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAF 60 Query: 61 MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120 +IMRQLGEMIVEEPVAGSFSHFAHKY GG+AGFLSGWN W+LY+LVGM+ELTAVGKY+ + Sbjct: 61 LIMRQLGEMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQF 120 Query: 121 WAPDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180 W P++PTW +AAAFF+LIN INL+NVK FGE EFWFAI+KV AIVGMI LG +LLVSG G Sbjct: 121 WWPEVPTWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKG 180 Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 G QAS++NLWSHGGFFPNG SG+++A+AIIMFSFGGLE++G TAAEA +PKTVIPKAINQ Sbjct: 181 GEQASISNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQ 240 Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 V+YRILIFYIGAL VLL+L PWD+LL TL A+GD YSGSPFVQ+FS++GS+TAAH+LNFV Sbjct: 241 VVYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFV 300 Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360 VLTAALSVYNSG YCNSRML G+AEQGDAP++L +I+ RGVPV ++ SA VTL+ V +N Sbjct: 301 VLTAALSVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVN 360 Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLA 420 YL PQ ALELLMSL VA LVINWAMIS +H KFR+ M Q P FKA W+P NY+CLA Sbjct: 361 YLFPQGALELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEPSFKAFWFPLSNYLCLA 420 Query: 421 FVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVIKNKRSAR 462 FV IL +ML +PGI++SV+AIPVWV F+W+CY ++ + AR Sbjct: 421 FVAGILIIMLWLPGIRMSVFAIPVWVGFLWLCYRLRARLLAR 462 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: 772 Number of extensions: 26 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: 464 Length adjustment: 33 Effective length of query: 438 Effective length of database: 431 Effective search space: 188778 Effective search space used: 188778 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