Align L-tyrosine transporter (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 417 bits (1073), Expect = e-121 Identities = 205/448 (45%), Positives = 293/448 (65%), Gaps = 12/448 (2%) Query: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 L+RGL+ RHI+L+ALG AIG GLFLGSA ++ AGP+++L Y + G F+IMR LGEM Sbjct: 7 LQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGEMA 66 Query: 71 VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWVS 130 V+ PVAGSFS +A Y G G+L+GWN W ++++ ++E+TAVG Y+ W PD+P W+ Sbjct: 67 VQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQWIW 126 Query: 131 AAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG--GPQASVTN 188 A A + + A+NLA VK +GE EFWFA+IKVV IV MI G ++V G G G ++N Sbjct: 127 ALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPTGISN 186 Query: 189 LWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILIF 248 LW+HGGF PNG G++MA+ ++MF++ G+EM+G TA EAD PK IP AIN V +RILIF Sbjct: 187 LWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRILIF 246 Query: 249 YIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAALSV 308 Y+GAL V++S+ PW+ L GSPFV F LG +AA I+NFVVLTAALS Sbjct: 247 YVGALFVIMSIYPWNEL---------GTHGSPFVMTFERLGIKSAAGIINFVVLTAALSS 297 Query: 309 YNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLNYLVPQHAL 368 N G Y RML +A+QG AP+ + G+P R++L S L VLLNYLVP Sbjct: 298 CNGGIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVF 357 Query: 369 ELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPL-FKALWYPYGNYICLAFVVFILG 427 + S + W ++ + K+R+ +++ Q++ L F+ ++PY +Y+ LAF+V ++G Sbjct: 358 VWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVG 417 Query: 428 VMLLIPGIQISVYAIPVWVVFMWVCYVI 455 +M P ++++ P+W+V + V Y + Sbjct: 418 LMGYFPDTRVALIVGPLWLVLLTVLYYV 445 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: 629 Number of extensions: 30 Number of successful extensions: 4 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: 454 Length adjustment: 33 Effective length of query: 438 Effective length of database: 421 Effective search space: 184398 Effective search space used: 184398 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