Align general amino acid permease AGP1 (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 213 bits (543), Expect = 1e-59 Identities = 139/433 (32%), Positives = 219/433 (50%), Gaps = 20/433 (4%) Query: 112 KSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQA 171 + D LK+ ++ RH+ +IALG IGTGL +G+ + L AGP+ +++GYAI G I + I++ Sbjct: 51 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGVIAFMIMRQ 109 Query: 172 CGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTS 231 GEM + + G ++ + D GF W Y + ++ V EL + YW Sbjct: 110 LGEM-VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 168 Query: 232 VNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGF 291 V V ++ + + IN+ + Y E EF+F K++ + G + G + V G G Sbjct: 169 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQA 228 Query: 292 IGGKYWHDPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAAK 351 W G F H F G+ L F+FGG E I IT AE P+K+IP A Sbjct: 229 SISNLWSHGGFF--PHG---FHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVN 283 Query: 352 QMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFINAV 411 Q+IYRIL ++ ++ +L L P+N + GG SP+V+ + G + + +N V Sbjct: 284 QVIYRILIFYICSLAVLLSLYPWNEV----AAGG----SPFVMIFSQIGSTLTANVLNVV 335 Query: 412 ILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSAL--FAVIAFC 469 +L + LS+ NS Y+++R+ L+EQG AP+ +DR G P +A+G+SAL F + Sbjct: 336 VLTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVN 395 Query: 470 AASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVWGS 529 P E L ++ L + W I L+HL+ RRAM G +L F W Sbjct: 396 YLIPAEALGLLMALVVAAL--VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNW-I 452 Query: 530 AYACIMMILILIA 542 A + +IL+++A Sbjct: 453 CLAFMALILVILA 465 Lambda K H 0.324 0.138 0.424 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: 756 Number of extensions: 31 Number of successful extensions: 6 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: 633 Length of database: 506 Length adjustment: 36 Effective length of query: 597 Effective length of database: 470 Effective search space: 280590 Effective search space used: 280590 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 53 (25.0 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