Align general amino acid permease AGP1 (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 221 bits (562), Expect = 7e-62 Identities = 139/434 (32%), Positives = 221/434 (50%), Gaps = 18/434 (4%) Query: 112 KSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQA 171 + LK+ ++ RH+ +IALG IGTGL +G+ L AGP+ +++GYAI G I + I++ Sbjct: 7 RQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFLIMRQ 65 Query: 172 CGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTS 231 GEM +V + G ++ + GF W Y + ++ V EL +++W Sbjct: 66 LGEM-IVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPE 124 Query: 232 VNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGF 291 V V +F+VLV IN+ + + E EF+F K++ + G LG + G G Sbjct: 125 VPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFSGTGGPQA 184 Query: 292 IGGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAA 350 W G F NG + G+ + F+FGG E + IT AE S P K IP A Sbjct: 185 SVSNLWDHGGFFPNG------YSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAI 238 Query: 351 KQMIYRILFLFLATIILLGFLVPYNSD-QLLGSTGGGTKASPYVIAVASHGVRVVPHFIN 409 Q++YR+L ++ + +L L P++ Q LG++G SP+V + G H +N Sbjct: 239 NQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILN 298 Query: 410 AVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAFC 469 V+L + LS+ NS Y ++R+ L+EQG APK +++ G PL+A+GVSAL +++ Sbjct: 299 FVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVL 358 Query: 470 AASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVW-- 527 + L A+ S + W I L+HL+FR+ M QG GFKS W Sbjct: 359 VNYLAPHEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGI---VPGFKS---FWFP 412 Query: 528 GSAYACIMMILILI 541 S Y C+ +++++ Sbjct: 413 FSNYLCLAFMVMIV 426 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: 695 Number of extensions: 35 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: 467 Length adjustment: 35 Effective length of query: 598 Effective length of database: 432 Effective search space: 258336 Effective search space used: 258336 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: 52 (24.6 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