Align general amino acid permease AGP1 (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 219 bits (559), Expect = 2e-61 Identities = 145/470 (30%), Positives = 235/470 (50%), Gaps = 30/470 (6%) Query: 116 LKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQACGEM 175 LK+ ++ RH+ +IALG IGTGL +G+ L AGP+ +++GYAI G I + I++ GEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFLIMRQLGEM 69 Query: 176 ALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTSVNPD 235 +V + G ++ + GF W Y + ++ V EL I++W + Sbjct: 70 -IVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTW 128 Query: 236 VFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGFIGGK 295 V ++F+V V IN + + E EF+F K++ + G +LG + G G Sbjct: 129 VSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSN 188 Query: 296 YWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAAKQMI 354 W G F NG G+ ++ F+FGG E + IT AE S PRK IP A Q++ Sbjct: 189 LWSHGGFFPNGG------MGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVV 242 Query: 355 YRILFLFLATIILLGFLVPYNSD-QLLGSTGGGTKASPYVIAVASHGVRVVPHFINAVIL 413 YRIL ++ + +L L P++ Q LG++G SP+V + G H +N V+L Sbjct: 243 YRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVL 302 Query: 414 LSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAFCAASP 473 + LS+ NS Y ++R+ L+EQG APK +++ G P+ A+ +SAL ++ Sbjct: 303 TAALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYV 362 Query: 474 KEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVW--GSAY 531 + L A+ S + W I ++H++FR+AM QG + FK+ W S Y Sbjct: 363 APQSALELLFALVVASLMINWALISITHIKFRKAMGEQGVT---PSFKT---FWFPFSNY 416 Query: 532 ACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIA-LYVGYKV 580 C + +++I +AI I E+ AMP+ + +YV Y++ Sbjct: 417 LC-LAFMVMIISVMLAIPGIS----------ESVYAMPVWVGIIYVAYRL 455 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: 692 Number of extensions: 35 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: 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