Align general amino acid permease AGP1 (characterized)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__Putida:PP_4495 Length = 472 Score = 195 bits (496), Expect = 3e-54 Identities = 130/432 (30%), Positives = 214/432 (49%), Gaps = 17/432 (3%) Query: 113 SDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQAC 172 S LK+ ++ RH+ +IALG IGTGL +G+ + AGP+ +++GYAI G I + I++ Sbjct: 8 SGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPS-MILGYAICGFIAFMIMRQL 66 Query: 173 GEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTSV 232 GEM +V + G ++ + GF W + ++ V EL + YW + Sbjct: 67 GEM-IVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHYWWPEI 125 Query: 233 NPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGFI 292 V F+VL+ IN+ + + EAEF+F K++ + LG + G+G Sbjct: 126 PTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMIGLGAYLLTSGSGGPEAT 185 Query: 293 GGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAAK 351 W G F NG G+ L F+FGG E + T AE P+ IP A Sbjct: 186 VANLWTHGGFFPNG------VSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAIN 239 Query: 352 QMIYRILFLFLATIILLGFLVPYNSDQLLGS---TGGGTKASPYVIAVASHGVRVVPHFI 408 Q+IYRIL ++ +++L L P+ D L+ S +GG +SP+V + G V + + Sbjct: 240 QVIYRILIFYVGALVVLLSLTPW--DNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLL 297 Query: 409 NAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAF 468 N V+L + LS+ NS Y +AR+ L ++EQG AP + +D+ G P+ ++ VSA +A Sbjct: 298 NFVVLTAALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAV 357 Query: 469 CAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVWG 528 + L+++ + + W I SHL+FR+ + G+ + FK+ +G Sbjct: 358 LLNYLMPQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQ---KPLFKALWYPYG 414 Query: 529 SAYACIMMILIL 540 + ++LIL Sbjct: 415 NYVVLAFVVLIL 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: 696 Number of extensions: 34 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: 472 Length adjustment: 36 Effective length of query: 597 Effective length of database: 436 Effective search space: 260292 Effective search space used: 260292 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