Align general amino acid permease AGP1 (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 201 bits (510), Expect = 8e-56 Identities = 133/438 (30%), Positives = 214/438 (48%), Gaps = 28/438 (6%) Query: 101 SSDNIGANTGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAI 160 +SDN A +LK+ ++ RH+ +IALG IGTGL +G + AGP+ +L+GYA+ Sbjct: 5 ASDNTDA-------TLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPS-VLLGYAV 56 Query: 161 MGSILYCIIQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVT 220 G I + I++ GEM +V + G ++ + + GF W Y + ++ V EL Sbjct: 57 AGIIAFFIMRQLGEM-VVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSA 115 Query: 221 ASMTIKYWTTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGII 280 + ++YW + + F++L+ IN+ + + E EF+F+ K+L + G + G Sbjct: 116 VGIYVQYWWPHIPTWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGY 175 Query: 281 IDVGGAGNDGFIGGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQ 339 + G W G F NG G+ + F+FGG E + IT AE Sbjct: 176 LLASGTAGPQASVSNLWQHGGFFPNG------ISGLVMAMAVIMFSFGGLELVGITAAEA 229 Query: 340 SNPRKAIPGAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASH 399 P K IP A Q+IYRIL ++ + +L L P+ TGG SP+V+ + Sbjct: 230 DEPEKTIPKATNQVIYRILIFYVGALGVLLSLYPWEKVV----TGG----SPFVLIFHAM 281 Query: 400 GVRVVPHFINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGV 459 +V +NAV+L + LS+ NS Y ++R+ L++QG APK +++ G PL A+GV Sbjct: 282 NSDIVATVLNAVVLTAALSVYNSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGV 341 Query: 460 SALFAVIAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELG 519 SAL + F L+ + + + W I + HL+FRR + G+ E Sbjct: 342 SALATAACVVINYFMPGEAFELLMGLVVSALIINWAMISIIHLKFRRDKRAAGQ---ETR 398 Query: 520 FKSQTGVWGSAYACIMMI 537 FKS G + Y C+ + Sbjct: 399 FKS-LGYPLTNYVCLAFL 415 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: 668 Number of extensions: 27 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: 465 Length adjustment: 35 Effective length of query: 598 Effective length of database: 430 Effective search space: 257140 Effective search space used: 257140 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