Align general amino acid permease AGP1 (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 221 bits (562), Expect = 7e-62 Identities = 144/445 (32%), Positives = 229/445 (51%), Gaps = 20/445 (4%) Query: 107 ANTGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILY 166 A T H + SL++ ++ RH+ +IALG IGTGL +G+ L AGP+ +++GYAI G I + Sbjct: 3 AETLH-TGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPS-MILGYAIGGFIAF 60 Query: 167 CIIQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIK 226 I++ GEM +V + G ++ + GF W Y + ++ V EL ++ Sbjct: 61 LIMRQLGEM-IVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQ 119 Query: 227 YWTTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGA 286 +W V F+VL+ IN+ + + E EF+F K+ + G +LG+ + V G Sbjct: 120 FWWPEVPTWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGK 179 Query: 287 GNDGFIGGKYWHDPGAF-NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKA 345 G + W G F NG F G+ L F+FGG E + IT AE + P+ Sbjct: 180 GGEQASISNLWSHGGFFPNG------FSGMLLALAIIMFSFGGLELVGITAAEAAEPKTV 233 Query: 346 IPGAAKQMIYRILFLFLATIILLGFLVPYNSDQL-LGSTGGGTKASPYVIAVASHGVRVV 404 IP A Q++YRIL ++ + +L L P+++ L LG+ G SP+V + G Sbjct: 234 IPKAINQVVYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTA 293 Query: 405 PHFINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFA 464 H +N V+L + LS+ NS Y ++R+ L+EQG AP+ I+ G P++A+GVSAL Sbjct: 294 AHLLNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVT 353 Query: 465 VIAFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQT 524 ++ + L++++ + + W I L+HL+FRRAM+ QG E FK+ Sbjct: 354 LLCVAVNYLFPQGALELLMSLAVAALVINWAMISLAHLKFRRAMQQQG---VEPSFKA-- 408 Query: 525 GVWG--SAYACIMMIL-ILIAQFWV 546 W S Y C+ + ILI W+ Sbjct: 409 -FWFPLSNYLCLAFVAGILIIMLWL 432 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: 666 Number of extensions: 29 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: 464 Length adjustment: 35 Effective length of query: 598 Effective length of database: 429 Effective search space: 256542 Effective search space used: 256542 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