Align general amino acid permease AGP1 (characterized)
to candidate PP_0284 PP_0284 gamma-aminobutyrate permease
Query= CharProtDB::CH_091105 (633 letters) >FitnessBrowser__Putida:PP_0284 Length = 461 Score = 202 bits (513), Expect = 3e-56 Identities = 138/438 (31%), Positives = 223/438 (50%), Gaps = 22/438 (5%) Query: 109 TGHKSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCI 168 +G+ S+ L + ++ RHV M+++ IG GL VG+G A+ AGPA +L+ YA G+++ + Sbjct: 2 SGNNSNDLAQGLKQRHVTMLSIAGVIGAGLFVGSGHAIAAAGPA-VLLAYAAAGTLVVLV 60 Query: 169 IQACGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYW 228 ++ GEMA V S TG ++ Y + GF + W+Y W+ V PLE A+ + W Sbjct: 61 MRMLGEMA-VASPDTGSFSTYADRAIGRWAGFTIGWLYWWFWVLVIPLEANAAAAILHAW 119 Query: 229 TTSVNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGN 288 +V+ F +I + + N+ + Y E EF+F K+L + GF +G G + Sbjct: 120 FPAVDLWAFSLIITLALTLTNLCSVKNYGEFEFWFALLKVLAIIGFIAVGCAALFGFVPS 179 Query: 289 DGFIGGKYWHDPGAF--NGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAI 346 G + D F NG A V A ++T F+F G+E + I AE +P K I Sbjct: 180 SQVSGTSHLFDTQGFMPNGLGA------VLAAMLTTMFSFMGTEIVTIAAAESKDPGKQI 233 Query: 347 PGAAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPH 406 A +I+RI +L +I L+ LVP+N D L TG Y ++ GV Sbjct: 234 SRATNSVIWRICLFYLVSIFLVVALVPWN-DPALAETGS------YQTVLSRIGVPNAKL 286 Query: 407 FINAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVI 466 ++ V+L++V S NS+ Y+S+R+ +LS++G AP + +A P +A+ +S A + Sbjct: 287 IVDIVVLIAVTSCLNSALYTSSRMLFSLSKRGDAPAIAQRTTKAATPHVAVLLSTAAAFL 346 Query: 467 AFCAASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQ--T 524 A QVF +LLA SG L + I +S LR R + +G ++ FK Sbjct: 347 CVFANFVAPAQVFEFLLASSGAIALLVYLVIAVSQLRMRAQREARGE---KITFKMWLFP 403 Query: 525 GVWGSAYACIMMILILIA 542 G+ + A I+ IL+++A Sbjct: 404 GLTWATIAFIVAILVVMA 421 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: 593 Number of extensions: 30 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: 461 Length adjustment: 35 Effective length of query: 598 Effective length of database: 426 Effective search space: 254748 Effective search space used: 254748 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