Align Aromatic amino acid permease, AroP (characterized)
to candidate PP_0284 PP_0284 gamma-aminobutyrate permease
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__Putida:PP_0284 Length = 461 Score = 354 bits (909), Expect = e-102 Identities = 179/435 (41%), Positives = 274/435 (62%), Gaps = 4/435 (0%) Query: 4 SNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQML 63 ++ L GL+ RH+TM+ + IGAGLF+G+G I AAGPAVLLAY AG +VVLVM+ML Sbjct: 5 NSNDLAQGLKQRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGTLVVLVMRML 64 Query: 64 GEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GVE 122 GEMA A P +GSFS Y + A G WAGF++GWLYW+ ++V+ E AAAI+ AWF V+ Sbjct: 65 GEMAVASPDTGSFSTYADRAIGRWAGFTIGWLYWWFWVLVIPLEANAAAAILHAWFPAVD 124 Query: 123 PWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVG 182 W SL+ + + NL +V+ +GEFE+WFA +KV II F+ +G A +FG++P S G Sbjct: 125 LWAFSLIITLALTLTNLCSVKNYGEFEFWFALLKVLAIIGFIAVGCAALFGFVPSSQVSG 184 Query: 183 TSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRI 242 TS+ GFMPNG+ V A +L F+F G EIVTIAAAES P + IS A +VIWRI Sbjct: 185 TSHLFDTQGFMPNGLGAVLAAMLTTMFSFMGTEIVTIAAAESKDPGKQISRATNSVIWRI 244 Query: 243 SVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFN 302 +FYL S+ ++ L+P+ A+T + + +L+ +P ++ ++++A+ S N Sbjct: 245 CLFYLVSIFLVVALVPWNDPALAETGS---YQTVLSRIGVPNAKLIVDIVVLIAVTSCLN 301 Query: 303 AQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDF 362 + +Y +SR++FS++ R DAP + + + + P AVLLS AF+ V + PA + +F Sbjct: 302 SALYTSSRMLFSLSKRGDAPAIAQRTTKAATPHVAVLLSTAAAFLCVFANFVAPAQVFEF 361 Query: 363 LLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALML 422 LL + G ++V+ +I +SQL++R + +A E T +MW P L T+ + ++ +M Sbjct: 362 LLASSGAIALLVYLVIAVSQLRMRAQREARGEKITFKMWLFPGLTWATIAFIVAILVVMA 421 Query: 423 GDAASRSQVYSVAIV 437 R+++ + A++ Sbjct: 422 LREDHRAEIIATALL 436 Lambda K H 0.327 0.140 0.428 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: 567 Number of extensions: 24 Number of successful extensions: 3 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: 463 Length of database: 461 Length adjustment: 33 Effective length of query: 430 Effective length of database: 428 Effective search space: 184040 Effective search space used: 184040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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