Align Aromatic amino acid permease, AroP (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 Length = 464 Score = 360 bits (925), Expect = e-104 Identities = 186/440 (42%), Positives = 269/440 (61%), Gaps = 4/440 (0%) Query: 4 SNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQML 63 S+ GL GL+ RH+TM+ + IGAGLF+G+G I AAGPAVLLAY AGA+VVLVM+ML Sbjct: 7 SSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRML 66 Query: 64 GEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GVE 122 GEMA A P +GSFS Y + A GHWAGF++GWLYW+ ++V+ E AA I+ AWF V Sbjct: 67 GEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVA 126 Query: 123 PWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVG 182 W +LV + NL +V+ +GEFE+WFA +KV II F+ +GI IFG+LP S G Sbjct: 127 IWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFLPTSQVSG 186 Query: 183 TSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRI 242 S+ GF+PNG+ V +L F+F G EIVTIAAAES P + IS A +VIWRI Sbjct: 187 VSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRI 246 Query: 243 SVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFN 302 +FYL S+ ++ L+P+ N A+ + +L IP ++ ++++A+ S N Sbjct: 247 GLFYLVSIFIVVALVPW---NDPILASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLN 303 Query: 303 AQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDF 362 + +Y SR++FS+ R DAP V + ++S P AV+LS AF++V Y PA + +F Sbjct: 304 SALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVFANYVAPAAVFEF 363 Query: 363 LLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALML 422 LL + G ++V+ +I +SQL++RK+ A E MW P L +V + + +ML Sbjct: 364 LLASSGAIALLVYLVIAISQLRMRKQRMARGEKIAFSMWLFPGLTYAVIVFIVAALTIML 423 Query: 423 GDAASRSQVYSVAIVYGFLV 442 A R ++ + ++ +V Sbjct: 424 FQEAHRVEILATGLLSALVV 443 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: 592 Number of extensions: 28 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: 464 Length adjustment: 33 Effective length of query: 430 Effective length of database: 431 Effective search space: 185330 Effective search space used: 185330 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