Align Aromatic amino acid permease, AroP (characterized)
to candidate GFF295 PS417_01505 gamma-aminobutyrate transporter
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__WCS417:GFF295 Length = 463 Score = 362 bits (929), Expect = e-104 Identities = 189/450 (42%), Positives = 278/450 (61%), Gaps = 5/450 (1%) Query: 3 KSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQM 62 +S+ L GL+ RH+TM+ + IGAGLF+G+G I AAGPAVLLAY AG +VVLVM+M Sbjct: 5 QSSNDLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGTLVVLVMRM 64 Query: 63 LGEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GV 121 L EMA A P +GSFS Y + A GHWAGF++GWLYW+ ++V+ E AA I+ AWF + Sbjct: 65 LAEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPDI 124 Query: 122 EPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFV 181 W+ +LV + NL +V+ +GEFE+WFA IKV I+ F+I+G+A IFG+LP S Sbjct: 125 AIWVFTLVITLLLTATNLFSVKNYGEFEFWFALIKVVAIVGFVILGLAAIFGFLPTSQVS 184 Query: 182 GTSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWR 241 G S+ GFMPNG+ V A +L F+F G EIVTIAAAES P + I+ A +VIWR Sbjct: 185 GVSHLFDTQGFMPNGMGAVLAAILTTMFSFMGTEIVTIAAAESKNPGQQITKATNSVIWR 244 Query: 242 ISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAF 301 I +FYL S+ ++ L+P+ N AA + +L IP ++ ++++A+ S Sbjct: 245 IGLFYLLSIFIVVSLVPW---NDPTLAAVGSYQTVLERMGIPNAKLIVDLVVLVAVTSCL 301 Query: 302 NAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLD 361 N+ +Y SR++FS+ R DAP V + + S P AVLLS AF++V Y PA + + Sbjct: 302 NSALYTASRMLFSLGRRGDAPAVAKRTNKSGTPYWAVLLSTGAAFLAVFANYVAPAAVFE 361 Query: 362 FLLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALM 421 FLL + G ++V+ +I +SQL++R++ A E +MW P L +V + G + +M Sbjct: 362 FLLASSGAIALLVYLVIAVSQLRMRQKRTAAGEKIVFKMWLFPGLTYAVMVFIVGTLTIM 421 Query: 422 LGDAASRSQVYSVAIVYGFLVLLSFVTVNS 451 L A R ++ + ++ LV+ + + V+S Sbjct: 422 LFQEAHRIEIIATGVL-SLLVVAAGLFVSS 450 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: 572 Number of extensions: 29 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: 463 Length adjustment: 33 Effective length of query: 430 Effective length of database: 430 Effective search space: 184900 Effective search space used: 184900 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