Align Aromatic amino acid permease, AroP (characterized)
to candidate PfGW456L13_375 transport permease protein of gamma-aminobutyrate
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_375 Length = 463 Score = 365 bits (936), Expect = e-105 Identities = 186/441 (42%), Positives = 274/441 (62%), Gaps = 4/441 (0%) Query: 3 KSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQM 62 +S+ GL GL+ RH+TM+ + IGAGLF+G+G I AAGPAVLLAY AG +VVLVM+M Sbjct: 5 QSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGMLVVLVMRM 64 Query: 63 LGEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GV 121 LGEMA A P +GSFS Y + A GHWAGF++GWLYW+ ++V+ E AA I+ AWF GV Sbjct: 65 LGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPGV 124 Query: 122 EPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFV 181 + W +LV + V NL +V+ +GEFE+WFA IKV II F+++G+ IFG+LPGS Sbjct: 125 DIWAFALVITMLLTVTNLFSVKNYGEFEFWFALIKVLAIIGFIVLGLMAIFGFLPGSQVS 184 Query: 182 GTSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWR 241 G S+ GF+PNG+ V +L F+F G EIVTIAAAES P + IS A +VIWR Sbjct: 185 GVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGKQISKATNSVIWR 244 Query: 242 ISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAF 301 I +FYL S+ ++ L+P+ N A+ + +L IP ++ ++++A+ S Sbjct: 245 IGLFYLVSIFIVVALVPW---NDPVLASLGSYQTVLERMGIPNAKMIVDIVVLVAVTSCL 301 Query: 302 NAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLD 361 N+ +Y +SR++FS+ R DAP + ++ + S P AV+LS AF++ Y PA + + Sbjct: 302 NSALYTSSRMLFSLGKRGDAPAMSTRTNKSGTPYWAVMLSTGAAFLATFANYVAPAAVFE 361 Query: 362 FLLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALM 421 FLL + G ++V+ +I +SQL++RK+ A E MW P L +V + + +M Sbjct: 362 FLLASSGAIALLVYLVIAISQLRMRKQRIARGEKIAFSMWLFPGLTYAVIVFIVAALTIM 421 Query: 422 LGDAASRSQVYSVAIVYGFLV 442 L A R ++ + ++ +V Sbjct: 422 LFQEAHRVEILATGLLSALVV 442 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: 597 Number of extensions: 26 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