Align Aromatic amino acid permease, AroP (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139 Length = 501 Score = 350 bits (897), Expect = e-101 Identities = 182/459 (39%), Positives = 273/459 (59%), Gaps = 8/459 (1%) Query: 4 SNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQML 63 SN L G + RH+TM+ + IGAGLF+G+G I AAGPAVLLAY+ +G +VVLVM+ML Sbjct: 42 SNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVLLAYLFSGLLVVLVMRML 101 Query: 64 GEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-GVE 122 GEMA A P +GSFS Y + A G WAGF++GWLYW+ ++V+ E A ++ WF ++ Sbjct: 102 GEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPQID 161 Query: 123 PWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVG 182 W+ +L ++ V NL +V +GEFE+WFA KV II F+ +G A++ GW+P G Sbjct: 162 TWLFALTSIILLVVTNLFSVSKYGEFEFWFAMAKVVAIIGFIGLGFAVLMGWIPEREASG 221 Query: 183 TSNFIGDH-GFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWR 241 S + +H GF PNG+S V + + F+F G E VTIAAAES P + I+ A R+VIWR Sbjct: 222 LSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESSNPAQNIAKATRSVIWR 281 Query: 242 ISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAF 301 I VFYL S+ V+ ++P+ N A+ + + L + NIP ++ ++++A+ S Sbjct: 282 IGVFYLLSIFVVISVVPW---NDPLLASVGSYQRALELMNIPHAKLMVDVVVLIAVASCM 338 Query: 302 NAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLD 361 N+ IY SR++FS+ R DAP+ S+ VP AV+ S Y+ PAGL Sbjct: 339 NSSIYIASRMLFSLGKRGDAPKPLKVTSSDGVPRAAVIASTVLGAGVTLFSYFMPAGLFQ 398 Query: 362 FLLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALM 421 FLL + G ++V+ +I +SQL++RK L + T +MW PWL L + + +A+M Sbjct: 399 FLLASSGAIALLVYLVIAVSQLRMRKILLRQNVTLTFKMWLFPWLTWLVIAFICAALAVM 458 Query: 422 LGDAASRSQVYSVAIVYGFLVLLSFVTVNSPLRGGRTPS 460 + R +V S G +++SF+ + + + G+ S Sbjct: 459 MVTPEHRMEVSS---TIGLALVISFIGLVTARQHGQPRS 494 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: 613 Number of extensions: 37 Number of successful extensions: 4 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: 501 Length adjustment: 34 Effective length of query: 429 Effective length of database: 467 Effective search space: 200343 Effective search space used: 200343 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: 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