Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_083529130.1 AS188_RS01250 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_001482365.1:WP_083529130.1 Length = 482 Score = 378 bits (970), Expect = e-109 Identities = 199/438 (45%), Positives = 282/438 (64%), Gaps = 6/438 (1%) Query: 9 GTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMAA 68 G L+ RHL MM LGSAIG GLF+G+G +R AGPAVLL++++A ++VLVM+ LGEMAA Sbjct: 23 GARLKARHLVMMALGSAIGTGLFIGSGAAVRTAGPAVLLSFLVACVLLVLVMRALGEMAA 82 Query: 69 ARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGA-WFGVEPWIPS 127 A P+ G+FS + E+A G G +LGWL+W +++V+ AE T AA ++ W E W+ + Sbjct: 83 ADPSPGAFSTWAENAMGRTVGRTLGWLWWAQIVVVVAAEATAAAQLLTELWPVTEQWVLA 142 Query: 128 LVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFI 187 LV +V F V+NLV VR GE E+WFA +KV ++ FL +G+AL+ G L + G N Sbjct: 143 LVFMVVFTVINLVKVRTLGETEFWFALMKVLAVLVFLAVGVALLLGLLEVPS-PGLRNLT 201 Query: 188 GDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYL 247 GF+P G++GVAA LL V FAFGG E+VTIAAAE++ P+ ++ A+R ++ RI VFY+ Sbjct: 202 AHGGFLPTGLTGVAAALLVVIFAFGGTELVTIAAAETEDPQHNVARAIRTILVRILVFYV 261 Query: 248 GSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYA 307 G+V V+ ++P+ + + SPF +L A +PG M II+LALLSA NA IY Sbjct: 262 GAVTVMVLVLPWND----EQLSVSPFVAVLEAAGVPGADVVMAVIIILALLSALNANIYG 317 Query: 308 TSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAV 367 +SR+++S+A R APR F+ LS VP AV++S+ F F +V L Y P +L ++LN V Sbjct: 318 SSRMLYSLARRGSAPRAFADLSDRGVPRTAVVVSVVFGFAAVVLNYLWPETVLLWMLNTV 377 Query: 368 GGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAAS 427 G +VVW + +SQ+ LR+ + +RMWA PWL L LLAG+V L L D A Sbjct: 378 GATCLVVWGLALVSQIVLRRRADRAGTVLPLRMWAFPWLSWFALALLAGIVLLGLLDDAV 437 Query: 428 RSQVYSVAIVYGFLVLLS 445 R Q+ A + + LL+ Sbjct: 438 RVQLLLTAGLVALIALLA 455 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: 599 Number of extensions: 24 Number of successful extensions: 5 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: 482 Length adjustment: 33 Effective length of query: 430 Effective length of database: 449 Effective search space: 193070 Effective search space used: 193070 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 24 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