Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_076479006.1 BW971_RS09675 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_900156495.1:WP_076479006.1 Length = 605 Score = 308 bits (789), Expect = 3e-88 Identities = 165/439 (37%), Positives = 251/439 (57%), Gaps = 10/439 (2%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 L L R L+M+ +G IGAGLF+G+GV I GP + Y +AG ++++VM+ L EMA Sbjct: 6 LNKSLSQRQLSMIAIGGVIGAGLFVGSGVVIHDTGPGTFITYALAGLLIIMVMRALAEMA 65 Query: 68 AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEP-WIP 126 A P++GSF+ Y A G+WAGFS+GWLYW+ ++V+G E A I+ W P W+ Sbjct: 66 VASPSTGSFADYSRRALGNWAGFSVGWLYWYFWVIVVGFEAIAGAKIVQYWIPSAPTWLT 125 Query: 127 SLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNF 186 +++ + NL +V FGEFEYWFA IKVA II FL++G+ +FG PG + + SN Sbjct: 126 AMLLLAAMTATNLFSVSSFGEFEYWFASIKVAAIIVFLVLGVVFVFGLWPGKS-MDFSNL 184 Query: 187 IGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFY 246 GF P G + + G++ V F+ G EI TIAAAES P A+S A +VI RI++FY Sbjct: 185 TSHGGFFPKGGTAITVGVVTVIFSMVGAEIATIAAAESQDPERAVSRAANSVIARIALFY 244 Query: 247 LGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIY 306 +GS ++ ++P+ D+ + SPF IP M A+++ A+LS N+ +Y Sbjct: 245 VGSAFLLVTILPWND----DSVSGSPFVAAFTEMGIPAADHIMNAVVLTAVLSCLNSGMY 300 Query: 307 ATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSV-GLQYWNPAGLLDFLLN 365 SR++F +A +++AP ++ VP NA+L S F+ V +W + FLLN Sbjct: 301 TGSRMLFVLAAKREAPAQLVAVTRRGVPRNAILASSVIGFLCVIAAAFWENT-IFTFLLN 359 Query: 366 AVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDA 425 + G ++ V+ +I +SQ LR ++ V+MW P L +LT + ++ M D Sbjct: 360 SSGAIILFVYLLIVVSQTVLR--FRSGSADLKVKMWFFPVLSLLTAAAILAILVQMGLDP 417 Query: 426 ASRSQVYSVAIVYGFLVLL 444 A RSQ+ + + +VLL Sbjct: 418 AVRSQLVLSLVSWAVVVLL 436 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: 678 Number of extensions: 43 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: 605 Length adjustment: 35 Effective length of query: 428 Effective length of database: 570 Effective search space: 243960 Effective search space used: 243960 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 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