Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_005459194.1 SACCYDRAFT_RS20860 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_000244975.1:WP_005459194.1 Length = 468 Score = 335 bits (860), Expect = 1e-96 Identities = 179/442 (40%), Positives = 259/442 (58%), Gaps = 13/442 (2%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 LG GLR RH+TM+ LG IGAGLF+G+ I GPA + Y +AG IV+ VM+M+GEMA Sbjct: 16 LGKGLRQRHVTMISLGGIIGAGLFVGSSTAIANIGPAATVTYALAGLIVLFVMRMIGEMA 75 Query: 68 AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEPWIPS 127 A P SF+ Y G GF+ GWLYW+ ++V+ E A ++ W W+ + Sbjct: 76 VALPGRSSFTEYVRAGLGDLGGFTAGWLYWYFWVIVVAVEAVAGAELLQRWVPAPMWLIA 135 Query: 128 LVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWL--PGSTFVGTSN 185 L V+ VVN AVR +GEFE+WFA IKVA II F+ +G+ FGW G TF N Sbjct: 136 LALVITMTVVNCFAVRSYGEFEFWFASIKVAAIIVFIALGLGYAFGWTSDAGPTF---GN 192 Query: 186 FIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVF 245 GF G++ V AG+ V FA G EI TIAAAESD+P ++++ R+VI R+ F Sbjct: 193 LTSGGGFFAMGLAAVFAGVPTVIFAICGAEIATIAAAESDEPAKSVAQMTRSVIVRVLTF 252 Query: 246 YLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQI 305 Y+G+VLVI ++P++ I + +SPF + +IP M I+V+A+LS N+ + Sbjct: 253 YVGAVLVIVAVVPWQKI----VSGQSPFVAAMDEMSIPAAGDIMNIIVVIAVLSCMNSGV 308 Query: 306 YATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLN 365 Y SR++F ++ R DAP +FS LS VP A+L +V+VG ++P GL FL+N Sbjct: 309 YVASRVLFGLSVRGDAPTMFSGLSKRRVPLRAILAGGVVGYVAVGAAIFSPDGLFAFLVN 368 Query: 366 AVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDA 425 A G +++V+ +I SQL+LR+ L+ +++MW PWL I+ + + ++ M + Sbjct: 369 ASGAIMLLVYLLIGFSQLRLRRRLEREGTSLSLKMWLFPWLTIVVIGAIVAVLVAMAFQS 428 Query: 426 ASRSQVY----SVAIVYGFLVL 443 A Q+Y SVA+V VL Sbjct: 429 ALAPQLYASLASVAVVLVAFVL 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: 536 Number of extensions: 28 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: 468 Length adjustment: 33 Effective length of query: 430 Effective length of database: 435 Effective search space: 187050 Effective search space used: 187050 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