Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_076475776.1 BW971_RS01220 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_900156495.1:WP_076475776.1 Length = 480 Score = 365 bits (938), Expect = e-105 Identities = 189/436 (43%), Positives = 269/436 (61%), Gaps = 7/436 (1%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 LGT L+ RH+TM+ + IGAGLF+G+ I AGPAVL++Y++AG +VVLVM+MLGEMA Sbjct: 30 LGTSLKPRHITMISIAGVIGAGLFVGSANAIEKAGPAVLISYLLAGTLVVLVMRMLGEMA 89 Query: 68 AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEPWIPS 127 A P +GSFS Y + A G WAGFS+GWLYW+ ++V+ E T AA+I+ G WI + Sbjct: 90 TANPDTGSFSVYSDRALGRWAGFSVGWLYWWFWVLVIPVEATAAASILSDLIGGAQWIWA 149 Query: 128 LVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFI 187 L V V NL++V +GEFE+WFA IKV I+AF+++G IFG PGS G SN Sbjct: 150 LAVTVLLTVTNLISVGNYGEFEFWFALIKVVAIVAFIVVGALAIFGVFPGSDVSGISNLW 209 Query: 188 GDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYL 247 GF+PNG V AG+L F+F G EIVTIAAAES P IS AV +VIWRIS+FY+ Sbjct: 210 KPDGFLPNGFGAVIAGMLVTMFSFMGTEIVTIAAAESPNPEAGISKAVNSVIWRISLFYI 269 Query: 248 GSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYA 307 GS+ V+ L+PY+ ++ + + +L IP M+ +I+ A+ S N+ +Y Sbjct: 270 GSIFVVVALLPYDKLD------DGSYQSVLEAIGIPHAKQIMDVVILTAVASCLNSALYT 323 Query: 308 TSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAV 367 SR++FS+ R+DAPRV KL+ + VP AVL SM F++V Y P + +LL Sbjct: 324 ASRMLFSLGERRDAPRVVRKLTGNGVPWVAVLASMVIGFLAVVGNYVLPDKIFAYLLATS 383 Query: 368 GGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAAS 427 G + V+ I SQL L ++++A S VRMW P+L + +V + ++ LM D + Sbjct: 384 GAVALFVYLAIATSQLVLGRKMRATGGRSAVRMWLFPYLTGVVIVFIIAVLILMAFD-PN 442 Query: 428 RSQVYSVAIVYGFLVL 443 + Q +I+ +++ Sbjct: 443 QQQAIGFSIISAVIIV 458 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: 618 Number of extensions: 32 Number of successful extensions: 2 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: 480 Length adjustment: 33 Effective length of query: 430 Effective length of database: 447 Effective search space: 192210 Effective search space used: 192210 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