Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_057509355.1 ABB28_RS14795 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_001431535.1:WP_057509355.1 Length = 460 Score = 396 bits (1018), Expect = e-115 Identities = 207/435 (47%), Positives = 283/435 (65%), Gaps = 6/435 (1%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 LG L+ R L MMGLGSAIGAGLFLG+GVG++ AGPAVLL+Y++AGA+V++VM LGEMA Sbjct: 16 LGHALKPRQLIMMGLGSAIGAGLFLGSGVGVQLAGPAVLLSYLVAGALVIIVMNALGEMA 75 Query: 68 AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGA-WFGVEPWIP 126 A +P SG+FS Y DA G AG ++GWL+W L++V+ AE GAA ++ W G+ + Sbjct: 76 ANKPTSGAFSVYAADALGPTAGATVGWLWWVQLVIVIAAEAVGAAGLLATVWTGLSVPMA 135 Query: 127 SLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNF 186 +L ++FF +NL+ V+ FGEFE+WFA +KVA I+ F+ IG AL+ GWLP +T G SNF Sbjct: 136 ALAFMLFFTAINLLGVKNFGEFEFWFAILKVAAILGFIAIGAALLLGWLPDATSPGLSNF 195 Query: 187 IGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFY 246 G+ GF P G++GV A LL V FAFGG EIV +AAAE++ P +I+ A+R V WRI VFY Sbjct: 196 TGNGGFAPTGLAGVGAALLVVIFAFGGTEIVAVAAAETEDPERSIARAIRTVAWRILVFY 255 Query: 247 LGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIY 306 +GS+ VI ++P+ S A +SPF +L ANIPG + + V+ALLSA NA +Y Sbjct: 256 IGSLSVIIAVVPWTS-----EALKSPFAAVLEAANIPGAGTAITLVAVIALLSALNANLY 310 Query: 307 ATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNA 366 SR++FS+A R++AP V VP AVL S+ F F + ++ P +L LLN Sbjct: 311 GASRMIFSLAQRREAPAVLGWADRRQVPVLAVLASVLFGFAATVMELVFPDRVLPVLLNI 370 Query: 367 VGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAA 426 VG ++VW + LSQL LR+ RM A PWL L L +LA + AL+L Sbjct: 371 VGSTCLLVWTLSLLSQLVLRRRADRAGVALPFRMAAFPWLTALALAILALIFALLLYGDQ 430 Query: 427 SRSQVYSVAIVYGFL 441 +R Q S+ ++ F+ Sbjct: 431 TRLQFLSMVVLTLFI 445 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: 601 Number of extensions: 29 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: 460 Length adjustment: 33 Effective length of query: 430 Effective length of database: 427 Effective search space: 183610 Effective search space used: 183610 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