Align Aromatic amino acid permease, AroP (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 328 bits (841), Expect = 2e-94 Identities = 177/431 (41%), Positives = 267/431 (61%), Gaps = 17/431 (3%) Query: 3 KSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQM 62 + + GL GL+ RH+TM+ LG IGAGLF+G+GV I++AGPA +++++I G +VVLVM+M Sbjct: 8 QQSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLLVVLVMRM 67 Query: 63 LGEMAAARPASGSFSRYGEDAF------GHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMG 116 LGEMA A P GSF Y +A+ G AGF GW+YW+ ++V+ E A+++ Sbjct: 68 LGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGASLVQ 127 Query: 117 AWF-GVEPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWL 175 W GV W SLV +V + NL++V+ FGEFE+WFA IKVA I+ FL + + G Sbjct: 128 FWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAGLFVLGMW 187 Query: 176 PGSTFVGTSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAV 235 PG+T ++ GF PNGI V G +A + G EIVTIAAAE+ +P++A++ A Sbjct: 188 PGAT-ASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETAEPQKAVARAT 246 Query: 236 RAVIWRISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVL 295 +VI R+ VFY+GSVL++ L+P+ S A +P+ L IP M A+++ Sbjct: 247 SSVITRVLVFYVGSVLLVVCLVPWNSAGIA-----TPYVSALNAMRIPAAAQIMNAVVLT 301 Query: 296 ALLSAFNAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWN 355 A+LSA N+ +YA+SR++F++ R DAP+ ++LS + VP A+L + F + +V + Y + Sbjct: 302 AVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAVVMSYVS 361 Query: 356 PAGLLDFLLNAVGGCLIVVWAMITLSQLKLRKELQAN-DEISTVRMWAHPWLGILTLVLL 414 P + FL+N+ G I V+ +I +SQL+LR L+ VRMWA P+ LT V + Sbjct: 362 PDKVFAFLVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFPY---LTWVAI 418 Query: 415 AGLVALMLGDA 425 AG+V +++ A Sbjct: 419 AGMVGIVVAMA 429 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: 581 Number of extensions: 36 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 474 Length adjustment: 33 Effective length of query: 430 Effective length of database: 441 Effective search space: 189630 Effective search space used: 189630 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 17 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