Align Aromatic amino acid permease, AroP (characterized)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 298 bits (763), Expect = 3e-85 Identities = 153/417 (36%), Positives = 243/417 (58%), Gaps = 15/417 (3%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 L L+ RH+TM+ LG IGAGLF+G+G I AGPA +L+Y+I G +V LVM MLGEMA Sbjct: 6 LKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFMLGEMA 65 Query: 68 AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEPWIP- 126 + P SGSFS Y G WAGF++GWLYWF ++ + E AI+ + PW+P Sbjct: 66 SRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFL---PWLPV 122 Query: 127 ---SLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGT 183 +L ++ N +VR FGE EYW +F KVA II F+++G +++FG PG G Sbjct: 123 PAGALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLGASILFGLQPGIPAPGL 182 Query: 184 SNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRIS 243 N GFMPNGIS V +G++ V F+ GG EI +AA ES+ P + + A+++VI R+ Sbjct: 183 LNLTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILRVM 242 Query: 244 VFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNA 303 VFY+GSV ++ MP+ +SP+ + +MA G M+ ++ ++ +S N+ Sbjct: 243 VFYVGSVSILILCMPWTD----KANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNS 298 Query: 304 QIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFL 363 +++ SR++FS++ R AP +F + + VP NA++L + +G+ + + L L Sbjct: 299 FLFSNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLML 358 Query: 364 LNAVGGCLIVVWAMITLSQLKLRKELQAND-EISTVRMWAHP---WLGILTLVLLAG 416 + G +++VW I ++ +R++ + + ++ R W +P W+ +L LV + G Sbjct: 359 AKSSGAFVMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLG 415 Score = 26.2 bits (56), Expect = 0.002 Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 4/51 (7%) Query: 117 AWF-GVEPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLII 166 AWF V W+ L V AV+ A F++WFA I+A+ + Sbjct: 396 AWFYPVSNWVALLALV---AVLGSQAFNPESRFQFWFAVSTALAIVAWYYV 443 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: 558 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 463 Length of database: 459 Length adjustment: 33 Effective length of query: 430 Effective length of database: 426 Effective search space: 183180 Effective search space used: 183180 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