Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= uniprot:A0A0C4YP23 (465 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 623 bits (1607), Expect = 0.0 Identities = 300/449 (66%), Positives = 365/449 (81%), Gaps = 9/449 (2%) Query: 12 TLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEM 71 +L+RGLKNRHIQLIALGGAIGTGLFLG A ++ AGPS++LGYA+ G IAF IMRQLGEM Sbjct: 10 SLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEM 69 Query: 72 VVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWA 131 +V+EPVAGSFSHFA+KY G +AGF+SGWNYWVLY+LV MAEL+AVG YVQ+WWP +PTWA Sbjct: 70 IVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWA 129 Query: 132 SALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVSNL 191 +A FF+LIN INL++VK+FGE EFWF+IVKV AIVGMI+ G +LL SG G QAS+SNL Sbjct: 130 TAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKGGEQASISNL 189 Query: 192 WQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIFY 251 W HGGFFPNG SG+++A+A+IMFSFGGLELVGITAAEA EP+ IPKA NQV+YRILIFY Sbjct: 190 WSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILIFY 249 Query: 252 VGALGVLLSLYPWEKVVT---------GGSPFVLIFHAMNSDIVATVLNAVVLTAALSVY 302 +GAL VLL+LYPW+ ++ GSPFV IF + SD A +LN VVLTAALSVY Sbjct: 250 IGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALSVY 309 Query: 303 NSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFE 362 NSGVYCNSRML+GLA+QG+AP++L+K+N RG+P+ A+GVSAL T CV +NY P A E Sbjct: 310 NSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQGALE 369 Query: 363 LLMGLVVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVM 422 LLM L V+AL+INWAMIS+ HLKFRR + G E FK+ +PL+NY+CLAF+AGIL +M Sbjct: 370 LLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEPSFKAFWFPLSNYLCLAFVAGILIIM 429 Query: 423 YLTPGLRISVYLIPAWLAVLGLSYRLRQK 451 PG+R+SV+ IP W+ L L YRLR + Sbjct: 430 LWLPGIRMSVFAIPVWVGFLWLCYRLRAR 458 Lambda K H 0.326 0.140 0.426 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: 709 Number of extensions: 30 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: 465 Length of database: 464 Length adjustment: 33 Effective length of query: 432 Effective length of database: 431 Effective search space: 186192 Effective search space used: 186192 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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