Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate BPHYT_RS07280 BPHYT_RS07280 amino acid permease
Query= uniprot:A0A0C4YP23 (465 letters) >FitnessBrowser__BFirm:BPHYT_RS07280 Length = 466 Score = 313 bits (801), Expect = 1e-89 Identities = 162/449 (36%), Positives = 257/449 (57%), Gaps = 2/449 (0%) Query: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 L+RGL + +IA+GGAIGTGLFLG I AGPSVL+ YA+ +IA +M L EM Sbjct: 18 LQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYAIGALIALLLMGCLAEMT 77 Query: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 V P +GSF +A Y +AGF+ + YW + E++A+ +Y++YW+P +P W Sbjct: 78 VAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTAIAVYMKYWFPAVPGWYW 137 Query: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVSNLW 192 +GF + IN SVK FG +E+ FS++K++AIVG I+ G Y++ A +N Sbjct: 138 IVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAYVVFGAPADSTIGFANYT 197 Query: 193 QHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIFYV 252 HGGFFP G+ G+ +A+ V +FS+ +E++ + A EA +P+K I +A ++R++ FY+ Sbjct: 198 SHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKAITRAFRATMFRLVFFYL 257 Query: 253 GALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCNSRM 312 L ++L++ PW T SPFV + A + A V+N V+L AALS NS +Y +RM Sbjct: 258 LTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVILVAALSAMNSQLYITTRM 317 Query: 313 LFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLVVSAL 372 +F L++ G AP+ L +N +G+P+AAL +S + A V+N P +F L+M + + Sbjct: 318 MFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVVYPDASFVLMMSVSMFGA 377 Query: 373 IINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLTPGLRISV 432 + W MI + H FR R G F+ GYP T+ + + L + T R+++ Sbjct: 378 MFTWLMIFVTHFFFRH--RHQGAPLAFRMWGYPGTSALGAGLMVSALVTTWFTREFRMTL 435 Query: 433 YLIPAWLAVLGLSYRLRQKQKRAEPALPE 461 + ++ L + Y + +++ E A E Sbjct: 436 VIGVPFIVSLLVVYFVWYRKRAVEGAAAE 464 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: 599 Number of extensions: 25 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: 465 Length of database: 466 Length adjustment: 33 Effective length of query: 432 Effective length of database: 433 Effective search space: 187056 Effective search space used: 187056 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