Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_058930993.1 AU252_RS12445 amino acid permease
Query= uniprot:A0A0C4YP23 (465 letters) >NCBI__GCF_001484605.1:WP_058930993.1 Length = 506 Score = 332 bits (852), Expect = 1e-95 Identities = 171/443 (38%), Positives = 268/443 (60%), Gaps = 9/443 (2%) Query: 10 DATLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLG 69 D + LK R IQ+IA+GGAIGTGLFLG + AGPS+++ YAV G AF I+R LG Sbjct: 30 DKGYHKSLKPRQIQMIAIGGAIGTGLFLGAGGRLNAAGPSLVIAYAVCGFFAFLILRALG 89 Query: 70 EMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQY------W 123 E+V+ P +GSF +A ++ G A F+SGW YW+ + ++ +++A +Y+ + W Sbjct: 90 ELVLHRPSSGSFVSYAREFFGEKAAFVSGWFYWLNWATTTIVDITAAALYMNFFGNYIPW 149 Query: 124 WPHIPTWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTA- 182 +P WA AL +++ A+NL SVK FGEMEFWF+++KV A+V +V G Y + GT Sbjct: 150 MAAVPQWAWALIALVVVLALNLVSVKVFGEMEFWFALIKVAALVVFLVVGTYFVIFGTPV 209 Query: 183 -GPQASVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATN 241 G +S L +GG FPNG+ +++ M ++F++ +ELVG A E + PEK +PKA N Sbjct: 210 DGQPVGLSLLSDNGGVFPNGLLPMIILMQGVLFAYASIELVGTAAGETENPEKIMPKAIN 269 Query: 242 QVIYRILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSV 301 V++RI +FYVG++ +L L P+ G SPFV F ++ V ++N VVLTAALS Sbjct: 270 SVVFRIAVFYVGSVILLALLLPYTSYEKGVSPFVTFFGSIGIQGVDVIMNLVVLTAALSS 329 Query: 302 YNSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAF 361 N+G+Y R+L ++ G+APK ++NK G+P + ++A + V +NY +P +AF Sbjct: 330 LNAGLYSTGRILRSMSVNGSAPKFAGRMNKAGVPYGGIAITAGVSLLGVPLNYLVPAQAF 389 Query: 362 ELLMGLVVSALIINWAMISIIHLKFRR-DKRAAGQETRFKSLGYPLTNYVCLAFLAGILY 420 E+++ + +I+ WA I + ++ +R + + F+ G P T Y+ L FLA +L Sbjct: 390 EIVLNVASVGIIMTWATIVLCQIQLQRWANKGWLKRPSFRMFGAPYTGYLSLLFLASVLV 449 Query: 421 VMYLTPGLRISVYLIPAWLAVLG 443 ++++ L + V I + L V G Sbjct: 450 MVFIDSPLTMLVTAIASVLMVFG 472 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: 595 Number of extensions: 28 Number of successful extensions: 4 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: 506 Length adjustment: 34 Effective length of query: 431 Effective length of database: 472 Effective search space: 203432 Effective search space used: 203432 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: 52 (24.6 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