Align Aromatic amino acid transport protein AroP (characterized, see rationale)
to candidate WP_058931453.1 AU252_RS15260 D-serine/D-alanine/glycine transporter
Query= uniprot:A0A0C4YP23 (465 letters) >NCBI__GCF_001484605.1:WP_058931453.1 Length = 498 Score = 358 bits (919), Expect = e-103 Identities = 174/445 (39%), Positives = 281/445 (63%), Gaps = 6/445 (1%) Query: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 L+R L NRHIQLIA+GGAIGTGLF+G +TI AGPSV+ Y + G + FF+MR +GE++ Sbjct: 15 LERQLSNRHIQLIAIGGAIGTGLFMGSGKTISAAGPSVIFVYMIIGFMLFFVMRAMGELL 74 Query: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 + SFS FA G +AGF +GW YW +++ +A++ A+ Y + WP +P W Sbjct: 75 LSNLHYKSFSDFAADLLGPWAGFFTGWTYWFCWVITGIADVIAIAAYSEELWPGVPLWIP 134 Query: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASG---TAGPQASVS 189 + +++ +NL +V++FGE EFWF+++K++AI +I+ G +++ SG AGP A+ + Sbjct: 135 GIATVVILLVLNLATVRAFGETEFWFALIKIIAIAALIIVGLFMIFSGFQSDAGP-ATFN 193 Query: 190 NLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILI 249 NLW HGG FPN G V + +F+F G+ELVG TAAEA +PEK +PKA N + R+L+ Sbjct: 194 NLWSHGGMFPNEFMGFVAGFQIAVFAFVGIELVGTTAAEAKDPEKNLPKAINSIPIRVLL 253 Query: 250 FYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCN 309 FYVGAL +L+S+ PW + G SPF+ +F AT++N VVL++A+S NSG+Y Sbjct: 254 FYVGALIILMSVTPWTQFQAGHSPFIAMFSLAGLGAAATIVNLVVLSSAMSSANSGIYST 313 Query: 310 SRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMP--GEAFELLMGL 367 SRM++GLA++G+AP +++ R +P AL +S + + +V+ Y G+AF+++ + Sbjct: 314 SRMVYGLAQEGDAPTVFSRLSSRKVPQNALFLSCILLLSGIVLMYAGKDIGKAFDMVTTV 373 Query: 368 VVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLTPG 427 + W++I +LKFR + + +++K G +V AF A +L+ + P Sbjct: 374 SAVCFVFVWSIILASYLKFRSRRPHLHESSKYKMPGGVPMVWVVFAFFAFVLWALTTQPD 433 Query: 428 LRISVYLIPAWLAVLGLSYRLRQKQ 452 +++ + P W +LG+++ + +K+ Sbjct: 434 TLVALLVTPIWFILLGVAWIILRKR 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: 559 Number of extensions: 20 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: 498 Length adjustment: 34 Effective length of query: 431 Effective length of database: 464 Effective search space: 199984 Effective search space used: 199984 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 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