Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter
Query= SwissProt::P0AAE0 (470 letters) >NCBI__GCF_001277995.1:WP_082353324.1 Length = 468 Score = 617 bits (1590), Expect = 0.0 Identities = 298/459 (64%), Positives = 365/459 (79%) Query: 11 DQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFV 70 D A + L R L+NRH+QLIAIGGAIGTGLFMGSGKTIS+AGPS+I VY IIGFMLFFV Sbjct: 3 DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62 Query: 71 MRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWF 130 MRAMGELLL+NL YKS D SD+LGP AG+ TGWTYWFCW+ TGMAD+VAIT Y Q+W+ Sbjct: 63 MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122 Query: 131 PDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSP 190 P++ W+ + I++L LNLA V++FGEMEFWFA+IKIVAIV+LI VG MV F +P Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAP 182 Query: 191 TGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAIN 250 G ASF +L GG+FP G++GF AGFQIA+FAFVGIEL GT AAETKDPE +LPRAIN Sbjct: 183 NGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAIN 242 Query: 251 SIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASS 310 SIPIRI++FYV AL VIM VTPW+ V P+ SPFV++F L G+PAAA +INFVV+TSAASS Sbjct: 243 SIPIRIVVFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASS 302 Query: 311 ANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIG 370 ANSG+FSTSRML+GL+ EG APK + LSKR VPA+GLTFS +CL+ V +LY +VI Sbjct: 303 ANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLYAGGTVIE 362 Query: 371 AFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVV 430 AFT+ITTVS++LFM VW+ IL +Y+VYR++ P LHEKS++KMP G +M V + FFV ++ Sbjct: 363 AFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVVVLVFFVAML 422 Query: 431 VLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELR 469 +L+LE DTR ALL TP+WFI LG+GW G + A+ R Sbjct: 423 GVLSLETDTRTALLATPVWFIILGVGWFATGGAKGAQRR 461 Lambda K H 0.329 0.141 0.440 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: 745 Number of extensions: 12 Number of successful extensions: 1 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: 470 Length of database: 468 Length adjustment: 33 Effective length of query: 437 Effective length of database: 435 Effective search space: 190095 Effective search space used: 190095 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 (21.8 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