Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease
Query= SwissProt::P0AAE0 (470 letters) >NCBI__GCF_000691145.1:WP_008347408.1 Length = 448 Score = 482 bits (1241), Expect = e-141 Identities = 228/446 (51%), Positives = 324/446 (72%), Gaps = 9/446 (2%) Query: 15 AEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 74 A+Q L+R+L+NRH+QLIAIGG IGTGLF+GSGK I LAGPSIIF Y+I+G +FFVMRA+ Sbjct: 2 AQQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRAL 61 Query: 75 GELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLS 134 GELLLS Y+S +D A D LGPWA + TGWTYWFCW++T MADV+A+ Y Q+WF D+ Sbjct: 62 GELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DIP 120 Query: 135 DWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVE 194 W+ ++ +++LL NL TVK+FGEMEFWFA+IK++ I+ LI VG+V++ + FQ+ G Sbjct: 121 QWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAG-P 179 Query: 195 ASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254 + +LW+ GG FP G++GF FQ+ +FA+VG+ELVG +AAET +P+K++P AIN IP+ Sbjct: 180 VTVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPL 239 Query: 255 RIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314 RI+ FYV A+ V++ + PW+ + +SPFV+ F L+G+P AA +INFVVLTSAAS+ NSG Sbjct: 240 RILFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNSG 299 Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374 +FSTSR+L+ L+ + P +F +L+K AVP+ L S I + G ++ + P AF + Sbjct: 300 MFSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPE--QAFGI 357 Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLT 434 +TT+SAI F++VW+IIL +L Y+K RP LH+ S +K P + + F ++V++ Sbjct: 358 VTTISAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIML 417 Query: 435 LEDDTRQALLVTPLWFIALGLGWLFI 460 D TR ALL+TP+WF G+LF+ Sbjct: 418 FADATRPALLLTPVWF-----GFLFL 438 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: 696 Number of extensions: 35 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: 470 Length of database: 448 Length adjustment: 33 Effective length of query: 437 Effective length of database: 415 Effective search space: 181355 Effective search space used: 181355 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