Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_008508798.1 BIBO1_RS14845 amino acid permease
Query= SwissProt::A0A0H2VDI7 (470 letters) >NCBI__GCF_000182725.1:WP_008508798.1 Length = 467 Score = 574 bits (1480), Expect = e-168 Identities = 271/442 (61%), Positives = 345/442 (78%) Query: 16 EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75 E L RNL+NRH+QLIAIGG IGTGLFMGSGK +SLAGPSI+ +Y I GFMLFFVMRA+G Sbjct: 16 EPHLARNLSNRHLQLIAIGGTIGTGLFMGSGKAVSLAGPSILLIYAITGFMLFFVMRALG 75 Query: 76 ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLSD 135 E+LLSNL+Y+SF+DFA D LGP A +FTGWTYW CW+VT +A+VVA++ Y FWFP L+ Sbjct: 76 EILLSNLQYRSFADFAGDYLGPCAQFFTGWTYWLCWIVTAVAEVVAVSGYVSFWFPHLAP 135 Query: 136 WVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195 W+ +L +I +LL+LNL TV+ FGE+EFWFA+IKI+ I+ LI+ G+ M+ F P G +A Sbjct: 136 WIPALGLITILLILNLPTVRNFGEIEFWFALIKIITIIGLIITGIYMLMTGFVLPNGTQA 195 Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255 S AHLWN GG+FP G GF AGFQI+VFAFVGIELVGT AAE ++P ++LP+AIN+IPIR Sbjct: 196 SIAHLWNHGGFFPNGSLGFIAGFQISVFAFVGIELVGTAAAEAENPMRNLPKAINNIPIR 255 Query: 256 IIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315 I++FY+ +L VI++VTPW+ V P SPFV +F L G+ AA INFVVLTSA+SS+NSG+ Sbjct: 256 IVLFYIGALFVIITVTPWNQVDPNSSPFVAMFSLAGIGIAAHFINFVVLTSASSSSNSGI 315 Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375 +STSRM++GLA G+APKAF+KLS R VP L FSCI LL VV+LY S+I FT++ Sbjct: 316 YSTSRMVYGLATVGLAPKAFSKLSNRKVPVHALIFSCIFLLSSVVLLYAGQSMIQVFTLV 375 Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLTL 435 TT+SA+LF+F+W+IIL SYL YR++ P HEKS +KMP G+ + FF FVL LT Sbjct: 376 TTISALLFIFIWSIILVSYLQYRRKHPERHEKSTFKMPGGRASVVMVFVFFAFVLWALTQ 435 Query: 436 EDDTRQALLVTPLWFIALGLGW 457 E DT A+ VTPLWF+ LG+ + Sbjct: 436 EPDTLAAMKVTPLWFVLLGIAY 457 Lambda K H 0.329 0.141 0.441 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: 771 Number of extensions: 26 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: 467 Length adjustment: 33 Effective length of query: 437 Effective length of database: 434 Effective search space: 189658 Effective search space used: 189658 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