Align D-serine/D-alanine/glycine transporter (characterized)
to candidate WP_009490181.1 C683_RS03825 amino acid permease
Query= SwissProt::A0A0H2VDI7 (470 letters) >NCBI__GCF_000313915.1:WP_009490181.1 Length = 448 Score = 470 bits (1209), Expect = e-137 Identities = 221/439 (50%), Positives = 323/439 (73%), Gaps = 3/439 (0%) Query: 15 AEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAM 74 +++ L R L+NRH+QLI+IGGAIGTGLF+ SGK+I++AGPS++ YMI+G +FF+MR++ Sbjct: 2 SQEKLERGLSNRHVQLISIGGAIGTGLFLASGKSIAIAGPSVLLAYMIVGMFVFFIMRSL 61 Query: 75 GELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLS 134 GELLL+NL+ SF + A LG + TGWTYWFCW+ M+D+ A+ Y ++WFP L Sbjct: 62 GELLLANLDCHSFVELAHQYLGRRWAFVTGWTYWFCWITVAMSDLTAVGMYMRYWFPHLP 121 Query: 135 DWVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVE 194 W+ +L +++ L+ LNL +VK+FGE+EFW A+IKI+AIV+LI VGL M+ H + G+ Sbjct: 122 QWIPALLMLLFLMALNLLSVKLFGEIEFWLALIKILAIVALIGVGLYMIFTHHKLENGIV 181 Query: 195 ASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254 ASFA+L+ DGG+FP G SGF FQ+AVF+F G+ELVG TA ET+DPEK+LP+AIN+IP+ Sbjct: 182 ASFANLYQDGGFFPHGFSGFILSFQLAVFSFTGVELVGLTAGETQDPEKTLPKAINNIPV 241 Query: 255 RIIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314 RI++FYV SL VIM+V PW+ + P +SPFV +F +G+ AAAS+INFVVL+SAAS+ NS Sbjct: 242 RILLFYVGSLAVIMAVQPWNIIDPTQSPFVTVFSSIGIAAAASIINFVVLSSAASACNSA 301 Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374 +FSTSRML+GLA++ APK FAKL+K + PA L S + + +V+ YV P G F++ Sbjct: 302 LFSTSRMLYGLAKDDNAPKTFAKLNKNSTPAMALLMSSVVVGITIVLNYVMPE--GVFSL 359 Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLT 434 I+ +S + F+F+WTII+ ++ + KQ ++ +++ K++ + + F ++V+ Sbjct: 360 ISGISTVCFLFIWTIIVICHMKFLKQTKD-EDRPKFRLKGAKVINILSLIFLALIIVICA 418 Query: 435 LEDDTRQALLVTPLWFIAL 453 + + TR AL +TP+WFIAL Sbjct: 419 VLESTRIALFITPIWFIAL 437 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: 635 Number of extensions: 24 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