Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter
Query= uniprot:A0A0C4YRF7 (472 letters) >NCBI__GCF_002095475.1:WP_084934657.1 Length = 463 Score = 427 bits (1099), Expect = e-124 Identities = 216/465 (46%), Positives = 307/465 (66%), Gaps = 5/465 (1%) Query: 1 MTDVRKLLNEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSY 60 M D K E EK L R L +RHIQ+IAIGGAIG GLF+G+G+ I++AGP ++ Y Sbjct: 1 MVDQSKEALIEAEQPEK-LRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 59 Query: 61 AIGGVAIFFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEIT 120 I G +FF+MRA+GELLL SF+ +A + +GP+AG+ TGW+YWF WVVTG+A++ Sbjct: 60 MIIGFMLFFVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVV 119 Query: 121 AVAVYVHYWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGL 180 A++ Y WFP W+ AL + +N V +FGE+EFWFA+IK+V IVA+I+ G+ Sbjct: 120 AISAYFQLWFPGFSIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGI 179 Query: 181 AIIFFGV-TPLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQN 239 ++ +P G TAS SN+W HGG P G G QI +FA+ G+EL+G A E ++ Sbjct: 180 VLVSMHYPSPNGTTASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKD 239 Query: 240 PEKVLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVN 299 P KVLP A N + RI++FYV AL+++MA+ PWN++ P SPFV +F IG+P AA+IVN Sbjct: 240 PHKVLPRAINAIPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVN 299 Query: 300 LVVITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVL 359 VV+T+AASS NSGIFST RML+ LA+ G A +AFGR+S++ VP+ + FS + +GV Sbjct: 300 FVVLTSAASSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVA 359 Query: 360 LNYIVPE--QVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYAN 417 L Y++P+ VF VT++S + ++ W+II+ ++L YRK R A F+MP + Sbjct: 360 LIYLIPDVMTVFTMVTTVSAILFMFVWTIILCSYLAYRKQ-HPQRHAASKFKMPLGKFMC 418 Query: 418 WLVVAFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRA 462 W+ +AF V VLL+L TR AL V P+WF +L +G+ + +A Sbjct: 419 WVCMAFFAFVLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRKA 463 Lambda K H 0.328 0.142 0.445 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: 716 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: 472 Length of database: 463 Length adjustment: 33 Effective length of query: 439 Effective length of database: 430 Effective search space: 188770 Effective search space used: 188770 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