Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate GFF344 PS417_01755 proline-specific permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 417 bits (1072), Expect = e-121 Identities = 202/444 (45%), Positives = 296/444 (66%), Gaps = 4/444 (0%) Query: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 +EK L RGL RHI+ +A+G AIG GLF G+ AI +AGP ++L+Y IGG A+F +MRAL Sbjct: 4 QEKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRAL 63 Query: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 GE+ ++ PV+GSF YA ++GP AGF GW+Y F ++ +A++TA +Y+ +WFPDV Sbjct: 64 GEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFPDVA 123 Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPT- 193 +W+ L + ++ +N V VFGE+EFW +L+KV IVAMI+ G I+ FG+ G T Sbjct: 124 RWVWVLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAGETQ 183 Query: 194 -ASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVV 252 + SNLW HGGFMP G G++ + +VMFA+ G+E+IG+TAGEA++P++V+P A N V Sbjct: 184 ASGLSNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAINAVP 243 Query: 253 WRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNS 312 RIL+FYV L ++MA+ PW ++ SPFV +F +G+ AA I+N+VVI+AA S+ NS Sbjct: 244 LRILLFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAVSAINS 303 Query: 313 GIFSTGRMLYTLAQFGQAPRAFGRVSSKHVP-SIAITFSAALMGIGVLLNYIVPEQVFVW 371 IF GRM+Y LAQ GQAP+ F ++S + VP + AAL+G GV+LNY++PE VF+ Sbjct: 304 DIFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLG-GVVLNYLIPENVFLV 362 Query: 372 VTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLL 431 + SI+ ++W W +I+ + R+++ +V + F +P PYA + FM+ V +L Sbjct: 363 IASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFVFGVL 422 Query: 432 SLDPGTRVALYVAPVWFALLGIGY 455 P T+ AL V VW LL + Y Sbjct: 423 GYFPDTQAALLVGAVWIVLLVVAY 446 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: 776 Number of extensions: 43 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 439 Effective length of database: 436 Effective search space: 191404 Effective search space used: 191404 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 17 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