Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 412 bits (1058), Expect = e-119 Identities = 203/443 (45%), Positives = 291/443 (65%), Gaps = 2/443 (0%) Query: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 + + L RGL RHI+ +A+G AIG GLF G+ AI AGP ++L+Y IGG A++ +MRAL Sbjct: 4 QSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMRAL 63 Query: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 GE+ + PV+GSF YA +GP AGF GW+Y F +V +A++TA +Y+ +WFPDVP Sbjct: 64 GEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPDVP 123 Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFG--VTPLGP 192 +WI L + ++ +N ++V VFGELEFW +L+KV IVAMI G+AI+ FG + G Sbjct: 124 RWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADGGV 183 Query: 193 TASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVV 252 NLWTHGGFMP G GV+ + +VMFA+ G+E+IG+TAGEA++P++V+P A N V Sbjct: 184 ATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINAVP 243 Query: 253 WRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNS 312 RIL+FYV L ++M+L PW+ + SPFV +F R+G+ AAA++N+VVI+AA S+ NS Sbjct: 244 LRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAINS 303 Query: 313 GIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWV 372 IF GRMLY +A QAPR F VS K VP + + A + GV+LNY++PE VF + Sbjct: 304 DIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFTLI 363 Query: 373 TSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLS 432 SI+ ++W W +I+++ + R+ ++ V A+ F +P P A AFM+ + +L Sbjct: 364 ASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGVLG 423 Query: 433 LDPGTRVALYVAPVWFALLGIGY 455 P TR AL V VW LL + + Sbjct: 424 WFPQTRAALLVGAVWLLLLVVAW 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: 785 Number of extensions: 49 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: 466 Length adjustment: 33 Effective length of query: 439 Effective length of database: 433 Effective search space: 190087 Effective search space used: 190087 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