Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate AO353_12275 AO353_12275 proline-specific permease
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12275 Length = 468 Score = 422 bits (1086), Expect = e-123 Identities = 201/438 (45%), Positives = 294/438 (67%), Gaps = 1/438 (0%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGL RHI+ +A+G AIG GLF G+ AI +AGP ++L+Y IGG A+F +MRALGE+ Sbjct: 8 LKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMA 67 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 ++ PV+GSF YA ++GP AGF GW+Y F V+ GMA++TA +Y+ +WFP+V +WI Sbjct: 68 VHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWIW 127 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGV-TPLGPTASFS 197 L ++++ +N V VFGE+EFW +L+KV IVAMI+ G I+ FG+ T G S Sbjct: 128 VLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDIS 187 Query: 198 NLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257 NLWT GGFMP G G++ + +VMFA+ G+E+IGVTAGEA++P+ VLP A N V RIL+ Sbjct: 188 NLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRILL 247 Query: 258 FYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFST 317 FYV ++++M++ PW ++ SPFV +F+++G+ AA I+N+VVITAA S+ NS IF Sbjct: 248 FYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIFGA 307 Query: 318 GRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISL 377 GRM++ LAQ G AP+ F +S VP + + + + +GVLLNY++PE VF+ + SI+ Sbjct: 308 GRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASIAT 367 Query: 378 VGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGT 437 ++W W +I+ + R+++ A +V + F +P PYA +AFM+ V +L P T Sbjct: 368 FATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFPDT 427 Query: 438 RVALYVAPVWFALLGIGY 455 + AL V VW LL + Y Sbjct: 428 QAALIVGVVWIVLLVLAY 445 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: 800 Number of extensions: 51 Number of successful extensions: 2 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: 468 Length adjustment: 33 Effective length of query: 439 Effective length of database: 435 Effective search space: 190965 Effective search space used: 190965 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