Align PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose (characterized)
to candidate WP_004095992.1 M988_RS13035 PTS system mannose/fructose/sorbose family transporter subunit IID
Query= TCDB::P69805 (286 letters) >NCBI__GCF_001655005.1:WP_004095992.1 Length = 288 Score = 183 bits (464), Expect = 4e-51 Identities = 108/254 (42%), Positives = 151/254 (59%), Gaps = 9/254 (3%) Query: 34 SWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHLEFFNTQPFVAAPILGVTLALE 93 S ++ER+Q+L FC SM P I++LYPE E R +A++RHL FFNT+ A I GV +A+E Sbjct: 42 SSSYERLQSLIFCASMTPIIKKLYPEKEE-RAEALKRHLNFFNTEQTFGAVIQGVAIAME 100 Query: 94 EQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLF 153 EQ+ G I D +I GIK GLMGPLAG+GD + W V P+ A+ A GS G +L Sbjct: 101 EQKTRGEPISDASITGIKTGLMGPLAGIGDSVIWAAVMPLLIAIFIPFAAKGSAFGGILP 160 Query: 154 FILFNLVRLATRYYGVAYGYSKGID-IVKDMGGGFLQKLTEGASILGLFVMGALVNKWTH 212 IL+ + LA Y V GY+ G D I+ + GG +++L GA++LGL +MGAL + Sbjct: 161 LILYTGITLAVSYGLVHKGYTLGRDSIITLLQGGRIKELIYGANVLGLIMMGALSASYVK 220 Query: 213 VNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTFACMWLLRKKVNPLWIIVGFF 272 + PL +S + G E V VQ ILD + PGL+PL F+ + L KK P + + Sbjct: 221 ITSPLKISAL---EGSEIV--VQQILDSIAPGLLPLAAVFSIYFYLTKK-GPRYTTILLS 274 Query: 273 VIGIAGYACGLLGL 286 V+ + C LLG+ Sbjct: 275 VV-VISVVCSLLGV 287 Lambda K H 0.326 0.143 0.436 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: 227 Number of extensions: 19 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: 286 Length of database: 288 Length adjustment: 26 Effective length of query: 260 Effective length of database: 262 Effective search space: 68120 Effective search space used: 68120 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 (21.6 bits) S2: 47 (22.7 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