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 BWI76_RS03970 BWI76_RS03970 PTS mannose/fructose/sorbose family transporter subunit IID
Query= TCDB::P69805 (286 letters) >FitnessBrowser__Koxy:BWI76_RS03970 Length = 283 Score = 209 bits (531), Expect = 7e-59 Identities = 108/284 (38%), Positives = 168/284 (59%), Gaps = 8/284 (2%) Query: 1 MSEMVDTTQTTTEKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPEN 60 +SE Q E ++T D+R VF RS + SWN+ER L F ++++P +++LYP Sbjct: 6 ISEETLRPQEQEETRITPRDLRRVFWRSFQMEFSWNYERQMNLAFVYALIPVLKKLYPRK 65 Query: 61 NEARKQAIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAG 120 E A++RHL FFNT P + +LG+T A+EE+ + +D AI+ +K LMGPLAG Sbjct: 66 EELAA-ALKRHLVFFNTTPHIVTLLLGITTAMEEKNSQQKNMDANAIDNVKASLMGPLAG 124 Query: 121 VGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIV 180 +GD FWGT+R + +G +A+ G++LGP+LF ++FN+ + R++ +GY G ++ Sbjct: 125 LGDSFFWGTLRLIATGIGTSLALKGNILGPILFLLVFNVPHILVRWFFTRWGYVLGTGVL 184 Query: 181 KDM-GGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILD 239 + + G ++ LT GASI+GL V+GA+ + IP+ E T VQ I++ Sbjct: 185 QRIQKSGMMESLTYGASIIGLMVVGAMTASMIDITIPVSFG------AGEAKTQVQDIIN 238 Query: 240 QLMPGLVPLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGL 283 ++P ++PLL WLL +KV PL II G ++GI G GL Sbjct: 239 DILPCMLPLLSFGIVYWLLGRKVKPLSIIGGMALVGILGSWIGL 282 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: 245 Number of extensions: 16 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: 283 Length adjustment: 26 Effective length of query: 260 Effective length of database: 257 Effective search space: 66820 Effective search space used: 66820 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 Apr 09 2024. 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