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_RS01725 BWI76_RS01725 PTS mannose/fructose/sorbose family transporter subunit IID
Query= TCDB::P69805 (286 letters) >FitnessBrowser__Koxy:BWI76_RS01725 Length = 274 Score = 343 bits (881), Expect = 2e-99 Identities = 169/272 (62%), Positives = 209/272 (76%), Gaps = 1/272 (0%) Query: 13 EKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHL 72 ++K+TQ D+ +FLRSNL Q S+NFER+ LGFC+ M+PAI+RLYP E + A++RHL Sbjct: 3 QRKITQGDLVSMFLRSNLQQASFNFERIHGLGFCYDMIPAIKRLYPLK-EDQVAALKRHL 61 Query: 73 EFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRP 132 FFNT P V P++GVT+A+EE RANGA IDDGAINGIKVGLMGPLAGVGDP+ WGT+RP Sbjct: 62 VFFNTTPAVCGPVIGVTVAMEEARANGAAIDDGAINGIKVGLMGPLAGVGDPLVWGTLRP 121 Query: 133 VFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDMGGGFLQKLT 192 + AALGA +A+SG+L+GPLLFF +FN VRLA ++YG+ G+ KG++IV +MGG LQKLT Sbjct: 122 ITAALGASLALSGNLVGPLLFFFIFNAVRLAMKWYGLQLGFRKGVNIVSEMGGNLLQKLT 181 Query: 193 EGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTF 252 EGASILGLFVMG LV KWT +N+PLVVS+ G TVQ ILDQL PGL+ L LT Sbjct: 182 EGASILGLFVMGVLVTKWTTINVPLVVSQTPGADGSTVTMTVQNILDQLCPGLLALGLTL 241 Query: 253 ACMWLLRKKVNPLWIIVGFFVIGIAGYACGLL 284 + LL KKVNP+W+I F +GI G A G L Sbjct: 242 LMVRLLNKKVNPVWLIFALFGLGILGNALGFL 273 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: 305 Number of extensions: 9 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: 286 Length of database: 274 Length adjustment: 26 Effective length of query: 260 Effective length of database: 248 Effective search space: 64480 Effective search space used: 64480 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