Align PTS system mannitol-specific cryptic EIICB component; EIICB-Mtl; EII-Mtl; EC 2.7.1.197 (characterized)
to candidate 17012 b2933 predicted fused mannitol-specific PTS enzymes: IIB component/IIC component (NCBI)
Query= SwissProt::P69826 (462 letters) >FitnessBrowser__Keio:17012 Length = 462 Score = 908 bits (2346), Expect = 0.0 Identities = 462/462 (100%), Positives = 462/462 (100%) Query: 1 MENKSARAKVQAFGGFLTAMVIPNIGAFIAWGFITALFIPTGWLPNEHFAKIVGPMITYL 60 MENKSARAKVQAFGGFLTAMVIPNIGAFIAWGFITALFIPTGWLPNEHFAKIVGPMITYL Sbjct: 1 MENKSARAKVQAFGGFLTAMVIPNIGAFIAWGFITALFIPTGWLPNEHFAKIVGPMITYL 60 Query: 61 LPVMIGSTGGHLVGGKRGAVMGGIGTIGVIVGAEIPMFLGSMIMGPLGGLVIKYVDKALE 120 LPVMIGSTGGHLVGGKRGAVMGGIGTIGVIVGAEIPMFLGSMIMGPLGGLVIKYVDKALE Sbjct: 61 LPVMIGSTGGHLVGGKRGAVMGGIGTIGVIVGAEIPMFLGSMIMGPLGGLVIKYVDKALE 120 Query: 121 KRIPAGFEMVINNFSLGIAGMLLCLLGFEVIGPAVLIANTFVKECIEALVHAGYLPLLSV 180 KRIPAGFEMVINNFSLGIAGMLLCLLGFEVIGPAVLIANTFVKECIEALVHAGYLPLLSV Sbjct: 121 KRIPAGFEMVINNFSLGIAGMLLCLLGFEVIGPAVLIANTFVKECIEALVHAGYLPLLSV 180 Query: 181 INEPAKVLFLNNAIDQGVYYPLGMQQASVNGKSIFFMVASNPGPGLGLLLAFTLFGKGMS 240 INEPAKVLFLNNAIDQGVYYPLGMQQASVNGKSIFFMVASNPGPGLGLLLAFTLFGKGMS Sbjct: 181 INEPAKVLFLNNAIDQGVYYPLGMQQASVNGKSIFFMVASNPGPGLGLLLAFTLFGKGMS 240 Query: 241 KRSAPGAMIIHFLGGIHELYFPYVLMKPLTIIAMIAGGMSGTWMFNLLDGGLVAGPSPGS 300 KRSAPGAMIIHFLGGIHELYFPYVLMKPLTIIAMIAGGMSGTWMFNLLDGGLVAGPSPGS Sbjct: 241 KRSAPGAMIIHFLGGIHELYFPYVLMKPLTIIAMIAGGMSGTWMFNLLDGGLVAGPSPGS 300 Query: 301 IFAYLALTPKGSFLATIAGVTVGTLVSFAITSLILKMEKTVETESEDEFAQSANAVKAMK 360 IFAYLALTPKGSFLATIAGVTVGTLVSFAITSLILKMEKTVETESEDEFAQSANAVKAMK Sbjct: 301 IFAYLALTPKGSFLATIAGVTVGTLVSFAITSLILKMEKTVETESEDEFAQSANAVKAMK 360 Query: 361 QEGAFSLSRVKRIAFVCDAGMGSSAMGATTFRKRLEKAGLAIEVKHYAIENVPADADIVV 420 QEGAFSLSRVKRIAFVCDAGMGSSAMGATTFRKRLEKAGLAIEVKHYAIENVPADADIVV Sbjct: 361 QEGAFSLSRVKRIAFVCDAGMGSSAMGATTFRKRLEKAGLAIEVKHYAIENVPADADIVV 420 Query: 421 THASLEGRVKRVTDKPLILINNYIGDPKLDTLFNQLTAEHKH 462 THASLEGRVKRVTDKPLILINNYIGDPKLDTLFNQLTAEHKH Sbjct: 421 THASLEGRVKRVTDKPLILINNYIGDPKLDTLFNQLTAEHKH 462 Lambda K H 0.323 0.141 0.414 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: 917 Number of extensions: 36 Number of successful extensions: 1 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: 462 Length of database: 462 Length adjustment: 33 Effective length of query: 429 Effective length of database: 429 Effective search space: 184041 Effective search space used: 184041 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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