Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_104914290.1 C3B54_RS05650 PTS mannitol transporter subunit IICB
Query= BRENDA::P00550 (637 letters) >NCBI__GCF_002950575.1:WP_104914290.1 Length = 371 Score = 409 bits (1051), Expect = e-118 Identities = 204/352 (57%), Positives = 260/352 (73%), Gaps = 1/352 (0%) Query: 6 KIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIG 65 + +Q G L+ MV+PNIGAFIAWG++TALFIPTGWLPNE+ A +VGPMI LLP+LIG Sbjct: 16 RASLQKLGGNLAGMVIPNIGAFIAWGLLTALFIPTGWLPNESFASMVGPMILNLLPILIG 75 Query: 66 YTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSG 125 YTGG++V G+RG V+G+I T+GVIVG D+PMFLG+MI GPL W +K D+ +D G Sbjct: 76 YTGGRIVHGQRGAVIGSIATVGVIVGTDIPMFLGAMIIGPLLAWILKQIDKVLDPITPPG 135 Query: 126 FEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAK 185 FEML+ NFS GI GM+ A+L +L IGP V A+S +L GV +MV + +LP+AS+ VEPAK Sbjct: 136 FEMLIGNFSLGISGMLGAMLGYLAIGPTVSAISTVLGNGVQWMVDNSLLPIASLIVEPAK 195 Query: 186 ILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGG 245 ILFLNNAINHG+ +PLG+ ++ E GKSI F++E NPGPG+G+L+A+ G + SA G Sbjct: 196 ILFLNNAINHGVLAPLGVVEAEETGKSILFMLETNPGPGLGILVAFWLAGPKILRGSAPG 255 Query: 246 AAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLA 305 A IIHFLGGIHEIYFPYVLM P++ILA ILGG TGV T + G GLV+ SPGSI A LA Sbjct: 256 AIIIHFLGGIHEIYFPYVLMKPQVILAAILGGATGVATFMVTGVGLVATPSPGSIFAYLA 315 Query: 306 MTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEED-DIEAATRRMQDMK 356 +TP+G + + G+ + AVSFVV+ LL+ SK D D EAA + MK Sbjct: 316 VTPQGDHLGVLLGIVLSAAVSFVVAWFLLRLSKSDASDADFEAAKAKSAAMK 367 Lambda K H 0.321 0.138 0.397 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: 677 Number of extensions: 27 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: 637 Length of database: 371 Length adjustment: 34 Effective length of query: 603 Effective length of database: 337 Effective search space: 203211 Effective search space used: 203211 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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