Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate 17012 b2933 predicted fused mannitol-specific PTS enzymes: IIB component/IIC component (NCBI)
Query= BRENDA::P00550 (637 letters) >FitnessBrowser__Keio:17012 Length = 462 Score = 476 bits (1225), Expect = e-139 Identities = 246/466 (52%), Positives = 326/466 (69%), Gaps = 10/466 (2%) Query: 6 KIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIG 65 + KVQ+FG FL+ MV+PNIGAFIAWG ITALFIPTGWLPNE AK+VGPMITYLLP++IG Sbjct: 7 RAKVQAFGGFLTAMVIPNIGAFIAWGFITALFIPTGWLPNEHFAKIVGPMITYLLPVMIG 66 Query: 66 YTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSG 125 TGG LVGG+RG V+G I T+GVIVGA++PMFLGSMI GPLGG IK+ D+ ++ +I +G Sbjct: 67 STGGHLVGGKRGAVMGGIGTIGVIVGAEIPMFLGSMIMGPLGGLVIKYVDKALEKRIPAG 126 Query: 126 FEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAK 185 FEM++NNFS GI GM+L +L F IGP V + + + +V LPL S+ EPAK Sbjct: 127 FEMVINNFSLGIAGMLLCLLGFEVIGPAVLIANTFVKECIEALVHAGYLPLLSVINEPAK 186 Query: 186 ILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGG 245 +LFLNNAI+ G++ PLG+QQ+ GKSIFF++ +NPGPG+G+LLA+ FG+G +K+SA G Sbjct: 187 VLFLNNAIDQGVYYPLGMQQASVNGKSIFFMVASNPGPGLGLLLAFTLFGKGMSKRSAPG 246 Query: 246 AAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLA 305 A IIHFLGGIHE+YFPYVLM P I+A+I GGM+G + +L GGLV+ SPGSI A LA Sbjct: 247 AMIIHFLGGIHELYFPYVLMKPLTIIAMIAGGMSGTWMFNLLDGGLVAGPSPGSIFAYLA 306 Query: 306 MTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESKGASPL 365 +TPKG++ A IAGV VSF +++++LK K E + +D A+S A Sbjct: 307 LTPKGSFLATIAGVTVGTLVSFAITSLILKMEKTVETES--------EDEFAQSANAVKA 358 Query: 366 SAGDVTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINNLPPDVD 425 + LS V++I CDAGMGSSAMGA RK+++ AGL+ I V + AI N+P D D Sbjct: 359 MKQEGAFSLSRVKRIAFVCDAGMGSSAMGATTFRKRLEKAGLA-IEVKHYAIENVPADAD 417 Query: 426 LVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQRH 471 +V+TH L E +++V I + N++ +L +L A +H Sbjct: 418 IVVTHASL-EGRVKRVTDKPLILINNYIGDPKLDTLFNQLTAEHKH 462 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: 740 Number of extensions: 38 Number of successful extensions: 3 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: 462 Length adjustment: 35 Effective length of query: 602 Effective length of database: 427 Effective search space: 257054 Effective search space used: 257054 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 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