Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_003463408.1 J416_RS01585 PTS mannitol transporter subunit IICB
Query= BRENDA::P00550 (637 letters) >NCBI__GCF_000359605.1:WP_003463408.1 Length = 473 Score = 530 bits (1364), Expect = e-155 Identities = 268/466 (57%), Positives = 340/466 (72%), Gaps = 5/466 (1%) Query: 6 KIKVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIG 65 + KVQ FG LS M+MPNI AFIAWG+ITALFIP G+ PNE LA LVGPMI YLLPLLIG Sbjct: 7 RAKVQRFGSHLSGMIMPNIAAFIAWGLITALFIPDGYFPNEELASLVGPMINYLLPLLIG 66 Query: 66 YTGGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSG 125 +TGG+LV RGGVVGA T+GVIVGAD+PMFLG+M GPLGG+ IK D KI G Sbjct: 67 FTGGRLVYDIRGGVVGATATIGVIVGADIPMFLGAMAMGPLGGYLIKKLDDVFQDKIGQG 126 Query: 126 FEMLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAK 185 FEML NNFSAGI+G +LA ++ IGPI+ ++++L AGV F++ +LPLA+I +EPAK Sbjct: 127 FEMLYNNFSAGILGAVLAGISLKIIGPIINGITQVLIAGVEFLINVGLLPLANIIIEPAK 186 Query: 186 ILFLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGG 245 +LFLNNAINHGI SP+ +QS E GKSI FL+E NPGPG+GVLLA+M FG G+A+ SA G Sbjct: 187 VLFLNNAINHGILSPIAAEQSSETGKSILFLLETNPGPGLGVLLAFMVFGTGAARSSASG 246 Query: 246 AAIIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLA 305 A+IIHF GGIHEIYFPY+LM P L+LAVI GG++GVFT TI GL + SPGSI+A++ Sbjct: 247 ASIIHFFGGIHEIYFPYILMKPALLLAVIGGGVSGVFTYTIFNAGLTATPSPGSIVALML 306 Query: 306 MTPKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESKGASPL 365 MTP G +F GV A VSF++++++LK S E +D+ AT +M++MK + AS Sbjct: 307 MTPPGDHFIIALGVIVATLVSFLIASVILKASN-SEGEDLSKATSQMEEMKGKKSKASDS 365 Query: 366 SAGD----VTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINNLP 421 G+ T V K++ ACDAGMGSSAMGA +L+ K + A + I VTN AIN+L Sbjct: 366 LRGNEEQASTQQAEDVNKVVFACDAGMGSSAMGASLLKDKFKKADIEGIDVTNKAINDLT 425 Query: 422 PDVDLVITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVA 467 + D++ITH+DLT+RA ++P A+HIS+ NFL+S Y L RL A Sbjct: 426 DEADIIITHKDLTDRAKEKIPSAEHISVENFLNSPKYDELVNRLKA 471 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: 800 Number of extensions: 41 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: 637 Length of database: 473 Length adjustment: 36 Effective length of query: 601 Effective length of database: 437 Effective search space: 262637 Effective search space used: 262637 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: 53 (25.0 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