Align Mannitol-specific phosphotransferase enzyme IIA component; EIIA; EIII; PTS system mannitol-specific EIIA component (characterized)
to candidate BWI76_RS24870 BWI76_RS24870 phosphocarrier, HPr family protein
Query= SwissProt::P17876 (144 letters) >FitnessBrowser__Koxy:BWI76_RS24870 Length = 271 Score = 110 bits (274), Expect = 2e-29 Identities = 49/128 (38%), Positives = 86/128 (67%), Gaps = 1/128 (0%) Query: 9 NIFLNQSFEDQNEAIEKAGQALVDAGAVTEDYIQAMKDREAVVSTFMGNGLAIPHGTDEA 68 +I ++ + ++EA+++ L +AG T Y+ M+DRE +ST++GNG+AIPHGT ++ Sbjct: 7 DIHFDREIKTKDEALQRVVGRLTEAGHTTAAYLNGMRDREGQISTYLGNGIAIPHGTPQS 66 Query: 69 KSAVLQSGLTLLQIPEGVQWGD-DVAKVVVGIAGKDGEHLDLLSKIAITFSEEENVDRIV 127 + AVL++G+ +L P+GV WG+ A ++VGIA +D EHLD+L ++ S+E + + Sbjct: 67 RDAVLKTGVKVLACPQGVDWGEQQTAYLIVGIAAQDSEHLDILRQLTHAMSDERVPEALS 126 Query: 128 NTKSPEEI 135 T+SP+ + Sbjct: 127 RTESPQAV 134 Lambda K H 0.311 0.130 0.351 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: 128 Number of extensions: 10 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: 144 Length of database: 271 Length adjustment: 20 Effective length of query: 124 Effective length of database: 251 Effective search space: 31124 Effective search space used: 31124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 45 (21.9 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