Align protein-Npi-phosphohistidine-D-mannitol phosphotransferase (EC 2.7.1.197) (characterized)
to candidate WP_008540051.1 HMPREF9454_RS11685 PTS mannitol transporter subunit IICBA
Query= BRENDA::P00550 (637 letters) >NCBI__GCF_000245775.1:WP_008540051.1 Length = 631 Score = 671 bits (1730), Expect = 0.0 Identities = 343/606 (56%), Positives = 441/606 (72%), Gaps = 14/606 (2%) Query: 8 KVQSFGRFLSNMVMPNIGAFIAWGIITALFIPTGWLPNETLAKLVGPMITYLLPLLIGYT 67 K+Q FGRFLS MVMPNIGAFIAWG++TALFIPTGW+PNE LA GPM +L+PLLIGY+ Sbjct: 13 KMQKFGRFLSGMVMPNIGAFIAWGLLTALFIPTGWIPNEYLAAAGGPMSKWLIPLLIGYS 72 Query: 68 GGKLVGGERGGVVGAITTMGVIVGADMPMFLGSMIAGPLGGWCIKHFDRWVDGKIKSGFE 127 GG + RGGV+GAI T G+I G+D+PMFLG+MI GP GGWCIK FD KI +GFE Sbjct: 73 GGSAIYQHRGGVLGAIATAGIIAGSDIPMFLGAMIVGPFGGWCIKKFDEAFQDKIPTGFE 132 Query: 128 MLVNNFSAGIIGMILAILAFLGIGPIVEALSKMLAAGVNFMVVHDMLPLASIFVEPAKIL 187 ML+NNFSAGI+G ILAILA+ +GP+V +L+ +L GV F+V ++PL SI VEPAK+L Sbjct: 133 MLINNFSAGILGGILAILAYAIVGPVVSSLNDILRGGVEFIVNLGLIPLVSILVEPAKVL 192 Query: 188 FLNNAINHGIFSPLGIQQSHELGKSIFFLIEANPGPGMGVLLAYMFFGRGSAKQSAGGAA 247 FLNNAINHG+FSP+GIQ+S ELGKSIFF+IE+NPGPG+GVLLA+ G+G AK SA GA Sbjct: 193 FLNNAINHGVFSPIGIQESQELGKSIFFMIESNPGPGLGVLLAFCLVGKGMAKSSAPGAV 252 Query: 248 IIHFLGGIHEIYFPYVLMNPRLILAVILGGMTGVFTLTILGGGLVSPASPGSILAVLAMT 307 IIHFLGGIHEIYFPY+LM P L+LAVI GM GVFTL++L GGL++PASPGSI A+LAMT Sbjct: 253 IIHFLGGIHEIYFPYILMKPILLLAVIPAGMAGVFTLSVLNGGLIAPASPGSIFAILAMT 312 Query: 308 PKGAYFANIAGVCAAMAVSFVVSAILLKTSKVKEEDDIEAATRRMQDMKAESKGASPLSA 367 PKGAYFANIA V A AVSFV+++I +K SK + +E A + MQDMK ++G+ + + Sbjct: 313 PKGAYFANIAAVVVATAVSFVIASIFIKASK-DDGSSLEEAQQNMQDMK--NRGSKRVES 369 Query: 368 GDVTNDLSHVRKIIVACDAGMGSSAMGAGVLRKKIQDAGLSQISVTNSAINNLPPDVDLV 427 DV S ++KII ACDAGMGSSAMGA LR K++ AG ISVTN AI N+P D +V Sbjct: 370 -DVVVKGSELKKIIYACDAGMGSSAMGASALRNKLKKAGYGYISVTNCAIGNIPSDAQIV 428 Query: 428 ITHRDLTERAMRQVPQAQHISLTNFLDSGLYTSLTERLVAAQRHTANEEKVKDSLKDSFD 487 ++H L +RA+ PQA+H+ + +F+ + +Y + +L Q A E+V DS +++ + Sbjct: 429 VSHEKLADRAIADSPQAEHLFVQDFIKNDVYDIILAKL---QNVEAKVEEVTDSKENAVE 485 Query: 488 DSSANLFKLGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTPTYLG 547 D + L ENI + TKEEAI+ AGE L K GYV EY+ ML RE+ TY+G Sbjct: 486 DETV----LKRENIKMCLDTVTKEEAIKMAGELLYKSGYVGKEYINGMLAREQDVSTYMG 541 Query: 548 ESIAVPHGTVEAKDRVLKTGVVFCQYPEGVRFGEEEDDIARLVIGIAARNNEHIQVITSL 607 IA+PHG KD V K+G+V Q+P GV FG + A+LV+GIA + +EH+ ++ ++ Sbjct: 542 RGIAIPHGENAVKDTVKKSGIVVLQFPNGVEFGTGK---AKLVVGIAGKGDEHLAILANI 598 Query: 608 TNALDD 613 ALD+ Sbjct: 599 AIALDE 604 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: 1029 Number of extensions: 49 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 637 Length of database: 631 Length adjustment: 38 Effective length of query: 599 Effective length of database: 593 Effective search space: 355207 Effective search space used: 355207 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: 54 (25.4 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