Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate GFF4493 PS417_22995 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::A0A0H3H456 (472 letters) >FitnessBrowser__WCS417:GFF4493 Length = 836 Score = 116 bits (291), Expect = 3e-30 Identities = 108/364 (29%), Positives = 170/364 (46%), Gaps = 22/364 (6%) Query: 125 MNALEAKRVQLGLPSQPQHASLTAA---PVDDRDAR-SVSVVIQNHNGLHVRPASKLVAA 180 + A+ ++V++G P A AA VD+ +A S SV I + GLH RPA+ + Sbjct: 136 LRAVAGQKVKVGEPLLQIVARSAAAVQTAVDNSEADVSASVRITHRGGLHARPAALIRKT 195 Query: 181 LAGFNADLVLEKGGKCVTPDSLNQIALLQVRRNDTLRLLARGPDADAAL----AAFQALA 236 F++ L G K + DSL + L + D +R+ RG DA+AAL AA A+ Sbjct: 196 AQDFSSQAQLHFGDKSASCDSLIGLMGLGIGEGDEVRVTCRGKDAEAALQALVAALSAVI 255 Query: 237 AENFGEPTEAAPARRPASADRVEGKVV---LYPQPQDRISR-ETSAAIG-----QQQLRL 287 E P A P R A ++G L P R++ E A +G +Q L Sbjct: 256 KEEHHVPVVAPPRRAHTEAGVLQGVCAAPGLVCGPLFRLTGIELPADVGNHSADEQLQHL 315 Query: 288 KRAIDRTLEDLSALTTLAEATFSADIAAIFSGHHTLLDDPDLYAAACDIIRDEQCSAAWA 347 A+++ ++ + A + + IF+ H LL+DP+L AA I ++ +A A Sbjct: 316 DTALEQVRSEIRSTLAHARQRKNVEEEDIFAAHLALLEDPNLLEAATRSI-EQGSAATHA 374 Query: 348 WQQVLSDLSQQYRHLDDAYLQARYIDIEDILHRTLRHLNERNEALP-QFSAPSILVADDI 406 W+ + L R D+ D+ R LR L EA + A SI+ A ++ Sbjct: 375 WRDAIQAQCAVLLALGKPLFAERANDLRDLQQRVLRAL--LGEAWHFELPAGSIVSAHEL 432 Query: 407 FPSTVLQLNAEQVKGICLQAGSELSHGAIIARQAGI-AMLCQQSDALTLQDGENVILDIP 465 PS +LQL+A+ GIC+ G SH AI+AR G+ ++ ++ L + G+ V+LD Sbjct: 433 TPSDLLQLSAQHAVGICMAEGGATSHVAILARGKGLPCVVALGAEVLDVPQGQRVVLDAV 492 Query: 466 GKRV 469 R+ Sbjct: 493 NGRL 496 Lambda K H 0.318 0.132 0.372 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: 738 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: 472 Length of database: 836 Length adjustment: 38 Effective length of query: 434 Effective length of database: 798 Effective search space: 346332 Effective search space used: 346332 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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