Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components
Query= SwissProt::D4GL26 (473 letters) >FitnessBrowser__Marino:GFF3781 Length = 978 Score = 134 bits (338), Expect = 1e-35 Identities = 114/380 (30%), Positives = 173/380 (45%), Gaps = 35/380 (9%) Query: 111 AAAGADIDTVIDVAMNALAAKQAQLGITPPAHAASLPAQAPDSDARSVTVTIRNHHGLHV 170 A G + +++ LA + G++ A A L +A +DA + VT+ N HGLH Sbjct: 267 AGPGDECHDLLERIDTFLAGDEPIQGLSAEALLARLSGEA--ADAVTAKVTLLNTHGLHA 324 Query: 171 RPASRLVAALAGMNADL---VLEKQGQCVKPDSLNQIALLQVRCHDAVTLSASGPDAERA 227 RPA +LV NA + +LE +G V SL ++ L R + LSA+G DA +A Sbjct: 325 RPAKQLVQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLLSATGDDASQA 384 Query: 228 LAAFESLAAEDFGEHPESMALKTSASTV-EKVQGKAVFYPLPLAQPARHP---------- 276 + + S GE + + V E Q A+ P+ A P Sbjct: 385 IQSLTSAIEGGLGEKVSPLRSADPQTKVPEAEQAPALTDDQPVKAVAASPGLALAPAFVM 444 Query: 277 ----------CSDVGQEERRLQQAIVDTLNDLNALAALAEKKYGASVAAIFSGHYTLLDD 326 D Q+ +RL QA+ L L AE G A I S H +L D Sbjct: 445 RQPTLEYPQFAEDSEQQIQRLNQAVDSADGQLRTLIRQAE---GGEAAPILSVHVEMLQD 501 Query: 327 PDLFDAACKVIRNDSCCAESAWYQVLMELSQQYQHLDDAYLQARFIDIEDILYRSLCHLK 386 DL+ A + I N+ AE+ W++ + ++ + L D L R D+ D+ R L +L Sbjct: 502 EDLYQATLEAI-NEGASAEAGWWKAIDTAARGQEALADRLLAERAADLRDVGRRVLSNLC 560 Query: 387 GRDIRLPTP-DVPAIIVADDIFPSAVVNLNAQLVKGICLREGSTLSHAAIIAQQAGIAFI 445 G + +PTP D P I+VADD+ PS V L+ V+G+ G SH+AI+A+ G+ + Sbjct: 561 G--VAMPTPPDTPYILVADDLGPSDVARLDTTRVRGLVTARGGATSHSAILARALGLPAV 618 Query: 446 CQQG-AVLDIIQPEDRLLID 464 G +L I+ D L++D Sbjct: 619 VGTGERILTILNGSD-LVVD 637 Lambda K H 0.320 0.133 0.380 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: 959 Number of extensions: 30 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: 473 Length of database: 978 Length adjustment: 39 Effective length of query: 434 Effective length of database: 939 Effective search space: 407526 Effective search space used: 407526 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 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