Align Mannitol 2-dehydrogenase; M2DH; MDH; EC 1.1.1.67 (uncharacterized)
to candidate Ac3H11_2939 D-arabinitol 4-dehydrogenase (EC 1.1.1.11)
Query= curated2:P33216 (477 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2939 Length = 463 Score = 250 bits (638), Expect = 8e-71 Identities = 171/459 (37%), Positives = 233/459 (50%), Gaps = 20/459 (4%) Query: 19 IVHIGVGNFHRAHQAVYLDDLFALGEGHDWAILGAGVRPTDARMREALAAQDNLSTVIEL 78 I+H+G+G+FHRAHQAVY+ L G DWAI G +RP A AL AQ T+ + Sbjct: 4 ILHLGLGSFHRAHQAVYMHQLRQQGST-DWAIAGGNLRPDMADTIAALQAQGGRYTLETV 62 Query: 79 DPAGHRARQV-GAMVGFLPVEADNAALIEAMSDPRIRIVSLTVTEGGYYVDASGAFD-PT 136 P G R+ V ++ +P + D A LI A +DP RI+S TVTE GYY+DA+ D T Sbjct: 63 TPQGERSYTVIESIQRVIPYQDDLAPLIAAGADPATRIISFTVTEAGYYLDAANQLDWAT 122 Query: 137 HPDIVADAAHPARPA---TAFGAILAALRARRDAGVTPFTVMSCDNLPGNGHVTRNAVVG 193 D+ AD A T +G + + LRAR AG P T+M+CDNL NG +R ++ Sbjct: 123 FADLRADLATVQAGQAGHTIYGGLASILRARMRAGAGPVTLMNCDNLRHNGDRSRGGLLQ 182 Query: 194 LAE-LYDAELAGWVKAQVAFPNGMVDRITPATGPHERELAQ-GFGLADPVPVTCEPFRQW 251 + L DA L GWV+ PN MVDRITP P E + G D + E F QW Sbjct: 183 FIDALGDAPLKGWVEQNTTSPNAMVDRITPRPTPDVAERVKTATGWDDKAALMGESFIQW 242 Query: 252 VIEDHFPAGRPALEKVGVTFTPHVHAYEAMKIRILNGGHAVIAYPSALMDIQLVHAAMAH 311 VIED F AGRPA EKVGV V A+E KIR+LN H+ IA+ L Q +H Sbjct: 243 VIEDDFIAGRPAWEKVGVEMVQSVQAHEEAKIRLLNATHSCIAWAGTLAGYQYIHEGTHD 302 Query: 312 PLIAAFLHKVEVEEILPHVPPVPDTSIPDYLTLIESRFSNPEIADTTRRLCLDGSNRQPK 371 I H ++ +P + P P + Y ++ RF NP IADT +R+ +D ++ P Sbjct: 303 AAIRQMAHDYVTDDAIPVLLPCP-IDLEAYRDVVLDRFGNPAIADTNQRVAMDAFSKIPG 361 Query: 372 FIVPSLRDNLAAGTVPKGLVLLSALWCRYC----FGTTDSGVVVEPNDPNWTALQDRARR 427 I P++RD LA + +L AL+ Y G + DP A+ Sbjct: 362 MIAPTIRDKLARNQPFDSVAVLPALFLAYLQRWHAGQIPYTYQDQAMDP---AVAHAICE 418 Query: 428 AKETPAEWLAMTEVYGDLAQN----DLLAAEFAAALEAV 462 A + A + A T ++G++A + D L +A L V Sbjct: 419 AADPVAAYAADTTLWGEMASHPRLVDTLRKAYARVLAFV 457 Lambda K H 0.321 0.136 0.418 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: 553 Number of extensions: 22 Number of successful extensions: 7 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: 477 Length of database: 463 Length adjustment: 33 Effective length of query: 444 Effective length of database: 430 Effective search space: 190920 Effective search space used: 190920 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 (21.9 bits) S2: 51 (24.3 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