Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate CA265_RS12755 CA265_RS12755 hydroxyacid dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Pedo557:CA265_RS12755 Length = 347 Score = 336 bits (861), Expect = 6e-97 Identities = 177/342 (51%), Positives = 231/342 (67%), Gaps = 4/342 (1%) Query: 15 GWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEI 74 G+AA++ L+P+ F RR G DV+ ++LFCGVCHSD H I N+W +P+VPGHEI Sbjct: 6 GYAAQNAETDLAPWNFERREVGPHDVQFEILFCGVCHSDLHQIKNDWFPGIFPMVPGHEI 65 Query: 75 VGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHC-ENTIDTYGSIYFDG-T 132 VG V +VG V+K KVGD G GC+V SC+ CE+C N E +C E TY + DG T Sbjct: 66 VGRVVKVGDHVKKFKVGDLAGTGCMVDSCQVCENCKQNLEQYCLEGNTQTYNGLERDGKT 125 Query: 133 MTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGL 192 T+GGYSD++V E F+L L L + APLLCAGITTYSPLK++ + K G K+ V+GL Sbjct: 126 PTYGGYSDSIVVREEFVLHVSDKLNLAAVAPLLCAGITTYSPLKHWKVGK-GHKLAVLGL 184 Query: 193 GGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGII 252 GGLGH+AVK AFGA+VTV+ S K ++A +KLGA F++ +D Q+K AR + D I+ Sbjct: 185 GGLGHMAVKFGVAFGAEVTVLSTSPKKEEDA-KKLGAHHFVVTTDPAQVKAARGTFDFIL 243 Query: 253 DTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEM 312 DTV H LL+ NG + VG P KP E+ FSLL GRK L G+ GGI ETQEM Sbjct: 244 DTVSAEHDFNMYLSLLRTNGIHICVGVPPKPAEIAAFSLLGGRKSLAGSGIGGIAETQEM 303 Query: 313 LDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIA 354 LDF A++NI +D+E+I + ++ A ER+ K DVRYRFVID+A Sbjct: 304 LDFCAENNIVSDIEMIDIKDIHHAYERMEKGDVRYRFVIDMA 345 Lambda K H 0.319 0.137 0.415 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: 356 Number of extensions: 14 Number of successful extensions: 4 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: 365 Length of database: 347 Length adjustment: 29 Effective length of query: 336 Effective length of database: 318 Effective search space: 106848 Effective search space used: 106848 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 (21.7 bits) S2: 49 (23.5 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