Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate 15701 b1580 predicted oxidoreductase, Zn-dependent and NAD(P)-binding (NCBI)
Query= BRENDA::Q1ACW3 (345 letters) >FitnessBrowser__Keio:15701 Length = 339 Score = 161 bits (408), Expect = 2e-44 Identities = 104/344 (30%), Positives = 171/344 (49%), Gaps = 13/344 (3%) Query: 7 MKALRYDKPESYAVVEVPLPTLRDNDVLIKVKACGVCGTDLHIHEGEF-IAKFPLIPGHE 65 MK++ +KP A+VE +PT +V +KVK G+CG+D HI+ G AK+P + GHE Sbjct: 1 MKSILIEKPNQLAIVEREIPTPSAGEVRVKVKLAGICGSDSHIYRGHNPFAKYPRVIGHE 60 Query: 66 TVGVVAAIGKDVKGFTVGERVCADNSELCNECFYCRRGQLLLCEKFEAHGVTMDGGFAEY 125 GV+ A+G+ V+ VGERV D C C+ C G+ +C GV DGGF+EY Sbjct: 61 FFGVIDAVGEGVESARVGERVAVDPVVSCGHCYPCSIGKPNVCTTLAVLGVHADGGFSEY 120 Query: 126 CAYPAGKVFKI-HNLSDVDATLLEPASCAAHGLEKIAPKIGSSVLMFGAGPTGLCLAQLP 184 PA +KI ++D A ++EP + AA+ P +VL++GAGP GL + Q+ Sbjct: 121 AVVPAKNAWKIPEAVADQYAVMIEPFTIAANVTGHGQPTENDTVLVYGAGPIGLTIVQVL 180 Query: 185 HN--GASHVVIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPYGFDIVVEA 242 +V++A +++ AK+ AD + +N Q +I ++ ++++A Sbjct: 181 KGVYNVKNVIVADRIDERLEKAKE-SGADWAI----NNSQTPLGEIFTEKGIKPTLIIDA 235 Query: 243 TGSPKILEDAINYVRRGGKLVVYGVYSDAARVSWPPSKIFGDEITIIGSFSETYMFPATI 302 P IL++A+ ++V+ G S+ + V I G E++I S FP I Sbjct: 236 ACHPSILKEAVTLASPAARIVLMGFSSEPSEVI--QQGITGKELSIFSSRLNANKFPIVI 293 Query: 303 GYLDTGKVKVEGIVNKTYKLEQWGECLEAMR--NKSAIKAAIVF 344 +L G +K E ++ T+ + + + K K + F Sbjct: 294 DWLSKGLIKPEKLITHTFDFQHVADAISLFEQDQKHCCKVLLTF 337 Lambda K H 0.320 0.138 0.420 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: 298 Number of extensions: 12 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: 345 Length of database: 339 Length adjustment: 29 Effective length of query: 316 Effective length of database: 310 Effective search space: 97960 Effective search space used: 97960 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: 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