Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate WP_099019607.1 CCS90_RS11000 L-threonine 3-dehydrogenase
Query= BRENDA::Q1ACW3 (345 letters) >NCBI__GCF_002591915.1:WP_099019607.1 Length = 340 Score = 150 bits (379), Expect = 5e-41 Identities = 98/278 (35%), Positives = 145/278 (52%), Gaps = 14/278 (5%) Query: 7 MKALRYDKPESYAVVE-VPLPTLRDNDVLIKVKACGVCGTDLHIHE-GEFIAKF---PLI 61 MKAL KPE +E VP+P + NDVLIK++ +CGTDLHI++ E+ AK PL+ Sbjct: 1 MKALVKKKPELGIWMEDVPMPEMGHNDVLIKIEKTAICGTDLHIYKWDEWSAKAIKPPLV 60 Query: 62 PGHETVGVVAAIGKDVKGFTVGERVCADNSELCNECFYCRRGQLLLCEKFEAHGVTMDGG 121 GHE VG + +G +VKG+ VG+RV A+ +C C CR G LC + GV +G Sbjct: 61 IGHEFVGHIVDMGSEVKGYEVGQRVSAEGHIVCGVCRNCRAGTPHLCPNTQGIGVNRNGA 120 Query: 122 FAEYCAYPAGKVFKI-HNLSDVDATLLEPASCAAH-GLEKIAPKIGSSVLMFGAGPTGLC 179 FAE+ + P ++ + + A +P AAH LE +G VL+ GAGP G+ Sbjct: 121 FAEFISMPVQNLWPVPDKIPSNLAAFFDPFGNAAHCALE--YDMVGEDVLITGAGPIGII 178 Query: 180 LAQL-PHNGASHVVIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPYGFDI 238 + H GA +VVI ++ LAK + P +K N GFD+ Sbjct: 179 ATGICKHVGARNVVITDVNDYRLSLAKDMGATRCVNVTKEKLPAV----MKEMNITGFDL 234 Query: 239 VVEATGSPKILEDAINYVRRGGKLVVYGVYSDAARVSW 276 +E +G+P D +N + GGK+ + G+ D +++W Sbjct: 235 GMEMSGNPMAFNDMLNSMYNGGKITLLGMLPDHTQINW 272 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: 331 Number of extensions: 21 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: 345 Length of database: 340 Length adjustment: 29 Effective length of query: 316 Effective length of database: 311 Effective search space: 98276 Effective search space used: 98276 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 24 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