Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate WP_042615137.1 ABB28_RS02015 L-threonine 3-dehydrogenase
Query= BRENDA::Q1ACW3 (345 letters) >NCBI__GCF_001431535.1:WP_042615137.1 Length = 344 Score = 142 bits (359), Expect = 1e-38 Identities = 100/295 (33%), Positives = 155/295 (52%), Gaps = 16/295 (5%) Query: 6 TMKAL-RYDKPESYAVVEVPLPTLRDNDVLIKVKACGVCGTDLHIHEGEFIAKFPLIPG- 63 TMKAL + + + + EVP+P N+VLIK++ +CGTDLHI+ + ++ + PG Sbjct: 4 TMKALVKREAAKGIWLEEVPVPVPGPNEVLIKLEKTAICGTDLHIYLWDEWSQRTITPGL 63 Query: 64 ---HETVGVVAAIGKDVKGFTVGERVCADNSELCNECFYCRRGQLLLCEKFEAHGVTMDG 120 HE VG VAA+G V G+ VG+RV A+ +C C CR G+ LC GV ++G Sbjct: 64 TIGHEFVGRVAALGSAVTGYEVGQRVSAEGHIVCGHCRNCRGGRQHLCPNTVGIGVNVNG 123 Query: 121 GFAEYCAYPAGKVFKI-HNLSDVDATLLEPASCAAH-GLEKIAPKIGSSVLMFGAGPTGL 178 FAEY PA ++ I + A +P AAH LE IG VL+ GAGP G+ Sbjct: 124 AFAEYMVMPATNLWPIPDQIPSELAAFFDPYGNAAHCALE--FNVIGEDVLITGAGPIGI 181 Query: 179 CLAQL-PHNGASHVVIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPYGFD 237 A + H GA +VV+ ++ LA + + ++ +N Q+ D +K + GFD Sbjct: 182 IAAGICKHIGARNVVVTDVNDFRLKLAADMGATRV---VNVAN-QSLKDVMKELHMEGFD 237 Query: 238 IVVEATGSPKILEDAINYVRRGGKLVVYGVYSDAARVSWPPSKIFGDEITIIGSF 292 + +E +G+P+ D ++ + GGK+ + G+ A W KI +T+ G + Sbjct: 238 VGLEMSGNPRAFNDMLDCMYHGGKIAMLGIMPRGAGCDW--DKIIFKGLTVQGIY 290 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: 328 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: 344 Length adjustment: 29 Effective length of query: 316 Effective length of database: 315 Effective search space: 99540 Effective search space used: 99540 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