Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AZOBR_RS16515 AZOBR_RS16515 S-(hydroxymethyl)glutathione dehydrogenase
Query= BRENDA::Q5JI69 (350 letters) >FitnessBrowser__azobra:AZOBR_RS16515 Length = 372 Score = 112 bits (280), Expect = 2e-29 Identities = 111/361 (30%), Positives = 170/361 (47%), Gaps = 52/361 (14%) Query: 18 ELVEVDVPKPGPGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQIMGHEVAGEVVEVG 77 E+ EV+V P GEVL++++AT +C TD + + S P I+GHE AG V EVG Sbjct: 17 EIEEVEVAAPRQGEVLVRIVATGVCHTDAYTLSGMD---SEGVFPAILGHEGAGIVEEVG 73 Query: 78 PGVEDLQVGDYISVETHIVCGKCYACKHNRYHVCQ---NTKIFGVDMDG----------- 123 PGV +QVGD++ CGKC C + ++CQ T+ G+ DG Sbjct: 74 PGVTSVQVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRATQGKGLMPDGTSRFTAKGQPV 133 Query: 124 -------VFAHYAIVPAKNAWKNPKDMPPEYAALQEPLGNAVDTVL------AGPIAGRS 170 F+ Y ++P K K P E L LG V T + A G + Sbjct: 134 FHYMGTSTFSEYTVLPEIAVAKINKAAPLEKVCL---LGCGVTTGMGAVRNTAKVEPGST 190 Query: 171 TLITGAGPLGL---LGIAVAKASGAYPVIVSEPSEFRRKLAKKVGADYVVNPFEED-PVK 226 I G G +GL +G +AKAS + ++ P +F ++AK++GA VVNP + D P++ Sbjct: 191 VAIFGLGGIGLSAIIGAVMAKASRIIGIDIN-PDKF--EIAKQLGATDVVNPKDYDRPIQ 247 Query: 227 FVM-DITDGAGVEVFLEFSGAPKALEQGLKAVTPG-GRVSLLGL--FPREVTIDFNNLI- 281 V+ ++TDG GV+ E G K + L+ G G ++G+ E++ L+ Sbjct: 248 EVLVEMTDG-GVDYSFECIGNVKVMRAALECCHKGWGESVIIGVAGAGEEISTRPFQLVT 306 Query: 282 --IFKALEVHGITGRHLWETWYTVSSLIQSGKLNLDPIITHKYKGFDKFEEAFELMRAGK 339 +++ G+ GR + G+ LD ITH G + +AF+LM GK Sbjct: 307 GRVWRGSAFGGVRGRSELPDYV---ERYLKGEFELDTFITHT-MGLEDINKAFDLMHEGK 362 Query: 340 T 340 + Sbjct: 363 S 363 Lambda K H 0.319 0.139 0.423 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: 344 Number of extensions: 29 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: 350 Length of database: 372 Length adjustment: 29 Effective length of query: 321 Effective length of database: 343 Effective search space: 110103 Effective search space used: 110103 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