Align S-(hydroxymethyl)glutathione dehydrogenase; EC 1.1.1.-; EC 1.1.1.1; EC 1.1.1.284 (characterized)
to candidate WP_057508427.1 ABB28_RS09645 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= CharProtDB::CH_002286 (369 letters) >NCBI__GCF_001431535.1:WP_057508427.1 Length = 369 Score = 672 bits (1734), Expect = 0.0 Identities = 316/369 (85%), Positives = 350/369 (94%) Query: 1 MKSRAAVAFAPGKPLEIVEIDVAPPKKGEVLIKVTHTGVCHTDAFTLSGDDPEGVFPVVL 60 MKSRAAVAF PG+PL+IVEIDVAPPKKGEVL+++THTGVCHTDAFTLSGDDPEG+FP VL Sbjct: 1 MKSRAAVAFGPGQPLKIVEIDVAPPKKGEVLVRITHTGVCHTDAFTLSGDDPEGLFPAVL 60 Query: 61 GHEGAGVVVEVGEGVTSVKPGDHVIPLYTAECGECEFCRSGKTNLCVAVRETQGKGLMPD 120 GHEGAG+VVEVGEGVTSV+PGDHVIPLYTAECGEC FC+SGKTNLCVAVR TQGKG+MPD Sbjct: 61 GHEGAGIVVEVGEGVTSVQPGDHVIPLYTAECGECLFCKSGKTNLCVAVRATQGKGVMPD 120 Query: 121 GTTRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKINPEANHEHVCLLGCGVTTGIGAVHN 180 GTTRFSYNG+P+YHYMGCSTFSEYTVVAEVSLA+INPEAN EHVCLLGCGVTTGIGAVHN Sbjct: 121 GTTRFSYNGEPIYHYMGCSTFSEYTVVAEVSLARINPEANPEHVCLLGCGVTTGIGAVHN 180 Query: 181 TAKVQPGDSVAVFGLGAIGLAVVQGARQAKAGRIIAIDTNPKKFDLARRFGATDCINPND 240 TAKVQ GDSVAVFGLG IGLAV+QGARQAKAGRIIAIDTNP KF+LAR FGATDC+NP++ Sbjct: 181 TAKVQEGDSVAVFGLGGIGLAVIQGARQAKAGRIIAIDTNPSKFELAREFGATDCVNPSE 240 Query: 241 YDKPIKDVLLDINKWGIDHTFECIGNVNVMRAALESAHRGWGQSVIIGVAVAGQEISTRP 300 ++ PI+ V++D+ WG+DH+FECIGNVNVMRAALE AHRGWGQSV+IGVA AG+EISTRP Sbjct: 241 HEAPIQQVVVDMTGWGVDHSFECIGNVNVMRAALECAHRGWGQSVVIGVAGAGKEISTRP 300 Query: 301 FQLVTGRVWKGSAFGGVKGRSQLPGMVEDAMKGDIDLEPFVTHTMSLDEINDAFDLMHEG 360 FQLVTGR WKGSAFGGVKGRSQLPGMVEDAMKGDI+L PFVTHTM LD+IN+AFDLMHEG Sbjct: 301 FQLVTGRTWKGSAFGGVKGRSQLPGMVEDAMKGDIELAPFVTHTMELDKINEAFDLMHEG 360 Query: 361 KSIRTVIRY 369 KSIR+V+ + Sbjct: 361 KSIRSVVHF 369 Lambda K H 0.319 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: 641 Number of extensions: 12 Number of successful extensions: 1 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: 369 Length of database: 369 Length adjustment: 30 Effective length of query: 339 Effective length of database: 339 Effective search space: 114921 Effective search space used: 114921 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 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