Align S-(hydroxymethyl)glutathione dehydrogenase; EC 1.1.1.-; EC 1.1.1.1; EC 1.1.1.284 (characterized)
to candidate Ac3H11_3163 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= CharProtDB::CH_002286 (369 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3163 Length = 371 Score = 654 bits (1688), Expect = 0.0 Identities = 311/369 (84%), Positives = 343/369 (92%) Query: 1 MKSRAAVAFAPGKPLEIVEIDVAPPKKGEVLIKVTHTGVCHTDAFTLSGDDPEGVFPVVL 60 MKSRAAVAF G+PL+IVEIDVAPPKKGEVLI++T TGVCHTDAFTLSGDDPEG+FPVVL Sbjct: 1 MKSRAAVAFKAGEPLKIVEIDVAPPKKGEVLIRITDTGVCHTDAFTLSGDDPEGLFPVVL 60 Query: 61 GHEGAGVVVEVGEGVTSVKPGDHVIPLYTAECGECEFCRSGKTNLCVAVRETQGKGLMPD 120 GHEGAG+VVEVGEGVTSVKPGDHVIPLYTAECGEC FC+SGKTNLCV+VR TQGKG+MPD Sbjct: 61 GHEGAGIVVEVGEGVTSVKPGDHVIPLYTAECGECLFCKSGKTNLCVSVRATQGKGVMPD 120 Query: 121 GTTRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKINPEANHEHVCLLGCGVTTGIGAVHN 180 GTTRFSYNGQP+YHYMGCSTFSEYTVVAEVSLAK+NP+AN E VCLLGCGVTTG+GAV N Sbjct: 121 GTTRFSYNGQPIYHYMGCSTFSEYTVVAEVSLAKVNPQANPEQVCLLGCGVTTGLGAVKN 180 Query: 181 TAKVQPGDSVAVFGLGAIGLAVVQGARQAKAGRIIAIDTNPKKFDLARRFGATDCINPND 240 TAKVQ GD+VAVFGLG IGLAV+QGA+ AKAGRIIA+DTNP KFDLAR FGATDCINP D Sbjct: 181 TAKVQEGDTVAVFGLGGIGLAVIQGAKLAKAGRIIAVDTNPSKFDLARTFGATDCINPKD 240 Query: 241 YDKPIKDVLLDINKWGIDHTFECIGNVNVMRAALESAHRGWGQSVIIGVAVAGQEISTRP 300 +DKPI+ V++++ WG+DH+FECIGNVNVMRAALE AHRGWGQSVIIGVA AGQEISTRP Sbjct: 241 FDKPIQQVIVEMTTWGVDHSFECIGNVNVMRAALECAHRGWGQSVIIGVAGAGQEISTRP 300 Query: 301 FQLVTGRVWKGSAFGGVKGRSQLPGMVEDAMKGDIDLEPFVTHTMSLDEINDAFDLMHEG 360 FQLVTGR W G+AFGGVKGRS+LPGMVEDAM G I LEPFVTHTM L +IN+AFDLMHEG Sbjct: 301 FQLVTGRKWLGTAFGGVKGRSELPGMVEDAMAGKIQLEPFVTHTMGLKDINEAFDLMHEG 360 Query: 361 KSIRTVIRY 369 KSIR+V++Y Sbjct: 361 KSIRSVVKY 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: 615 Number of extensions: 16 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: 371 Length adjustment: 30 Effective length of query: 339 Effective length of database: 341 Effective search space: 115599 Effective search space used: 115599 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