Align S-(hydroxymethyl)glutathione dehydrogenase; EC 1.1.1.-; EC 1.1.1.1; EC 1.1.1.284 (characterized)
to candidate BPHYT_RS25430 BPHYT_RS25430 S-(hydroxymethyl)glutathione dehydrogenase
Query= CharProtDB::CH_002286 (369 letters) >FitnessBrowser__BFirm:BPHYT_RS25430 Length = 369 Score = 655 bits (1689), Expect = 0.0 Identities = 311/369 (84%), Positives = 342/369 (92%) Query: 1 MKSRAAVAFAPGKPLEIVEIDVAPPKKGEVLIKVTHTGVCHTDAFTLSGDDPEGVFPVVL 60 MKSRAAVAFAPGKPLEIVEIDV PP+KGEVL+K+THTGVCHTDAFTLSGDDPEG+FPVVL Sbjct: 1 MKSRAAVAFAPGKPLEIVEIDVEPPRKGEVLVKITHTGVCHTDAFTLSGDDPEGLFPVVL 60 Query: 61 GHEGAGVVVEVGEGVTSVKPGDHVIPLYTAECGECEFCRSGKTNLCVAVRETQGKGLMPD 120 GHEGAG+VVEVGEGVTSVKPGDHVIPLYTAECGEC FC+SGKTNLCV+VR TQGKG+MPD Sbjct: 61 GHEGAGIVVEVGEGVTSVKPGDHVIPLYTAECGECLFCKSGKTNLCVSVRATQGKGVMPD 120 Query: 121 GTTRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKINPEANHEHVCLLGCGVTTGIGAVHN 180 GT+RFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKI+P+ANHE VCLLGCGVTTG+GAV N Sbjct: 121 GTSRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKIDPQANHEQVCLLGCGVTTGLGAVKN 180 Query: 181 TAKVQPGDSVAVFGLGAIGLAVVQGARQAKAGRIIAIDTNPKKFDLARRFGATDCINPND 240 TAKVQ GD+VAVFGLG IGLAV+QGA+ A AGRIIA+DTNP KFDLAR FGATDC+NP D Sbjct: 181 TAKVQEGDTVAVFGLGGIGLAVIQGAKLATAGRIIAVDTNPGKFDLARAFGATDCVNPKD 240 Query: 241 YDKPIKDVLLDINKWGIDHTFECIGNVNVMRAALESAHRGWGQSVIIGVAVAGQEISTRP 300 ++KPI+ V++D+ WG+DH+FECIG+VNVMRAALE AHRGWGQSV+IGVA AGQEISTRP Sbjct: 241 HEKPIQQVIVDMTGWGVDHSFECIGSVNVMRAALECAHRGWGQSVVIGVAGAGQEISTRP 300 Query: 301 FQLVTGRVWKGSAFGGVKGRSQLPGMVEDAMKGDIDLEPFVTHTMSLDEINDAFDLMHEG 360 FQLVTGR W G+AFGGVKGRSQLPGMVEDAM+G I L PFVTHT L IN+AFDLMHEG Sbjct: 301 FQLVTGRRWLGTAFGGVKGRSQLPGMVEDAMEGKIQLAPFVTHTKPLSGINEAFDLMHEG 360 Query: 361 KSIRTVIRY 369 KSIRTV+ Y Sbjct: 361 KSIRTVVHY 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: 642 Number of extensions: 17 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 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