Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate PP_3671 PP_3671 Oxidoreductase, aldo/keto reductase family
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Putida:PP_3671 Length = 274 Score = 159 bits (402), Expect = 6e-44 Identities = 96/262 (36%), Positives = 145/262 (55%), Gaps = 7/262 (2%) Query: 14 GVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREE 73 G+++P GLG + + G+E T++V+ A+ GYR IDTA Y+NE VG +++S V RE+ Sbjct: 9 GLDLPAIGLGTWPM-TGSECTQAVRQALDVGYRHIDTATAYENEAAVGQALRDSDVPREQ 67 Query: 74 LFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYKDTWRALEKLY--- 130 + +T+KVW + + + E SL L + +DL+ IHWPG D D R+++ L Sbjct: 68 IHLTTKVWWDRLEPKAMRQSLEDSLRALGTEQVDLFHIHWPGTD--WDLARSIDTLVALR 125 Query: 131 KDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWS 190 +GK R IGV+NF + L ++++ QVE+H L+Q+ L D+ +G + L A++ Sbjct: 126 DEGKARHIGVANFPLGLLRQVVETLGAPLSAIQVEYHVLLSQQPLLDFARGHDLLLTAYT 185 Query: 191 PLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDL-QHGVVTIPKSIKEHRIIENADIFDFE 249 PL +GQ V+ IA KH +QV L+W L Q GV IPK+ + N Sbjct: 186 PLARGQAAAQPVIQAIARKHGVLPSQVALKWLLDQDGVAAIPKASSRENQLANLAALTVP 245 Query: 250 LSQEDMDKIDALNKDERVGPNP 271 L ED I L KD+RV P Sbjct: 246 LDDEDRTAIAGLPKDQRVVSPP 267 Lambda K H 0.316 0.135 0.397 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: 193 Number of extensions: 11 Number of successful extensions: 3 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: 276 Length of database: 274 Length adjustment: 25 Effective length of query: 251 Effective length of database: 249 Effective search space: 62499 Effective search space used: 62499 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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