Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate RR42_RS17795 RR42_RS17795 aldo/keto reductase
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__Cup4G11:RR42_RS17795 Length = 277 Score = 121 bits (303), Expect = 2e-32 Identities = 94/279 (33%), Positives = 140/279 (50%), Gaps = 15/279 (5%) Query: 8 TVKLHNGVEMPWFGLGVFKVENGN----EATESVKAAIKNGYRSIDTAAIY---KNEEGV 60 TV L G + G+G + + + E +++ + G IDTA +Y ++EE V Sbjct: 3 TVSLPGGESVAALGMGTWNMGDQPAARAEELATLRLGLDLGLTLIDTAEMYGDGRSEELV 62 Query: 61 GIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYK 120 G I R+E+F+ SKV+ + G +AA E+SL RL D LDLYL+HW G Sbjct: 63 GEAIAGR---RDEVFLVSKVYPHNAGRTGAVAACERSLRRLGTDRLDLYLLHWRGGVPLA 119 Query: 121 DTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPM-VNQVEFH--PRLTQKELRD 177 +T A L K GKIR GVSN + + L + K + NQ+ ++ R + +L Sbjct: 120 ETMEAFMALRKAGKIRYFGVSNLDLDDMRALWRVPGGKEVAANQLLYNLTRRGIEWDLLP 179 Query: 178 YCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDL-QHGVVTIPKSIKE 236 + + G+ L A+SP+ Q LL N L A+KH S Q L W L Q GV+ IPK+ Sbjct: 180 WLREHGVPLMAYSPIEQATLLRNPRLAGFAKKHGISPVQAALGWLLAQQGVIAIPKTSHR 239 Query: 237 HRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELL 275 R+ EN LS + + ++DA + GP+P +L Sbjct: 240 ERLRENHGALALRLSAQQLAELDAAFQPPD-GPHPLAML 277 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: 182 Number of extensions: 12 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: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 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