Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate BPHYT_RS15795 BPHYT_RS15795 hypothetical protein
Query= SwissProt::O32210 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS15795 Length = 281 Score = 106 bits (265), Expect = 5e-28 Identities = 87/281 (30%), Positives = 137/281 (48%), Gaps = 9/281 (3%) Query: 3 TSLKDTVKLHNGVEMPWFGLGVFKVEN--GNEATE--SVKAAIKNGYRSIDTAAIYKNEE 58 TS +V L +G +P G G +++ A E +++ I+ G IDTA +Y + Sbjct: 2 TSEIASVSLPDGERIPKLGQGTWEMGELPARRAAEIDALRCGIELGMTLIDTAEMYGDGA 61 Query: 59 GVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDK 118 + + R+++F SKV+ + +AA E+SL+RL+ D LDLYL+HW G Sbjct: 62 TESLLGEALAGLRDKVFRVSKVYPHNASRRGVIAACEQSLKRLKTDQLDLYLLHWRGSVP 121 Query: 119 YKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELL-KDAEIKPMVNQVEFH--PRLTQKEL 175 +T E L + GKIR GVSNF +EEL+ NQ+ ++ R + +L Sbjct: 122 LAETVEGFEALRRAGKIRHWGVSNFDTEDMEELVATPGGDACATNQILYNVARRGPEFDL 181 Query: 176 RDYCKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDL-QHGVVTIPKSI 234 + + + A+SP+ +L L IA+ SV Q+ L W L Q GV IPK+ Sbjct: 182 LPWLAARKMPGMAYSPVDHARLPRRSPLDDIADARGVSVFQIALAWVLRQPGVCAIPKAA 241 Query: 235 KEHRIIENADIFDFELSQEDMDKIDALNKDERVGPNPDELL 275 + + +N +L +++ IDA K R G P E+L Sbjct: 242 RVEHVRDNHRASQLQLGADELAAIDAHFKPPR-GKRPLEML 281 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: 181 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: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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