Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate PP_1649 PP_1649 D-lactate dehydrogenase
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__Putida:PP_1649 Length = 342 Score = 162 bits (411), Expect = 9e-45 Identities = 120/349 (34%), Positives = 174/349 (49%), Gaps = 35/349 (10%) Query: 1 MKRPRVFVTREVFPEALELLSKYYDVEVWDKYQP--------PPYETLLSKAREADALYT 52 M PR + R AL S++YD E + K P L A AD Sbjct: 1 MTHPRHALQRSSTMRALLFSSQHYDQESFTKAAGGTALELHFQPARLTLDTAALADGFEV 60 Query: 53 L---LTDRIDCDLLSQ--APRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAE 107 + + D +D +L + A R++A + G++++D+ A RLG+ V P A AE Sbjct: 61 VCAFINDELDAPVLQRLAAAGTRLIALRSAGYNHVDLAAAQRLGLAVVRVPAYSPHAVAE 120 Query: 108 FTWALILAAARRVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVA 167 ALILA RR+ A + R G++ + G +L GKT+G++G G+IG A Sbjct: 121 HAVALILALNRRLHRAYNRTREGDFTLHG-------LTGFDLHGKTVGVVGTGQIGVAFA 173 Query: 168 EIGKAFGMRIIYHSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESE 227 I FG +++ + E+ LGA Y L +LLRE+ I+S+H PLT+ TRHLI Sbjct: 174 RIMAGFGCQLLAYDPYPNPEL-LALGARYLPLPELLREARIISLHCPLTEHTRHLINAQS 232 Query: 228 LKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAALDVFEEE-----------PLNPN 276 L ++ A+L+NTGRGA+VDT AL+ AL+ G + LDV+EEE PL + Sbjct: 233 LAQLQPGAMLINTGRGALVDTPALIDALKSGQLGYLGLDVYEEEAQLFFEDRSDLPLQDD 292 Query: 277 --HPLTAFKNVVLAPHAASATRETRLRMAMMAAENLVAFAQGKVPPNLV 323 L F NV++ H A TRE +A +N+ +A G P NLV Sbjct: 293 VLARLLTFPNVIITAHQAFLTREALDAIAATTLDNINRWAAGN-PQNLV 340 Lambda K H 0.322 0.136 0.406 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: 280 Number of extensions: 12 Number of successful extensions: 4 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: 335 Length of database: 342 Length adjustment: 28 Effective length of query: 307 Effective length of database: 314 Effective search space: 96398 Effective search space used: 96398 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 (21.9 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