Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate RR42_RS33330 RR42_RS33330 hydroxyacid dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Cup4G11:RR42_RS33330 Length = 312 Score = 214 bits (545), Expect = 2e-60 Identities = 132/323 (40%), Positives = 178/323 (55%), Gaps = 13/323 (4%) Query: 1 MKPKVFITRQIPENGIKMIEKFYEIE-LWKDPKAPPRGVLLEKVREVDALVTLVTDKVDK 59 MKP++ ++P + + Y++ LW + P L E AL T VD Sbjct: 1 MKPRLAQHGRLPAALEASLAEHYDVHPLWAE--TDPAAFLASHGGEFAALTTRAAIGVDA 58 Query: 60 ELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRI 119 ++ P LK+I+ + VG D ID++ A RGI V TP VL D AD AF LL+ VAR Sbjct: 59 AMIAAMPNLKVISSFGVGLDKIDLDAARARGIAVGYTPDVLNDCVADTAFGLLMDVARGF 118 Query: 120 VEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYY 179 AD FVR GEW K++ L + GK +GIVG GRIG+ +A+R GF M++ Y+ Sbjct: 119 SAADRFVRRGEWPKAQFP------LATRVSGKRMGIVGMGRIGRVIARRGVGFDMEVRYH 172 Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 SR +A L + +DF+ + ET H++ + L+ + PN LIN Sbjct: 173 SRRPAQDAPYR---HEPSLSELARWADFLVIATAGGPETRHLVSAEVLEALGPNGFLINI 229 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREG 299 +RG VVD AL+ AL +G IAGAGLDVFE EP + LF L NVVL PHI SATHE R Sbjct: 230 ARGTVVDETALVDALVQGRIAGAGLDVFENEPQVPQALFALDNVVLLPHIASATHETRNA 289 Query: 300 MAELVAKNLIA-FAKGEIPPNLV 321 MA+LV +NL + FA G + + V Sbjct: 290 MADLVFENLQSFFASGAVKASAV 312 Lambda K H 0.317 0.137 0.392 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: 259 Number of extensions: 16 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: 331 Length of database: 312 Length adjustment: 28 Effective length of query: 303 Effective length of database: 284 Effective search space: 86052 Effective search space used: 86052 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: 48 (23.1 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