Align 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized)
to candidate CA265_RS01080 CA265_RS01080 6-phosphogluconate dehydrogenase
Query= curated2:P77161 (292 letters) >FitnessBrowser__Pedo557:CA265_RS01080 Length = 285 Score = 155 bits (391), Expect = 1e-42 Identities = 97/283 (34%), Positives = 148/283 (52%), Gaps = 6/283 (2%) Query: 2 KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVAD-ELLSLGAVSVETARQVTEASDIIF 60 K+G+IGLG MG PMA L AG+ + V + L +GA +T + + +D++ Sbjct: 5 KIGWIGLGNMGIPMAEQLINAGYAVMVYNRSKDKEASLKEMGASIAQTPQDLITTTDVVI 64 Query: 61 IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120 +MV D + ++ GE G + GK I++MS++SP +K A G YLDAPVS Sbjct: 65 VMVSDDAAIAQIFNGEGGLLRVETSGKIIINMSTVSPSISKEMAALCKANGNFYLDAPVS 124 Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180 G A G L IMVGG+E VF +VKP+ E +GK LVG NG G + K+A ++AL Sbjct: 125 GSVKQAETGQLVIMVGGEEDVFNQVKPILEKMGKLAKLVGENGAGNSAKLAINSLLALYA 184 Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240 + ++E +LFA+K G + + + + ++ G+ +I + F + KDLN Sbjct: 185 QGLAETVLFANKQGIKTSDLLELINNAAIGNIFTKIKGDAIIADHYKAAFALKHIVKDLN 244 Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQAL 283 L AKA ++ P T F AA G + D A+++ L Sbjct: 245 L----AKAEGISSPLAKTALNTFGDAAAKYGEE-DIIAIIKQL 282 Lambda K H 0.318 0.135 0.376 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: 207 Number of extensions: 10 Number of successful extensions: 2 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: 292 Length of database: 285 Length adjustment: 26 Effective length of query: 266 Effective length of database: 259 Effective search space: 68894 Effective search space used: 68894 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 (21.7 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