Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate BWI76_RS16900 BWI76_RS16900 4-hydroxy-2-oxovalerate aldolase
Query= curated2:Q07179 (382 letters) >FitnessBrowser__Koxy:BWI76_RS16900 Length = 338 Score = 70.1 bits (170), Expect = 9e-17 Identities = 76/271 (28%), Positives = 113/271 (41%), Gaps = 36/271 (13%) Query: 5 RTLALCDTTLRDGEQTAGVAFSLAEKKAIARALDRAGVAEIEV-------------GIAA 51 + L + D TLRDG +SL + IARALD AGV IEV G A Sbjct: 4 KKLYISDVTLRDGMHAIRHQYSLDNVRQIARALDSAGVDSIEVAHGDGLQGSSFNYGFGA 63 Query: 52 ---MGWAEVAEIRAVVAEIAHATPVVWCRLRMHDLDMAQKTGVKRVHFAVPTSTAQLEGK 108 + W E A A+IA T ++ +HDL A + G + V A + A + Sbjct: 64 HSDLEWIEAAAESVSQAKIA--TLLLPGIGTLHDLKNAYQAGARVVRVATHCTEADV--- 118 Query: 109 LRVDRDWILRETAALVFCASDRGLQVSVGAEDASRTDPDFLIRLAEVAAAAGAIRFRIAD 168 +A + A + G+ + T P+ L + A + GA + D Sbjct: 119 -----------SAQHIAFARELGMDTVGFLMMSHMTAPEQLAQQALKMESYGATCIYVVD 167 Query: 169 TLGLL---DPLGAFRLVAELSARISLPIEMHAHNDFGMATANTIMAAHAGATHLSVTVNG 225 + G + D FR + + + MHAH++ + AN+I A G + ++ G Sbjct: 168 SGGAMNMRDIRDRFRALKAV-LKPETATGMHAHHNLSLGVANSIAAVEEGCDRIDASLAG 226 Query: 226 LGERAGNAACEEVGAALEAGGIDTGLDLCAL 256 +G AGNA E AA + G + G DL AL Sbjct: 227 MGAGAGNAPLEVFIAAADKLGWNHGTDLYAL 257 Lambda K H 0.321 0.134 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: 262 Number of extensions: 14 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: 382 Length of database: 338 Length adjustment: 29 Effective length of query: 353 Effective length of database: 309 Effective search space: 109077 Effective search space used: 109077 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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