Align D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate Echvi_0155 Echvi_0155 ketose-bisphosphate aldolases
Query= SwissProt::Q8VS16 (284 letters) >FitnessBrowser__Cola:Echvi_0155 Length = 274 Score = 178 bits (452), Expect = 1e-49 Identities = 99/243 (40%), Positives = 143/243 (58%), Gaps = 4/243 (1%) Query: 22 AFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAGTGNVVAIARDLAKIWDLPLAVHL 81 A N +NLET+Q V++ A+ + P+IL T + Y G VA+ R K + + +HL Sbjct: 19 ATNFYNLETLQGVLKAASAMDEPVILQLTKSSIDYMGLNTAVAMGRAALKEYGVEGWIHL 78 Query: 82 DHHEDLADITRKVQAGIRSVMIDGSHSPFEENVALVKSVVELSHRYDASVEAELGRLGGV 141 DH + + AG SVMIDGS PFEENV + + VV +H+Y A+VEAELG + Sbjct: 79 DHGGSVELAQACLDAGFDSVMIDGSELPFEENVKITQEVVRRAHKYGANVEAELGYVA-- 136 Query: 142 EDDLGVDAKDALYTNPEQGREFVARTGIDSLAVVIGTAHGLYAAEPKLGFAALPPISERV 201 LG + +T E+ + FV +TG+D+LA+ IGTAHG Y EPKL F L I+ Sbjct: 137 --KLGQSHEHQGFTTAEEAKTFVEQTGVDALAISIGTAHGFYKQEPKLQFDLLSEIAAAT 194 Query: 202 DVPLVLHGASKLPDSDIRRAISLGVCKVNVATELKIAFSDALKHYFEENPDANEPRHYMK 261 + LVLHG+S +P+ +R+AIS G+CKVN+ATE+K F L+ +N + + + + K Sbjct: 195 EATLVLHGSSGVPEEQLRKAISGGICKVNLATEIKNIFMKTLQQLLLQNEEIDLRKVFPK 254 Query: 262 PAK 264 K Sbjct: 255 ATK 257 Lambda K H 0.319 0.135 0.389 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: 7 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: 284 Length of database: 274 Length adjustment: 26 Effective length of query: 258 Effective length of database: 248 Effective search space: 63984 Effective search space used: 63984 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 (21.7 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