Align Probable fructose-bisphosphate aldolase; FBP aldolase; FBPA; Fructose-1,6-bisphosphate aldolase; EC 4.1.2.13 (characterized)
to candidate Echvi_0155 Echvi_0155 ketose-bisphosphate aldolases
Query= SwissProt::P13243 (285 letters) >FitnessBrowser__Cola:Echvi_0155 Length = 274 Score = 167 bits (422), Expect = 3e-46 Identities = 108/265 (40%), Positives = 151/265 (56%), Gaps = 8/265 (3%) Query: 12 TAKEKGYAVGQFNLNNLEFTQAILQAAEEEKSPVILGVSEGAGRYMGGFKTVVAMVKALM 71 TA+++G F NLE Q +L+AA PVIL +++ + YMG T VAM +A + Sbjct: 11 TAQKRGLLATNFY--NLETLQGVLKAASAMDEPVILQLTKSSIDYMG-LNTAVAMGRAAL 67 Query: 72 EEYKVTVPVAIHLDHGSSFESCAKAIHAGFTSVMIDASHHPFEENVATTAKVVELAHFHG 131 +EY V IHLDHG S E + AGF SVMID S PFEENV T +VV AH +G Sbjct: 68 KEYGVEG--WIHLDHGGSVELAQACLDAGFDSVMIDGSELPFEENVKITQEVVRRAHKYG 125 Query: 132 VSVEAELGTVGGQEDDVIAEGVIYADPKECQELVERTGIDCLAPALGSVHGPYKGEPNLG 191 +VEAELG V +G A+ E + VE+TG+D LA ++G+ HG YK EP L Sbjct: 126 ANVEAELGYVAKLGQSHEHQGFTTAE--EAKTFVEQTGVDALAISIGTAHGFYKQEPKLQ 183 Query: 192 FKEMEEIGKSTGLPLVLHGGTGIPTADIKKSISLGTAKINVNTENQISSAKAVRETLAAK 251 F + EI +T LVLHG +G+P ++K+IS G K+N+ TE + K +++ L + Sbjct: 184 FDLLSEIAAATEATLVLHGSSGVPEEQLRKAISGGICKVNLATEIKNIFMKTLQQ-LLLQ 242 Query: 252 PDEYDPRKYLGPAREAIKETVIGKM 276 +E D RK A + + + V K+ Sbjct: 243 NEEIDLRKVFPKATKEVTDLVSYKL 267 Lambda K H 0.313 0.131 0.367 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: 189 Number of extensions: 8 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: 285 Length of database: 274 Length adjustment: 26 Effective length of query: 259 Effective length of database: 248 Effective search space: 64232 Effective search space used: 64232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 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