Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate WP_028990577.1 G579_RS0113435 fructose-bisphosphate aldolase class I
Query= BRENDA::Q8L207 (343 letters) >NCBI__GCF_000423825.1:WP_028990577.1 Length = 341 Score = 336 bits (861), Expect = 6e-97 Identities = 190/343 (55%), Positives = 229/343 (66%), Gaps = 10/343 (2%) Query: 3 ERLEDIALTLVGAGKGILAADESTATIGKRFESIGVECTEDNRRAYREMLFTAKEAMESA 62 + LE L GKGILAADES TI KRF I V TE+NRR+YREMLF+ + Sbjct: 4 QELEATVAALTAPGKGILAADESFGTIEKRFRKINVPSTEENRRSYREMLFSTP-GLGEF 62 Query: 63 ISGVILFDETLRQKASTGQMLTDLIRDAGAVPGIKVDTGAKPLAAFPQETITEGLDGLRE 122 I GVILFDETLRQ+ S G + L+R G VPGIKVD G PL FP E +T+GLDGL E Sbjct: 63 IGGVILFDETLRQRGSDGTPIPQLLRAQGIVPGIKVDKGTVPLPNFPDEVVTQGLDGLAE 122 Query: 123 RLKDYYTLGARFAKWRAVIAIDAQTLPTRGAISQNAQALARYAALCQEAGLVPIVEPEVL 182 RL +Y LGARFAKWRAV+ I A +P+R I++NA ALARYAA+CQ GLVPIVEPEVL Sbjct: 123 RLAEYRYLGARFAKWRAVLRIGA-GMPSRRCITENANALARYAAICQAQGLVPIVEPEVL 181 Query: 183 MDGPSRQHSITRCFEVTKVVLHTVFKELFEARVLFEGMILKPNMVIDGKDA-RIASVEEV 241 +DG HS +VT+ VLH VF L E RV E M+LKP+MV+ G D+ S E V Sbjct: 182 IDG---DHSFASAAQVTEDVLHQVFHALHEQRVTLELMLLKPSMVVPGADSGESVSAEAV 238 Query: 242 AEKTVHVLKQTVPAAVPGIAFLSGGQTDEEATAHLSAMNA----LGALPWKLTFSYGRAL 297 A T+ L++ VPAAVPGI FLSGGQ +EEATAHL+A+N G PW L+FSY RAL Sbjct: 239 ASATLACLRRAVPAAVPGIFFLSGGQGNEEATAHLNAINVQAGQAGQAPWVLSFSYARAL 298 Query: 298 QAAALKAWAGKNENIVVAQKAFCHRARMNHLAALGQWTKDQEK 340 QA AL+AW G+ N AQ+ RAR+N LA G+++ E+ Sbjct: 299 QAPALEAWRGEAANREAAQRVLHQRARLNSLARQGRYSAALEQ 341 Lambda K H 0.319 0.132 0.378 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: 332 Number of extensions: 25 Number of successful extensions: 6 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: 343 Length of database: 341 Length adjustment: 29 Effective length of query: 314 Effective length of database: 312 Effective search space: 97968 Effective search space used: 97968 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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