Align Probable fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Probable fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate YP_004144350.1 Mesci_5202 deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase
Query= curated2:Q9YG90 (272 letters) >NCBI__GCF_000185905.1:YP_004144350.1 Length = 266 Score = 108 bits (271), Expect = 9e-29 Identities = 83/267 (31%), Positives = 126/267 (47%), Gaps = 15/267 (5%) Query: 7 VGKRVRLSRIL--PDGRSVIFAFDHGIEHGPGEIPEERLD--PRLLIREVVEAGVDAIMT 62 +G +VRL+R+ P G A DH + G G++ + L P L R +V D + Sbjct: 3 LGTKVRLARLFSHPSGNLFGGAVDHFV--GYGDVRKGGLADLPGALARVMV-GKPDYVSI 59 Query: 63 TPGIARLTWDIWANRVAMIIKVSGKTSIRPQDDQFLQSAISSVDEVVALGGDGVAATVYW 122 PG AR W +A + +++I+ T D + I++ ++ V G D +A + Sbjct: 60 QPGTARHLWPQYAGKASLVIQAGCFTP-----DDRISELIATPEDAVRAGADALAVAIPV 114 Query: 123 GSQFEDKMLERWTRIRLRAEKLGLPALQLAYPRG--PHIKNRYAVDIVAYGARAAMETGA 180 E K + T A + G+P + YPR K + D +AY AR E+G Sbjct: 115 RGATEGKYIRWLTDSVNAAARYGMPVVAHIYPRDFTDGAKIVFTPDEIAYAARIGYESGV 174 Query: 181 DLIKTYYTGSTESFRRVVSAAGGVPVLMSGGARTPSPQEFLHKVYSVMEAGGGGVVVGRN 240 D+IK YTG ESFR V VPV+++GG +T + L + + AG G VVGRN Sbjct: 175 DVIKIGYTGDFESFRETVRTCP-VPVVIAGGPKTDTLLGALQQTADAIRAGARGAVVGRN 233 Query: 241 IFQAGDIRAMVKAIRAIVHEGFDPEKA 267 ++ GD A R ++HEG + A Sbjct: 234 LWGHGDPEKAAIAFRGVIHEGLSAQDA 260 Lambda K H 0.320 0.137 0.403 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: 190 Number of extensions: 13 Number of successful extensions: 3 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: 272 Length of database: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 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: 47 (22.7 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