Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate Echvi_1588 Echvi_1588 deoxyribose-phosphate aldolase
Query= BRENDA::Q9AIP7 (220 letters) >FitnessBrowser__Cola:Echvi_1588 Length = 221 Score = 189 bits (480), Expect = 4e-53 Identities = 100/211 (47%), Positives = 138/211 (65%), Gaps = 1/211 (0%) Query: 3 INQYIDHTLLKPESRQDQIDKLIREAKTYNFASVCINPTWVSYAAKALEGTDIKVCTVIG 62 IN Y++HT L P Q++++I EA Y F VC+ P WV + LE T I V TV+G Sbjct: 4 INTYLEHTALNPVLTDQQVNRVIHEAMKYRFLGVCVPPFWVKKVKRELENTGITVVTVVG 63 Query: 63 FPLGATTSAVKAFETKDAISHGADEVDMVINIGQAKSG-HFAFVEEDIRAVVEASGDKLV 121 FPLG + K FET+ AI +GADE+D+V ++ K+G ++ +E + V KL+ Sbjct: 64 FPLGYQMTETKVFETQKAIENGADEIDVVWSLSAFKAGMNWPKIELVKLSSVCHEAGKLL 123 Query: 122 KVIIETCLLTDKEKIKACQAAVAAGADFVKTSTGFSTAGARLDDVRLMRQTVGPDVGVKA 181 KVI+ET L E +AC+ AG D VKTSTGF+ +GARL++V+LMR+ + VG+KA Sbjct: 124 KVIVETAYLETDELRQACKICSDAGVDIVKTSTGFAPSGARLEEVKLMREFLPDQVGIKA 183 Query: 182 AGGTRSLEDAQAFIEAGATRIGTSAGVTIME 212 +GG ++LE A+AF+ AGA RIGTSAGV IME Sbjct: 184 SGGIKTLEQAKAFVTAGADRIGTSAGVQIME 214 Lambda K H 0.316 0.131 0.366 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: 176 Number of extensions: 8 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: 220 Length of database: 221 Length adjustment: 22 Effective length of query: 198 Effective length of database: 199 Effective search space: 39402 Effective search space used: 39402 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 45 (21.9 bits)
Align candidate Echvi_1588 Echvi_1588 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00126.hmm # target sequence database: /tmp/gapView.6038.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00126 [M=211] Accession: TIGR00126 Description: deoC: deoxyribose-phosphate aldolase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-75 239.9 0.2 1.1e-75 239.7 0.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1588 Echvi_1588 deoxyribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1588 Echvi_1588 deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.7 0.2 1.1e-75 1.1e-75 2 210 .. 4 213 .. 3 214 .. 0.95 Alignments for each domain: == domain 1 score: 239.7 bits; conditional E-value: 1.1e-75 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLkgteveictvvgFPlGasttevkllE 75 ++++++htal++ t+++++++++eA+ky+f vcv p +v+ k++L++t +++ tvvgFPlG + te+k++E lcl|FitnessBrowser__Cola:Echvi_1588 4 INTYLEHTALNPVLTDQQVNRVIHEAMKYRFLGVCVPPFWVKKVKRELENTGITVVTVVGFPLGYQMTETKVFE 77 5789********************************************************************** PP TIGR00126 76 akeaieeGAdEvDvviniaalkdkneevviedikavveaca..kvllKvilEtalLtdeekkkAseisieagad 147 +++aie+GAdE+Dvv ++a+k++ + ie +k + +c + llKvi+Eta+L +e+++A++i+ +ag+d lcl|FitnessBrowser__Cola:Echvi_1588 78 TQKAIENGADEIDVVWSLSAFKAGMNWPKIELVK-LSSVCHeaGKLLKVIVETAYLETDELRQACKICSDAGVD 150 **********************998877776665.3444443489***************************** PP TIGR00126 148 fvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaavaii 210 vKtstgf+ gA +e+v+lm++ d+vg+KasGG++t e+a+a++ aga+rig+sa+v+i+ lcl|FitnessBrowser__Cola:Echvi_1588 151 IVKTSTGFAPSGARLEEVKLMREFLPDQVGIKASGGIKTLEQAKAFVTAGADRIGTSAGVQIM 213 *************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (221 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.51 // [ok]
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