Align Deoxyribose-phosphate aldolase; DERA; EC 4.1.2.4; 2-deoxy-D-ribose 5-phosphate aldolase; Phosphodeoxyriboaldolase; Deoxyriboaldolase (uncharacterized)
to candidate BWI76_RS23665 BWI76_RS23665 2-deoxyribose-5-phosphate aldolase
Query= curated2:A6T962 (249 letters) >FitnessBrowser__Koxy:BWI76_RS23665 Length = 249 Score = 476 bits (1224), Expect = e-139 Identities = 238/249 (95%), Positives = 243/249 (97%) Query: 1 MKAIKNKGQDKTMNETTHRFARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWT 60 MK IKNK QD+TMNETT RFARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWT Sbjct: 1 MKVIKNKEQDETMNETTRRFARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWT 60 Query: 61 RFLSTLLPQQGTGEVMIGGPVGFPGGGHTTDTKVQEVRQLIADGAREVDMVVNIGKVLSG 120 RFLSTLLPQQGTGEVMIGGPVGFPGGGH TDTKVQEVRQLIADGAREVDMVVNIGKVLSG Sbjct: 61 RFLSTLLPQQGTGEVMIGGPVGFPGGGHATDTKVQEVRQLIADGAREVDMVVNIGKVLSG 120 Query: 121 DYDYVREDLRRVVEAAAPVPAKVILETHYLNEEQIRRVCEIAVEVGMKWVKTSTGWAPTG 180 DYDYVREDLRRVV+AAAPVPAKVILETHYLNEEQIRRVC+IAVEVGMKWVKTSTGWAPTG Sbjct: 121 DYDYVREDLRRVVDAAAPVPAKVILETHYLNEEQIRRVCDIAVEVGMKWVKTSTGWAPTG 180 Query: 181 ATVEKVRIIADQLKGRIDIKGAGGIRDLATVRALYQLGVRRFGMSHGAVTKVLAELEQHP 240 ATVEKV IIADQLKGRIDIKGAGGIRDLATVRALYQLG+RRFGMSHGAV+KVL ELEQHP Sbjct: 181 ATVEKVSIIADQLKGRIDIKGAGGIRDLATVRALYQLGIRRFGMSHGAVSKVLTELEQHP 240 Query: 241 ERFPELNAD 249 ERFPELNAD Sbjct: 241 ERFPELNAD 249 Lambda K H 0.319 0.135 0.393 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: 298 Number of extensions: 5 Number of successful extensions: 1 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: 249 Length of database: 249 Length adjustment: 24 Effective length of query: 225 Effective length of database: 225 Effective search space: 50625 Effective search space used: 50625 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: 46 (22.3 bits)
Align candidate BWI76_RS23665 BWI76_RS23665 (2-deoxyribose-5-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.13979.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-57 179.3 0.0 4.4e-57 178.9 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS23665 BWI76_RS23665 2-deoxyribose-5-ph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS23665 BWI76_RS23665 2-deoxyribose-5-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.9 0.0 4.4e-57 4.4e-57 2 207 .. 20 228 .. 19 231 .. 0.98 Alignments for each domain: == domain 1 score: 178.9 bits; conditional E-value: 4.4e-57 TIGR00126 2 lakliDhtalkadtteedietlcaeAkkykfaavcvnpsyvslAkelLk..gt.eveictvvgFPlGastt 69 +a+l+D++a++a +te+d+ ++ + A +y++++v v p + ++ lL gt ev i vgFP G + t lcl|FitnessBrowser__Koxy:BWI76_RS23665 20 FARLVDLSAVQATSTEADVRACAELAARYNIISVHVLPCWTRFLSTLLPqqGTgEVMIGGPVGFPGGGHAT 90 689********************************************9767999***************** PP TIGR00126 70 evkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekkkAsei 140 ++k+ E ++ i+ GA EvD+v+ni+++ +++ + v ed++ vv+a+a v+ KvilEt +L +e++++ ++i lcl|FitnessBrowser__Koxy:BWI76_RS23665 91 DTKVQEVRQLIADGAREVDMVVNIGKVLSGDYDYVREDLRRVVDAAAPVPAKVILETHYLNEEQIRRVCDI 161 *********************************************************************** PP TIGR00126 141 sieagadfvKtstgfsakgAtvedvrlmkkvvgdevgvKasGGvrtaedalalieagaerigasaav 207 ++e g ++vKtstg++ +gAtve v ++ + ++++ +K +GG+r+ ++ al + g r+g s++ lcl|FitnessBrowser__Koxy:BWI76_RS23665 162 AVEVGMKWVKTSTGWAPTGATVEKVSIIADQLKGRIDIKGAGGIRDLATVRALYQLGIRRFGMSHGA 228 ***************************************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (249 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: 00:00:00.02 # Mc/sec: 2.61 // [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