Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate SM_b21300 SM_b21300 deoxyribose-phosphate aldolase
Query= BRENDA::Q9Y315 (318 letters) >FitnessBrowser__Smeli:SM_b21300 Length = 334 Score = 369 bits (946), Expect = e-107 Identities = 188/313 (60%), Positives = 238/313 (76%), Gaps = 2/313 (0%) Query: 5 NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64 N G ELDLSW+ +VN A RR + + RRTVKK+ QAAWLLKAVT IDLTTL+GDDT Sbjct: 23 NDGVELDLSWVLDQRVNLSAAERRVQTLPGRRTVKKDAQAAWLLKAVTCIDLTTLNGDDT 82 Query: 65 SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124 + ++RLC KA+ P+R+D+L AL M D+GITT A+CVY V AV+AL+ +G IPVA+ Sbjct: 83 AERVKRLCAKARQPVRQDILDALGMGDRGITTGAICVYHRFVSTAVEALEGSG--IPVAA 140 Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184 V+ GFPAG +L EI+ +V DGA EID+VI R VLTG W+ALYDE+R FR ACG+ Sbjct: 141 VSTGFPAGLVPHDVKLREIKASVADGAREIDIVITREHVLTGNWQALYDEMRDFRAACGD 200 Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244 AH+K ILATG+L TL NV +AS++ MMAG+DFIKTSTGKE VNAT V + MLR IR + Sbjct: 201 AHVKAILATGDLKTLRNVARASLVCMMAGADFIKTSTGKEGVNATLLVTLAMLRMIRAYE 260 Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304 +TG K+G+KPAGGI AKD L + L+KEELG EWL+P+LFR+GAS+LL+DIERQ+ HH Sbjct: 261 ERTGIKVGYKPAGGISVAKDVLNYQFLMKEELGREWLEPDLFRVGASSLLADIERQLEHH 320 Query: 305 VTGRYAAYHDLPM 317 V+G Y+A + P+ Sbjct: 321 VSGAYSALNRHPI 333 Lambda K H 0.320 0.133 0.397 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: 355 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: 318 Length of database: 334 Length adjustment: 28 Effective length of query: 290 Effective length of database: 306 Effective search space: 88740 Effective search space used: 88740 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: 48 (23.1 bits)
Align candidate SM_b21300 SM_b21300 (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.6668.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-46 143.5 0.9 1.3e-45 141.5 0.9 1.8 1 lcl|FitnessBrowser__Smeli:SM_b21300 SM_b21300 deoxyribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b21300 SM_b21300 deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 141.5 0.9 1.3e-45 1.3e-45 3 201 .. 69 292 .. 67 297 .. 0.91 Alignments for each domain: == domain 1 score: 141.5 bits; conditional E-value: 1.3e-45 TIGR00126 3 akliDhtalkadtteedietlcaeAkky................kfaavcvnpsyvslAkelLkgteveictv. 59 + iD+t+l+ d+t e +++lca+A ++ + a+cv+ ++vs A+e L+g+ + +++v lcl|FitnessBrowser__Smeli:SM_b21300 69 VTCIDLTTLNGDDTAERVKRLCAKARQPvrqdildalgmgdrgiTTGAICVYHRFVSTAVEALEGSGIPVAAVs 142 578**********************9988888888888777776788*************************97 PP TIGR00126 60 vgFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdee 133 +gFP+G ++vkl E k++++ GA E+D+vi + +n+++ +++++ ac+++++K+il t+ L+ lcl|FitnessBrowser__Smeli:SM_b21300 143 TGFPAGLVPHDVKLREIKASVADGAREIDIVITREHVLTGNWQALYDEMRDFRAACGDAHVKAILATGDLKTLR 216 8*********************************************************************9876 PP TIGR00126 134 kk.kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieagae 199 + +As +++ agadf+Ktstg+ ++At+ m ++++ +vg K++GG+ a+d+l++ e lcl|FitnessBrowser__Smeli:SM_b21300 217 NVaRASLVCMMAGADFIKTSTGKEGVNATLLVTLAMLRMIRAyeertgiKVGYKPAGGISVAKDVLNYQFLMKE 290 655**************************987777777777778899999**************9998655555 PP TIGR00126 200 ri 201 + lcl|FitnessBrowser__Smeli:SM_b21300 291 EL 292 55 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (334 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 2.18 // [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