Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate GFF3226 PGA1_c32790 putative deoxyribose-phosphate aldolase
Query= BRENDA::Q9Y315 (318 letters) >FitnessBrowser__Phaeo:GFF3226 Length = 329 Score = 371 bits (953), Expect = e-107 Identities = 188/307 (61%), Positives = 234/307 (76%), Gaps = 4/307 (1%) Query: 5 NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64 N G ELDL W ++ N A+ RR + RR+VKK QAAWLLKA+T IDLTTLSGDDT Sbjct: 20 NPGMELDLDWALGVEANTSAIERRCATLPGRRSVKKNHQAAWLLKAITLIDLTTLSGDDT 79 Query: 65 SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124 +QRLC KA+ P+R DL++AL+M ITT AVCVY + AV AL G IPVA+ Sbjct: 80 VGRVQRLCAKARQPVRADLMQALDMEP--ITTGAVCVYHDMIETAVAALDGTG--IPVAA 135 Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184 V+ GFP G + RL EI +V+ GA EID+VI+R VL+G W+ALYDE++ FR+ACG+ Sbjct: 136 VSTGFPGGLSPFHLRLAEIEESVKAGAKEIDIVISRRHVLSGNWQALYDEMKAFREACGD 195 Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244 AH+K ILATGELGTL NV +AS+I MMAG+DFIKTSTGKE+VNAT PV++VM+R IRD+ Sbjct: 196 AHVKAILATGELGTLRNVARASLICMMAGADFIKTSTGKESVNATLPVSLVMIRTIRDYH 255 Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304 +TG ++G+KPAGGI AKDSL +LSL+KEELGD WL+P+LFR GAS+LL DIERQ+ HH Sbjct: 256 ERTGYRVGYKPAGGISKAKDSLVYLSLIKEELGDRWLQPDLFRFGASSLLGDIERQLEHH 315 Query: 305 VTGRYAA 311 VTG Y+A Sbjct: 316 VTGAYSA 322 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: 339 Number of extensions: 10 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: 318 Length of database: 329 Length adjustment: 28 Effective length of query: 290 Effective length of database: 301 Effective search space: 87290 Effective search space used: 87290 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 GFF3226 PGA1_c32790 (putative 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.24239.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-49 152.2 0.0 1.5e-48 151.1 0.0 1.5 1 lcl|FitnessBrowser__Phaeo:GFF3226 PGA1_c32790 putative deoxyribose Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3226 PGA1_c32790 putative deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 151.1 0.0 1.5e-48 1.5e-48 3 203 .. 66 289 .. 64 293 .. 0.93 Alignments for each domain: == domain 1 score: 151.1 bits; conditional E-value: 1.5e-48 TIGR00126 3 akliDhtalkadtteedietlcaeAkky..............kfaavcvnpsyvslAkelLkgteveictv.vgFP 63 +liD+t+l+ d+t +++lca+A ++ + avcv+ +++ A+ L gt + +++v +gFP lcl|FitnessBrowser__Phaeo:GFF3226 66 ITLIDLTTLSGDDTVGRVQRLCAKARQPvradlmqaldmepiTTGAVCVYHDMIETAVAALDGTGIPVAAVsTGFP 141 679**********************99887777777777777788*************************978*** PP TIGR00126 64 lGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtd.eekkkAs 138 G s + +l+E +e++++GA+E+D+vi + + ++n+++ ++++ka eac+++++K+il t++L ++ +As lcl|FitnessBrowser__Phaeo:GFF3226 142 GGLSPFHLRLAEIEESVKAGAKEIDIVISRRHVLSGNWQALYDEMKAFREACGDAHVKAILATGELGTlRNVARAS 217 ******************************************************************6615666*** PP TIGR00126 139 eisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieagaeriga 203 i++ agadf+Ktstg+ ++At+ +m ++++d +vg K++GG+ a+d l +++ e +g lcl|FitnessBrowser__Phaeo:GFF3226 218 LICMMAGADFIKTSTGKESVNATLPVSLVMIRTIRDyhertgyRVGYKPAGGISKAKDSLVYLSLIKEELGD 289 *************************99*********************************999988888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (329 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 2.09 // [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