Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate 3609633 Dshi_3016 deoxyribose-phosphate aldolase (RefSeq)
Query= BRENDA::Q9Y315 (318 letters) >FitnessBrowser__Dino:3609633 Length = 339 Score = 368 bits (945), Expect = e-106 Identities = 189/309 (61%), Positives = 235/309 (76%), Gaps = 4/309 (1%) Query: 5 NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64 N G LDL W+ VN AV RRA + RR+VKK+ QAAWLLKAVT IDLTTL+GDDT Sbjct: 30 NPGLPLDLDWVRSAAVNTSAVERRAASLPGRRSVKKDHQAAWLLKAVTLIDLTTLAGDDT 89 Query: 65 SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124 + ++RLC KA+ P+ ++L AL M +TT AVCVY V AV+AL+ +G IPVA+ Sbjct: 90 AGRVRRLCAKARQPVAPEVLAALGMGP--VTTGAVCVYHDMVHVAVEALEGSG--IPVAA 145 Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184 V+ GFPAG + R+ EI +V GA EID+VI+R VLTG W+ALYDE+R FR ACG+ Sbjct: 146 VSTGFPAGLSPFHLRVAEIEESVAAGAAEIDIVISRRHVLTGNWQALYDEMRAFRAACGD 205 Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244 AH+K ILATGELG L NV +AS++ MMAG+DFIKTSTGKE+VNAT PV++VM+RAIRD+ Sbjct: 206 AHVKAILATGELGDLGNVARASLVCMMAGADFIKTSTGKESVNATLPVSLVMIRAIRDYE 265 Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304 TG K+G+KPAGGI AKD+L +LSL+KEELGD WL+P+LFR GAS+LL DIERQ+ HH Sbjct: 266 AATGVKVGYKPAGGISKAKDALVYLSLIKEELGDRWLQPDLFRFGASSLLGDIERQLEHH 325 Query: 305 VTGRYAAYH 313 VTG Y+A H Sbjct: 326 VTGAYSATH 334 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: 367 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: 318 Length of database: 339 Length adjustment: 28 Effective length of query: 290 Effective length of database: 311 Effective search space: 90190 Effective search space used: 90190 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: 49 (23.5 bits)
Align candidate 3609633 Dshi_3016 (deoxyribose-phosphate aldolase (RefSeq))
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.9560.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-48 151.3 0.3 2.6e-48 150.3 0.3 1.4 1 lcl|FitnessBrowser__Dino:3609633 Dshi_3016 deoxyribose-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609633 Dshi_3016 deoxyribose-phosphate aldolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 150.3 0.3 2.6e-48 2.6e-48 3 203 .. 76 299 .. 74 303 .. 0.94 Alignments for each domain: == domain 1 score: 150.3 bits; conditional E-value: 2.6e-48 TIGR00126 3 akliDhtalkadtteedietlcaeAkky..............kfaavcvnpsyvslAkelLkgteveictv.vgFPl 64 +liD+t+l d+t + +lca+A ++ + avcv+ +v++A+e L+g+ + +++v +gFP+ lcl|FitnessBrowser__Dino:3609633 76 VTLIDLTTLAGDDTAGRVRRLCAKARQPvapevlaalgmgpvTTGAVCVYHDMVHVAVEALEGSGIPVAAVsTGFPA 152 689**********************998888888878777777889************************978**** PP TIGR00126 65 GasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdeekk.kAsei 140 G s + +++E +e++++GA E+D+vi + + +n+++ +++++a ac+++++K+il t++L d + +As + lcl|FitnessBrowser__Dino:3609633 153 GLSPFHLRVAEIEESVAAGAAEIDIVISRRHVLTGNWQALYDEMRAFRAACGDAHVKAILATGELGDLGNVaRASLV 229 *******************************************************************87666***** PP TIGR00126 141 sieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieagaeriga 203 ++ agadf+Ktstg+ ++At+ +m ++++d +vg K++GG+ a+dal +++ e +g lcl|FitnessBrowser__Dino:3609633 230 CMMAGADFIKTSTGKESVNATLPVSLVMIRAIRDyeaatgvKVGYKPAGGISKAKDALVYLSLIKEELGD 299 ***********************999**********************************9988888875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (339 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3.32 // [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