Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate BPHYT_RS25815 BPHYT_RS25815 deoxyribose-phosphate aldolase
Query= BRENDA::Q9Y315 (318 letters) >FitnessBrowser__BFirm:BPHYT_RS25815 Length = 336 Score = 364 bits (935), Expect = e-105 Identities = 186/314 (59%), Positives = 238/314 (75%), Gaps = 2/314 (0%) Query: 5 NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64 N G D SW+ ++VN AV RR + RR+VKK+ QAAWLLKAVT IDLTTL+GDDT Sbjct: 25 NPGMPFDASWLDGLRVNQSAVERRTATLGTRRSVKKDAQAAWLLKAVTCIDLTTLNGDDT 84 Query: 65 SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124 ++RLC KA+ P+R DLL+AL + +GITT AVCVY V AV AL +G IPVA+ Sbjct: 85 EGRVRRLCAKARQPVRADLLEALGLAPQGITTGAVCVYHRFVAAAVDALHGSG--IPVAA 142 Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184 V+ GFPAG +L+EI +V DGA EID+V+ R VLTG W+ALYDE+R FR ACG Sbjct: 143 VSTGFPAGLIPHPLKLKEIEASVADGAQEIDIVVTREYVLTGNWQALYDEVRDFRAACGP 202 Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244 AHLKTILATG++ TL+NV +ASM+ MMAG+DFIKTSTGKE VNAT V++VM+R IR++ Sbjct: 203 AHLKTILATGDIRTLSNVARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREYQ 262 Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304 +TG IGFKPAGG+ +AK L++ L+KEELG WL+PELFRIGAS+LL+DIERQ+ H+ Sbjct: 263 ERTGVLIGFKPAGGVSTAKSVLSYQILMKEELGRAWLEPELFRIGASSLLADIERQLEHY 322 Query: 305 VTGRYAAYHDLPMS 318 V+GRY+A++ P++ Sbjct: 323 VSGRYSAFNRHPVA 336 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: 323 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: 336 Length adjustment: 28 Effective length of query: 290 Effective length of database: 308 Effective search space: 89320 Effective search space used: 89320 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 BPHYT_RS25815 BPHYT_RS25815 (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.29143.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-44 138.4 0.1 4.7e-44 136.4 0.1 1.8 1 lcl|FitnessBrowser__BFirm:BPHYT_RS25815 BPHYT_RS25815 deoxyribose-phosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS25815 BPHYT_RS25815 deoxyribose-phosphate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 136.4 0.1 4.7e-44 4.7e-44 3 202 .. 71 295 .. 69 300 .. 0.92 Alignments for each domain: == domain 1 score: 136.4 bits; conditional E-value: 4.7e-44 TIGR00126 3 akliDhtalkadtteedietlcaeAkky................kfaavcvnpsyvslAkelLkgtevei 56 + iD+t+l+ d+te + +lca+A ++ + avcv+ ++v A++ L+g+ + + lcl|FitnessBrowser__BFirm:BPHYT_RS25815 71 VTCIDLTTLNGDDTEGRVRRLCAKARQPvradllealglapqgiTTGAVCVYHRFVAAAVDALHGSGIPV 140 578**********************9988888888887777766788*********************** PP TIGR00126 57 ctv.vgFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilE 125 ++v +gFP+G + kl E +++++ GA+E+D+v+ + +n+++ +++++ ac+ ++lK il lcl|FitnessBrowser__BFirm:BPHYT_RS25815 141 AAVsTGFPAGLIPHPLKLKEIEASVADGAQEIDIVVTREYVLTGNWQALYDEVRDFRAACGPAHLKTILA 210 **978***************************************************************** PP TIGR00126 126 talLtd.eekkkAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrta 187 t+ ++ +++ +As +++ agadf+Ktstg+ ++At++ +m +++++ +g+K++GGv ta lcl|FitnessBrowser__BFirm:BPHYT_RS25815 211 TGDIRTlSNVARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREyqertgvLIGFKPAGGVSTA 280 **997625666***************************99999999999999999999************ PP TIGR00126 188 edalalieagaerig 202 + +l++ e +g lcl|FitnessBrowser__BFirm:BPHYT_RS25815 281 KSVLSYQILMKEELG 295 **9988666555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (336 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: 2.12 // [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