Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_097030588.1 CRO07_RS10010 deoxyribose-phosphate aldolase
Query= BRENDA::Q9Y315 (318 letters) >NCBI__GCF_900207575.1:WP_097030588.1 Length = 307 Score = 357 bits (917), Expect = e-103 Identities = 183/308 (59%), Positives = 235/308 (76%), Gaps = 4/308 (1%) Query: 10 LDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDTSSNIQ 69 LDL W+++ Q N PA+ RRA + A R VKK+ QAAWL KA++ IDLT LSGDDT ++ Sbjct: 3 LDLEWVAQAQANAPAIARRAASLPATRGVKKDHQAAWLCKAISLIDLTALSGDDTPGRVR 62 Query: 70 RLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVASVAAGF 129 RLC KA+ P+R DLL AL M +G+TT AVCVY V AV+AL +G IPVA+V+ GF Sbjct: 63 RLCAKARQPVRPDLLAALGM--EGLTTGAVCVYHEMVETAVRALDGSG--IPVAAVSTGF 118 Query: 130 PAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGEAHLKT 189 PAG + + RL EI +V GA+EID+VI+R VLTG W+ALYDE+ Q R+A G AH+K Sbjct: 119 PAGLSPYRLRLAEIGESVAAGASEIDIVISRRHVLTGDWQALYDEMCQMRQAAGSAHVKA 178 Query: 190 ILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFFWKTGN 249 ILATGELG+L NV +AS++ MMAG+DFIKTSTGKE VNAT PV++ M+RAIRD+ +TG Sbjct: 179 ILATGELGSLRNVARASLVCMMAGADFIKTSTGKEPVNATLPVSLTMIRAIRDYQDRTGF 238 Query: 250 KIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHHVTGRY 309 +IGFKPAGGI AK++L +L+++KEELG WL+P+LFR GAS+LL DIERQ+ HHVTG Y Sbjct: 239 RIGFKPAGGISKAKEALVYLAMMKEELGHPWLQPDLFRFGASSLLGDIERQLDHHVTGCY 298 Query: 310 AAYHDLPM 317 +A + P+ Sbjct: 299 SAANRHPL 306 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: 326 Number of extensions: 12 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: 307 Length adjustment: 27 Effective length of query: 291 Effective length of database: 280 Effective search space: 81480 Effective search space used: 81480 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 WP_097030588.1 CRO07_RS10010 (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.3430743.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-45 140.3 0.0 5.7e-45 139.4 0.0 1.4 1 NCBI__GCF_900207575.1:WP_097030588.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900207575.1:WP_097030588.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 139.4 0.0 5.7e-45 5.7e-45 3 203 .. 44 267 .. 42 271 .. 0.94 Alignments for each domain: == domain 1 score: 139.4 bits; conditional E-value: 5.7e-45 TIGR00126 3 akliDhtalkadtteedietlcaeAkky..............kfaavcvnpsyvslAkelLkgteveictv.v 60 +liD+tal+ d+t+ + +lca+A ++ + avcv+ ++v+ A++ L g+ + +++v + NCBI__GCF_900207575.1:WP_097030588.1 44 ISLIDLTALSGDDTPGRVRRLCAKARQPvrpdllaalgmeglTTGAVCVYHEMVETAVRALDGSGIPVAAVsT 116 689**********************99888888888877777788*************************978 PP TIGR00126 61 gFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdee 133 gFP+G s + +l+E e++++GA E+D+vi + + +++++ ++++ + +a++ +++K+il t++L NCBI__GCF_900207575.1:WP_097030588.1 117 GFPAGLSPYRLRLAEIGESVAAGASEIDIVISRRHVLTGDWQALYDEMCQMRQAAGSAHVKAILATGELGSLR 189 *********************************************************************9876 PP TIGR00126 134 kk.kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieaga 198 + +As +++ agadf+Ktstg+ ++At+ m ++++d ++g+K++GG+ a++al ++++ NCBI__GCF_900207575.1:WP_097030588.1 190 NVaRASLVCMMAGADFIKTSTGKEPVNATLPVSLTMIRAIRDyqdrtgfRIGFKPAGGISKAKEALVYLAMMK 262 665***************************988889999999999************************9999 PP TIGR00126 199 eriga 203 e +g NCBI__GCF_900207575.1:WP_097030588.1 263 EELGH 267 98886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (211 nodes) Target sequences: 1 (307 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: 00:00:00.00 # Mc/sec: 11.10 // [ok]
This GapMind analysis is from Sep 24 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