Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_011736875.1 PPRO_RS15095 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000015045.1:WP_011736875.1 Length = 430 Score = 414 bits (1065), Expect = e-120 Identities = 218/422 (51%), Positives = 289/422 (68%), Gaps = 1/422 (0%) Query: 9 DPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTG-IA 67 D DF ++FA LS E+ V+ +V EI+ VR GD ALLD +RRFDR++ + Sbjct: 8 DTDFGERFAVILSRGEEIDRAVEGSVAEIIADVRSRGDQALLDLTRRFDRLETSSVAELE 67 Query: 68 VTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAV 127 V E EIDAA A A + +L+ A +R+ + H +Q + T+ + LG + T +E V Sbjct: 68 VGETEIDAALAAVAADDLASLRHAVERVTRFHEKQRQQTWLSTEEPDIMLGQKVTPLERV 127 Query: 128 GLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRV 187 G+YVPGG ASYPSSV+MNA+PA+VAGV I+MV P P G +NP VL AARL+GV I+R+ Sbjct: 128 GIYVPGGKASYPSSVIMNAVPARVAGVREILMVTPTPGGEVNPHVLAAARLSGVDRIFRI 187 Query: 188 GGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDN 247 GGAQA+AALAYGT TI V KI GPGN YVA AK++VFG VGIDMIAGPSE+L++ D Sbjct: 188 GGAQAVAALAYGTATIPRVDKITGPGNIYVATAKKLVFGQVGIDMIAGPSEILVINDGSG 247 Query: 248 NPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGA 307 + +A+DLL+QAEHD A SIL+T D +F V VERQL L+R A ASW +GA Sbjct: 248 DTAHVASDLLSQAEHDELASSILITTDRSFGERVAGEVERQLGLLSRESIARASWESYGA 307 Query: 308 VILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCN 367 +I+ ++A+ +NRIA EHLE+AVAD + +P I NAG+IF+G +TPE GDY+ G N Sbjct: 308 IIVAGSLDEAVAFSNRIAPEHLELAVADPFSLLPAITNAGAIFMGHWTPEAAGDYLAGPN 367 Query: 368 HVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427 H LPT +ARF S LSV D++K++S++ L L+ LG + IA EGL+AHA+SV+IR Sbjct: 368 HTLPTGGTARFFSPLSVDDFVKKSSIVCLSEGGLKRLGRDIVRIAGLEGLEAHARSVSIR 427 Query: 428 LN 429 L+ Sbjct: 428 LD 429 Lambda K H 0.318 0.134 0.375 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: 496 Number of extensions: 20 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: 430 Length of database: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_011736875.1 PPRO_RS15095 (histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))
# 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.aa/TIGR00069.hmm # target sequence database: /tmp/gapView.13319.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00069 [M=393] Accession: TIGR00069 Description: hisD: histidinol dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-169 549.9 0.0 2.2e-169 549.7 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736875.1 PPRO_RS15095 histidinol dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736875.1 PPRO_RS15095 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 549.7 0.0 2.2e-169 2.2e-169 1 393 [] 33 427 .. 33 427 .. 0.99 Alignments for each domain: == domain 1 score: 549.7 bits; conditional E-value: 2.2e-169 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 v+eii+dvr++Gd+All++t++fd++ ++++l+v e e+++al+av ++ ++l++a+e++++fhek lcl|NCBI__GCF_000015045.1:WP_011736875.1 33 VAEIIADVRSRGDQALLDLTRRFDRLetsSVAELEVGETEIDAALAAVAADDLASLRHAVERVTRFHEK 101 789**********************966677899*********************************** PP TIGR00069 67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135 q+++++ +++e++++lgqkv+plervg+YvPgGka+ypS+v+m+avpA+vAgv+ei++vtP+ g+vn lcl|NCBI__GCF_000015045.1:WP_011736875.1 102 QRQQTWLSTEEPDIMLGQKVTPLERVGIYVPGGKASYPSSVIMNAVPARVAGVREILMVTPTP-GGEVN 169 **************************************************************6.9**** PP TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204 p+vlaaa+l gvd+++++GGaqa+aalayGt+t+p+vdki+GPGniyV++AKklvfg+vgidmiaGPsE lcl|NCBI__GCF_000015045.1:WP_011736875.1 170 PHVLAAARLSGVDRIFRIGGAQAVAALAYGTATIPRVDKITGPGNIYVATAKKLVFGQVGIDMIAGPSE 238 ********************************************************************* PP TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 +lvi d s + ++va+DllsqaEHde a++il+tt++++ e+v eve+ql l+r++ia++s+e++ga lcl|NCBI__GCF_000015045.1:WP_011736875.1 239 ILVINDGSGDTAHVASDLLSQAEHDELASSILITTDRSFGERVAGEVERQLGLLSRESIARASWESYGA 307 ********************************************************************* PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342 ii++ +l+ea+++sn++ApEHLel+++dp +ll+ i+naG++f+G++tpea+gdy+aGpnh+LPT+gtA lcl|NCBI__GCF_000015045.1:WP_011736875.1 308 IIVAGSLDEAVAFSNRIAPEHLELAVADPFSLLPAITNAGAIFMGHWTPEAAGDYLAGPNHTLPTGGTA 376 ********************************************************************* PP TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 rf s+lsv+dF+k++s++ ls+ +l++l+++++++a +EgLeaHa++v++R lcl|NCBI__GCF_000015045.1:WP_011736875.1 377 RFFSPLSVDDFVKKSSIVCLSEGGLKRLGRDIVRIAGLEGLEAHARSVSIR 427 *************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (430 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.96 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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