Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_092345237.1 BLU87_RS04780 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_900107645.1:WP_092345237.1 Length = 430 Score = 403 bits (1036), Expect = e-117 Identities = 217/428 (50%), Positives = 289/428 (67%) Query: 1 MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60 M+ L+ +DPDF + EV + ++ V+ I+ VR+ GD AL + S +FDRID Sbjct: 1 MMRILKFSDPDFSAQLQRIEQRADEVPDVIEETVKTIIADVRKRGDVALFELSAKFDRID 60 Query: 61 LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 L I V+ AEID A A ++ L+LA DRI +HA+Q + TD V LG Sbjct: 61 LTVETIEVSAAEIDTALAAVSDESMAGLQLAADRIAAYHAKQKQETWLSTDEDDVLLGQM 120 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 ++ VG+YVPGG A+YPSSVLMNA+PAKVAGV ++MVVP P G +NP VL AA++AG Sbjct: 121 VRPLDRVGIYVPGGKAAYPSSVLMNAVPAKVAGVAEVIMVVPMPGGEVNPHVLAAAKIAG 180 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V I+++GGAQA+AALAYGT ++ V KI GPGN YVA AK++VFG V IDMIAGPSE+L Sbjct: 181 VDRIFKLGGAQAVAALAYGTASVPRVDKITGPGNIYVAIAKKLVFGQVDIDMIAGPSEIL 240 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 ++ D N IAADLL+QAEHD A +IL+T+ E A AV++ VE+QL L+R A Sbjct: 241 VINDGSGNAAHIAADLLSQAEHDELASAILVTSSETMAIAVQDEVEKQLQQLSRETIARQ 300 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S DFGA+IL +D +AI +NRIA EHLE+AV + A + IR+AG+IF+G +TPE G Sbjct: 301 SIDDFGAIILAEDLSEAIEFSNRIAPEHLELAVDNPFAILSAIRHAGAIFMGHHTPEAAG 360 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY+ G NH LPT +ARF S LS+ D++K++S+L L+ L I+IA EGL+AH Sbjct: 361 DYLAGPNHTLPTGGTARFFSPLSLDDFVKKSSILSFTEGGLQRLSQEIIQIAELEGLEAH 420 Query: 421 AQSVAIRL 428 A+SV+IRL Sbjct: 421 AKSVSIRL 428 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: 476 Number of extensions: 26 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_092345237.1 BLU87_RS04780 (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.25878.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-170 553.4 5.0 1.9e-170 553.2 5.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092345237.1 BLU87_RS04780 histidinol dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092345237.1 BLU87_RS04780 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 553.2 5.0 1.9e-170 1.9e-170 1 393 [] 34 427 .. 34 427 .. 0.99 Alignments for each domain: == domain 1 score: 553.2 bits; conditional E-value: 1.9e-170 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 vk+ii+dvrk+Gd Al+e++ kfd++ ++e+++vs++e+++al+av++e + l+laa++i+++h+kq lcl|NCBI__GCF_900107645.1:WP_092345237.1 34 VKTIIADVRKRGDVALFELSAKFDRIdlTVETIEVSAAEIDTALAAVSDESMAGLQLAADRIAAYHAKQ 102 899**********************977899************************************** PP TIGR00069 68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136 ++e++ +++e++vllgq+vrpl+rvg+YvPgGkaaypS+vlm+avpAkvAgv e+++v P+ g+vnp lcl|NCBI__GCF_900107645.1:WP_092345237.1 103 KQETWLSTDEDDVLLGQMVRPLDRVGIYVPGGKAAYPSSVLMNAVPAKVAGVAEVIMVVPMP-GGEVNP 170 *************************************************************6.9***** PP TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205 +vlaaak++gvd+++k+GGaqa+aalayGt++vp+vdki+GPGniyV+ AKklvfg+v+idmiaGPsE+ lcl|NCBI__GCF_900107645.1:WP_092345237.1 171 HVLAAAKIAGVDRIFKLGGAQAVAALAYGTASVPRVDKITGPGNIYVAIAKKLVFGQVDIDMIAGPSEI 239 ********************************************************************* PP TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274 lvi d s n++++aaDllsqaEHde a+ailvt+se++a +v++eve+ql++l+r++ia++s+++ gai lcl|NCBI__GCF_900107645.1:WP_092345237.1 240 LVINDGSGNAAHIAADLLSQAEHDELASAILVTSSETMAIAVQDEVEKQLQQLSRETIARQSIDDFGAI 308 ********************************************************************* PP TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343 il++dl+ea+e+sn++ApEHLel++++p ++l+ i++aG++f+G++tpea+gdy+aGpnh+LPT+gtAr lcl|NCBI__GCF_900107645.1:WP_092345237.1 309 ILAEDLSEAIEFSNRIAPEHLELAVDNPFAILSAIRHAGAIFMGHHTPEAAGDYLAGPNHTLPTGGTAR 377 ********************************************************************* PP TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 f s+ls++dF+k++s+ ++++ +l++l+++++++ae+EgLeaHa++v++R lcl|NCBI__GCF_900107645.1:WP_092345237.1 378 FFSPLSLDDFVKKSSILSFTEGGLQRLSQEIIQIAELEGLEAHAKSVSIR 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: 11.68 // [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