Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_027457733.1 K420_RS0108805 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000519045.1:WP_027457733.1 Length = 432 Score = 408 bits (1049), Expect = e-118 Identities = 213/428 (49%), Positives = 287/428 (67%), Gaps = 1/428 (0%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61 + L D DF + L+ + E+++R V I+ V+ GD+A+++Y+ +FDR+ Sbjct: 3 IQRLSTVDADFLSQLKTLLAFEAAADENIERTVANILADVKTRGDAAVIEYTNQFDRLTA 62 Query: 62 EKT-GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 + + + + E+ AA D PA AL+ A RI +H RQ + YT+A G LG Sbjct: 63 KAMIDLELRQDELHAALDGLPAERRAALEAAAGRIRAYHERQKMEGWSYTEADGTMLGQM 122 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 T ++ VGLYVPGG A+YPSSVLMNA+PAKVAGV ++MVVP P G N LVL AA LAG Sbjct: 123 ITPLDRVGLYVPGGKAAYPSSVLMNAIPAKVAGVKELIMVVPTPGGEKNQLVLAAACLAG 182 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V ++ +GGAQA+ ALAYGT+T+ V KIVGPGNAYVA AKR VFG VGIDM+AGPSE+L Sbjct: 183 VDRVFTMGGAQAVGALAYGTQTVPQVDKIVGPGNAYVATAKRRVFGIVGIDMVAGPSEIL 242 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 +V+D NPDW+A DL +QAEHD AQSIL+ + AF V+ ++E+ L T+ R E Sbjct: 243 VVSDGSGNPDWVAMDLFSQAEHDELAQSILICTNAAFIERVQASIEKLLPTMPRQEVIRT 302 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S + GA ILV+D ++A+ +ANR+A EHLE+A+ + + +V +I +AG+IFIG YT E +G Sbjct: 303 SLTNRGAFILVRDMDEAVAIANRVAPEHLELALDNPDPWVGKIHHAGAIFIGHYTSESLG 362 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY G NHVLPT+ SARFSS L V D+ KRTSL+K+ + LG A +A+ EGL AH Sbjct: 363 DYCAGPNHVLPTSGSARFSSPLGVYDFQKRTSLIKVSKVGAQTLGKIASTLAQGEGLPAH 422 Query: 421 AQSVAIRL 428 A+S RL Sbjct: 423 AKSAEFRL 430 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: 455 Number of extensions: 18 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: 432 Length adjustment: 32 Effective length of query: 398 Effective length of database: 400 Effective search space: 159200 Effective search space used: 159200 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_027457733.1 K420_RS0108805 (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.31265.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-165 534.6 0.1 1e-164 534.4 0.1 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027457733.1 K420_RS0108805 histidinol dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027457733.1 K420_RS0108805 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.4 0.1 1e-164 1e-164 1 393 [] 35 429 .. 35 429 .. 0.98 Alignments for each domain: == domain 1 score: 534.4 bits; conditional E-value: 1e-164 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkle...slrvseeeleealeavdeelkealelaaeniekfhek 66 v++i++dv+++Gd+A++eyt++fd+++++ +l++ ++el++al+ +++e ++ale+aa +i+++he+ lcl|NCBI__GCF_000519045.1:WP_027457733.1 35 VANILADVKTRGDAAVIEYTNQFDRLTAKamiDLELRQDELHAALDGLPAERRAALEAAAGRIRAYHER 103 789**********************9555333799********************************** PP TIGR00069 67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135 q+ e +++++++g++lgq+++pl+rvglYvPgGkaaypS+vlm+a+pAkvAgvke+++v P+ g+ n lcl|NCBI__GCF_000519045.1:WP_027457733.1 104 QKMEGWSYTEADGTMLGQMITPLDRVGLYVPGGKAAYPSSVLMNAIPAKVAGVKELIMVVPTP-GGEKN 171 **************************************************************6.99*** PP TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204 + vlaaa l+gvd+v+++GGaqa++alayGt+tvp+vdkivGPGn+yV++AK+ vfg vgidm+aGPsE lcl|NCBI__GCF_000519045.1:WP_027457733.1 172 QLVLAAACLAGVDRVFTMGGAQAVGALAYGTQTVPQVDKIVGPGNAYVATAKRRVFGIVGIDMVAGPSE 240 ********************************************************************* PP TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 +lv++d s np++va+Dl+sqaEHde aq+il++t+++++e+v++++e+ l +++r+e++++sl+++ga lcl|NCBI__GCF_000519045.1:WP_027457733.1 241 ILVVSDGSGNPDWVAMDLFSQAEHDELAQSILICTNAAFIERVQASIEKLLPTMPRQEVIRTSLTNRGA 309 ********************************************************************* PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342 ilv+d++ea++++n++ApEHLel+ ++p ++ ki++aG++f+G+yt+e+lgdy+aGpnhvLPTsg+A lcl|NCBI__GCF_000519045.1:WP_027457733.1 310 FILVRDMDEAVAIANRVAPEHLELALDNPDPWVGKIHHAGAIFIGHYTSESLGDYCAGPNHVLPTSGSA 378 ********************************************************************* PP TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 rf+s+l+v+dF+kr+s++++sk ++++l++ +++la+ EgL aHa+++e R lcl|NCBI__GCF_000519045.1:WP_027457733.1 379 RFSSPLGVYDFQKRTSLIKVSKVGAQTLGKIASTLAQGEGLPAHAKSAEFR 429 ***********************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (432 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: 10.33 // [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