Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Dsui_1411 Dsui_1411 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >FitnessBrowser__PS:Dsui_1411 Length = 435 Score = 420 bits (1080), Expect = e-122 Identities = 217/429 (50%), Positives = 294/429 (68%), Gaps = 1/429 (0%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61 + L D DF+Q+ L+ + E++++ V I+ V+ GD+A+++Y+ RFDR+ + Sbjct: 6 IKRLNSADADFQQRLDELLAFEGAQDENIEKTVVGILADVKARGDAAVVEYTNRFDRLSV 65 Query: 62 E-KTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 + + +AE+ AA D PA AL+ A RI +H RQL YT+A G LG Sbjct: 66 AGMAALELPKAELQAALDGLPAERRAALEAAAQRIRTYHERQLGAGFTYTEADGTMLGQM 125 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 T ++ VGLYVPGG A+YPSSVLMNA+PAKVAGV ++MVVP P G N LVL AA LAG Sbjct: 126 VTPLDRVGLYVPGGKAAYPSSVLMNALPAKVAGVKELIMVVPTPGGEHNALVLAAACLAG 185 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V ++ +GGAQA+AALAYGTET+ V KIVGPGNAYVA AKR VFG VGIDM+AGPSE+L Sbjct: 186 VDRVFTIGGAQAVAALAYGTETVPQVDKIVGPGNAYVACAKRRVFGIVGIDMVAGPSEIL 245 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 ++AD +PDW+A DL +QAEHD AQSIL+ D A+ V+ ++++ L T+ R + Sbjct: 246 VLADGSTDPDWVAMDLFSQAEHDELAQSILICPDAAYIEKVQASIDKLLPTMPRRDVIRT 305 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S + GA+ILV+D E+A+ +ANR+A EHLE+++A+ +A+V +I +AG+IFIG YT E +G Sbjct: 306 SLENRGALILVRDLEEAVAMANRVAPEHLELSLAEPDAWVEKIHHAGAIFIGPYTSESLG 365 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY G NHVLPT+ SARFSS L V D+ KRTSL+++ + LG A +A EGL AH Sbjct: 366 DYCAGPNHVLPTSGSARFSSPLGVYDFQKRTSLIRVSRAGAQTLGRIAATLADGEGLPAH 425 Query: 421 AQSVAIRLN 429 AQS RL+ Sbjct: 426 AQSARYRLD 434 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: 499 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: 435 Length adjustment: 32 Effective length of query: 398 Effective length of database: 403 Effective search space: 160394 Effective search space used: 160394 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 Dsui_1411 Dsui_1411 (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.20227.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-164 532.4 0.1 4.6e-164 532.2 0.1 1.0 1 lcl|FitnessBrowser__PS:Dsui_1411 Dsui_1411 histidinol dehydrogena Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1411 Dsui_1411 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.2 0.1 4.6e-164 4.6e-164 2 393 .] 39 432 .. 38 432 .. 0.99 Alignments for each domain: == domain 1 score: 532.2 bits; conditional E-value: 4.6e-164 TIGR00069 2 keiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesveve 75 i++dv+++Gd+A++eyt++fd++ +++l+++++el++al+ +++e ++ale+aa++i+++he+ql + ++++ lcl|FitnessBrowser__PS:Dsui_1411 39 VGILADVKARGDAAVVEYTNRFDRLsvaGMAALELPKAELQAALDGLPAERRAALEAAAQRIRTYHERQLGAGFTYT 115 579*********************955566799******************************************** PP TIGR00069 76 teegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevyk 152 +++g++lgq+v+pl+rvglYvPgGkaaypS+vlm+a+pAkvAgvke+++v P+ g+ n+ vlaaa l+gvd+v++ lcl|FitnessBrowser__PS:Dsui_1411 116 EADGTMLGQMVTPLDRVGLYVPGGKAAYPSSVLMNALPAKVAGVKELIMVVPTP-GGEHNALVLAAACLAGVDRVFT 191 *****************************************************6.9********************* PP TIGR00069 153 vGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHd 229 +GGaqa+aalayGtetvp+vdkivGPGn+yV+ AK+ vfg vgidm+aGPsE+lv+ad s++p++va+Dl+sqaEHd lcl|FitnessBrowser__PS:Dsui_1411 192 IGGAQAVAALAYGTETVPQVDKIVGPGNAYVACAKRRVFGIVGIDMVAGPSEILVLADGSTDPDWVAMDLFSQAEHD 268 ***************************************************************************** PP TIGR00069 230 edaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeell 306 e aq+il++++++ +ekv++++++ l +++r++++++sle++ga+ilv+dleea++++n++ApEHLel ++p +++ lcl|FitnessBrowser__PS:Dsui_1411 269 ELAQSILICPDAAYIEKVQASIDKLLPTMPRRDVIRTSLENRGALILVRDLEEAVAMANRVAPEHLELSLAEPDAWV 345 ***************************************************************************** PP TIGR00069 307 kkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgL 383 +ki++aG++f+G+yt+e+lgdy+aGpnhvLPTsg+Arf+s+l+v+dF+kr+s++++s++++++l++ +++la+ EgL lcl|FitnessBrowser__PS:Dsui_1411 346 EKIHHAGAIFIGPYTSESLGDYCAGPNHVLPTSGSARFSSPLGVYDFQKRTSLIRVSRAGAQTLGRIAATLADGEGL 422 ***************************************************************************** PP TIGR00069 384 eaHaeavevR 393 aHa++++ R lcl|FitnessBrowser__PS:Dsui_1411 423 PAHAQSARYR 432 ******9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (435 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: 9.30 // [ok]
This GapMind analysis is from Apr 09 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