Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate BPHYT_RS17710 BPHYT_RS17710 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >FitnessBrowser__BFirm:BPHYT_RS17710 Length = 440 Score = 396 bits (1018), Expect = e-115 Identities = 209/432 (48%), Positives = 291/432 (67%), Gaps = 5/432 (1%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61 + L T PDF++ A L+ + E ++R+V +I++ V+ GD+A+L+Y++RFDR++ Sbjct: 5 IRKLDSTAPDFQKSLHAVLAFEASEDEAIERSVAQILNDVKARGDAAVLEYTQRFDRVEA 64 Query: 62 EKT-GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDD----RYTDALGVE 116 + + + +E++AA + AL+ A R+ +H +Q + +YT+A G Sbjct: 65 KSVDALELPMSELEAALENLEPKRRAALEAAAARVRGYHEKQKIECGSHSWQYTEADGTV 124 Query: 117 LGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAA 176 LG + T ++ G+YVPGG A+YPSSVLMNA+PA+VAGV IVMVVP PDG NPLVL AA Sbjct: 125 LGQKVTPLDRAGIYVPGGKAAYPSSVLMNAIPARVAGVREIVMVVPTPDGVKNPLVLAAA 184 Query: 177 RLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGP 236 L GV ++ +GGAQA+ ALAYGT TI V KI GPGNAYVA+AKR VFGTVGIDMIAGP Sbjct: 185 LLGGVDRVFTIGGAQAVGALAYGTATIPAVDKICGPGNAYVASAKRRVFGTVGIDMIAGP 244 Query: 237 SEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTE 296 SE+L++ D +P W+A DL +QAEHD AQSIL+ D+AF V++A++ L T+ R + Sbjct: 245 SEILVLCDGTTDPRWVAMDLFSQAEHDELAQSILLCPDDAFIGRVKDAIDELLPTMPRRD 304 Query: 297 TASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTP 356 S D GA+I V+D E A +AN IA EHLEI+ + + IR+AG+IF+G YT Sbjct: 305 VIRKSLEDRGALIKVRDMEQACAIANDIAPEHLEISALEPHHWGQLIRHAGAIFLGRYTS 364 Query: 357 EVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEG 416 E +GDY G NHVLPT+R+ARFSS L V D+ KR+S++++ +E + LG A E+A EG Sbjct: 365 ESLGDYCAGPNHVLPTSRTARFSSPLGVYDFFKRSSVIEVSAEGAQTLGEIAAELAYGEG 424 Query: 417 LDAHAQSVAIRL 428 L AHA+S R+ Sbjct: 425 LQAHARSAEYRM 436 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: 23 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: 440 Length adjustment: 32 Effective length of query: 398 Effective length of database: 408 Effective search space: 162384 Effective search space used: 162384 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 BPHYT_RS17710 BPHYT_RS17710 (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.9016.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-161 522.6 0.0 4.6e-161 522.3 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS17710 BPHYT_RS17710 histidinol dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS17710 BPHYT_RS17710 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 522.3 0.0 4.6e-161 4.6e-161 1 393 [] 37 435 .. 37 435 .. 0.98 Alignments for each domain: == domain 1 score: 522.3 bits; conditional E-value: 4.6e-161 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 v++i++dv+++Gd+A+leyt++fd+v ++++l+++ +ele+ale+++++ ++ale+aa++++ +hekq lcl|FitnessBrowser__BFirm:BPHYT_RS17710 37 VAQILNDVKARGDAAVLEYTQRFDRVeakSVDALELPMSELEAALENLEPKRRAALEAAAARVRGYHEKQ 106 789***********************666667899*********************************** PP TIGR00069 68 lpes....veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgk 133 + e +++++++g++lgqkv+pl+r+g+YvPgGkaaypS+vlm+a+pA+vAgv+eiv+v P+ dg lcl|FitnessBrowser__BFirm:BPHYT_RS17710 107 KIECgshsWQYTEADGTVLGQKVTPLDRAGIYVPGGKAAYPSSVLMNAIPARVAGVREIVMVVPTP-DGV 175 95433345*********************************************************6.*** PP TIGR00069 134 vnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPs 203 np vlaaa l gvd+v+++GGaqa++alayGt+t+p+vdki+GPGn+yV+ AK+ vfg+vgidmiaGPs lcl|FitnessBrowser__BFirm:BPHYT_RS17710 176 KNPLVLAAALLGGVDRVFTIGGAQAVGALAYGTATIPAVDKICGPGNAYVASAKRRVFGTVGIDMIAGPS 245 ********************************************************************** PP TIGR00069 204 EvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 E+lv++d +++p++va+Dl+sqaEHde aq+il++++++++ +v+++++e l +++r+++++ksle++ga lcl|FitnessBrowser__BFirm:BPHYT_RS17710 246 EILVLCDGTTDPRWVAMDLFSQAEHDELAQSILLCPDDAFIGRVKDAIDELLPTMPRRDVIRKSLEDRGA 315 ********************************************************************** PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343 +i v+d+e+a++++n++ApEHLe+ + +p+++ + i++aG++flG+yt+e+lgdy+aGpnhvLPTs+tAr lcl|FitnessBrowser__BFirm:BPHYT_RS17710 316 LIKVRDMEQACAIANDIAPEHLEISALEPHHWGQLIRHAGAIFLGRYTSESLGDYCAGPNHVLPTSRTAR 385 ********************************************************************** PP TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 f+s+l+v+dF+kr+sv+e+s e++++l+e +++la EgL+aHa+++e R lcl|FitnessBrowser__BFirm:BPHYT_RS17710 386 FSSPLGVYDFFKRSSVIEVSAEGAQTLGEIAAELAYGEGLQAHARSAEYR 435 **********************************************9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (440 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: 00:00:00.01 # Mc/sec: 13.08 // [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