Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_093427940.1 BM272_RS06415 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_900112605.1:WP_093427940.1 Length = 437 Score = 399 bits (1026), Expect = e-116 Identities = 212/423 (50%), Positives = 286/423 (67%), Gaps = 2/423 (0%) Query: 8 TDPD-FEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGI 66 TD D F+ L+ + + V+ VR+I+ VR GD+A+++ + R DR D Sbjct: 9 TDEDGFDAALDRLLAWEEGTDDRVEGIVRDILTDVRTRGDTAVVEQTNRLDRRDAATMAD 68 Query: 67 AVTEAE-IDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIE 125 AE + A +A P++ +AL+ A +RI +H Q + +YT+A G LG + T ++ Sbjct: 69 LELPAERLQRALEALPSAQRQALETAAERIRGYHRHQCQESWQYTEADGTVLGQQVTPMD 128 Query: 126 AVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIY 185 GLYVPGG A+YPSSVLMNA+PAKVAGV +VMVVPAPDG LN LVL AA +AGV ++ Sbjct: 129 RAGLYVPGGKAAYPSSVLMNALPAKVAGVGELVMVVPAPDGELNDLVLAAAAVAGVDRVF 188 Query: 186 RVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADK 245 +GGAQA+AALAYGTET+ V KIVGPGN +VA AKR+VFGTVGIDMIAGPSE+L+V D Sbjct: 189 TLGGAQAVAALAYGTETVPAVDKIVGPGNIFVATAKRMVFGTVGIDMIAGPSEILVVCDG 248 Query: 246 DNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDF 305 + +P+W+A DL +QAEHD AQ+IL+ D A+ V EA++R L T+ R +S Sbjct: 249 ETDPEWVAVDLFSQAEHDEDAQAILVCPDAAYLDRVAEAMDRLLPTMGRETIIRSSLAAR 308 Query: 306 GAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGG 365 GA+I +D +DA + NR+A EHLE++VA+ EA ++R+AG+IF+G YT E +GDY G Sbjct: 309 GALIQCRDLDDAAAVINRVAPEHLELSVAEPEALAAKVRHAGAIFLGRYTSESLGDYCAG 368 Query: 366 CNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVA 425 NHVLPT+R+ARFSS L V D+ KR+SL+ + ALGP A +A EGL AHA++ Sbjct: 369 PNHVLPTSRTARFSSPLGVYDFQKRSSLIGCSAAGAAALGPTAAALADGEGLGAHAEAAR 428 Query: 426 IRL 428 RL Sbjct: 429 RRL 431 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: 542 Number of extensions: 25 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 430 Length of database: 437 Length adjustment: 32 Effective length of query: 398 Effective length of database: 405 Effective search space: 161190 Effective search space used: 161190 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_093427940.1 BM272_RS06415 (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.26833.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-161 523.3 0.2 2.7e-161 523.1 0.2 1.0 1 NCBI__GCF_900112605.1:WP_093427940.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900112605.1:WP_093427940.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 523.1 0.2 2.7e-161 2.7e-161 1 393 [] 36 430 .. 36 430 .. 0.99 Alignments for each domain: == domain 1 score: 523.1 bits; conditional E-value: 2.7e-161 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 v++i++dvr++Gd+A++e t+++d+ ++++l++++e+l++alea++++ ++ale+aae+i+ +h++q +e NCBI__GCF_900112605.1:WP_093427940.1 36 VRDILTDVRTRGDTAVVEQTNRLDRRdaaTMADLELPAERLQRALEALPSAQRQALETAAERIRGYHRHQCQE 108 899*********************976668889**************************************** PP TIGR00069 71 sveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaak 143 s+++++++g++lgq+v+p++r+glYvPgGkaaypS+vlm+a+pAkvAgv e+v+v P dg++n+ vlaaa+ NCBI__GCF_900112605.1:WP_093427940.1 109 SWQYTEADGTVLGQQVTPMDRAGLYVPGGKAAYPSSVLMNALPAKVAGVGELVMVVPAP-DGELNDLVLAAAA 180 **********************************************************6.************* PP TIGR00069 144 llgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpe 216 ++gvd+v+++GGaqa+aalayGtetvp+vdkivGPGni+V++AK++vfg+vgidmiaGPsE+lv++d +++pe NCBI__GCF_900112605.1:WP_093427940.1 181 VAGVDRVFTLGGAQAVAALAYGTETVPAVDKIVGPGNIFVATAKRMVFGTVGIDMIAGPSEILVVCDGETDPE 253 ************************************************************************* PP TIGR00069 217 lvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsne 289 +va+Dl+sqaEHdedaqailv+++++ +++v e++++ l ++ r++i+++sl+ +ga+i ++dl++a++++n+ NCBI__GCF_900112605.1:WP_093427940.1 254 WVAVDLFSQAEHDEDAQAILVCPDAAYLDRVAEAMDRLLPTMGRETIIRSSLAARGALIQCRDLDDAAAVINR 326 ************************************************************************* PP TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362 +ApEHLel +++pe+l+ k+++aG++flG+yt+e+lgdy+aGpnhvLPTs+tArf+s+l+v+dF+kr+s++ + NCBI__GCF_900112605.1:WP_093427940.1 327 VAPEHLELSVAEPEALAAKVRHAGAIFLGRYTSESLGDYCAGPNHVLPTSRTARFSSPLGVYDFQKRSSLIGC 399 ************************************************************************* PP TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393 s +++++l++++++la+ EgL aHaea++ R NCBI__GCF_900112605.1:WP_093427940.1 400 SAAGAAALGPTAAALADGEGLGAHAEAARRR 430 ***************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (437 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 25.29 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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