Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013451397.1 CALNI_RS06400 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000183405.1:WP_013451397.1 Length = 419 Score = 362 bits (928), Expect = e-104 Identities = 194/423 (45%), Positives = 278/423 (65%), Gaps = 18/423 (4%) Query: 5 LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64 L+++D D+E+K+ + V I+D V++ GDSAL YS++FD E Sbjct: 14 LKRSD-DYEEKYLS--------------TVLSIIDDVKKNGDSALKIYSKKFDNNPDEN- 57 Query: 65 GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAI 124 + VT+ E+ +A+D L+LA+ IE++H QL K + + G LG + T + Sbjct: 58 -LEVTKKEMISAYDNIDEQLKLDLQLAKKNIEEYHKNQLEKS-WFIEKEGTILGQKITPL 115 Query: 125 EAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEI 184 + VG+YVPGG ASYPS+VLMN +PAKVAGV +++V PA DG ++ +VL A +AGV +I Sbjct: 116 DKVGVYVPGGKASYPSTVLMNVIPAKVAGVKEVIVVTPAKDGKISEIVLAACYIAGVDKI 175 Query: 185 YRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVAD 244 +++GGAQAIAAL+YGTETI V KIVGPGN YVA AK++VFG V IDMIAGPSE+LI+AD Sbjct: 176 FKIGGAQAIAALSYGTETIPKVDKIVGPGNIYVALAKKLVFGRVDIDMIAGPSEILIIAD 235 Query: 245 KDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRD 304 NP+++AAD+L+QAEHD A SI +T+ A +E+ + L +L + + A S + Sbjct: 236 DSANPEYVAADMLSQAEHDELASSITITDSPNLAKEIEKYLNIHLKSLPKKDIAEKSLKQ 295 Query: 305 FGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVG 364 +G VI+VK+ +A+ L+N IA EHLE+AV + +P+I++AG+IF+G YTPE +GDY Sbjct: 296 YGGVIVVKNINEAVELSNSIAPEHLELAVKNPFELLPKIKHAGAIFLGHYTPEAMGDYFA 355 Query: 365 GCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSV 424 G NH LPT +ARFSS L D+ KR+S++ + +A++E LDAHA SV Sbjct: 356 GPNHTLPTGGTARFSSPLGTYDFFKRSSIISYTRDSFLKQRENVYRLAKSEDLDAHALSV 415 Query: 425 AIR 427 +R Sbjct: 416 KVR 418 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: 450 Number of extensions: 15 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: 419 Length adjustment: 32 Effective length of query: 398 Effective length of database: 387 Effective search space: 154026 Effective search space used: 154026 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_013451397.1 CALNI_RS06400 (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.17720.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-176 571.0 0.2 8.8e-176 570.8 0.2 1.0 1 lcl|NCBI__GCF_000183405.1:WP_013451397.1 CALNI_RS06400 histidinol dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183405.1:WP_013451397.1 CALNI_RS06400 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 570.8 0.2 8.8e-176 8.8e-176 1 393 [] 28 418 .. 28 418 .. 0.99 Alignments for each domain: == domain 1 score: 570.8 bits; conditional E-value: 8.8e-176 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlp 69 v +ii+dv+k+Gd+Al+ y++kfd+ e+l+v+++e+ +a++++de+lk +l+la++nie++h++ql+ lcl|NCBI__GCF_000183405.1:WP_013451397.1 28 VLSIIDDVKKNGDSALKIYSKKFDNNPDENLEVTKKEMISAYDNIDEQLKLDLQLAKKNIEEYHKNQLE 96 668****************************************************************** PP TIGR00069 70 esveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpav 138 +s+++e +eg++lgqk++pl++vg+YvPgGka+ypStvlm+++pAkvAgvke++vvtP k dgk+++ v lcl|NCBI__GCF_000183405.1:WP_013451397.1 97 KSWFIE-KEGTILGQKITPLDKVGVYVPGGKASYPSTVLMNVIPAKVAGVKEVIVVTPAK-DGKISEIV 163 ***887.789*************************************************6.******** PP TIGR00069 139 laaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlv 207 laa+ ++gvd+++k+GGaqaiaal+yGtet+pkvdkivGPGniyV+ AKklvfg+v+idmiaGPsE+l+ lcl|NCBI__GCF_000183405.1:WP_013451397.1 164 LAACYIAGVDKIFKIGGAQAIAALSYGTETIPKVDKIVGPGNIYVALAKKLVFGRVDIDMIAGPSEILI 232 ********************************************************************* PP TIGR00069 208 iadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiil 276 iad+sanpe+vaaD+lsqaEHde a++i +t+s +la+++e+ ++ +l++l++k+iaeksl+++g +i+ lcl|NCBI__GCF_000183405.1:WP_013451397.1 233 IADDSANPEYVAADMLSQAEHDELASSITITDSPNLAKEIEKYLNIHLKSLPKKDIAEKSLKQYGGVIV 301 ********************************************************************* PP TIGR00069 277 vddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfa 345 v++++ea+elsn++ApEHLel++k+p ell+kik+aG++flG+ytpea+gdy+aGpnh+LPT+gtArf+ lcl|NCBI__GCF_000183405.1:WP_013451397.1 302 VKNINEAVELSNSIAPEHLELAVKNPFELLPKIKHAGAIFLGHYTPEAMGDYFAGPNHTLPTGGTARFS 370 ********************************************************************* PP TIGR00069 346 sglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 s+l+++dF+kr+s+++++++++ + +e+v +la+ E+L+aHa +v+vR lcl|NCBI__GCF_000183405.1:WP_013451397.1 371 SPLGTYDFFKRSSIISYTRDSFLKQRENVYRLAKSEDLDAHALSVKVR 418 **********************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (419 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: 10.13 // [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