Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013538076.1 THEAM_RS06690 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000185805.1:WP_013538076.1 Length = 443 Score = 382 bits (980), Expect = e-110 Identities = 194/396 (48%), Positives = 278/396 (70%), Gaps = 2/396 (0%) Query: 33 AVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPASTVEALKLAR 92 AV EI++ VR+ D+A+ Y+++FDR++L + V+E EI+ AF+ P V+A++ A Sbjct: 34 AVLEIIENVRQFRDTAVFGYAKKFDRVELTPENVKVSEREIEEAFNRVPKEVVKAIEFAV 93 Query: 93 DRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAKVA 152 +R+ + H Q ++ + G+ LG + T +++ G+YVPGG ASYPSSV+MNA+PAKVA Sbjct: 94 ERVRRFHEHQ-KENSYFVTEPGIVLGQKVTPLDSAGIYVPGGKASYPSSVVMNAVPAKVA 152 Query: 153 GVDRIVMVVPAPDG-NLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVG 211 GV+++VM+ PA +NP LVAA+L+GV+EIYRVGGA +AA+A+GTE+I V KIVG Sbjct: 153 GVEKVVMITPAIGSLEVNPYTLVAAKLSGVNEIYRVGGAHGVAAVAFGTESIPKVDKIVG 212 Query: 212 PGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILM 271 PGN YVA AK+ +FGTV IDM+AGPSE+L++AD+ NPDW+A DLL+QAEHD A + L+ Sbjct: 213 PGNIYVALAKKFLFGTVDIDMVAGPSEILVIADESANPDWVATDLLSQAEHDELAGAFLV 272 Query: 272 TNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHLEI 331 T+ + A V +AVE +L L+R E A + +FG V L +D + +AN IA EHLE+ Sbjct: 273 THSDRVAQEVVKAVEEKLKKLSRKEIARKAIENFGTVFLTEDVNHSCDVANEIAPEHLEV 332 Query: 332 AVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRT 391 A + + RI++AG+IF+G YT E +GDYV G NHVLPT SARF S L V D++KR+ Sbjct: 333 ATKEPFGLLDRIKHAGAIFLGHYTCESLGDYVLGPNHVLPTGGSARFFSPLGVYDFIKRS 392 Query: 392 SLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427 S++ + E + +G AA E+A EGL+AH +V +R Sbjct: 393 SVIYVTPEGFKQVGWAARELAECEGLEAHRLAVEVR 428 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: 493 Number of extensions: 24 Number of successful extensions: 3 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: 443 Length adjustment: 32 Effective length of query: 398 Effective length of database: 411 Effective search space: 163578 Effective search space used: 163578 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_013538076.1 THEAM_RS06690 (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.14157.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-168 545.1 0.4 6.7e-168 544.9 0.4 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013538076.1 THEAM_RS06690 histidinol dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185805.1:WP_013538076.1 THEAM_RS06690 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 544.9 0.4 6.7e-168 6.7e-168 1 393 [] 35 428 .. 35 428 .. 0.99 Alignments for each domain: == domain 1 score: 544.9 bits; conditional E-value: 6.7e-168 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 v eiie+vr+ d+A++ y++kfd+v ++e+++vse e+eea ++v++e+++a+e a+e++++fhe+q lcl|NCBI__GCF_000185805.1:WP_013538076.1 35 VLEIIENVRQFRDTAVFGYAKKFDRVelTPENVKVSEREIEEAFNRVPKEVVKAIEFAVERVRRFHEHQ 103 679**********************977889************************************** PP TIGR00069 68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136 +++s+ te+g++lgqkv+pl+++g+YvPgGka+ypS+v+m+avpAkvAgv+++v++tP + +vnp lcl|NCBI__GCF_000185805.1:WP_013538076.1 104 KENSY-FVTEPGIVLGQKVTPLDSAGIYVPGGKASYPSSVVMNAVPAKVAGVEKVVMITPAIGSLEVNP 171 99985.5679***************************************************9899**** PP TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205 +l+aakl gv+e+y+vGGa+++aa+a+Gte++pkvdkivGPGniyV+ AKk +fg+v+idm+aGPsE+ lcl|NCBI__GCF_000185805.1:WP_013538076.1 172 YTLVAAKLSGVNEIYRVGGAHGVAAVAFGTESIPKVDKIVGPGNIYVALAKKFLFGTVDIDMVAGPSEI 240 ********************************************************************* PP TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274 lviadesanp++va+DllsqaEHde a a+lvt+s+++a++v ++vee+l++l+rkeia+k++e+ g++ lcl|NCBI__GCF_000185805.1:WP_013538076.1 241 LVIADESANPDWVATDLLSQAEHDELAGAFLVTHSDRVAQEVVKAVEEKLKKLSRKEIARKAIENFGTV 309 ********************************************************************* PP TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343 +l++d+++ ++++ne+ApEHLe++tk+p ll++ik+aG++flG+yt+e+lgdyv GpnhvLPT+g+Ar lcl|NCBI__GCF_000185805.1:WP_013538076.1 310 FLTEDVNHSCDVANEIAPEHLEVATKEPFGLLDRIKHAGAIFLGHYTCESLGDYVLGPNHVLPTGGSAR 378 ********************************************************************* PP TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 f s+l+v+dF+kr+sv++++ e++++++ a+++lae EgLeaH+ avevR lcl|NCBI__GCF_000185805.1:WP_013538076.1 379 FFSPLGVYDFIKRSSVIYVTPEGFKQVGWAARELAECEGLEAHRLAVEVR 428 ************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (443 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: 13.75 // [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