Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_011612464.1 TERY_RS14125 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000014265.1:WP_011612464.1 Length = 454 Score = 368 bits (945), Expect = e-106 Identities = 195/399 (48%), Positives = 267/399 (66%), Gaps = 1/399 (0%) Query: 31 DRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPASTVEALKL 90 + VREI+ VR +GD ALL+Y+ FD I L + ++ +E+DAA+ + +++L Sbjct: 31 ETTVREILRNVREKGDEALLNYTSEFDHITLTSEELKISGSELDAAYQQVNKDLLSSIRL 90 Query: 91 ARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAK 150 A +I+ H +Q+PK V LG R+T ++ GLYVPGG A+YPS+VLMNA+PA+ Sbjct: 91 AAKQIKAFHRQQIPKSWVQFGDDEVVLGKRYTPVDRAGLYVPGGQAAYPSTVLMNAIPAQ 150 Query: 151 VAGVDRIVMVVPAPDGN-LNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVAKI 209 VA V +IVMV P G +NP VLVAA+ AG+ EIYR+GGAQAIAALAYGTETI V I Sbjct: 151 VAKVPKIVMVTPPSQGKKINPAVLVAAQEAGIQEIYRIGGAQAIAALAYGTETIPKVDVI 210 Query: 210 VGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQSI 269 GPGN YV AK+IV+GTVGID +AGPSEVLI+AD + NP ++AAD+LAQAEHD+ A +I Sbjct: 211 TGPGNIYVTLAKKIVYGTVGIDSLAGPSEVLIIADSEANPVYVAADMLAQAEHDSLAAAI 270 Query: 270 LMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHL 329 L+T D A V VERQL R + +G V++V FEDA+ L+N+ A EHL Sbjct: 271 LLTTDLELARQVVVEVERQLEDHPRRTLTEKAIAHYGLVVVVSSFEDAVELSNQFAPEHL 330 Query: 330 EIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMK 389 E+ V+D + IR+AG+IF+G TPE +GDY+ G NH LPT+ +AR++S L V ++K Sbjct: 331 ELEVSDPWELLENIRHAGAIFLGYSTPEAVGDYLAGPNHTLPTSGAARYASALGVETFLK 390 Query: 390 RTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428 +SL++ L+ + +A AEGL +HA SV +R+ Sbjct: 391 HSSLVQYSPTALQKVASDIDLLATAEGLHSHANSVRLRM 429 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: 477 Number of extensions: 20 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: 454 Length adjustment: 32 Effective length of query: 398 Effective length of database: 422 Effective search space: 167956 Effective search space used: 167956 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_011612464.1 TERY_RS14125 (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.13990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-171 555.3 2.4 5.5e-171 555.0 2.4 1.1 1 lcl|NCBI__GCF_000014265.1:WP_011612464.1 TERY_RS14125 histidinol dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011612464.1 TERY_RS14125 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 555.0 2.4 5.5e-171 5.5e-171 1 393 [] 34 428 .. 34 428 .. 0.99 Alignments for each domain: == domain 1 score: 555.0 bits; conditional E-value: 5.5e-171 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 v+ei+++vr++GdeAll+yt++fd++ + e+l++s +el++a+++v+++l ++++laa++i++fh++q lcl|NCBI__GCF_000014265.1:WP_011612464.1 34 VREILRNVREKGDEALLNYTSEFDHItlTSEELKISGSELDAAYQQVNKDLLSSIRLAAKQIKAFHRQQ 102 89***********************9778899************************************* PP TIGR00069 68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136 +p+s+ + ++v+lg++++p++r+glYvPgG+aaypStvlm+a+pA+vA v++iv+vtPp++ +k+np lcl|NCBI__GCF_000014265.1:WP_011612464.1 103 IPKSWVQFGDDEVVLGKRYTPVDRAGLYVPGGQAAYPSTVLMNAIPAQVAKVPKIVMVTPPSQGKKINP 171 *************************************************************98889*** PP TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205 avl+aa+ +g++e+y++GGaqaiaalayGtet+pkvd+i+GPGniyVt AKk+v+g+vgid++aGPsEv lcl|NCBI__GCF_000014265.1:WP_011612464.1 172 AVLVAAQEAGIQEIYRIGGAQAIAALAYGTETIPKVDVITGPGNIYVTLAKKIVYGTVGIDSLAGPSEV 240 ********************************************************************* PP TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274 l+iad++anp +vaaD+l+qaEHd+ a+ail+tt+ ela++v eve+qle+++r++++ek+++++g + lcl|NCBI__GCF_000014265.1:WP_011612464.1 241 LIIADSEANPVYVAADMLAQAEHDSLAAAILLTTDLELARQVVVEVERQLEDHPRRTLTEKAIAHYGLV 309 ********************************************************************* PP TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343 ++v+++e+a+elsn++ApEHLel+++dp+ell++i++aG++flG tpea+gdy+aGpnh+LPTsg+Ar lcl|NCBI__GCF_000014265.1:WP_011612464.1 310 VVVSSFEDAVELSNQFAPEHLELEVSDPWELLENIRHAGAIFLGYSTPEAVGDYLAGPNHTLPTSGAAR 378 ********************************************************************* PP TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 +as+l+ve+Flk++s++++s +al+++a+++ la aEgL+ Ha++v+ R lcl|NCBI__GCF_000014265.1:WP_011612464.1 379 YASALGVETFLKHSSLVQYSPTALQKVASDIDLLATAEGLHSHANSVRLR 428 ***********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (454 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: 11.76 // [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