Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012171673.1 AZC_RS16245 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000010525.1:WP_012171673.1 Length = 430 Score = 552 bits (1422), Expect = e-162 Identities = 285/418 (68%), Positives = 327/418 (78%), Gaps = 1/418 (0%) Query: 12 FEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEA 71 F FA FL+ KRE S DV AV +I+ VR GD+AL+DYSR FDR++LE I VTEA Sbjct: 12 FPDAFATFLASKREASTDVAVAVADIIAGVRARGDAALIDYSRTFDRVELEGR-IRVTEA 70 Query: 72 EIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYV 131 EI+AA P T EALK A+ RIE HHARQLP D+RYTDA+GVELG RWT ++AVGLYV Sbjct: 71 EIEAALAEVPQDTFEALKFAKARIEAHHARQLPADERYTDAVGVELGQRWTPVDAVGLYV 130 Query: 132 PGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVGGAQ 191 PGGTA+YPSSVLMNA+PAKVAGV R+ MVVP+PDG + PLVL AARLAGV E+YRVGGAQ Sbjct: 131 PGGTAAYPSSVLMNAVPAKVAGVPRVAMVVPSPDGVIAPLVLAAARLAGVDEVYRVGGAQ 190 Query: 192 AIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDW 251 A+AALAYGTETI PV KIVGPGNAYVAAAKR VFG VGIDMIAGPSEVLI+AD + N W Sbjct: 191 AVAALAYGTETIAPVDKIVGPGNAYVAAAKRQVFGKVGIDMIAGPSEVLILADGNANAAW 250 Query: 252 IAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILV 311 IAADLLAQAEHD AAQSIL+T+ A AV AVE QL TL R E A ASWRD GA+ILV Sbjct: 251 IAADLLAQAEHDAAAQSILVTDSPVLADAVTRAVEAQLTTLPRREIAEASWRDHGAIILV 310 Query: 312 KDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLP 371 ++A+PL +R+A EHLEI DA+A RIR+AG+IF+G YTPE IGDYVGG NHVLP Sbjct: 311 GSMDEALPLVDRVAPEHLEIHADDADALADRIRHAGAIFVGAYTPEAIGDYVGGTNHVLP 370 Query: 372 TARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRLN 429 TARSARFSSGL V D++KRTS+LK L +GPAA+ +A E LDAH +S+ IR N Sbjct: 371 TARSARFSSGLGVYDFLKRTSILKCSPASLNVIGPAAVRLAEVERLDAHGRSILIRTN 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: 586 Number of extensions: 22 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: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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_012171673.1 AZC_RS16245 (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.666145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-167 542.5 3.5 3.9e-167 542.4 3.5 1.0 1 NCBI__GCF_000010525.1:WP_012171673.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012171673.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 542.4 3.5 3.9e-167 3.9e-167 1 393 [] 34 426 .. 34 426 .. 0.99 Alignments for each domain: == domain 1 score: 542.4 bits; conditional E-value: 3.9e-167 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkle.slrvseeeleealeavdeelkealelaaeniekfhekqlpesv 72 v++ii+ vr++Gd+Al++y+++fd+v+le ++rv+e+e+e+al++v++++ eal+ a+++ie+ h++qlp++ NCBI__GCF_000010525.1:WP_012171673.1 34 VADIIAGVRARGDAALIDYSRTFDRVELEgRIRVTEAEIEAALAEVPQDTFEALKFAKARIEAHHARQLPADE 106 789***********************87658****************************************** PP TIGR00069 73 eveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakll 145 ++++ gv lgq+++p+++vglYvPgG+aaypS+vlm+avpAkvAgv+++++v P dg ++p vlaaa+l+ NCBI__GCF_000010525.1:WP_012171673.1 107 RYTDAVGVELGQRWTPVDAVGLYVPGGTAAYPSSVLMNAVPAKVAGVPRVAMVVPSP-DGVIAPLVLAAARLA 178 ********************************************************6.*************** PP TIGR00069 146 gvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelv 218 gvdevy+vGGaqa+aalayGtet+ +vdkivGPGn+yV+aAK++vfg+vgidmiaGPsEvl++ad +an++++ NCBI__GCF_000010525.1:WP_012171673.1 179 GVDEVYRVGGAQAVAALAYGTETIAPVDKIVGPGNAYVAAAKRQVFGKVGIDMIAGPSEVLILADGNANAAWI 251 ************************************************************************* PP TIGR00069 219 aaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyA 291 aaDll+qaEHd+ aq+ilvt+s la++v+++ve+ql++l+r+eiae+s++++gaiilv +++eal l++++A NCBI__GCF_000010525.1:WP_012171673.1 252 AADLLAQAEHDAAAQSILVTDSPVLADAVTRAVEAQLTTLPRREIAEASWRDHGAIILVGSMDEALPLVDRVA 324 ************************************************************************* PP TIGR00069 292 pEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelsk 364 pEHLe++++d+ +l+++i++aG++f+G+ytpea+gdyv G+nhvLPT+++Arf+sgl+v+dFlkr+s+ ++s NCBI__GCF_000010525.1:WP_012171673.1 325 PEHLEIHADDADALADRIRHAGAIFVGAYTPEAIGDYVGGTNHVLPTARSARFSSGLGVYDFLKRTSILKCSP 397 ************************************************************************* PP TIGR00069 365 ealeelaeaveklaeaEgLeaHaeavevR 393 ++l+ +++a+++lae+E L+aH +++ +R NCBI__GCF_000010525.1:WP_012171673.1 398 ASLNVIGPAAVRLAEVERLDAHGRSILIR 426 **************************988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (430 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 25.32 // [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