Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_020177037.1 A3OQ_RS0119050 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000385335.1:WP_020177037.1 Length = 433 Score = 573 bits (1478), Expect = e-168 Identities = 296/429 (68%), Positives = 339/429 (79%) Query: 1 MVTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID 60 M L PDF+ F + L+ KRE SEDVD V+ I+ V GD AL+++S++FDR+D Sbjct: 1 MPLRLDMRSPDFKSAFDSLLAMKREASEDVDHTVQAIIAAVVARGDEALIEFSKKFDRVD 60 Query: 61 LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 LE G+ VT AE+DAA APA V AL+LA +RI H RQ P+D R+TD LGVELG R Sbjct: 61 LEALGLRVTPAEVDAAVAIAPADAVAALRLAHERIIAFHERQKPQDLRFTDPLGVELGWR 120 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 W +EAVGLYVPGGTASYPSSVLMNA PAKVAGV R+VMVVPAPDG +NPLVL AA LAG Sbjct: 121 WLPVEAVGLYVPGGTASYPSSVLMNAAPAKVAGVSRLVMVVPAPDGKINPLVLAAAHLAG 180 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V EIYRVGGA A+AALAYGT+TI PVAKIVGPGNAYVAAAKR VFGTVGIDMIAGPSEVL Sbjct: 181 VDEIYRVGGAHAVAALAYGTKTIAPVAKIVGPGNAYVAAAKRRVFGTVGIDMIAGPSEVL 240 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 I+ADK NP+WIAADLLAQAEHD+AAQSIL+T+D A A AVE AVERQL L R E A+ Sbjct: 241 ILADKSANPEWIAADLLAQAEHDSAAQSILITDDAALASAVEAAVERQLANLPRKEIAAP 300 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 SWRDFGA+I V DAIPLA+R+A EHLEI DAE +RNAG+IFIG YTPE IG Sbjct: 301 SWRDFGAIIEVASLMDAIPLADRLAPEHLEIMAEDAEGIASHVRNAGAIFIGAYTPEAIG 360 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DYVGG NHVLPTARSARFSSGL+VLD+MK+TS+LK S L LGPAA+ + +AEGLDAH Sbjct: 361 DYVGGSNHVLPTARSARFSSGLNVLDFMKKTSILKCDSASLAVLGPAAVALGKAEGLDAH 420 Query: 421 AQSVAIRLN 429 A+SV +RL+ Sbjct: 421 ARSVQMRLD 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: 581 Number of extensions: 20 Number of successful extensions: 1 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: 433 Length adjustment: 32 Effective length of query: 398 Effective length of database: 401 Effective search space: 159598 Effective search space used: 159598 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_020177037.1 A3OQ_RS0119050 (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.458889.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-161 524.2 3.8 1.5e-161 524.0 3.8 1.0 1 NCBI__GCF_000385335.1:WP_020177037.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000385335.1:WP_020177037.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 524.0 3.8 1.5e-161 1.5e-161 1 393 [] 34 427 .. 34 427 .. 0.99 Alignments for each domain: == domain 1 score: 524.0 bits; conditional E-value: 1.5e-161 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkle..slrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 v++ii++v ++GdeAl+e+++kfd+v+le lrv+ +e+++a++ +++ ++al+la+e+i +fhe+q+p++ NCBI__GCF_000385335.1:WP_020177037.1 34 VQAIIAAVVARGDEALIEFSKKFDRVDLEalGLRVTPAEVDAAVAIAPADAVAALRLAHERIIAFHERQKPQD 106 899***********************6652268**************************************** PP TIGR00069 72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144 + ++ gv lg ++ p+e+vglYvPgG+a+ypS+vlm+a pAkvAgv+++v+v P dgk+np vlaaa+l NCBI__GCF_000385335.1:WP_020177037.1 107 LRFTDPLGVELGWRWLPVEAVGLYVPGGTASYPSSVLMNAAPAKVAGVSRLVMVVPAP-DGKINPLVLAAAHL 178 *********************************************************6.************** PP TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217 +gvde+y+vGGa+a+aalayGt+t+ +v kivGPGn+yV+aAK+ vfg+vgidmiaGPsEvl++ad+sanpe+ NCBI__GCF_000385335.1:WP_020177037.1 179 AGVDEIYRVGGAHAVAALAYGTKTIAPVAKIVGPGNAYVAAAKRRVFGTVGIDMIAGPSEVLILADKSANPEW 251 ************************************************************************* PP TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290 +aaDll+qaEHd+ aq+il+t++++la++ve++ve+ql++l+rkeia s+++ gaii v++l +a+ l++++ NCBI__GCF_000385335.1:WP_020177037.1 252 IAADLLAQAEHDSAAQSILITDDAALASAVEAAVERQLANLPRKEIAAPSWRDFGAIIEVASLMDAIPLADRL 324 ************************************************************************* PP TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqels 363 ApEHLe++++d+e ++++++naG++f+G+ytpea+gdyv G+nhvLPT+++Arf+sgl+v dF+k++s+ +++ NCBI__GCF_000385335.1:WP_020177037.1 325 APEHLEIMAEDAEGIASHVRNAGAIFIGAYTPEAIGDYVGGSNHVLPTARSARFSSGLNVLDFMKKTSILKCD 397 ************************************************************************* PP TIGR00069 364 kealeelaeaveklaeaEgLeaHaeavevR 393 +++l+ l++a+++l +aEgL+aHa++v++R NCBI__GCF_000385335.1:WP_020177037.1 398 SASLAVLGPAAVALGKAEGLDAHARSVQMR 427 ****************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (433 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 17.23 // [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