Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate WP_037576905.1 BS73_RS27295 histidinol dehydrogenase
Query= curated2:Q9RH05 (430 letters) >NCBI__GCF_000744815.1:WP_037576905.1 Length = 439 Score = 258 bits (659), Expect = 3e-73 Identities = 157/407 (38%), Positives = 228/407 (56%), Gaps = 16/407 (3%) Query: 30 VSRDVSAIIADVKKRGDVAIAELTQKFDRHDLNKGGWQ-----LTQEEIKKACDSLPSEL 84 V VS +++D++K G A+ +++ D GWQ ++ E+K+ DSL EL Sbjct: 34 VVETVSRMLSDIEKNGMDAVLRYSRELD-------GWQGGDVEISAAELKRTGDSLSPEL 86 Query: 85 MDALKLAATRIRY--CHENQLPESSEMTDAAGVRMGVRWQAVEAAGLYVPGGRAAYCSSV 142 AL A R R + + + E GV G ++ V G Y+P G +S Sbjct: 87 RQALAAGAERTRLFAVEQREHLQDFETELIPGVVTGQKYLPVPRVGAYLPAGNFPILASA 146 Query: 143 LMNAVPAKVAGVKRLVMVTP-TPDGFVNPAVIAAAVISEVDEIWKIGGAQAVAALALGTE 201 M AK A V ++ TP T + +PAV+ AA +S VD + +GG QA+AA+A G Sbjct: 147 FMTVGVAKAADVPTVLACTPPTAEQGGHPAVLYAAYLSGVDRAFALGGVQALAAMAFGLL 206 Query: 202 KIKPVDVVVGPGNAWVAEAKRQLYGQVGIDMVAGPSEIVVVADKDNDPEWLAADLLSQAE 261 +P D++VG GNA+V EAKRQL+G+VGID++AGPSE+ V+AD+ DPE +AADLL QAE Sbjct: 207 GDQPADMLVGAGNAYVTEAKRQLFGRVGIDLLAGPSEVAVIADETADPELVAADLLGQAE 266 Query: 262 HDPTSQSILISDSEDLIEKTIEAVGRRLEKLETQKVARESWDKHGATILVQSLDEAPALV 321 H S + L++ S +L +E V ++L +L T+ +A +W HG + + A L+ Sbjct: 267 HGRQSPASLVTTSRELGLAVLEEVEKQLRQLPTRDIAEPAWRDHGTVYVAEDRQTAVELM 326 Query: 322 DRLAPEHLELAVADPDALFANVHHSGSVFLGRYTPEAIGDY-VGGPNHVLPTGRRARFSS 380 D LAPEHLE+ AD D N+ + GS+FLG ++ A D + G NHVLPTGR AR S+ Sbjct: 327 DLLAPEHLEVISADDDYYHQNLKNYGSIFLGAWSTVAYSDKGIAGTNHVLPTGRGARASA 386 Query: 381 GLSVIDFMKRTTYLNCSQEALSKIGPAAVTLAKAEGLPAHAESVISR 427 GLSV F+K T+ S EA + ++ EG+ AH + R Sbjct: 387 GLSVSRFLKPLTFQKVSAEATPDLAAHVEAISDFEGMAAHRATATLR 433 Lambda K H 0.316 0.132 0.377 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: 461 Number of extensions: 18 Number of successful extensions: 4 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: 439 Length adjustment: 32 Effective length of query: 398 Effective length of database: 407 Effective search space: 161986 Effective search space used: 161986 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 (21.6 bits) S2: 51 (24.3 bits)
Align candidate WP_037576905.1 BS73_RS27295 (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.240127.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-131 425.2 0.0 1.7e-131 425.0 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037576905.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037576905.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.0 0.0 1.7e-131 1.7e-131 1 393 [] 38 433 .. 38 433 .. 0.98 Alignments for each domain: == domain 1 score: 425.0 bits; conditional E-value: 1.7e-131 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes.. 71 v+++++d++k+G +A+l+y++++d+++ ++++s++el++ +++++el++al++ ae+ + f+ +q+++ NCBI__GCF_000744815.1:WP_037576905.1 38 VSRMLSDIEKNGMDAVLRYSRELDGWQGGDVEISAAELKRTGDSLSPELRQALAAGAERTRLFAVEQREHLqd 110 78899**********************************************************9999865334 PP TIGR00069 72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144 +e+e +gv++gqk+ p+ rvg+Y+P+G+ + +++++mt+ Ak A v++++++tPp+ ++ +pavl+aa l NCBI__GCF_000744815.1:WP_037576905.1 111 FETELIPGVVTGQKYLPVPRVGAYLPAGNFPILASAFMTVGVAKAADVPTVLACTPPTAEQGGHPAVLYAAYL 183 99999****************************************************98888*********** PP TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217 gvd+ +++GG+qa+aa+a+G+ +++d++vG Gn+yVt+AK+++fg+vgid++aGPsEv+viade+a+pel NCBI__GCF_000744815.1:WP_037576905.1 184 SGVDRAFALGGVQALAAMAFGLLGDQPADMLVGAGNAYVTEAKRQLFGRVGIDLLAGPSEVAVIADETADPEL 256 ************************************************************************* PP TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290 vaaDll qaEH++++ a lvtts+el +v eeve+ql++l++++iae +++++g++ +++d + a+el++ + NCBI__GCF_000744815.1:WP_037576905.1 257 VAADLLGQAEHGRQSPASLVTTSRELGLAVLEEVEKQLRQLPTRDIAEPAWRDHGTVYVAEDRQTAVELMDLL 329 ************************************************************************* PP TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdy.vaGpnhvLPTsgtArfasglsvedFlkrisvqel 362 ApEHLe+ +d + +++kn+Gs+flG+++++a++d+ +aG+nhvLPT++ Ar+++glsv++Flk +++q++ NCBI__GCF_000744815.1:WP_037576905.1 330 APEHLEVISADDDYYHQNLKNYGSIFLGAWSTVAYSDKgIAGTNHVLPTGRGARASAGLSVSRFLKPLTFQKV 402 *************************************989********************************* PP TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393 s ea+ +la +ve+++++Eg++aH+++++ R NCBI__GCF_000744815.1:WP_037576905.1 403 SAEATPDLAAHVEAISDFEGMAAHRATATLR 433 *************************998877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (439 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: 32.14 // [ok]
This GapMind analysis is from Jul 26 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