Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_037581586.1 BS73_RS28925 histidinol dehydrogenase
Query= SwissProt::P9WNW9 (444 letters) >NCBI__GCF_000744815.1:WP_037581586.1 Length = 435 Score = 553 bits (1426), Expect = e-162 Identities = 292/437 (66%), Positives = 336/437 (76%), Gaps = 8/437 (1%) Query: 7 VLTRIDLRGAELTAAELRAALPRGGADVEAVLPTVRPIVAAVAERGAEAALDFGASFDGV 66 +++RIDLRG+ + RA LPR DVEA L VRPI V RG EA ++ FDGV Sbjct: 1 MISRIDLRGS---TDDPRALLPRAELDVEAALEKVRPICEDVHHRGVEALIEITERFDGV 57 Query: 67 RPHAIRVPDAALDAALAGLDCDVCEALQVMVERTRAVHSGQRRTDVTTTLGPGATVTERW 126 R RVP L ALA LD V AL+V +ER R VH QRRTD TT + PG TVTERW Sbjct: 58 RLTTTRVPVEELHKALAELDPKVRAALEVSIERARKVHREQRRTDHTTQVVPGGTVTERW 117 Query: 127 VPVERVGLYVPGGNAVYPSSVVMNVVPAQAAGVDSLVVASPPQAQWDGMPHPTILAAARL 186 VPVERVGLYVPGG AVYPSSVVMNVVPAQ AGV+SL V SPPQ +DG+PHPTILAA L Sbjct: 118 VPVERVGLYVPGGRAVYPSSVVMNVVPAQEAGVESLAVTSPPQPDFDGLPHPTILAACAL 177 Query: 187 LGVDEVWAVGGAQAVALLAYGGTDTDGAALTPVDMITGPGNIYVTAAKRLCRSRVGIDAE 246 LGVDEV+AVGGAQAVA+ AYG + PV+++TGPGNI+V AAKRL + R+GIDAE Sbjct: 178 LGVDEVYAVGGAQAVAMFAYGTEEC-----RPVNLVTGPGNIWVAAAKRLLKGRIGIDAE 232 Query: 247 AGPTEIAILADHTADPVHVAADLISQAEHDELAASVLVTPSEDLADATDAELAGQLQTTV 306 AGPTEIAILAD TADP HVAAD+ISQAEHD LAA+VLVT S LADA + EL Q++ T Sbjct: 233 AGPTEIAILADSTADPRHVAADMISQAEHDPLAAAVLVTDSLALADAVEKELEPQVRATK 292 Query: 307 HRERVTAALTGRQSAIVLVDDVDAAVLVVNAYAAEHLEIQTADAPQVASRIRSAGAIFVG 366 H ER+ AL GRQS IVLVDD+D + VV+AYAAEHLEIQTADA VA+R+R+AGAIF+G Sbjct: 293 HSERIATALDGRQSGIVLVDDIDQGLKVVDAYAAEHLEIQTADAHAVAARVRNAGAIFIG 352 Query: 367 PWSPVSLGDYCAGSNHVLPTAGCARHSSGLSVQTFLRGIHVVEYTEAALKDVSGHVITLA 426 W+PVSLGDY AGSNHVLPT GCA HSSGLSVQ+FLRGIHVV+Y+ AL +V+GHV+ LA Sbjct: 353 AWAPVSLGDYAAGSNHVLPTGGCACHSSGLSVQSFLRGIHVVDYSREALAEVAGHVVNLA 412 Query: 427 TAEDLPAHGEAVRRRFE 443 AEDLP HG+A+R RFE Sbjct: 413 NAEDLPGHGDAIRARFE 429 Lambda K H 0.317 0.132 0.383 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: 545 Number of extensions: 14 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: 444 Length of database: 435 Length adjustment: 32 Effective length of query: 412 Effective length of database: 403 Effective search space: 166036 Effective search space used: 166036 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_037581586.1 BS73_RS28925 (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.243784.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-149 484.5 2.8 1.6e-149 484.3 2.8 1.0 1 NCBI__GCF_000744815.1:WP_037581586.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037581586.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 484.3 2.8 1.6e-149 1.6e-149 1 393 [] 32 427 .. 32 427 .. 0.99 Alignments for each domain: == domain 1 score: 484.3 bits; conditional E-value: 1.6e-149 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 v++i+edv+++G eAl+e+te+fd+v+l++ rv+ eel++al+++d+++++ale ++e+ +k+h++q++++++ NCBI__GCF_000744815.1:WP_037581586.1 32 VRPICEDVHHRGVEALIEITERFDGVRLTTTRVPVEELHKALAELDPKVRAALEVSIERARKVHREQRRTDHT 104 799********************************************************************** PP TIGR00069 74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkk..dgkvnpavlaaakl 144 ++ +g +++++++p+ervglYvPgG+a ypS+v+m++vpA+ Agv++++v++Pp+ dg +p++laa++l NCBI__GCF_000744815.1:WP_037581586.1 105 TQVVPGGTVTERWVPVERVGLYVPGGRAVYPSSVVMNVVPAQEAGVESLAVTSPPQPdfDGLPHPTILAACAL 177 *******************************************************7756899*********** PP TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217 lgvdevy+vGGaqa+a++ayGte++++v+ ++GPGni+V+aAK+l+ g++gid aGP+E++++ad++a+p++ NCBI__GCF_000744815.1:WP_037581586.1 178 LGVDEVYAVGGAQAVAMFAYGTEECRPVNLVTGPGNIWVAAAKRLLKGRIGIDAEAGPTEIAILADSTADPRH 250 ************************************************************************* PP TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslek.ngaiilvddleealelsne 289 vaaD++sqaEHd+ a+a+lvt+s +la++ve+e+e q+++++++e + ++l+ ++ i+lvdd+++ l+++++ NCBI__GCF_000744815.1:WP_037581586.1 251 VAADMISQAEHDPLAAAVLVTDSLALADAVEKELEPQVRATKHSERIATALDGrQSGIVLVDDIDQGLKVVDA 323 ***************************************************976899**************** PP TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362 yA+EHLe+qt+d+++++ +++naG++f+G+++p++lgdy+aG+nhvLPT+g+A ++sglsv++Fl+ i+v+++ NCBI__GCF_000744815.1:WP_037581586.1 324 YAAEHLEIQTADAHAVAARVRNAGAIFIGAWAPVSLGDYAAGSNHVLPTGGCACHSSGLSVQSFLRGIHVVDY 396 ************************************************************************* PP TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393 s+eal+e+a +v++la+aE+L H +a+++R NCBI__GCF_000744815.1:WP_037581586.1 397 SREALAEVAGHVVNLANAEDLPGHGDAIRAR 427 ****************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (435 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: 29.96 // [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