Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (uncharacterized)
to candidate WP_066329740.1 BLR17_RS09345 histidinol dehydrogenase
Query= curated2:Q9RH05 (430 letters) >NCBI__GCF_900100165.1:WP_066329740.1 Length = 431 Score = 299 bits (766), Expect = 1e-85 Identities = 168/412 (40%), Positives = 254/412 (61%), Gaps = 5/412 (1%) Query: 22 ERRESEGDVSRDVSAIIADVKKRGDVAIAELTQKFDRHDLNKGGWQLTQEEIKKACDSLP 81 E ++ V V +I VK GD A+ EL++KFD+ + ++L+ I++ +S+P Sbjct: 13 EAETNDKKVREIVENLIEQVKTEGDKALFELSEKFDKW--SPESFRLSANAIEEIINSVP 70 Query: 82 SELMDALKLAATRIRYC--HENQLPESSEMTDAAGVRMGVRWQAVEAAGLYVPGGRAAYC 139 +++++ +K A ++R H+ E+ GV +G + V + G Y+PGGR Sbjct: 71 AQVIEDIKFAQAQVRNFAQHQKDSMRDIEVETLPGVFLGHKNVPVNSVGCYIPGGRYPMV 130 Query: 140 SSVLMNAVPAKVAGVKRLVMVTPTPDGFVNPAVIAAAVISEVDEIWKIGGAQAVAALALG 199 +S M+ + AKVAGVKR+V TP +G + A IAA ++ DEI+ +GG QA+AA+ALG Sbjct: 131 ASAHMSVLTAKVAGVKRVVACTPPINGKIPAATIAAMAMAGADEIYILGGVQAIAAMALG 190 Query: 200 TEKIKPVDVVVGPGNAWVAEAKRQLYGQVGIDMVAGPSEIVVVADKDNDPEWLAADLLSQ 259 TE I+ VD++VGPGN++VAEAKRQL+G++GID++AGP+E +V+AD+ +D E A DLL Q Sbjct: 191 TESIESVDMIVGPGNSYVAEAKRQLFGKIGIDLLAGPTETLVIADETSDAEICAVDLLGQ 250 Query: 260 AEHDPTSQSILISDSEDLIEKTIEAVGRRLEKLETQKVARESWDKHGATILVQSLDEAPA 319 AEH PTS SIL+++SE L +TI + R+L+ L T VA +W +G ILV ++DE A Sbjct: 251 AEHGPTSPSILLTNSEKLAYETIAEIERQLKVLPTADVASIAWKDYGQIILVDTIDEMVA 310 Query: 320 LVDRLAPEHLELAVADPDALFANVHHSGSVFLGRYTPEAIGDYVGGPNHVLPTGRRARFS 379 DR+A EH+++ ADP N+ + G++FLG+YT A GD V G NH LPT A+++ Sbjct: 311 EADRIASEHVQVMTADPRYFLKNMTNYGALFLGKYTNVAYGDKVIGTNHTLPTKHGAKYT 370 Query: 380 SGLSVIDFMKRTTYLNC-SQEALSKIGPAAVTLAKAEGLPAHAESVISRLNK 430 GL V F+K +Y + EA + IG L + E H E R+ + Sbjct: 371 GGLWVGKFLKTCSYQEIRTPEASAMIGEYCSRLCEIENFYGHKEQADIRVRR 422 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: 419 Number of extensions: 11 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: 431 Length adjustment: 32 Effective length of query: 398 Effective length of database: 399 Effective search space: 158802 Effective search space used: 158802 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_066329740.1 BLR17_RS09345 (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.215927.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-145 470.1 0.9 4e-145 469.9 0.9 1.0 1 NCBI__GCF_900100165.1:WP_066329740.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066329740.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.9 0.9 4e-145 4e-145 1 393 [] 25 419 .. 25 419 .. 0.98 Alignments for each domain: == domain 1 score: 469.9 bits; conditional E-value: 4e-145 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpes.. 71 v+++ie+v++eGd+Al+e++ekfdk+++es+r+s++ +ee ++v+++++e+++ a++++++f+++q+++ NCBI__GCF_900100165.1:WP_066329740.1 25 VENLIEQVKTEGDKALFELSEKFDKWSPESFRLSANAIEEIINSVPAQVIEDIKFAQAQVRNFAQHQKDSMrd 97 789************************************************************9999976545 PP TIGR00069 72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144 +evet +gv+lg+k +p+++vg+Y+PgG++++++++ m +++AkvAgvk++v++tPp +gk+ +a++aa+++ NCBI__GCF_900100165.1:WP_066329740.1 98 IEVETLPGVFLGHKNVPVNSVGCYIPGGRYPMVASAHMSVLTAKVAGVKRVVACTPPI-NGKIPAATIAAMAM 169 9********************************************************6.9************* PP TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217 +g+de+y +GG+qaiaa+a Gte++++vd+ivGPGn+yV++AK+++fg++gid++aGP+E lviade++++e+ NCBI__GCF_900100165.1:WP_066329740.1 170 AGADEIYILGGVQAIAAMALGTESIESVDMIVGPGNSYVAEAKRQLFGKIGIDLLAGPTETLVIADETSDAEI 242 ************************************************************************* PP TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290 +a+Dll qaEH++++ +il+t+se+la ++ +e+e+ql+ l+++++a+ +++++g+iilvd+++e+++ ++++ NCBI__GCF_900100165.1:WP_066329740.1 243 CAVDLLGQAEHGPTSPSILLTNSEKLAYETIAEIERQLKVLPTADVASIAWKDYGQIILVDTIDEMVAEADRI 315 ************************************************************************* PP TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel. 362 A EH++++t+dp+ +lk+++n+G++flG+yt +a+gd+v G+nh+LPT+ A++++gl+v +Flk++s+qe+ NCBI__GCF_900100165.1:WP_066329740.1 316 ASEHVQVMTADPRYFLKNMTNYGALFLGKYTNVAYGDKVIGTNHTLPTKHGAKYTGGLWVGKFLKTCSYQEIr 388 ***********************************************************************93 PP TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393 + ea + ++e +++l+e+E++ H+e +++R NCBI__GCF_900100165.1:WP_066329740.1 389 TPEASAMIGEYCSRLCEIENFYGHKEQADIR 419 46788899******************99988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (431 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: 15.03 // [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