Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_066326079.1 BLR17_RS14020 histidinol dehydrogenase
Query= SwissProt::P06988 (434 letters) >NCBI__GCF_900100165.1:WP_066326079.1 Length = 427 Score = 397 bits (1021), Expect = e-115 Identities = 215/423 (50%), Positives = 282/423 (66%), Gaps = 7/423 (1%) Query: 13 TAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEE 72 T + +L RP + ++ I TV +I V+ GD A+ +Y+ +FD +V+A E Sbjct: 8 TPDTWASILERPTKTVND-IEATVKEIFAAVQKDGDAAVAKYTTQFDGVYFENSEVTAAE 66 Query: 73 IAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIP 132 I A +SDEL A+++A N+E FH AQK V +ET GV+C Q RP+ VGLYIP Sbjct: 67 IEVAINTISDELTAAISLAKANVEKFHQAQKTTRVSIETAEGVQCWQEKRPIQKVGLYIP 126 Query: 133 GGSAPLFSTVLMLATPASIAGCKKVVLCSPPP----IADEILYAAQLCGVQDVFNVGGAQ 188 GG+APLFSTVLMLA PA IAGC ++VLCSPP I ILYAA LCGV + VGG Q Sbjct: 127 GGTAPLFSTVLMLAVPAKIAGCSEIVLCSPPDKNGNINPAILYAANLCGVTKIIKVGGIQ 186 Query: 189 AIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGAT 248 AIA + FGT+++PKV KIFGPGN +VT AK+ +Q G AIDMPAGPSE+LV+AD A Sbjct: 187 AIAGMTFGTKAIPKVYKIFGPGNQYVTVAKQLATQF--GVAIDMPAGPSELLVVADDTAV 244 Query: 249 PDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLI 308 P FVASDLLSQAEHG DSQVIL++ + M V ++ QL LPR A +A+ S+ I Sbjct: 245 PAFVASDLLSQAEHGVDSQVILVSTSKAMIDAVESEIQAQLELLPRKTIAEKAIANSKSI 304 Query: 309 VTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHV 368 ++ + +++ N+YGPEH I+ T N VD I +AGSVF+G+++PESAGDYASGTNH Sbjct: 305 FVENDSIALDLINEYGPEHFIVCTANNDFYVDGIQNAGSVFIGNYTPESAGDYASGTNHT 364 Query: 369 LPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVN 428 LPT GY S + L F K MT Q++S++G + + IE +A AE L AH+NAVTLR+ Sbjct: 365 LPTNGYAKNYSGVNLDSFMKSMTFQKISEKGIQNIGTAIEVMAEAEGLQAHRNAVTLRLK 424 Query: 429 ALK 431 +L+ Sbjct: 425 SLE 427 Lambda K H 0.315 0.128 0.356 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: 446 Number of extensions: 16 Number of successful extensions: 3 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: 434 Length of database: 427 Length adjustment: 32 Effective length of query: 402 Effective length of database: 395 Effective search space: 158790 Effective search space used: 158790 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_066326079.1 BLR17_RS14020 (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.239745.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-159 516.5 6.6 3.1e-159 516.3 6.6 1.0 1 NCBI__GCF_900100165.1:WP_066326079.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066326079.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.3 6.6 3.1e-159 3.1e-159 1 393 [] 30 422 .. 30 422 .. 0.99 Alignments for each domain: == domain 1 score: 516.3 bits; conditional E-value: 3.1e-159 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 vkei+++v+k Gd+A+ +yt++fd+v e+ +v+++e+e a +++++el +a++la++n+ekfh++q++++v+ NCBI__GCF_900100165.1:WP_066326079.1 30 VKEIFAAVQKDGDAAVAKYTTQFDGVYFENSEVTAAEIEVAINTISDELTAAISLAKANVEKFHQAQKTTRVS 102 89*********************************************************************** PP TIGR00069 74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllg 146 +et+egv++ q rp+++vglY+PgG+a+++Stvlm+avpAk+Ag++eiv+++Pp+k+g++npa+l+aa+l+g NCBI__GCF_900100165.1:WP_066326079.1 103 IETAEGVQCWQEKRPIQKVGLYIPGGTAPLFSTVLMLAVPAKIAGCSEIVLCSPPDKNGNINPAILYAANLCG 175 ************************************************************************* PP TIGR00069 147 vdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfg.evgidmiaGPsEvlviadesanpelv 218 v++++kvGG qaia +++Gt+ +pkv ki+GPGn+yVt AK+l ++ v+idm+aGPsE+lv+ad++a p++v NCBI__GCF_900100165.1:WP_066326079.1 176 VTKIIKVGGIQAIAGMTFGTKAIPKVYKIFGPGNQYVTVAKQLATQfGVAIDMPAGPSELLVVADDTAVPAFV 248 *******************************************99669************************* PP TIGR00069 219 aaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyA 291 a+DllsqaEH+ d+q+ilv+ts++++++ve+e+++qle l+rk+iaek+++ n++ i v++ + al+l+ney+ NCBI__GCF_900100165.1:WP_066326079.1 249 ASDLLSQAEHGVDSQVILVSTSKAMIDAVESEIQAQLELLPRKTIAEKAIA-NSKSIFVENDSIALDLINEYG 320 ***************************************************.66777789999********** PP TIGR00069 292 pEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelsk 364 pEH +++t+++ +++ i+naGsvf+G+ytpe++gdy++G+nh+LPT+g+A+ +sg+++++F+k++++q++s+ NCBI__GCF_900100165.1:WP_066326079.1 321 PEHFIVCTANNDFYVDGIQNAGSVFIGNYTPESAGDYASGTNHTLPTNGYAKNYSGVNLDSFMKSMTFQKISE 393 ************************************************************************* PP TIGR00069 365 ealeelaeaveklaeaEgLeaHaeavevR 393 +++++++ a+e +aeaEgL+aH++av+ R NCBI__GCF_900100165.1:WP_066326079.1 394 KGIQNIGTAIEVMAEAEGLQAHRNAVTLR 422 **************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (427 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.17 // [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