Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_011814898.1 HHAL_RS10670 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000015585.1:WP_011814898.1 Length = 439 Score = 386 bits (992), Expect = e-112 Identities = 209/427 (48%), Positives = 278/427 (65%), Gaps = 1/427 (0%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61 + L T PDF A S +++ V E+V+ VR GD+ALLDY+RRFD + Sbjct: 4 IKRLSTTQPDFWDSLDALTSWGSHPGASIEQRVAEVVEGVRTGGDAALLDYTRRFDGREA 63 Query: 62 EKTG-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 + + + ++ AA + EAL+ A RI + RQ + Y DA G LG + Sbjct: 64 DSVAALEIPTEQVVAAHEQIAPEMREALEQAAARIRDYAQRQRLESWEYQDADGNRLGQQ 123 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 TA++ VG+YVPGG A+YPSSVLMNA+PA+VAGV I+M VPAP G L+PLVL AA +AG Sbjct: 124 VTALDRVGVYVPGGKAAYPSSVLMNAVPARVAGVQEIIMTVPAPGGELSPLVLAAAHVAG 183 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V I+ +GGAQA+AALAYGTET+ V KIVGPGNAYVA AKR V+G VGIDMIAGPSEVL Sbjct: 184 VDRIFTLGGAQAVAALAYGTETVPAVDKIVGPGNAYVAEAKRRVYGVVGIDMIAGPSEVL 243 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 +++D +P+WIA DL +QAEHD AQ++L+ D F V+ A+ER L + R+E Sbjct: 244 VISDGQADPEWIAMDLFSQAEHDEEAQALLVCPDFVFLDQVQAAMERLLPDMERSEIIRT 303 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S + GA+I V+D E+A +AN +A EHLE++VA+ + IR+AG+IF+G Y+ E +G Sbjct: 304 SLAERGALICVRDLEEAQQVANYVAPEHLELSVAEPDRLAEGIRHAGAIFLGHYSAESLG 363 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY G NH LPT+R+ARF+S L V D+ KR++ L AL A +AR EGL AH Sbjct: 364 DYCAGPNHTLPTSRTARFASPLGVYDFQKRSTTLACSPAGAAALAGTAAVMARGEGLTAH 423 Query: 421 AQSVAIR 427 A+S R Sbjct: 424 ARSAEYR 430 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: 506 Number of extensions: 24 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: 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_011814898.1 HHAL_RS10670 (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.24896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-162 525.7 1.5 5e-162 525.5 1.5 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011814898.1 HHAL_RS10670 histidinol dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011814898.1 HHAL_RS10670 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 525.5 1.5 5e-162 5e-162 1 393 [] 36 430 .. 36 430 .. 0.99 Alignments for each domain: == domain 1 score: 525.5 bits; conditional E-value: 5e-162 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 v+e++e vr+ Gd+All+yt++fd+ ++++l++++e++ +a+e++ +e++eale+aa++i++++++ lcl|NCBI__GCF_000015585.1:WP_011814898.1 36 VAEVVEGVRTGGDAALLDYTRRFDGReadSVAALEIPTEQVVAAHEQIAPEMREALEQAAARIRDYAQR 104 789**********************9556667899********************************** PP TIGR00069 67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135 q+ es+e+++++g lgq+v++l+rvg+YvPgGkaaypS+vlm+avpA+vAgv+ei+++ P g+++ lcl|NCBI__GCF_000015585.1:WP_011814898.1 105 QRLESWEYQDADGNRLGQQVTALDRVGVYVPGGKAAYPSSVLMNAVPARVAGVQEIIMTVPAP-GGELS 172 **************************************************************6.9**** PP TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204 p vlaaa+++gvd+++++GGaqa+aalayGtetvp+vdkivGPGn+yV++AK+ v+g vgidmiaGPsE lcl|NCBI__GCF_000015585.1:WP_011814898.1 173 PLVLAAAHVAGVDRIFTLGGAQAVAALAYGTETVPAVDKIVGPGNAYVAEAKRRVYGVVGIDMIAGPSE 241 ********************************************************************* PP TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 vlvi+d +a+pe++a+Dl+sqaEHde+aqa+lv+++ ++++v++++e+ l ++er+ei+++sl+++ga lcl|NCBI__GCF_000015585.1:WP_011814898.1 242 VLVISDGQADPEWIAMDLFSQAEHDEEAQALLVCPDFVFLDQVQAAMERLLPDMERSEIIRTSLAERGA 310 ********************************************************************* PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342 +i+v+dleea +++n +ApEHLel +++p +l++ i++aG++flG+y++e+lgdy+aGpnh+LPTs+tA lcl|NCBI__GCF_000015585.1:WP_011814898.1 311 LICVRDLEEAQQVANYVAPEHLELSVAEPDRLAEGIRHAGAIFLGHYSAESLGDYCAGPNHTLPTSRTA 379 ********************************************************************* PP TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 rfas+l+v+dF+kr+++ +s +++++la +++ +a+ EgL+aHa+++e R lcl|NCBI__GCF_000015585.1:WP_011814898.1 380 RFASPLGVYDFQKRSTTLACSPAGAAALAGTAAVMARGEGLTAHARSAEYR 430 ***********************************************9988 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 13.56 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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