Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_022947719.1 H035_RS0104045 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000421465.1:WP_022947719.1 Length = 434 Score = 400 bits (1028), Expect = e-116 Identities = 215/428 (50%), Positives = 281/428 (65%), Gaps = 1/428 (0%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID- 60 + L DP F ++ ++ + ++V + V EI+ RVR+EGD+A+L Y+RRFDR+D Sbjct: 5 IRRLNGDDPGFAEQLTQLVAWTADFDQNVHQTVLEILGRVRQEGDAAVLAYTRRFDRLDR 64 Query: 61 LEKTGIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 L + A ++ A P +AL+ A RI + RQ Y D LG LG + Sbjct: 65 LSVAELEFPRARLEEALTTLPTEQRQALENAAARIRAYAERQKLASWHYRDELGNLLGQQ 124 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 T ++ VGLYVPGG A+YPSSVLMNA+PAKVAGV ++MVVP P G N LVL AA +AG Sbjct: 125 ITPLDRVGLYVPGGKAAYPSSVLMNAVPAKVAGVTELIMVVPTPGGEANRLVLAAAAVAG 184 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V ++RVGGAQA+AALAYGTETI V KIVGPGN YVA AK++VFG VGIDMIAGPSE+L Sbjct: 185 VDRVFRVGGAQAVAALAYGTETIPQVDKIVGPGNIYVATAKKLVFGQVGIDMIAGPSEIL 244 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 I+AD +PDWIA DL +QAEHD AQ+IL+ DEA+ V ++ +QL + R Sbjct: 245 IIADGTTDPDWIAMDLFSQAEHDEDAQAILLCPDEAYLDRVAASIAKQLPGMERRAVIRT 304 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S GA+I V+D A +ANRIA EHLE++VAD EA +P +R+AG+IF+G +T E +G Sbjct: 305 SLEKRGALIKVRDLNQACEIANRIAPEHLEVSVADPEALLPELRHAGAIFLGPHTAEALG 364 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY G NHVLPT+ +ARFSS L V D+ KRTSL+ + L A +A+ E L AH Sbjct: 365 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRTSLIGCTALGASPLAETARILAKGESLTAH 424 Query: 421 AQSVAIRL 428 A+S R+ Sbjct: 425 ARSAEYRI 432 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: 525 Number of extensions: 26 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: 434 Length adjustment: 32 Effective length of query: 398 Effective length of database: 402 Effective search space: 159996 Effective search space used: 159996 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_022947719.1 H035_RS0104045 (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.32087.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-164 532.3 0.0 4.9e-164 532.1 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022947719.1 H035_RS0104045 histidinol dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022947719.1 H035_RS0104045 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.1 0.0 4.9e-164 4.9e-164 1 393 [] 37 431 .. 37 431 .. 0.99 Alignments for each domain: == domain 1 score: 532.1 bits; conditional E-value: 4.9e-164 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 v ei+ +vr+eGd+A+l+yt++fd++ ++++l+ ++++leeal++++ e ++ale+aa++i++++e+ lcl|NCBI__GCF_000421465.1:WP_022947719.1 37 VLEILGRVRQEGDAAVLAYTRRFDRLdrlSVAELEFPRARLEEALTTLPTEQRQALENAAARIRAYAER 105 6789********************98777899************************************* PP TIGR00069 67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135 q+ +s+++++e g llgq+++pl+rvglYvPgGkaaypS+vlm+avpAkvAgv+e+++v P+ g++n lcl|NCBI__GCF_000421465.1:WP_022947719.1 106 QKLASWHYRDELGNLLGQQITPLDRVGLYVPGGKAAYPSSVLMNAVPAKVAGVTELIMVVPTP-GGEAN 173 **************************************************************6.9**** PP TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204 + vlaaa+++gvd+v++vGGaqa+aalayGtet+p+vdkivGPGniyV++AKklvfg+vgidmiaGPsE lcl|NCBI__GCF_000421465.1:WP_022947719.1 174 RLVLAAAAVAGVDRVFRVGGAQAVAALAYGTETIPQVDKIVGPGNIYVATAKKLVFGQVGIDMIAGPSE 242 ********************************************************************* PP TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 +l+iad +++p+++a+Dl+sqaEHdedaqail++++e+ +++v +++++ql +er+ ++++slek+ga lcl|NCBI__GCF_000421465.1:WP_022947719.1 243 ILIIADGTTDPDWIAMDLFSQAEHDEDAQAILLCPDEAYLDRVAASIAKQLPGMERRAVIRTSLEKRGA 311 ********************************************************************* PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342 +i v+dl++a+e++n++ApEHLe+ ++dpe+ll+++++aG++flG++t+ealgdy+aGpnhvLPTsgtA lcl|NCBI__GCF_000421465.1:WP_022947719.1 312 LIKVRDLNQACEIANRIAPEHLEVSVADPEALLPELRHAGAIFLGPHTAEALGDYCAGPNHVLPTSGTA 380 ********************************************************************* PP TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 rf+s+l+v+dF+kr+s++ ++ +++ lae+++ la+ E L+aHa+++e R lcl|NCBI__GCF_000421465.1:WP_022947719.1 381 RFSSPLGVYDFQKRTSLIGCTALGASPLAETARILAKGESLTAHARSAEYR 431 ***********************************************9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (434 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 11.46 // [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