Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate 3607568 Dshi_0979 Histidinol dehydrogenase (RefSeq)
Query= BRENDA::Q8G2R2 (430 letters) >FitnessBrowser__Dino:3607568 Length = 438 Score = 490 bits (1261), Expect = e-143 Identities = 252/425 (59%), Positives = 312/425 (73%) Query: 5 LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64 L + FE FA L+ KRE + DVD V I+ VR GD+A+++ + RFDR+ L Sbjct: 5 LSSAEAGFEAAFAQLLTMKREDAVDVDDTVAGIIADVRARGDAAVIELTSRFDRLTLTPQ 64 Query: 65 GIAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAI 124 +A + EI A AL+LA +RI +HARQ+P+D R+T+ G ELG RWT + Sbjct: 65 TLAFSAEEIAAEIAKVSEEDRAALELAAERIRAYHARQMPQDARWTEPTGAELGWRWTPV 124 Query: 125 EAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEI 184 A GLYVPGG ASYPSSVLMNA+PA+VAGV+R+V+ P PDG +NPLVL+AA L+GV + Sbjct: 125 SAAGLYVPGGLASYPSSVLMNAIPAQVAGVERLVICAPTPDGVVNPLVLLAASLSGVDTV 184 Query: 185 YRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVAD 244 YRVGGAQAIAALAYGTETI PV KI GPGNA+VAAAKR VFG VGIDMIAGPSE+L++AD Sbjct: 185 YRVGGAQAIAALAYGTETIAPVDKITGPGNAFVAAAKRRVFGRVGIDMIAGPSEILVIAD 244 Query: 245 KDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRD 304 +DN+PDWIA DLL+QAEHD +AQSIL+T+D AF AV AVE +L TL R A SWRD Sbjct: 245 RDNDPDWIAVDLLSQAEHDESAQSILITDDAAFGQAVAAAVEARLETLERRAIAGPSWRD 304 Query: 305 FGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVG 364 FGAVI V+D +A L+NRIA EHLE+ VAD + I +AG+IF+G +TPE IGDY+G Sbjct: 305 FGAVITVRDLAEAAELSNRIAPEHLELCVADPDGLAEHITHAGAIFLGAWTPEAIGDYIG 364 Query: 365 GCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSV 424 G NHVLPTARSARFSSGLSV+D++KRT+L K+ L +GPAA +A +E L+AH SV Sbjct: 365 GPNHVLPTARSARFSSGLSVMDFVKRTTLAKMTPAALAEIGPAAERLAISESLEAHGLSV 424 Query: 425 AIRLN 429 RL+ Sbjct: 425 RARLD 429 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: 552 Number of extensions: 24 Number of successful extensions: 1 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: 438 Length adjustment: 32 Effective length of query: 398 Effective length of database: 406 Effective search space: 161588 Effective search space used: 161588 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 3607568 Dshi_0979 (Histidinol dehydrogenase (RefSeq))
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.16877.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-164 532.1 0.2 5.9e-164 531.9 0.2 1.0 1 lcl|FitnessBrowser__Dino:3607568 Dshi_0979 Histidinol dehydrogena Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607568 Dshi_0979 Histidinol dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 531.9 0.2 5.9e-164 5.9e-164 1 393 [] 34 427 .. 34 427 .. 0.99 Alignments for each domain: == domain 1 score: 531.9 bits; conditional E-value: 5.9e-164 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesveve 75 v+ ii+dvr++Gd+A++e+t++fd++ ++++l+ s+ee++++ ++v+ee ++alelaae+i+++h++q+p++ + lcl|FitnessBrowser__Dino:3607568 34 VAGIIADVRARGDAAVIELTSRFDRLtlTPQTLAFSAEEIAAEIAKVSEEDRAALELAAERIRAYHARQMPQDARWT 110 678**********************977889********************************************** PP TIGR00069 76 teegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvdevyk 152 + +g lg +++p++++glYvPgG a+ypS+vlm+a+pA+vAgv+++v+++P+ dg vnp vl aa+l gvd+vy+ lcl|FitnessBrowser__Dino:3607568 111 EPTGAELGWRWTPVSAAGLYVPGGLASYPSSVLMNAIPAQVAGVERLVICAPTP-DGVVNPLVLLAASLSGVDTVYR 186 *****************************************************6.********************** PP TIGR00069 153 vGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHd 229 vGGaqaiaalayGtet+ +vdki+GPGn++V+aAK+ vfg+vgidmiaGPsE+lviad++ +p+++a+DllsqaEHd lcl|FitnessBrowser__Dino:3607568 187 VGGAQAIAALAYGTETIAPVDKITGPGNAFVAAAKRRVFGRVGIDMIAGPSEILVIADRDNDPDWIAVDLLSQAEHD 263 ***************************************************************************** PP TIGR00069 230 edaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeell 306 e+aq+il+t+++++ ++v ++ve++le+ler+ ia s+++ ga+i+v+dl+ea+elsn++ApEHLel+++dp l+ lcl|FitnessBrowser__Dino:3607568 264 ESAQSILITDDAAFGQAVAAAVEARLETLERRAIAGPSWRDFGAVITVRDLAEAAELSNRIAPEHLELCVADPDGLA 340 ***************************************************************************** PP TIGR00069 307 kkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgL 383 ++i++aG++flG++tpea+gdy+ GpnhvLPT+++Arf+sglsv+dF+kr+++++++ +al+e+++a+e+la E L lcl|FitnessBrowser__Dino:3607568 341 EHITHAGAIFLGAWTPEAIGDYIGGPNHVLPTARSARFSSGLSVMDFVKRTTLAKMTPAALAEIGPAAERLAISESL 417 ***************************************************************************** PP TIGR00069 384 eaHaeavevR 393 eaH +v++R lcl|FitnessBrowser__Dino:3607568 418 EAHGLSVRAR 427 *******998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (438 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: 00:00:00.02 # Mc/sec: 7.45 // [ok]
This GapMind analysis is from Apr 09 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