Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate GFF871 PS417_04420 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >FitnessBrowser__WCS417:GFF871 Length = 440 Score = 399 bits (1026), Expect = e-116 Identities = 211/428 (49%), Positives = 281/428 (65%), Gaps = 1/428 (0%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61 + L DPDF LS + + V+ V +I+ VR GD+AL+D++R+FD +D+ Sbjct: 7 IARLNAADPDFAHHLDHLLSWESVSDDSVNGRVLDIIKAVRERGDAALVDFTRQFDGLDV 66 Query: 62 EKTGIAVTEAE-IDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 + E ++ A A EAL++A R+ +H +Q YT+A G LG + Sbjct: 67 ASMSDLILPRERLELALTRITAPQREALEVAAARVRSYHEKQKQDSWSYTEADGTVLGQK 126 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180 T ++ GLYVPGG ASYPSSVLMNA+PAKVAGV +VMVVP P G +N LVL AA +AG Sbjct: 127 VTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVTEVVMVVPTPRGEINELVLAAACIAG 186 Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240 V ++ +GGAQA+AALAYGTE++ V K+VGPGN YVA AKR VFG VGIDMIAGPSE+L Sbjct: 187 VDRVFTIGGAQAVAALAYGTESVPKVDKVVGPGNIYVATAKRHVFGQVGIDMIAGPSEIL 246 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 +V D +PDWIA DL +QAEHD AQ+IL++ D F V ++ + L T+ R E Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASINKLLPTMDRAEIIEK 306 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S GA+ILV+D E AI +ANRIA EHLE++VAD +A++P IR+AG+IF+G +T E +G Sbjct: 307 SINGRGALILVRDMEQAIEVANRIAPEHLELSVADPQAWLPSIRHAGAIFMGRHTSEALG 366 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY G NHVLPT+ +ARFSS L V D+ KR+S++ + LG A +AR E L AH Sbjct: 367 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSPQGASELGKTASVLARGESLSAH 426 Query: 421 AQSVAIRL 428 A+S R+ Sbjct: 427 ARSAEYRI 434 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: 494 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: 440 Length adjustment: 32 Effective length of query: 398 Effective length of database: 408 Effective search space: 162384 Effective search space used: 162384 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 GFF871 PS417_04420 (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.25047.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-166 540.6 0.1 1.5e-166 540.4 0.1 1.0 1 lcl|FitnessBrowser__WCS417:GFF871 PS417_04420 histidinol dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF871 PS417_04420 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 540.4 0.1 1.5e-166 1.5e-166 1 393 [] 39 433 .. 39 433 .. 0.99 Alignments for each domain: == domain 1 score: 540.4 bits; conditional E-value: 1.5e-166 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 v +ii++vr++Gd+Al+++t++fd++ ++++l +++e+le al+++++ +eale aa++++++hekq+++s++ lcl|FitnessBrowser__WCS417:GFF871 39 VLDIIKAVRERGDAALVDFTRQFDGLdvaSMSDLILPRERLELALTRITAPQREALEVAAARVRSYHEKQKQDSWS 114 679**********************9666788999***************************************** PP TIGR00069 74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllgvde 149 +++++g++lgqkv+pl+r+glYvPgGka+ypS+vlm+a+pAkvAgv+e+v+v P+ +g++n+ vlaaa ++gvd+ lcl|FitnessBrowser__WCS417:GFF871 115 YTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVTEVVMVVPTP-RGEINELVLAAACIAGVDR 189 *******************************************************6.9****************** PP TIGR00069 150 vykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelvaaDllsq 225 v+++GGaqa+aalayGte+vpkvdk+vGPGniyV++AK++vfg+vgidmiaGPsE+lv++d +++p+++a+Dl+sq lcl|FitnessBrowser__WCS417:GFF871 190 VFTIGGAQAVAALAYGTESVPKVDKVVGPGNIYVATAKRHVFGQVGIDMIAGPSEILVVCDGQTDPDWIAMDLFSQ 265 **************************************************************************** PP TIGR00069 226 aEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkd 301 aEHdedaqailv++++e+++kv +++++ l +++r+ei+eks++ +ga+ilv+d+e+a+e++n++ApEHLel ++d lcl|FitnessBrowser__WCS417:GFF871 266 AEHDEDAQAILVSPDAEFLDKVAASINKLLPTMDRAEIIEKSINGRGALILVRDMEQAIEVANRIAPEHLELSVAD 341 **************************************************************************** PP TIGR00069 302 peellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeavekl 377 p+++l++i++aG++f+G++t+ealgdy+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++ +s ++++el+++++ l lcl|FitnessBrowser__WCS417:GFF871 342 PQAWLPSIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSPQGASELGKTASVL 417 **************************************************************************** PP TIGR00069 378 aeaEgLeaHaeavevR 393 a+ E L+aHa+++e R lcl|FitnessBrowser__WCS417:GFF871 418 ARGESLSAHARSAEYR 433 ************9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (440 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: 9.38 // [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