Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Synpcc7942_1519 Synpcc7942_1519 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >FitnessBrowser__SynE:Synpcc7942_1519 Length = 434 Score = 390 bits (1003), Expect = e-113 Identities = 205/398 (51%), Positives = 277/398 (69%), Gaps = 1/398 (0%) Query: 31 DRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAFDAAPASTVEALKL 90 + +VREIV V+R GD+AL+++++ FD L+ + V+ AE+DAA+ P ++A++L Sbjct: 31 EASVREIVQAVQRRGDAALIEFTQEFDGFALQAENLRVSGAELDAAYQQIPKELLDAIRL 90 Query: 91 ARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTASYPSSVLMNAMPAK 150 A +IE H +++PK A G LG R+T ++ GLYVPGG A+YPS+VLMNA+PAK Sbjct: 91 AHHQIEAFHRQRVPKSWVQFGADGEVLGKRYTPVDRAGLYVPGGRAAYPSTVLMNAVPAK 150 Query: 151 VAGVDRIVMVVP-APDGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVAKI 209 VAGV+R+V+ P PDG+LNP VLVAA+ AG+ EIYRVGGAQAIAALAYGT TI V I Sbjct: 151 VAGVERVVITTPPGPDGSLNPAVLVAAQEAGIEEIYRVGGAQAIAALAYGTATIPKVDVI 210 Query: 210 VGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQSI 269 GPGN YV AK++V+GTVGID +AGPSEVLI+AD+ NP W+AADLLAQAEHD A +I Sbjct: 211 SGPGNIYVTLAKKLVYGTVGIDSLAGPSEVLIIADRSANPRWVAADLLAQAEHDPLAAAI 270 Query: 270 LMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHL 329 L+T D A V VERQL R + +G I+V E A+ L+N+ A EHL Sbjct: 271 LITPDLELATQVGFEVERQLQDHPRRLVTEKAIAHYGLAIVVDSLETAVKLSNQFAPEHL 330 Query: 330 EIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMK 389 E+ V D A V ++R+AG+IF+G TPE IGDYV G NH LPT+ +AR++S LSV ++K Sbjct: 331 ELEVEDPWALVEQVRHAGAIFLGSLTPEAIGDYVAGPNHTLPTSGAARYASALSVETFLK 390 Query: 390 RTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427 +SL++ + L+ + A +A AEGL++HA+SV +R Sbjct: 391 SSSLIEYTAASLQRVARAVDVLATAEGLESHAESVRLR 428 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: 485 Number of extensions: 21 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 Synpcc7942_1519 Synpcc7942_1519 (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.18591.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-173 561.6 1.3 6.4e-173 561.4 1.3 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1519 Synpcc7942_1519 histidinol dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1519 Synpcc7942_1519 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 561.4 1.3 6.4e-173 6.4e-173 1 393 [] 34 428 .. 34 428 .. 1.00 Alignments for each domain: == domain 1 score: 561.4 bits; conditional E-value: 6.4e-173 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 v+ei+++v+++Gd+Al+e+t++fd++ ++e+lrvs +el++a++++++el +a++la+++ie+fh+++ lcl|FitnessBrowser__SynE:Synpcc7942_1519 34 VREIVQAVQRRGDAALIEFTQEFDGFalQAENLRVSGAELDAAYQQIPKELLDAIRLAHHQIEAFHRQR 102 89***********************878999************************************** PP TIGR00069 68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136 +p+s+ + ++g +lg++++p++r+glYvPgG+aaypStvlm+avpAkvAgv+++v++tPp dg++np lcl|FitnessBrowser__SynE:Synpcc7942_1519 103 VPKSWVQFGADGEVLGKRYTPVDRAGLYVPGGRAAYPSTVLMNAVPAKVAGVERVVITTPPGPDGSLNP 171 ********************************************************************* PP TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205 avl+aa+ +g++e+y+vGGaqaiaalayGt+t+pkvd+i GPGniyVt AKklv+g+vgid++aGPsEv lcl|FitnessBrowser__SynE:Synpcc7942_1519 172 AVLVAAQEAGIEEIYRVGGAQAIAALAYGTATIPKVDVISGPGNIYVTLAKKLVYGTVGIDSLAGPSEV 240 ********************************************************************* PP TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274 l+iad+sanp++vaaDll+qaEHd+ a+ail+t++ ela++v eve+ql++++r+ ++ek+++++g lcl|FitnessBrowser__SynE:Synpcc7942_1519 241 LIIADRSANPRWVAADLLAQAEHDPLAAAILITPDLELATQVGFEVERQLQDHPRRLVTEKAIAHYGLA 309 ********************************************************************* PP TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343 i+vd+le a++lsn++ApEHLel+++dp++l++++++aG++flG+ tpea+gdyvaGpnh+LPTsg+Ar lcl|FitnessBrowser__SynE:Synpcc7942_1519 310 IVVDSLETAVKLSNQFAPEHLELEVEDPWALVEQVRHAGAIFLGSLTPEAIGDYVAGPNHTLPTSGAAR 378 ********************************************************************* PP TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 +as+lsve+Flk++s++e++ ++l+++a+av la aEgLe Hae+v+ R lcl|FitnessBrowser__SynE:Synpcc7942_1519 379 YASALSVETFLKSSSLIEYTAASLQRVARAVDVLATAEGLESHAESVRLR 428 ***********************************************998 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.54 // [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