Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate Pf6N2E2_3252 Histidinol dehydrogenase (EC 1.1.1.23)
Query= BRENDA::Q8G2R2 (430 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 Length = 445 Score = 394 bits (1011), Expect = e-114 Identities = 207/428 (48%), Positives = 281/428 (65%), Gaps = 1/428 (0%) Query: 2 VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61 + L DPDF LS + + V++ V +I+ VR GD+AL++++++FD + + Sbjct: 7 IRRLNAVDPDFAHHLDHLLSWESVSDDSVNQRVLDIIKAVRERGDAALVEFTQKFDGLQV 66 Query: 62 EKTGIAVTEAE-IDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120 + E ++ A EAL+ A R+ +H RQ YT+A G LG + Sbjct: 67 ASMADLILPRERLELALTRITVPQREALEKAASRVRDYHERQKQDSWSYTEADGTVLGQK 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 VDRVFTIGGAQAVAALAYGTESVPRVDKVVGPGNIYVATAKRHVFGQVGIDMIAGPSEIL 246 Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300 +V D +PDWIA DL +QAEHD AQ+IL++ D F V ++++ L T+ R E + Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASIDKLLPTMDRAEIINT 306 Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360 S GA+I V+D E AI +ANRIA EHLE++VAD +A++P+IR+AG+IF+G +T E +G Sbjct: 307 SINGRGALIHVRDMEQAIEVANRIAPEHLELSVADPQAWLPQIRHAGAIFMGRHTSEALG 366 Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420 DY G NHVLPT+ +ARFSS L V D+ KR+S++ + LG A +AR E L AH Sbjct: 367 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSEQGASELGKTASVLARGESLSAH 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: 491 Number of extensions: 29 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: 445 Length adjustment: 32 Effective length of query: 398 Effective length of database: 413 Effective search space: 164374 Effective search space used: 164374 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 Pf6N2E2_3252 (Histidinol dehydrogenase (EC 1.1.1.23))
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.2588.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-166 538.2 0.1 7.9e-166 538.0 0.1 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 Histidinol dehydrogenase (EC 1.1 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 Histidinol dehydrogenase (EC 1.1.1.23) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 538.0 0.1 7.9e-166 7.9e-166 1 393 [] 39 433 .. 39 433 .. 0.99 Alignments for each domain: == domain 1 score: 538.0 bits; conditional E-value: 7.9e-166 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaenie 61 v +ii++vr++Gd+Al+e+t+kfd++ ++++l +++e+le al++++ +eale+aa++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 39 VLDIIKAVRERGDAALVEFTQKFDGLqvaSMADLILPRERLELALTRITVPQREALEKAASRVR 102 679*********************99556677889***************************** PP TIGR00069 62 kfhekqlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvv 125 ++he+q+++s+++++++g++lgqkv+pl+r+glYvPgGka+ypS+vlm+a+pAkvAgv+e+v+v lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 103 DYHERQKQDSWSYTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVTEVVMV 166 **************************************************************** PP TIGR00069 126 tPpkkdgkvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKkl 189 P+ +g++n+ vlaaa ++gvd+v+++GGaqa+aalayGte+vp+vdk+vGPGniyV++AK++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 167 VPTP-RGEINELVLAAACIAGVDRVFTIGGAQAVAALAYGTESVPRVDKVVGPGNIYVATAKRH 229 ***6.9********************************************************** PP TIGR00069 190 vfgevgidmiaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeevee 253 vfg+vgidmiaGPsE+lv++d +++p+++a+Dl+sqaEHdedaqailv++++e+++kv +++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 230 VFGQVGIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAEFLDKVAASIDK 293 **************************************************************** PP TIGR00069 254 qleelerkeiaekslekngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvfl 317 l +++r+ei+++s++ +ga+i v+d+e+a+e++n++ApEHLel ++dp+++l++i++aG++f+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 294 LLPTMDRAEIINTSINGRGALIHVRDMEQAIEVANRIAPEHLELSVADPQAWLPQIRHAGAIFM 357 **************************************************************** PP TIGR00069 318 GeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaE 381 G++t+ealgdy+aGpnhvLPTsgtArf+s+l+v+dF+kr+s++ +s+++++el+++++ la+ E lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 358 GRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSEQGASELGKTASVLARGE 421 **************************************************************** PP TIGR00069 382 gLeaHaeavevR 393 L+aHa+++e R lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3252 422 SLSAHARSAEYR 433 ********9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (445 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: 13.49 // [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