Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012284033.1 HM1_RS13880 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000019165.1:WP_012284033.1 Length = 426 Score = 367 bits (943), Expect = e-106 Identities = 199/412 (48%), Positives = 270/412 (65%), Gaps = 2/412 (0%) Query: 18 AFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAF 77 A+L K V V E++ VR +G +AL Y++RFD D++++ V+EAEIDAA+ Sbjct: 14 AYLQKKSFDDVAVAERVAEVIANVRNQGTAALFAYTKRFDGADVDESNFRVSEAEIDAAY 73 Query: 78 DAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTAS 137 S + AL+ A + I + H +QL +A G LG +E VG+YVPGG AS Sbjct: 74 SQVDPSVLAALRRACENIRRFHEKQLRPSWIEPEADGTMLGQLIRPLERVGVYVPGGLAS 133 Query: 138 YPSSVLMNAMPAKVAGVDRIVMVVP-APDGNLNPLVLVAARLAGVSEIYRVGGAQAIAAL 196 YPSSVLMNA+PAKVAGV ++VM P DG++NP LVAA+ AGV E+YR+GGAQA+AA+ Sbjct: 134 YPSSVLMNAVPAKVAGVPQVVMATPPGKDGSINPYSLVAAKEAGVDEVYRMGGAQAVAAM 193 Query: 197 AYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADL 256 A+G ++ V KI GPGN YV AK+ V+GTV IDM+AGPSEVL++AD+ P ++AAD Sbjct: 194 AFGVG-LKAVDKITGPGNIYVTLAKKQVYGTVDIDMLAGPSEVLVIADESAAPAYVAADF 252 Query: 257 LAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFED 316 L+QAEHD A ++L+T A A AVE + RQL TL R E + RD GA+ +VKD E+ Sbjct: 253 LSQAEHDVRAATVLVTPSAALADAVEAEIARQLATLPRREIMEQALRDNGAIFIVKDLEE 312 Query: 317 AIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSA 376 A ++NR A EHLE+ A + ++ AG+IF+G Y+PE +GDY G NHVLPT +A Sbjct: 313 ACQVSNRFAPEHLEVLTEAPFALLGKLTQAGAIFLGPYSPEPVGDYFAGPNHVLPTGGTA 372 Query: 377 RFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428 RF S L+V + K+TSL+ + I +A+AEGLDAHA +VA+RL Sbjct: 373 RFYSPLNVDTFQKKTSLIAYSKVRFDRDAKDIIALAKAEGLDAHANAVAVRL 424 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: 476 Number of extensions: 13 Number of successful extensions: 4 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: 426 Length adjustment: 32 Effective length of query: 398 Effective length of database: 394 Effective search space: 156812 Effective search space used: 156812 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_012284033.1 HM1_RS13880 (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.25211.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-173 561.0 0.9 9.7e-173 560.8 0.9 1.0 1 lcl|NCBI__GCF_000019165.1:WP_012284033.1 HM1_RS13880 histidinol dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012284033.1 HM1_RS13880 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 560.8 0.9 9.7e-173 9.7e-173 1 393 [] 30 423 .. 30 423 .. 0.99 Alignments for each domain: == domain 1 score: 560.8 bits; conditional E-value: 9.7e-173 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 v+e+i++vr++G +Al++yt++fd++ + +++rvse+e+++a+++vd+++ +al++a eni++fhekq lcl|NCBI__GCF_000019165.1:WP_012284033.1 30 VAEVIANVRNQGTAALFAYTKRFDGAdvDESNFRVSEAEIDAAYSQVDPSVLAALRRACENIRRFHEKQ 98 789*********************98667889************************************* PP TIGR00069 68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnp 136 l+ s+ +++g++lgq++rplervg+YvPgG a+ypS+vlm+avpAkvAgv+++v++tPp kdg++np lcl|NCBI__GCF_000019165.1:WP_012284033.1 99 LRPSWIEPEADGTMLGQLIRPLERVGVYVPGGLASYPSSVLMNAVPAKVAGVPQVVMATPPGKDGSINP 167 ********************************************************************* PP TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205 l+aak +gvdevy++GGaqa+aa+a+G+ +++vdki+GPGniyVt AKk+v+g+v+idm+aGPsEv lcl|NCBI__GCF_000019165.1:WP_012284033.1 168 YSLVAAKEAGVDEVYRMGGAQAVAAMAFGV-GLKAVDKITGPGNIYVTLAKKQVYGTVDIDMLAGPSEV 235 ******************************.9************************************* PP TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngai 274 lviadesa p++vaaD+lsqaEHd +a+++lvt+s++la++ve+e+++ql++l+r+ei+e++l++ngai lcl|NCBI__GCF_000019165.1:WP_012284033.1 236 LVIADESAAPAYVAADFLSQAEHDVRAATVLVTPSAALADAVEAEIARQLATLPRREIMEQALRDNGAI 304 ********************************************************************* PP TIGR00069 275 ilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtAr 343 ++v+dleea+++sn++ApEHLe+ t+ p +ll k+++aG++flG+y+pe++gdy+aGpnhvLPT+gtAr lcl|NCBI__GCF_000019165.1:WP_012284033.1 305 FIVKDLEEACQVSNRFAPEHLEVLTEAPFALLGKLTQAGAIFLGPYSPEPVGDYFAGPNHVLPTGGTAR 373 ********************************************************************* PP TIGR00069 344 fasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 f+s+l+v++F+k++s++ +sk +++ a+++++la+aEgL+aHa+av+vR lcl|NCBI__GCF_000019165.1:WP_012284033.1 374 FYSPLNVDTFQKKTSLIAYSKVRFDRDAKDIIALAKAEGLDAHANAVAVR 423 ***********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (426 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 13.36 // [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