Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_012502672.1 CPAR_RS07305 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000020505.1:WP_012502672.1 Length = 428 Score = 334 bits (857), Expect = 3e-96 Identities = 185/422 (43%), Positives = 257/422 (60%), Gaps = 3/422 (0%) Query: 8 TDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIA 67 T P E L+ + + V EI+ RVR EGD A+LDY+ RF + LE + Sbjct: 6 TFPQDEAALKEQLNRTVSFDPEAQKTVDEILHRVRTEGDKAILDYTERFQGVRLES--MM 63 Query: 68 VTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAV 127 V + EIDAA+ + + L+ A I H + K Y GV LG R T +E Sbjct: 64 VPQEEIDAAYAESDPEFISILEEAYANITAFHRNEAEKSFFYEQKGGVILGQRVTPMEKA 123 Query: 128 GLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAP-DGNLNPLVLVAARLAGVSEIYR 186 LYVPGG A+YPSSVLMNA PA+VAGVD I M P +G +NP +L AA++AG++ +YR Sbjct: 124 LLYVPGGKAAYPSSVLMNAAPAQVAGVDEIYMTTPCDAEGKVNPHILAAAKVAGITSVYR 183 Query: 187 VGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKD 246 +GGAQA+AA AYGT +I V + GPGN YVA AK+ VFG V ID IAGPSEV+++AD+ Sbjct: 184 LGGAQAVAAFAYGTASIPKVDIVTGPGNKYVALAKKQVFGHVSIDSIAGPSEVVVIADEK 243 Query: 247 NNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFG 306 +P++I D+ AQAEHD A ++L+T A A AV+EA R T+ R E + + D G Sbjct: 244 ADPEFIVMDMFAQAEHDPDASAVLITPSAAVAKAVQEAAARLASTMLRGEVITKALTDNG 303 Query: 307 AVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGC 366 +++ ++A +++ IA EHLE+ V + +P +R+AG+IF+G ++ E +GDY G Sbjct: 304 GIVVTNSMQEACKVSDMIAPEHLELHVENPWEILPDLRHAGAIFMGPWSCETVGDYFAGP 363 Query: 367 NHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAI 426 NH LPT +ARF S LSV D++K TS++ +L G A EGL AHA++V + Sbjct: 364 NHTLPTNGTARFFSPLSVRDFVKHTSIIAWSKGELGRAGEKIARFADHEGLQAHAEAVRV 423 Query: 427 RL 428 RL Sbjct: 424 RL 425 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: 396 Number of extensions: 20 Number of successful extensions: 3 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: 428 Length adjustment: 32 Effective length of query: 398 Effective length of database: 396 Effective search space: 157608 Effective search space used: 157608 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_012502672.1 CPAR_RS07305 (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.1319074.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-166 540.8 2.3 1.3e-166 540.6 2.3 1.0 1 NCBI__GCF_000020505.1:WP_012502672.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000020505.1:WP_012502672.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 540.6 2.3 1.3e-166 1.3e-166 1 393 [] 32 424 .. 32 424 .. 1.00 Alignments for each domain: == domain 1 score: 540.6 bits; conditional E-value: 1.3e-166 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlpesve 73 v ei+++vr+eGd+A+l+yte+f++v+les+ v++ee+++a+++ d+e+++ le+a++ni++fh+++ ++s++ NCBI__GCF_000020505.1:WP_012502672.1 32 VDEILHRVRTEGDKAILDYTERFQGVRLESMMVPQEEIDAAYAESDPEFISILEEAYANITAFHRNEAEKSFF 104 789********************************************************************** PP TIGR00069 74 veteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakllg 146 +e++ gv+lgq+v+p+e++ lYvPgGkaaypS+vlm+a pA+vAgv+ei+++tP + +gkvnp++laaak++g NCBI__GCF_000020505.1:WP_012502672.1 105 YEQKGGVILGQRVTPMEKALLYVPGGKAAYPSSVLMNAAPAQVAGVDEIYMTTPCDAEGKVNPHILAAAKVAG 177 ************************************************************************* PP TIGR00069 147 vdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpelva 219 +++vy++GGaqa+aa+ayGt+++pkvd+++GPGn+yV+ AKk+vfg+v+id+iaGPsEv+viade+a+pe+++ NCBI__GCF_000020505.1:WP_012502672.1 178 ITSVYRLGGAQAVAAFAYGTASIPKVDIVTGPGNKYVALAKKQVFGHVSIDSIAGPSEVVVIADEKADPEFIV 250 ************************************************************************* PP TIGR00069 220 aDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsneyAp 292 +D+++qaEHd+da+a+l+t+s+++a++v+e+ ++ ++++ r e+++k+l++ng i+++++++ea+++s+ +Ap NCBI__GCF_000020505.1:WP_012502672.1 251 MDMFAQAEHDPDASAVLITPSAAVAKAVQEAAARLASTMLRGEVITKALTDNGGIVVTNSMQEACKVSDMIAP 323 ************************************************************************* PP TIGR00069 293 EHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqelske 365 EHLel++++p+e+l+++++aG++f+G++++e++gdy+aGpnh+LPT+gtArf s+lsv+dF+k++s++ sk NCBI__GCF_000020505.1:WP_012502672.1 324 EHLELHVENPWEILPDLRHAGAIFMGPWSCETVGDYFAGPNHTLPTNGTARFFSPLSVRDFVKHTSIIAWSKG 396 ************************************************************************* PP TIGR00069 366 aleelaeaveklaeaEgLeaHaeavevR 393 +l + +e+++++a+ EgL+aHaeav+vR NCBI__GCF_000020505.1:WP_012502672.1 397 ELGRAGEKIARFADHEGLQAHAEAVRVR 424 **************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (428 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: 00:00:00.00 # Mc/sec: 17.05 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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