Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_038208762.1 Q392_RS14285 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000745855.1:WP_038208762.1 Length = 463 Score = 389 bits (998), Expect = e-112 Identities = 208/444 (46%), Positives = 288/444 (64%), Gaps = 20/444 (4%) Query: 5 LRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKT 64 L FE F A L + +++ V +I+ V+R GD+A+L+Y+RRFD + Sbjct: 10 LSTASASFEADFKARLHWSADTDAAIEQRVADILADVQRRGDAAVLEYTRRFDGLAAGSM 69 Query: 65 G-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDR---YTDALGVELGSR 120 + +T+A+ AAF++ PA+ +AL+ A +R+ +H Q Y DA G LG + Sbjct: 70 AQLELTQADFRAAFESLPAAQRDALRSAAERVRSYHEAQKKASGESWTYRDADGTLLGQK 129 Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAP---------------- 164 T ++ VG+YVPGG A+YPSS+LMNA+PA VAGV I+MVVP P Sbjct: 130 VTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAGVQEIIMVVPTPAKGSVATGGSGTEPAA 189 Query: 165 DGNLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIV 224 G N LVL AA +AGV+ + +GGAQA+AALAYGT T+ V KI GPGNAYVAAAKR V Sbjct: 190 QGERNVLVLAAAHVAGVTRAFTIGGAQAVAALAYGTATVPAVDKITGPGNAYVAAAKRRV 249 Query: 225 FGTVGIDMIAGPSEVLIVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEA 284 FGTVGIDMIAGPSE+L++AD PDW+A DL +QAEHD AQSIL++ D A+ AV+ Sbjct: 250 FGTVGIDMIAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILLSPDAAYIDAVQRE 309 Query: 285 VERQLHTLARTETASASWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIR 344 ++R L + R + +AS GA+I +D E+A ++NRIA EHLE++ + + P +R Sbjct: 310 IDRLLPDMPRAQIIAASLTGRGALIHTRDMEEACAISNRIAPEHLEVSSREPHRWEPLLR 369 Query: 345 NAGSIFIGGYTPEVIGDYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRAL 404 +AG+IF+G +T E +GDY G NHVLPT+ +ARFSS L V D+ KR+SL+++ + +AL Sbjct: 370 HAGAIFLGAFTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSLIEVSEQGAQAL 429 Query: 405 GPAAIEIARAEGLDAHAQSVAIRL 428 GP A E+A EGL AHA++ +RL Sbjct: 430 GPIAAELAYGEGLQAHARAAEMRL 453 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: 531 Number of extensions: 26 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: 463 Length adjustment: 33 Effective length of query: 397 Effective length of database: 430 Effective search space: 170710 Effective search space used: 170710 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_038208762.1 Q392_RS14285 (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.3857076.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-156 508.1 0.3 2e-155 503.8 0.3 2.0 1 NCBI__GCF_000745855.1:WP_038208762.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038208762.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 503.8 0.3 2e-155 2e-155 1 393 [] 39 452 .. 39 452 .. 0.95 Alignments for each domain: == domain 1 score: 503.8 bits; conditional E-value: 2e-155 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekqlpe 70 v++i++dv+++Gd+A+leyt++fd++ ++++l+++++++++a e+++++ ++al+ aae+++++he+q+++ NCBI__GCF_000745855.1:WP_038208762.1 39 VADILADVQRRGDAAVLEYTRRFDGLaagSMAQLELTQADFRAAFESLPAAQRDALRSAAERVRSYHEAQKKA 111 789**********************98888999*************************************987 PP TIGR00069 71 s...veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkv...... 134 s +++++++g+llgqkv+pl+rvg+YvPgGkaaypS++lm+a+pA+vAgv+ei++v P+ +g+v NCBI__GCF_000745855.1:WP_038208762.1 112 SgesWTYRDADGTLLGQKVTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAGVQEIIMVVPTPAKGSVatggsg 184 6677******************************************************997655544122222 PP TIGR00069 135 .........npavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidm 198 n vlaaa+++gv++ +++GGaqa+aalayGt+tvp+vdki+GPGn+yV+aAK+ vfg+vgidm NCBI__GCF_000745855.1:WP_038208762.1 185 tepaaqgerNVLVLAAAHVAGVTRAFTIGGAQAVAALAYGTATVPAVDKITGPGNAYVAAAKRRVFGTVGIDM 257 2111111115679************************************************************ PP TIGR00069 199 iaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekn 271 iaGPsE+lv+ad s+ p++va+Dl+sqaEHde aq+il++++++ +++v++e+++ l +++r++i+ +sl+ + NCBI__GCF_000745855.1:WP_038208762.1 258 IAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILLSPDAAYIDAVQREIDRLLPDMPRAQIIAASLTGR 330 ************************************************************************* PP TIGR00069 272 gaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArf 344 ga+i ++d+eea+++sn++ApEHLe+ ++p+++ + +++aG++flG+ t+e+lgdy+aGpnhvLPTsgtArf NCBI__GCF_000745855.1:WP_038208762.1 331 GALIHTRDMEEACAISNRIAPEHLEVSSREPHRWEPLLRHAGAIFLGAFTSESLGDYCAGPNHVLPTSGTARF 403 ************************************************************************* PP TIGR00069 345 asglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 +s+l+v+dF+kr+s++e+s++++++l++ +++la EgL+aHa+a+e+R NCBI__GCF_000745855.1:WP_038208762.1 404 SSPLGVYDFQKRSSLIEVSEQGAQALGPIAAELAYGEGLQAHARAAEMR 452 **********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (463 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: 14.66 // [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