Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_028951054.1 Q385_RS0107405 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000619805.1:WP_028951054.1 Length = 428 Score = 352 bits (903), Expect = e-101 Identities = 190/411 (46%), Positives = 271/411 (65%), Gaps = 7/411 (1%) Query: 19 FLSGKREVSEDV-DRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAF 77 +L + +V D+ + AV+EI+ V+ GD AL++Y+ +FD+I + + + E++ A+ Sbjct: 19 YLIKRADVETDLYETAVKEIIKNVKERGDEALVEYTEKFDKIKINPEDLIIPFEELERAY 78 Query: 78 DAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTAS 137 D A ++A +R+ + H Q K + + G+ LG + +E VGLYVPGG A+ Sbjct: 79 DEIEEEVRWAFEVAYERLYEFHELQKEKSF-FKEEDGMILGQKVIPLERVGLYVPGGKAA 137 Query: 138 YPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVGGAQAIAALA 197 YPSSVLMNA+PA+VAGV+ IV+ P P N L AA + G+ +YR+GGAQA+AA+A Sbjct: 138 YPSSVLMNAVPARVAGVEEIVICSPNP----NKYTLAAAFICGIDTVYRIGGAQAVAAMA 193 Query: 198 YGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADLL 257 YGTET++ V KIVGPGN YVA AK+ VFG V IDMIAGPSE+L++AD+ N W+AADLL Sbjct: 194 YGTETVKKVDKIVGPGNIYVALAKKNVFGVVDIDMIAGPSEILVIADETANYKWVAADLL 253 Query: 258 AQAEHDTAAQSILMTNDEAFAHAVEEAVERQ-LHTLARTETASASWRDFGAVILVKDFED 316 +QAEHD A SIL+T E A V++ + + L +R E A S ++G +V+D E Sbjct: 254 SQAEHDELAASILITTSEELAKNVKDYLYNELLKAFSRKEIAEKSLNNYGHAFIVEDLEK 313 Query: 317 AIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSA 376 A LAN +A EHLEI + + +I++AG+IF+G Y+ E +GDY+ G NHVLPT+RSA Sbjct: 314 ACELANYLAPEHLEIVTENPFDLLNKIKHAGAIFLGHYSTEPLGDYILGPNHVLPTSRSA 373 Query: 377 RFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427 RFSS L V D++KR+S++ + E + AI +A +EGL+AHA SV IR Sbjct: 374 RFSSPLGVYDFVKRSSVIYVSKEGFERVANHAINMANSEGLEAHALSVKIR 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: 429 Number of extensions: 19 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: 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_028951054.1 Q385_RS0107405 (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.665866.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-170 553.2 0.2 2.2e-170 553.0 0.2 1.0 1 NCBI__GCF_000619805.1:WP_028951054.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028951054.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 553.0 0.2 2.2e-170 2.2e-170 1 393 [] 35 424 .. 35 424 .. 0.98 Alignments for each domain: == domain 1 score: 553.0 bits; conditional E-value: 2.2e-170 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 vkeii++v+++GdeAl+eytekfdk+ ++e+l ++ eele+a+++++ee++ a+e a+e++ +fhe q+++s NCBI__GCF_000619805.1:WP_028951054.1 35 VKEIIKNVKERGDEALVEYTEKFDKIkiNPEDLIIPFEELERAYDEIEEEVRWAFEVAYERLYEFHELQKEKS 107 89**********************9977889**************************************9998 PP TIGR00069 72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144 + ++e+g++lgqkv plervglYvPgGkaaypS+vlm+avpA+vAgv+eiv+++P+ n+ +laaa + NCBI__GCF_000619805.1:WP_028951054.1 108 -FFKEEDGMILGQKVIPLERVGLYVPGGKAAYPSSVLMNAVPARVAGVEEIVICSPN-----PNKYTLAAAFI 174 .68889***************************************************.....599******** PP TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217 +g+d+vy++GGaqa+aa+ayGtetv+kvdkivGPGniyV+ AKk vfg v+idmiaGPsE+lviade+an ++ NCBI__GCF_000619805.1:WP_028951054.1 175 CGIDTVYRIGGAQAVAAMAYGTETVKKVDKIVGPGNIYVALAKKNVFGVVDIDMIAGPSEILVIADETANYKW 247 ************************************************************************* PP TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeq.leelerkeiaekslekngaiilvddleealelsne 289 vaaDllsqaEHde a++il+ttseela++v++ + ++ l++ +rkeiaeksl+++g ++v+dle+a+el+n NCBI__GCF_000619805.1:WP_028951054.1 248 VAADLLSQAEHDELAASILITTSEELAKNVKDYLYNElLKAFSRKEIAEKSLNNYGHAFIVEDLEKACELANY 320 *******************************998766167789****************************** PP TIGR00069 290 yApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqel 362 +ApEHLe+ t++p +ll+kik+aG++flG+y++e+lgdy+ GpnhvLPTs++Arf+s+l+v+dF+kr+sv+++ NCBI__GCF_000619805.1:WP_028951054.1 321 LAPEHLEIVTENPFDLLNKIKHAGAIFLGHYSTEPLGDYILGPNHVLPTSRSARFSSPLGVYDFVKRSSVIYV 393 ************************************************************************* PP TIGR00069 363 skealeelaeaveklaeaEgLeaHaeavevR 393 ske++e++a++++++a+ EgLeaHa +v++R NCBI__GCF_000619805.1:WP_028951054.1 394 SKEGFERVANHAINMANSEGLEAHALSVKIR 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 17.72 // [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