Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013841335.1 DESRU_RS06590 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000215085.1:WP_013841335.1 Length = 432 Score = 394 bits (1011), Expect = e-114 Identities = 206/412 (50%), Positives = 275/412 (66%), Gaps = 1/412 (0%) Query: 18 AFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDLEKTGIAVTEAEIDAAF 77 A L G+ E + V I+ VR GD AL ++RRFD L + VT+ EID A+ Sbjct: 15 ALLKGRSGGQEGIASRVAAIMQEVRERGDIALCGFTRRFDGASLTPEQLRVTDEEIDQAY 74 Query: 78 DAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGLYVPGGTAS 137 + +LKLARDRI K+H +QL + T+ G LG T ++ VG+YVPGGTAS Sbjct: 75 SMVDQEVLTSLKLARDRIRKYHQKQLTRSWFDTEPNGTLLGQLITPLDRVGVYVPGGTAS 134 Query: 138 YPSSVLMNAMPAKVAGVDRIVMVVP-APDGNLNPLVLVAARLAGVSEIYRVGGAQAIAAL 196 YPSSVLMNA+PAKVAGV ++VMV P DG LNP LVAAR AGV EIY+ GGAQAIAAL Sbjct: 135 YPSSVLMNAVPAKVAGVSQVVMVTPPGADGKLNPYTLVAAREAGVDEIYKAGGAQAIAAL 194 Query: 197 AYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNPDWIAADL 256 AYGTETI PV KI GPGN +V AKR+V+G V IDM+AGPSEVL+VAD NP++ AAD+ Sbjct: 195 AYGTETIAPVDKITGPGNIFVTLAKRMVYGQVDIDMLAGPSEVLVVADASANPEYAAADM 254 Query: 257 LAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVILVKDFED 316 L+QAEHD A ++L+T+ A V + +E+Q+ L R + A + + A+++ E+ Sbjct: 255 LSQAEHDVLASAVLLTHHRELAEWVRQELEKQVALLPRQDLAREALANHSALVITGSLEE 314 Query: 317 AIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHVLPTARSA 376 ++ LAN A EHLE+ V + ++ RIR+AG++F+G ++PE +GDY+ G NHVLPT +A Sbjct: 315 SLELANAFAPEHLELLVEEPFRWLSRIRHAGAVFLGAHSPEPVGDYLAGPNHVLPTGGTA 374 Query: 377 RFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428 RF S L+V +MK++S++ E L LGP I +A EGL AHA +V +RL Sbjct: 375 RFYSPLNVDTFMKKSSIISFSKENLELLGPDIIRLAEVEGLQAHANAVRVRL 426 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: 462 Number of extensions: 14 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: 432 Length adjustment: 32 Effective length of query: 398 Effective length of database: 400 Effective search space: 159200 Effective search space used: 159200 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_013841335.1 DESRU_RS06590 (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.3887205.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-174 565.0 0.0 6.1e-174 564.8 0.0 1.0 1 NCBI__GCF_000215085.1:WP_013841335.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841335.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 564.8 0.0 6.1e-174 6.1e-174 1 393 [] 31 425 .. 31 425 .. 0.99 Alignments for each domain: == domain 1 score: 564.8 bits; conditional E-value: 6.1e-174 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv..kleslrvseeeleealeavdeelkealelaaeniekfhekqlpes 71 v++i+++vr++Gd Al +t++fd++ ++e+lrv++ee+++a++ vd+e+ ++l+la ++i+k+h+kql++s NCBI__GCF_000215085.1:WP_013841335.1 31 VAAIMQEVRERGDIALCGFTRRFDGAslTPEQLRVTDEEIDQAYSMVDQEVLTSLKLARDRIRKYHQKQLTRS 103 789**********************977899****************************************** PP TIGR00069 72 veveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvnpavlaaakl 144 ++ ++ +g+llgq+++pl+rvg+YvPgG+a+ypS+vlm+avpAkvAgv+++v+vtPp dgk+np +l+aa+ NCBI__GCF_000215085.1:WP_013841335.1 104 WFDTEPNGTLLGQLITPLDRVGVYVPGGTASYPSSVLMNAVPAKVAGVSQVVMVTPPGADGKLNPYTLVAARE 176 ************************************************************************* PP TIGR00069 145 lgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEvlviadesanpel 217 +gvde+yk+GGaqaiaalayGtet+ +vdki+GPGni+Vt AK++v+g+v+idm+aGPsEvlv+ad+sanpe+ NCBI__GCF_000215085.1:WP_013841335.1 177 AGVDEIYKAGGAQAIAALAYGTETIAPVDKITGPGNIFVTLAKRMVYGQVDIDMLAGPSEVLVVADASANPEY 249 ************************************************************************* PP TIGR00069 218 vaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslekngaiilvddleealelsney 290 aaD+lsqaEHd a+a+l+t+++elae v++e+e+q++ l+r+++a+++l++++a++++ +lee lel+n++ NCBI__GCF_000215085.1:WP_013841335.1 250 AAADMLSQAEHDVLASAVLLTHHRELAEWVRQELEKQVALLPRQDLAREALANHSALVITGSLEESLELANAF 322 ************************************************************************* PP TIGR00069 291 ApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtArfasglsvedFlkrisvqels 363 ApEHLel +++p ++l++i++aG+vflG+++pe++gdy+aGpnhvLPT+gtArf+s+l+v++F+k++s++++s NCBI__GCF_000215085.1:WP_013841335.1 323 APEHLELLVEEPFRWLSRIRHAGAVFLGAHSPEPVGDYLAGPNHVLPTGGTARFYSPLNVDTFMKKSSIISFS 395 ************************************************************************* PP TIGR00069 364 kealeelaeaveklaeaEgLeaHaeavevR 393 ke+le l++++++lae+EgL+aHa+av+vR NCBI__GCF_000215085.1:WP_013841335.1 396 KENLELLGPDIIRLAEVEGLQAHANAVRVR 425 ****************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (432 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: 17.53 // [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