Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_011372131.1 SUDEN_RS02595 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000012965.1:WP_011372131.1 Length = 430 Score = 340 bits (871), Expect = 7e-98 Identities = 181/419 (43%), Positives = 262/419 (62%), Gaps = 3/419 (0%) Query: 12 FEQKFAAFLS-GKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDR-IDLEKTGIAVT 69 F+ +F L GK +++ V V I+D ++ + AL ++ +FD+ + + ++ Sbjct: 11 FKAEFKELLERGKMDIAH-VSATVGTIIDEIKSNKNQALKEHITKFDKWTPVSDEDLKIS 69 Query: 70 EAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAVGL 129 + A++ + AL L+ DRI+ +H +Q P+ + G LG R T +++ GL Sbjct: 70 TESMSRAYENLDKALKAALHLSYDRIKAYHEKQKPRSWFDDEPNGTILGQRVTPVDSAGL 129 Query: 130 YVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRVGG 189 Y+PGG A+YPSS+LMN +PA+VAGV IV+ P P+ N L+L A L GVSE+Y+VGG Sbjct: 130 YIPGGKAAYPSSLLMNVIPAQVAGVQNIVVCTPTPENEPNELLLAACHLCGVSEVYKVGG 189 Query: 190 AQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDNNP 249 A AIAA+AYGTETI V I GPGN +VA AK++VFG V IDMIAGPSE+ I+AD NP Sbjct: 190 ASAIAAMAYGTETIPKVDVITGPGNIFVATAKKMVFGDVNIDMIAGPSEIGILADDSANP 249 Query: 250 DWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGAVI 309 +A D+L+QAEHD A SIL+T + A A++ +E L L R + A S GA+I Sbjct: 250 SHMAVDMLSQAEHDEMASSILITPSQKLADAIKAEIENWLKILPRQKIARESIEKRGAII 309 Query: 310 LVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCNHV 369 + D ++AI L N IA EHLE+A +P I++AG+IF+G TPE +GDY+ G NH Sbjct: 310 VTSDMQEAIDLMNEIAPEHLEVATLSPFELLPLIKHAGAIFLGHNTPEAVGDYMAGPNHT 369 Query: 370 LPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIRL 428 LPT +A+F S L V ++MK+TS++ ++ + +G IA+ EGL AH QS+ +RL Sbjct: 370 LPTGGTAKFFSPLGVENFMKKTSIISFSAKAINEIGEECALIAKIEGLTAHEQSIRVRL 428 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: 393 Number of extensions: 21 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: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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_011372131.1 SUDEN_RS02595 (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.29339.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-170 552.5 0.3 3.7e-170 552.3 0.3 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011372131.1 SUDEN_RS02595 histidinol dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011372131.1 SUDEN_RS02595 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 552.3 0.3 3.7e-170 3.7e-170 1 393 [] 33 427 .. 33 427 .. 0.99 Alignments for each domain: == domain 1 score: 552.3 bits; conditional E-value: 3.7e-170 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 v +ii++++++ ++Al+e+ +kfdk+ + e+l++s+e++++a+e++d++lk+al+l++++i+++hek lcl|NCBI__GCF_000012965.1:WP_011372131.1 33 VGTIIDEIKSNKNQALKEHITKFDKWtpvSDEDLKISTESMSRAYENLDKALKAALHLSYDRIKAYHEK 101 678**********************9777889************************************* PP TIGR00069 67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135 q+p+s++ ++ +g++lgq+v+p++++glY+PgGkaaypS++lm+++pA+vAgv++ivv+tP+ +++ n lcl|NCBI__GCF_000012965.1:WP_011372131.1 102 QKPRSWFDDEPNGTILGQRVTPVDSAGLYIPGGKAAYPSSLLMNVIPAQVAGVQNIVVCTPTP-ENEPN 169 **************************************************************6.899** PP TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204 + +laa++l+gv+evykvGGa+aiaa+ayGtet+pkvd+i+GPGni+V++AKk+vfg+v+idmiaGPsE lcl|NCBI__GCF_000012965.1:WP_011372131.1 170 ELLLAACHLCGVSEVYKVGGASAIAAMAYGTETIPKVDVITGPGNIFVATAKKMVFGDVNIDMIAGPSE 238 ********************************************************************* PP TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 + ++ad+sanp+++a+D+lsqaEHde a++il+t+s++la+++++e+e+ l+ l+r++ia++s+ek+ga lcl|NCBI__GCF_000012965.1:WP_011372131.1 239 IGILADDSANPSHMAVDMLSQAEHDEMASSILITPSQKLADAIKAEIENWLKILPRQKIARESIEKRGA 307 ********************************************************************* PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342 ii+++d++ea++l+ne+ApEHLe++t +p ell+ ik+aG++flG++tpea+gdy+aGpnh+LPT+gtA lcl|NCBI__GCF_000012965.1:WP_011372131.1 308 IIVTSDMQEAIDLMNEIAPEHLEVATLSPFELLPLIKHAGAIFLGHNTPEAVGDYMAGPNHTLPTGGTA 376 ********************************************************************* PP TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 +f s+l+ve+F+k++s++++s +a++e++e+++ +a++EgL+aH+++++vR lcl|NCBI__GCF_000012965.1:WP_011372131.1 377 KFFSPLGVENFMKKTSIISFSAKAINEIGEECALIAKIEGLTAHEQSIRVR 427 *************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (430 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: 00:00:00.01 # Mc/sec: 10.82 // [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