Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate WP_013554303.1 NITSA_RS06905 histidinol dehydrogenase
Query= BRENDA::Q8G2R2 (430 letters) >NCBI__GCF_000186245.1:WP_013554303.1 Length = 431 Score = 353 bits (905), Expect = e-102 Identities = 192/421 (45%), Positives = 262/421 (62%), Gaps = 1/421 (0%) Query: 9 DPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRID-LEKTGIA 67 D F + F L + V V ++ +R EG++AL + RFDR + + + Sbjct: 8 DERFPEIFEELLGRGAMDIDQVTETVAALLKEIREEGNAALRRHIARFDRWEPADDAALQ 67 Query: 68 VTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSRWTAIEAV 127 V AE+ A++A +AL LA DRI+ +H + LPK + G LG + T ++ Sbjct: 68 VDPAEMAMAYEAIAPELRDALHLAYDRIKAYHEKLLPKSWFEYEKNGSMLGQKVTPVDRA 127 Query: 128 GLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAGVSEIYRV 187 GLY+PGG A+YPSS+LMNA+PA VAGV+ IV+ P PD +N L+L A L G+ ++++V Sbjct: 128 GLYIPGGKAAYPSSLLMNAVPAIVAGVEEIVVCTPTPDNEINVLLLAACHLCGIKKVFKV 187 Query: 188 GGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVLIVADKDN 247 GGA AI A+AYGTETI V I GPGN +VA AK++V+G V IDMIAGPSE+ I+AD Sbjct: 188 GGASAIGAMAYGTETIPKVDVITGPGNIFVATAKKLVYGEVNIDMIAGPSEIGILADGSA 247 Query: 248 NPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASASWRDFGA 307 PDW+A DLL+QAEHD A SIL+T+D A V + VE+ L L R A S + GA Sbjct: 248 RPDWVAMDLLSQAEHDEMASSILITDDAELAKRVVDEVEKALSKLEREAIARKSIEERGA 307 Query: 308 VILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIGDYVGGCN 367 +I+ D +AI L N+IA EHLE+ A + I++AG+IF+G YTPE IGDY+ G N Sbjct: 308 IIVTSDMAEAIDLMNQIAPEHLEVMTASPMELLGSIKHAGAIFLGHYTPEPIGDYIAGPN 367 Query: 368 HVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAHAQSVAIR 427 H LPT +A+F S LSV ++K++SL+ + +R LG A +A EGL AH SV IR Sbjct: 368 HTLPTGGTAKFYSPLSVEHFLKKSSLIMMTEAGVRELGDACALLAHTEGLTAHEASVRIR 427 Query: 428 L 428 L Sbjct: 428 L 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: 416 Number of extensions: 15 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: 431 Length adjustment: 32 Effective length of query: 398 Effective length of database: 399 Effective search space: 158802 Effective search space used: 158802 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_013554303.1 NITSA_RS06905 (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.19888.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-169 549.3 0.3 3.5e-169 549.1 0.3 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013554303.1 NITSA_RS06905 histidinol dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013554303.1 NITSA_RS06905 histidinol dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 549.1 0.3 3.5e-169 3.5e-169 1 393 [] 33 427 .. 33 427 .. 0.99 Alignments for each domain: == domain 1 score: 549.1 bits; conditional E-value: 3.5e-169 TIGR00069 1 vkeiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhek 66 v+++++++r+eG++Al+++ +fd++ + ++l+v +e++ a+ea+ +el++al+la+++i+++hek lcl|NCBI__GCF_000186245.1:WP_013554303.1 33 VAALLKEIREEGNAALRRHIARFDRWepaDDAALQVDPAEMAMAYEAIAPELRDALHLAYDRIKAYHEK 101 67899********************97666679************************************ PP TIGR00069 67 qlpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkkdgkvn 135 lp+s++ +++g++lgqkv+p++r+glY+PgGkaaypS++lm+avpA vAgv+eivv+tP+ d+++n lcl|NCBI__GCF_000186245.1:WP_013554303.1 102 LLPKSWFEYEKNGSMLGQKVTPVDRAGLYIPGGKAAYPSSLLMNAVPAIVAGVEEIVVCTPTP-DNEIN 169 **************************************************************6.999** PP TIGR00069 136 pavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsE 204 +laa++l+g+++v+kvGGa+ai+a+ayGtet+pkvd+i+GPGni+V++AKklv+gev+idmiaGPsE lcl|NCBI__GCF_000186245.1:WP_013554303.1 170 VLLLAACHLCGIKKVFKVGGASAIGAMAYGTETIPKVDVITGPGNIFVATAKKLVYGEVNIDMIAGPSE 238 ********************************************************************* PP TIGR00069 205 vlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaeksleknga 273 + ++ad sa p++va+DllsqaEHde a++il+t+++ela++v +eve+ l++ler+ ia+ks+e++ga lcl|NCBI__GCF_000186245.1:WP_013554303.1 239 IGILADGSARPDWVAMDLLSQAEHDEMASSILITDDAELAKRVVDEVEKALSKLEREAIARKSIEERGA 307 ********************************************************************* PP TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342 ii+++d++ea++l+n++ApEHLe++t++p+ell +ik+aG++flG+ytpe++gdy+aGpnh+LPT+gtA lcl|NCBI__GCF_000186245.1:WP_013554303.1 308 IIVTSDMAEAIDLMNQIAPEHLEVMTASPMELLGSIKHAGAIFLGHYTPEPIGDYIAGPNHTLPTGGTA 376 ********************************************************************* PP TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393 +f+s+lsve+Flk++s++ +++++++el++a++ la++EgL+aH+++v++R lcl|NCBI__GCF_000186245.1:WP_013554303.1 377 KFYSPLSVEHFLKKSSLIMMTEAGVRELGDACALLAHTEGLTAHEASVRIR 427 *************************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (431 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: 11.33 // [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