Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_057506750.1 ABB28_RS00540 bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_001431535.1:WP_057506750.1 Length = 357 Score = 374 bits (960), Expect = e-108 Identities = 188/354 (53%), Positives = 248/354 (70%), Gaps = 5/354 (1%) Query: 6 LFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPQLLKLQKAGYKLVMITNQDGLGTQSFP 65 LFIDRDGTLI EP +D Q+D ++KL F VIP L+KL+ AG++ V+++NQDGLG++S+P Sbjct: 5 LFIDRDGTLIEEP-ADHQIDAYEKLRFVRDVIPALIKLRDAGWQFVIVSNQDGLGSESYP 63 Query: 66 QADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAMDRANS 125 QA FD PH LMM +F SQG+ F +VLI P + RKP + L+ YL ++++D A S Sbjct: 64 QAIFDAPHALMMHVFESQGITFRDVLIDTSWPHENLPTRKPGIGLMTAYLQDRSIDWARS 123 Query: 126 YVIGDRATDIQLAENMGINGLRYDRETL----NWPMIGEQLTRRDRYAHVVRNTKETQID 181 ++GDR TDIQ A+N+ I G + E +WP I L R A V RNTKET+I Sbjct: 124 AMVGDRLTDIQFAQNLNIRGFQLRTEEFGGDWDWPAIAHALADAPRTAVVQRNTKETRIR 183 Query: 182 VQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALGE 241 V++ LD + +I+TG+ FFDHML+QI HGG + I +GDL+ID+HHT+EDTGLALG+ Sbjct: 184 VELDLDAQAEPRIHTGLPFFDHMLEQIGKHGGISVRIQAEGDLHIDEHHTIEDTGLALGQ 243 Query: 242 ALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEHF 301 AL+ ALGDKRGI R+GF LPMDE LA ALD SGRP+ + EF +RVGDL TE++ HF Sbjct: 244 ALREALGDKRGIGRYGFTLPMDETLASAALDFSGRPYFVFDGEFKRERVGDLPTELVPHF 303 Query: 302 FRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355 FRSL G+ L+L+ +G NDHH+VE+ FKA R LR A+ +G LPS+KG L Sbjct: 304 FRSLCEAAGLNLNLQVRGDNDHHKVEACFKALARALRTAVARQGTELPSTKGAL 357 Lambda K H 0.322 0.140 0.420 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: 400 Number of extensions: 11 Number of successful extensions: 5 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: 355 Length of database: 357 Length adjustment: 29 Effective length of query: 326 Effective length of database: 328 Effective search space: 106928 Effective search space used: 106928 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_057506750.1 ABB28_RS00540 (bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB)
to HMM TIGR01261 (hisB: histidinol-phosphatase (EC 3.1.3.15))
# 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/TIGR01261.hmm # target sequence database: /tmp/gapView.18062.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01261 [M=161] Accession: TIGR01261 Description: hisB_Nterm: histidinol-phosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-73 229.5 0.0 9.6e-73 229.1 0.0 1.1 1 lcl|NCBI__GCF_001431535.1:WP_057506750.1 ABB28_RS00540 bifunctional histi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057506750.1 ABB28_RS00540 bifunctional histidinol-phosphatase/imidazoleglycerol-phospha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 229.1 0.0 9.6e-73 9.6e-73 2 160 .. 3 164 .. 2 165 .. 0.98 Alignments for each domain: == domain 1 score: 229.1 bits; conditional E-value: 9.6e-73 TIGR01261 2 kilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedfdkp 70 +ilfidrdGtlieeP d q+da+ekl++ ++vipal+kl++ag+++v+v+nqdGlG+es+P++ fd p lcl|NCBI__GCF_001431535.1:WP_057506750.1 3 PILFIDRDGTLIEEPA-DHQIDAYEKLRFVRDVIPALIKLRDAGWQFVIVSNQDGLGSESYPQAIFDAP 70 89*************9.**************************************************** PP TIGR01261 71 halmlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenl 139 halm+++f+s+Gi+f+dvli+ +++++n +rkP i+l+++yl++++id++rs+++Gdr td+q+a+nl lcl|NCBI__GCF_001431535.1:WP_057506750.1 71 HALMMHVFESQGITFRDVLIDTSWPHENLPTRKPGIGLMTAYLQDRSIDWARSAMVGDRLTDIQFAQNL 139 ********************************************************************* PP TIGR01261 140 girglkykeeeln....wkeiakel 160 +irg+++++ee++ w ia+ l lcl|NCBI__GCF_001431535.1:WP_057506750.1 140 NIRGFQLRTEEFGgdwdWPAIAHAL 164 ***********98887799999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (357 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: 10.23 // [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