Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate N515DRAFT_2935 N515DRAFT_2935 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::Q9S5G5 (355 letters) >FitnessBrowser__Dyella79:N515DRAFT_2935 Length = 354 Score = 387 bits (994), Expect = e-112 Identities = 196/355 (55%), Positives = 242/355 (68%), Gaps = 1/355 (0%) Query: 1 MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPQLLKLQKAGYKLVMITNQDGLG 60 MS+K LF+DRDG LI EP +D Q+D ++KLA PGVI L + AGY+LVM+TNQDGLG Sbjct: 1 MSRKLLFVDRDGCLIEEP-ADEQIDSYEKLALLPGVIAALQRCVAAGYELVMVTNQDGLG 59 Query: 61 TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120 T SFP+A F GPH L+M+I SQGV+F EVLI P D D RKP + ++ YLA+ Sbjct: 60 TDSFPEAHFTGPHELLMRILASQGVRFREVLIDRSFPRDGLDTRKPGIGMLRHYLADDGW 119 Query: 121 DRANSYVIGDRATDIQLAENMGINGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180 RA S ++GDR TD+Q A NMG+ G + L W I QL R A V RNT+ET+I Sbjct: 120 SRAASAMVGDRQTDLQFAANMGVRGFLVGPKGLAWEEIAHQLLDAPRTATVTRNTRETRI 179 Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240 V+V LDR K TG+GFFDHML+QI HGGF +E+ GD ID+HHT+ED LALG Sbjct: 180 TVRVDLDRVAEPKAQTGLGFFDHMLEQIGKHGGFALELECDGDTRIDEHHTIEDCALALG 239 Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300 +AL+ ALGDKRGI R+GF LPMDE A ALD+SGRP+ ++ F +RVGD+ TE++ H Sbjct: 240 QALRQALGDKRGIARYGFTLPMDESQASAALDLSGRPYFVFEGSFPRERVGDVPTELVPH 299 Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355 FFRSL T+G LHL G N HH VE+ FK R LRQA+R EG LPS+KG L Sbjct: 300 FFRSLCETLGANLHLSVYGDNAHHMVEACFKVVARALRQALRREGSELPSTKGAL 354 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: 426 Number of extensions: 16 Number of successful extensions: 3 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: 354 Length adjustment: 29 Effective length of query: 326 Effective length of database: 325 Effective search space: 105950 Effective search space used: 105950 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 N515DRAFT_2935 N515DRAFT_2935 (imidazoleglycerol-phosphate dehydratase)
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.8257.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-63 196.8 0.0 1.2e-62 196.3 0.0 1.2 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 N515DRAFT_2935 imidazoleglycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 N515DRAFT_2935 imidazoleglycerol-phosphate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 196.3 0.0 1.2e-62 1.2e-62 2 160 .. 4 161 .. 3 162 .. 0.99 Alignments for each domain: == domain 1 score: 196.3 bits; conditional E-value: 1.2e-62 TIGR01261 2 kilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedf 67 k+lf+drdG lieeP d q+d++ekl+l ++vi+al + +agy+lv+vtnqdGlGt+sfP+++f lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 4 KLLFVDRDGCLIEEPA-DEQIDSYEKLALLPGVIAALQRCVAAGYELVMVTNQDGLGTDSFPEAHF 68 89*************9.99*********************************************** PP TIGR01261 68 dkphalmlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdl 133 +ph+l++ i+ s+G+ f++vli+++f+ d ++rkP i++l++yl+++ ++ s+++Gdr+tdl lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 69 TGPHELLMRILASQGVRFREVLIDRSFPRDGLDTRKPGIGMLRHYLADDGWSRAASAMVGDRQTDL 134 ****************************************************************** PP TIGR01261 134 qlaenlgirglkykeeelnwkeiakel 160 q+a n+g+rg+ + l+w+eia++l lcl|FitnessBrowser__Dyella79:N515DRAFT_2935 135 QFAANMGVRGFLVGPKGLAWEEIAHQL 161 *************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (354 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: 14.54 // [ok]
This GapMind analysis is from Apr 09 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