Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate 6937803 Sama_1944 imidazole glycerol-phosphate dehydratase/histidinol phosphatase (RefSeq)
Query= SwissProt::Q9S5G5 (355 letters) >FitnessBrowser__SB2B:6937803 Length = 355 Score = 457 bits (1176), Expect = e-133 Identities = 221/355 (62%), Positives = 269/355 (75%) Query: 1 MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPQLLKLQKAGYKLVMITNQDGLG 60 M QK LFIDRDGTLI EP +D QVD KL FEP IP LL+LQKAGY+L+M++NQDGLG Sbjct: 1 MPQKMLFIDRDGTLIEEPVTDKQVDSLSKLVFEPTAIPALLRLQKAGYRLIMVSNQDGLG 60 Query: 61 TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120 T SFPQ DFD PHNLMMQ+F SQGV+FDEVLICPH + C CRKPK+ LV+ +L + + Sbjct: 61 TPSFPQEDFDAPHNLMMQVFESQGVKFDEVLICPHFNDENCSCRKPKLGLVKSFLTQGLV 120 Query: 121 DRANSYVIGDRATDIQLAENMGINGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180 D S VIGDR TD++L MGI +Y RETL W I + L + R A VVR T+ET I Sbjct: 121 DFTASAVIGDRDTDVELGNAMGIKSFKYQRETLGWNAIADSLLAKGRCATVVRTTRETDI 180 Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240 V V LD G ++I+TG+GFFDHMLDQIATHG F +++NV GDL IDDHH+VEDT LALG Sbjct: 181 RVTVDLDTPGNNQIDTGIGFFDHMLDQIATHGNFSLKLNVDGDLEIDDHHSVEDTALALG 240 Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300 +AL+ ALGDKRGI RFGF LPMDE +C +DISGRP ++++A F+ +VG+++TEM+ H Sbjct: 241 DALRQALGDKRGIGRFGFALPMDEASGQCLMDISGRPFIKFEASFSRDKVGEMATEMVPH 300 Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355 FFRS + + TLH+ G NDHH+VE+LFK GRTLRQAI +EGD LPSSKGVL Sbjct: 301 FFRSFADGLRCTLHIGCDGDNDHHKVEALFKVLGRTLRQAIAIEGDALPSSKGVL 355 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: 447 Number of extensions: 15 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: 355 Length adjustment: 29 Effective length of query: 326 Effective length of database: 326 Effective search space: 106276 Effective search space used: 106276 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 6937803 Sama_1944 (imidazole glycerol-phosphate dehydratase/histidinol phosphatase (RefSeq))
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.9548.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-77 244.8 0.0 2.3e-77 244.1 0.0 1.3 1 lcl|FitnessBrowser__SB2B:6937803 Sama_1944 imidazole glycerol-pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937803 Sama_1944 imidazole glycerol-phosphate dehydratase/histidinol phosphatase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.1 0.0 2.3e-77 2.3e-77 1 160 [. 3 162 .. 3 163 .. 0.99 Alignments for each domain: == domain 1 score: 244.1 bits; conditional E-value: 2.3e-77 TIGR01261 1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklkeagyklvlvtnqdGlGtesfPkedfdkphalmlqi 77 qk+lfidrdGtlieeP +d qvd+l kl +e+++ipall+l++agy+l++v+nqdGlGt+sfP+edfd ph+lm+q+ lcl|FitnessBrowser__SB2B:6937803 3 QKMLFIDRDGTLIEEPVTDKQVDSLSKLVFEPTAIPALLRLQKAGYRLIMVSNQDGLGTPSFPQEDFDAPHNLMMQV 79 79*************************************************************************** PP TIGR01261 78 fkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkykeeelnwk 154 f+s+G++fd+vlicphf+++nc+crkPk++l++++l + +d s+viGdr+td++l + +gi+++ky++e+l+w+ lcl|FitnessBrowser__SB2B:6937803 80 FESQGVKFDEVLICPHFNDENCSCRKPKLGLVKSFLTQGLVDFTASAVIGDRDTDVELGNAMGIKSFKYQRETLGWN 156 ***************************************************************************** PP TIGR01261 155 eiakel 160 ia++l lcl|FitnessBrowser__SB2B:6937803 157 AIADSL 162 **9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (355 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: 13.39 // [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