Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate WP_012383261.1 BIND_RS01235 imidazole glycerol phosphate synthase subunit HisH
Query= BRENDA::Q5NMD4 (213 letters) >NCBI__GCF_000019845.1:WP_012383261.1 Length = 226 Score = 217 bits (552), Expect = 2e-61 Identities = 115/217 (52%), Positives = 144/217 (66%), Gaps = 15/217 (6%) Query: 9 VALIDYGAGNLRSVANAL----LASGLARENLVVTANPDEVLQADRVVLPGVGAFASCMQ 64 VA++DYG+GNL S A +G A + VT +P+ V ADR+VLPGVGAFA C + Sbjct: 13 VAIVDYGSGNLHSAHKAFERAASETGYAG-TIAVTHDPEAVALADRIVLPGVGAFADCRR 71 Query: 65 ALKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPND 124 L A+P M+ A+E AV +G+PFLGICVGMQLLA +G E+ GL WIKG+V L P D Sbjct: 72 GLNAVPGMIEAMEHAVRREGKPFLGICVGMQLLATRGLEHETTAGLDWIKGEVAALEPTD 131 Query: 125 PSCKVPHMGWNQIGLTTDSHPLLRAG--------EAYFLHSYAFVPEDESTLLATTEHGG 176 S K+PHMGWN + HPLL AG AYF+HSYAF P+ E+ L+ATT++GG Sbjct: 132 KSLKIPHMGWNTL-TALRPHPLL-AGIPLGAEGLHAYFVHSYAFRPQREADLIATTDYGG 189 Query: 177 LVTAAVGRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213 VTA +G NI G QFHPEKSQ+ GL +S FL W+P Sbjct: 190 PVTAMIGEANIAGTQFHPEKSQTLGLALISNFLKWHP 226 Lambda K H 0.318 0.136 0.409 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: 195 Number of extensions: 9 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: 213 Length of database: 226 Length adjustment: 22 Effective length of query: 191 Effective length of database: 204 Effective search space: 38964 Effective search space used: 38964 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: 45 (21.9 bits)
Align candidate WP_012383261.1 BIND_RS01235 (imidazole glycerol phosphate synthase subunit HisH)
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))
# 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/TIGR01855.hmm # target sequence database: /tmp/gapView.17856.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01855 [M=198] Accession: TIGR01855 Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-63 198.1 0.0 7.9e-63 197.9 0.0 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012383261.1 BIND_RS01235 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012383261.1 BIND_RS01235 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.9 0.0 7.9e-63 7.9e-63 1 197 [. 13 223 .. 13 224 .. 0.91 Alignments for each domain: == domain 1 score: 197.9 bits; conditional E-value: 7.9e-63 TIGR01855 1 ivvidygvgNlksvkkalervgaes......evvkdskelekadklvlPGVGafkeamkklrele..le 61 ++++dyg+gNl+s +ka+er+ e+ v++d +++ ad++vlPGVGaf+++ + l+ +e lcl|NCBI__GCF_000019845.1:WP_012383261.1 13 VAIVDYGSGNLHSAHKAFERAASETgyagtiAVTHDPEAVALADRIVLPGVGAFADCRRGLNAVPgmIE 81 79***********999999876553222222688999*************************9977788 PP TIGR01855 62 llaekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkes 127 ++++ v++++kp+lgiC+GmQll+ ++ E++++ gl +ikg+v le + k+Ph+GWn+++ ++ + lcl|NCBI__GCF_000019845.1:WP_012383261.1 82 AMEHAVRREGKPFLGICVGMQLLATRGLEHETTAGLDWIKGEVAALEPTDkslKIPHMGWNTLTALRPH 150 99999999**************************************9887789**************** PP TIGR01855 128 ellkgle...eearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllk 193 +ll+g+ e+ ++YfvHsYa +++ e +++a++dyg +a++ + ni+g+QFHPEkS++ Gl+l++ lcl|NCBI__GCF_000019845.1:WP_012383261.1 151 PLLAGIPlgaEGLHAYFVHSYAFRPQREADLIATTDYGGPVTAMIGEANIAGTQFHPEKSQTLGLALIS 219 ******733256689****************************************************** PP TIGR01855 194 nfle 197 nfl+ lcl|NCBI__GCF_000019845.1:WP_012383261.1 220 NFLK 223 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (226 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: 6.21 // [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