Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate 3607381 Dshi_0795 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (RefSeq)
Query= BRENDA::Q5NMD4 (213 letters) >FitnessBrowser__Dino:3607381 Length = 212 Score = 199 bits (505), Expect = 4e-56 Identities = 103/211 (48%), Positives = 134/211 (63%), Gaps = 11/211 (5%) Query: 11 LIDYGAGNLRSVANALLASGLARE----NLVVTANPDEVLQADRVVLPGVGAFASCMQAL 66 L+DY +GNL S A +ARE + VT++PD V +ADR+VLPG GAF +C L Sbjct: 5 LVDYDSGNLHSAEKAF--ERMAREVDGGEICVTSDPDLVARADRIVLPGDGAFPACRAGL 62 Query: 67 KAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPNDPS 126 + + A+E+AV + RPFLGICVGMQL+A G EY G GWI G+V + P+DP+ Sbjct: 63 EGFAGLFEAIEEAVTARARPFLGICVGMQLMATTGREYEDTPGFGWIDGEVVKITPSDPA 122 Query: 127 CKVPHMGWNQIGLTTDSHPLLR----AGEAYFLHSYAFVPEDESTLLATTEHGGLVTAAV 182 KVPHMGWN + + HP+L AYF+HSY D +TLLA ++GG VTA V Sbjct: 123 LKVPHMGWNDL-VIDRPHPVLEGVATGDHAYFVHSYHMQVTDPATLLAHCDYGGPVTAVV 181 Query: 183 GRDNIMGVQFHPEKSQSYGLEFLSRFLDWNP 213 GRD ++G QFHPEKSQ+ GL ++ FL W P Sbjct: 182 GRDTMVGAQFHPEKSQAAGLRMIANFLTWRP 212 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: 179 Number of extensions: 6 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: 212 Length adjustment: 21 Effective length of query: 192 Effective length of database: 191 Effective search space: 36672 Effective search space used: 36672 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 3607381 Dshi_0795 (imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (RefSeq))
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.21704.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-63 199.9 0.0 2.1e-63 199.7 0.0 1.0 1 lcl|FitnessBrowser__Dino:3607381 Dshi_0795 imidazole glycerol pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607381 Dshi_0795 imidazole glycerol phosphate synthase, glutamine amidotransferase subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.7 0.0 2.1e-63 2.1e-63 2 197 .. 4 209 .. 3 210 .. 0.94 Alignments for each domain: == domain 1 score: 199.7 bits; conditional E-value: 2.1e-63 TIGR01855 2 vvidygvgNlksvkkalerv.....gaesevvkdskelekadklvlPGVGafkeamkklrele..lellaekvvkkk 71 v++dy++gNl+s +ka+er+ g e v++d + + +ad++vlPG Gaf ++ + l+ + e+++e v+++ lcl|FitnessBrowser__Dino:3607381 4 VLVDYDSGNLHSAEKAFERMarevdGGEICVTSDPDLVARADRIVLPGDGAFPACRAGLEGFAglFEAIEEAVTARA 80 79****************99332233356799999*************************9988889999999**** PP TIGR01855 72 kpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkesellkgleeearvYfvHsY 145 +p+lgiC+GmQl++ ++ E ++++g g+i+g+v+k++ + kvPh+GWn + + + +++l+g+ +++++YfvHsY lcl|FitnessBrowser__Dino:3607381 81 RPFLGICVGMQLMATTGREYEDTPGFGWIDGEVVKITPSDpalKVPHMGWNDLVIDRPHPVLEGVATGDHAYFVHSY 157 *************************************988899********************************** PP TIGR01855 146 aveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfle 197 ++++++ ++la +dyg +a+v +d++vg+QFHPEkS+++Gl+++ nfl lcl|FitnessBrowser__Dino:3607381 158 HMQVTDPATLLAHCDYGGPVTAVVGRDTMVGAQFHPEKSQAAGLRMIANFLT 209 *************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (212 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: 6.43 // [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