Align imidazole glycerol-phosphate synthase (subunit 1/2) (EC 4.3.2.10) (characterized)
to candidate AZOBR_RS01670 AZOBR_RS01670 imidazole glycerol phosphate synthase
Query= BRENDA::Q5NMD4 (213 letters) >FitnessBrowser__azobra:AZOBR_RS01670 Length = 214 Score = 231 bits (589), Expect = 8e-66 Identities = 117/211 (55%), Positives = 150/211 (71%), Gaps = 8/211 (3%) Query: 8 TVALIDYGAGNLRSVANAL--LASGL-ARENLVVTANPDEVLQADRVVLPGVGAFASCMQ 64 TVALIDYG+GNLRS A AL A+G A ++VT++ D V +ADRVVLPGVGAFA C + Sbjct: 3 TVALIDYGSGNLRSAAKALERAAAGCHASFQVLVTSDADAVRKADRVVLPGVGAFADCKR 62 Query: 65 ALKAIPDMVPALEKAVLEKGRPFLGICVGMQLLADQGEEYGVHQGLGWIKGKVTPLRPND 124 L +P M+ AL++ V KGRPFLGICVGMQL+A++G EYGV +GLGWIKG+V L P D Sbjct: 63 GLSEVPGMLDALDEVVHGKGRPFLGICVGMQLMAERGREYGVTEGLGWIKGEVVKLEPAD 122 Query: 125 PSCKVPHMGWNQIGLTTDSHPLL----RAGEAYFLHSYAFVPEDESTLLATTEHGGLVTA 180 P+ K+PHMGWN++ + + HPLL AYF+HSY F E ++A+ ++GG A Sbjct: 123 PTLKIPHMGWNELDIRRE-HPLLAGLPERAHAYFVHSYRFAVERPEDVIASADYGGPFAA 181 Query: 181 AVGRDNIMGVQFHPEKSQSYGLEFLSRFLDW 211 VGRDN++G QFHPEKSQ GL ++ FL W Sbjct: 182 VVGRDNLVGTQFHPEKSQETGLALVANFLTW 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: 204 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: 214 Length adjustment: 22 Effective length of query: 191 Effective length of database: 192 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 AZOBR_RS01670 AZOBR_RS01670 (imidazole glycerol phosphate synthase)
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.12229.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-71 224.7 0.0 5.6e-71 224.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS01670 AZOBR_RS01670 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS01670 AZOBR_RS01670 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 224.5 0.0 5.6e-71 5.6e-71 1 197 [. 4 211 .. 4 212 .. 0.93 Alignments for each domain: == domain 1 score: 224.5 bits; conditional E-value: 5.6e-71 TIGR01855 1 ivvidygvgNlksvkkalervg......aesevvkdskelekadklvlPGVGafkeamkklrele..le 61 +++idyg+gNl+s +kaler+ +++ v++d+++++kad++vlPGVGaf+++ + l+e l+ lcl|FitnessBrowser__azobra:AZOBR_RS01670 4 VALIDYGSGNLRSAAKALERAAagchasFQVLVTSDADAVRKADRVVLPGVGAFADCKRGLSEVPgmLD 72 789***************9864112211567899999**************************987788 PP TIGR01855 62 llaekvvkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek...kvPhiGWnevevvkes 127 +l e v k++p+lgiC+GmQl++e++ E + ++glg+ikg+v+kle + k+Ph+GWne+++ +e+ lcl|FitnessBrowser__azobra:AZOBR_RS01670 73 ALDEVVHGKGRPFLGICVGMQLMAERGREYGVTEGLGWIKGEVVKLEPADptlKIPHMGWNELDIRREH 141 9988888999*************************************998899**************** PP TIGR01855 128 ellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfl 196 +ll+gl e a++YfvHsY+ +e e+v+a+adyg f a+v +dn+vg+QFHPEkS++tGl+l+ nfl lcl|FitnessBrowser__azobra:AZOBR_RS01670 142 PLLAGLPERAHAYFVHSYRFAVERPEDVIASADYGGPFAAVVGRDNLVGTQFHPEKSQETGLALVANFL 210 *******************************************************************98 PP TIGR01855 197 e 197 lcl|FitnessBrowser__azobra:AZOBR_RS01670 211 T 211 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (214 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: 4.78 // [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