Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate RR42_RS18895 RR42_RS18895 imidazole glycerol phosphate synthase
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__Cup4G11:RR42_RS18895 Length = 217 Score = 303 bits (776), Expect = 2e-87 Identities = 148/217 (68%), Positives = 170/217 (78%), Gaps = 5/217 (2%) Query: 1 MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60 M I +VDYGMGNLRSVAQALR APEADV++ + IRAADRVVLPGQGAMPDCM +L Sbjct: 1 MTTIAIVDYGMGNLRSVAQALRAAAPEADVQVVDQPEAIRAADRVVLPGQGAMPDCMGAL 60 Query: 61 RESGVQDAVIEASRTKPLFGVCVGEQMLFDWSEE-----GDTPGLGLLPGKVVRFDLEGM 115 SG+Q AVIEA+ +KP+ GVCVGEQMLFD+S+E G TP LGLLPG+V+RF+LEGM Sbjct: 61 GASGLQQAVIEAAASKPMLGVCVGEQMLFDFSKESRTQDGSTPCLGLLPGEVIRFELEGM 120 Query: 116 RQDDGSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGR 175 Q DGS +KVPQMGWN V Q HPLW GI D ++FYFVHSYY + AH+ G+T YG Sbjct: 121 TQPDGSRYKVPQMGWNRVRQVRSHPLWAGIPDESWFYFVHSYYVHAQDPAHIAGETDYGV 180 Query: 176 DFACAVARDNIFATQFHPEKSASAGLQLYRNFVHWKP 212 F AVARDNIFATQFHPEKSA+ GL+LYRNFVHW P Sbjct: 181 LFTSAVARDNIFATQFHPEKSAAMGLRLYRNFVHWNP 217 Lambda K H 0.322 0.137 0.431 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: 237 Number of extensions: 7 Number of successful extensions: 2 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: 212 Length of database: 217 Length adjustment: 22 Effective length of query: 190 Effective length of database: 195 Effective search space: 37050 Effective search space used: 37050 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: 45 (21.9 bits)
Align candidate RR42_RS18895 RR42_RS18895 (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.6825.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-63 199.5 0.0 3e-63 199.3 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS18895 RR42_RS18895 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS18895 RR42_RS18895 imidazole glycerol phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.3 0.0 3e-63 3e-63 1 197 [. 4 214 .. 4 215 .. 0.91 Alignments for each domain: == domain 1 score: 199.3 bits; conditional E-value: 3e-63 TIGR01855 1 ivvidygvgNlksvkkalerv..gaesevvkdskelekadklvlPGVGafkeamkklrelelellaekv 67 i+++dyg+gNl+sv++al+++ +a ++vv++ ++++ ad++vlPG Ga+ ++m l ++l++ + + lcl|FitnessBrowser__Cup4G11:RR42_RS18895 4 IAIVDYGMGNLRSVAQALRAAapEADVQVVDQPEAIRAADRVVLPGQGAMPDCMGALGASGLQQAVIE- 71 79****************987336788999999****************************7777555. PP TIGR01855 68 vkkkkpvlgiClGmQllfekseEgke....vkglglikgkvkkleaek.........kvPhiGWnevev 123 ++++kp+lg+C+G Q+lf+ s+E+++ +++lgl++g+v ++e e kvP++GWn+v lcl|FitnessBrowser__Cup4G11:RR42_RS18895 72 AAASKPMLGVCVGEQMLFDFSKESRTqdgsTPCLGLLPGEVIRFELEGmtqpdgsryKVPQMGWNRVRQ 140 55667******************6541122679***********9876777889999************ PP TIGR01855 124 vkesellkgleeearvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkll 192 v++++l +g+ +e+ +YfvHsY+v+ ++ ++ +dyg f++av++dni+++QFHPEkS+++Gl+l lcl|FitnessBrowser__Cup4G11:RR42_RS18895 141 VRSHPLWAGIPDESWFYFVHSYYVHAQDPAHIAGETDYGVLFTSAVARDNIFATQFHPEKSAAMGLRLY 209 ********************************************************************* PP TIGR01855 193 knfle 197 +nf++ lcl|FitnessBrowser__Cup4G11:RR42_RS18895 210 RNFVH 214 ***97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (217 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.38 // [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