Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate Synpcc7942_1481 Synpcc7942_1481 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >FitnessBrowser__SynE:Synpcc7942_1481 Length = 217 Score = 161 bits (408), Expect = 7e-45 Identities = 92/209 (44%), Positives = 128/209 (61%), Gaps = 12/209 (5%) Query: 3 KIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRE 62 +I VVDY MGNL S + L A A+ ++ + A I AAD V+LPG GA M LR+ Sbjct: 6 QIAVVDYDMGNLHSACKGLE--AAGANPIVTADPATILAADGVLLPGVGAFDPAMDHLRD 63 Query: 63 SGVQDAVIEASRT-KPLFGVCVGEQMLFDWSEEGDTPGLGLLPGKVVRFDLEGMRQDDGS 121 + + + +A+ + KP G+C+G Q+LF+ SEEG + GLG+LPG+V RF R + G Sbjct: 64 RQLIEPLHQAATSGKPFLGICLGLQLLFEASEEGQSAGLGILPGRVQRF-----RSEPGL 118 Query: 122 LFKVPQMGWNHVH-QTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYG-RDFAC 179 + +P MGWN + Q PLW+ + + +FYFVH+YY VP+E +G + Sbjct: 119 V--IPHMGWNQLQLQQPDCPLWQNLGADPWFYFVHTYYVVPSEPTLTAATVQHGSQPVTA 176 Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFV 208 A+ARD ++A QFHPEKSA AGLQL NFV Sbjct: 177 AIARDRLWAVQFHPEKSAKAGLQLLANFV 205 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: 158 Number of extensions: 11 Number of successful extensions: 5 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 Synpcc7942_1481 Synpcc7942_1481 (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.4969.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-66 209.7 0.0 2.1e-66 209.5 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1481 Synpcc7942_1481 imidazole glycer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1481 Synpcc7942_1481 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.5 0.0 2.1e-66 2.1e-66 1 196 [. 7 205 .. 7 207 .. 0.95 Alignments for each domain: == domain 1 score: 209.5 bits; conditional E-value: 2.1e-66 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 i+v+dy++gNl+s k le++ga++ v++d ++ ad ++lPGVGaf+ am++lr+++ +e l ++++ lcl|FitnessBrowser__SynE:Synpcc7942_1481 7 IAVVDYDMGNLHSACKGLEAAGANPIVTADPATILAADGVLLPGVGAFDPAMDHLRDRQlIEPL-HQAA 74 79*********************************************************55555.9999 PP TIGR01855 69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek..kvPhiGWnevevvk.esellkgle 134 +++kp+lgiClG+Qllfe seEg ++ glg+++g+v+++++e +Ph+GWn+++ ++ +++l ++l lcl|FitnessBrowser__SynE:Synpcc7942_1481 75 TSGKPFLGICLGLQLLFEASEEG-QSAGLGILPGRVQRFRSEPglVIPHMGWNQLQLQQpDCPLWQNLG 142 9*********************6.68***************99999*********9987356******* PP TIGR01855 135 eearvYfvHsYaveleeeeavlakadyg.ekfvaavekdnivgvQFHPEkSgktGlkllknfl 196 ++ +YfvH+Y+v+++e + a++++g + +aa+++d++ +vQFHPEkS+k+Gl+ll nf+ lcl|FitnessBrowser__SynE:Synpcc7942_1481 143 ADPWFYFVHTYYVVPSEPTLTAATVQHGsQPVTAAIARDRLWAVQFHPEKSAKAGLQLLANFV 205 ***************************626799****************************98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.28 // [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