Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_086508671.1 BZY95_RS03880 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_002151265.1:WP_086508671.1 Length = 213 Score = 213 bits (541), Expect = 3e-60 Identities = 118/213 (55%), Positives = 141/213 (66%), Gaps = 6/213 (2%) Query: 4 IVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSLRES 63 I V+DYGMGNL SVA+AL HV E V I+ + I+ A R+VLPGQGA+ DCM L + Sbjct: 3 IAVIDYGMGNLHSVAKALEHVTHE-HVVITRDPRRIQGATRLVLPGQGAIRDCMGELERT 61 Query: 64 GVQDAVIE--ASRTKPLFGVCVGEQMLFDWSEE-GDTPGLGLLPGKVVRFDLEGMRQDDG 120 ++ V E AS++KPL G+CVG+QML D SEE G P LG L GKV RF ++ M D G Sbjct: 62 ELRGLVQELLASQSKPLLGICVGQQMLLDHSEESGGIPCLGFLSGKVKRFPVD-MVDDHG 120 Query: 121 SLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGR-DFAC 179 KVP MGWN VHQ HPLWEGI + FYFVHSYY + A V+G T YGR + Sbjct: 121 QRLKVPHMGWNLVHQHHEHPLWEGIDQDEHFYFVHSYYVAAEDDACVLGTTRYGRIEAHV 180 Query: 180 AVARDNIFATQFHPEKSASAGLQLYRNFVHWKP 212 AV RD FA QFHPEKS+ AGL+L NFV+W P Sbjct: 181 AVGRDATFAVQFHPEKSSRAGLKLLENFVNWAP 213 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: 171 Number of extensions: 9 Number of successful extensions: 6 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: 213 Length adjustment: 21 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_086508671.1 BZY95_RS03880 (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.22001.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-68 214.4 0.0 7.8e-68 214.2 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508671.1 BZY95_RS03880 imidazole glycerol Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508671.1 BZY95_RS03880 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 214.2 0.0 7.8e-68 7.8e-68 1 197 [. 3 210 .. 3 211 .. 0.94 Alignments for each domain: == domain 1 score: 214.2 bits; conditional E-value: 7.8e-68 TIGR01855 1 ivvidygvgNlksvkkalervgaese.vvkdskelekadklvlPGVGafkeamkklrele.lellaekv 67 i+vidyg+gNl+sv+kale+v e++ +++d ++++ a++lvlPG Ga +++m +l+++e + l++e + lcl|NCBI__GCF_002151265.1:WP_086508671.1 3 IAVIDYGMGNLHSVAKALEHVTHEHVvITRDPRRIQGATRLVLPGQGAIRDCMGELERTElRGLVQELL 71 79*******************98865157788****************************777888889 PP TIGR01855 68 vkkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek........kvPhiGWnevevvkese 128 ++++kp+lgiC+G Q+l+++seE++ ++lg+++gkvk++ ++ kvPh+GWn v+ +e++ lcl|NCBI__GCF_002151265.1:WP_086508671.1 72 ASQSKPLLGICVGQQMLLDHSEESGGIPCLGFLSGKVKRFPVDMvddhgqrlKVPHMGWNLVHQHHEHP 140 999*************************************988788889999***************** PP TIGR01855 129 llkgleeearvYfvHsYaveleeeeavlakadyge.kfvaavekdnivgvQFHPEkSgktGlkllknfl 196 l +g+++++++YfvHsY+v e++ vl ++ yg+ + av +d+ ++vQFHPEkS+++Glkll+nf+ lcl|NCBI__GCF_002151265.1:WP_086508671.1 141 LWEGIDQDEHFYFVHSYYVAAEDDACVLGTTRYGRiEAHVAVGRDATFAVQFHPEKSSRAGLKLLENFV 209 *********************************65278899***************************9 PP TIGR01855 197 e 197 + lcl|NCBI__GCF_002151265.1:WP_086508671.1 210 N 210 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (213 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: 5.08 // [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