Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate WP_011020951.1 MA_RS04735 imidazole glycerol phosphate synthase subunit HisH
Query= reanno::HerbieS:HSERO_RS20325 (212 letters) >NCBI__GCF_000007345.1:WP_011020951.1 Length = 202 Score = 166 bits (419), Expect = 4e-46 Identities = 93/212 (43%), Positives = 132/212 (62%), Gaps = 17/212 (8%) Query: 1 MNKIVVVDYGMGNLRSVAQALRHVAPEADVRISGEVADIRAADRVVLPGQGAMPDCMRSL 60 M +IV++DYG+GNLRSV + L HV A+ ISG +I AD ++LPG GA D M+ L Sbjct: 1 MKRIVIIDYGLGNLRSVQKGLEHVG--ANPAISGNPEEILTADGIILPGVGAFIDAMKCL 58 Query: 61 RESGVQDAVIE-ASRTKPLFGVCVGEQMLFDWSEEGD-TPGLGLLPGKVVRFDLEGMRQD 118 ++ + E A KP+ G+C+G+Q+L SEEG T GL L+ G+V+RF Sbjct: 59 IP--LKGVIAEFAESGKPMLGICLGQQVLMSSSEEGRLTGGLDLIQGRVLRFPK------ 110 Query: 119 DGSLFKVPQMGWNHVHQTSRHPLWEGIADNAFFYFVHSYYAVPAESAHVVGQTPYGRDFA 178 S KVP MGWN++ HPL++GI+D +F YFVHSYY V + + + YG DF+ Sbjct: 111 --SELKVPHMGWNNIRIKQDHPLFKGISDGSFVYFVHSYY-VDTTAENTLASCEYGLDFS 167 Query: 179 CAV--ARDNIFATQFHPEKSASAGLQLYRNFV 208 +V ++ N+ TQFHPEKS + GL++ +NFV Sbjct: 168 ASVVNSKGNVMGTQFHPEKSGTTGLKILKNFV 199 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: 131 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: 202 Length adjustment: 21 Effective length of query: 191 Effective length of database: 181 Effective search space: 34571 Effective search space used: 34571 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_011020951.1 MA_RS04735 (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.20248.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-72 228.3 0.0 4.2e-72 228.2 0.0 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011020951.1 MA_RS04735 imidazole glycerol ph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011020951.1 MA_RS04735 imidazole glycerol phosphate synthase subunit HisH # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 228.2 0.0 4.2e-72 4.2e-72 1 198 [] 4 201 .. 4 201 .. 0.96 Alignments for each domain: == domain 1 score: 228.2 bits; conditional E-value: 4.2e-72 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvk 69 iv+idyg+gNl+sv+k le+vga++ ++ + +e+ +ad ++lPGVGaf +amk l l+ ++ ++ ++ lcl|NCBI__GCF_000007345.1:WP_011020951.1 4 IVIIDYGLGNLRSVQKGLEHVGANPAISGNPEEILTADGIILPGVGAFIDAMKCLIPLK-GVI-AEFAE 70 89*****************************************************9988.455.8999* PP TIGR01855 70 kkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaek.kvPhiGWnevevvkesellkgleeea 137 ++kp+lgiClG Q+l+++seEg+ + gl li+g+v ++ +++ kvPh+GWn++ ++++++l+kg+++++ lcl|NCBI__GCF_000007345.1:WP_011020951.1 71 SGKPMLGICLGQQVLMSSSEEGRLTGGLDLIQGRVLRFPKSElKVPHMGWNNIRIKQDHPLFKGISDGS 139 **************************************98888************************** PP TIGR01855 138 rvYfvHsYaveleeeeavlakadygekfvaav..ekdnivgvQFHPEkSgktGlkllknflel 198 vYfvHsY+v ++ e++la+++yg +f a+v +k+n++g+QFHPEkSg+tGlk+lknf+e+ lcl|NCBI__GCF_000007345.1:WP_011020951.1 140 FVYFVHSYYVDTTA-ENTLASCEYGLDFSASVvnSKGNVMGTQFHPEKSGTTGLKILKNFVEM 201 ************98.89*************9955589***********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (202 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: 8.46 // [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