Align IGP synthase glutamine amidotransferase subunit; EC 2.4.2.- (characterized)
to candidate 201227 SO2070 amidotransferase HisH (NCBI ptt file)
Query= CharProtDB::CH_024511 (196 letters) >FitnessBrowser__MR1:201227 Length = 221 Score = 196 bits (498), Expect = 3e-55 Identities = 105/212 (49%), Positives = 140/212 (66%), Gaps = 17/212 (8%) Query: 2 NVVILDTGCANLNSVKSAIARHGYEPKVSRDPDVVLLADKLFLPGVGTAQAAMDQVRERE 61 +VVI+DTGCANL+SV+ A R G V+ D + A ++ LPGVG+A AAM + E+ Sbjct: 9 DVVIIDTGCANLSSVRFAFERLGANVLVTDDKASIKAAKRVVLPGVGSAGAAMASLTEKA 68 Query: 62 LFDLIKACTQPVLGICLGMQLLGRRSEESNGVDL---------LGIIDEDVPKMTDF--- 109 L +LI+ TQPVLG+CLGMQ+L S+E G L LGII ++ ++ Sbjct: 69 LVELIQGLTQPVLGVCLGMQMLTLLSKERGGQALDCQAHDCKCLGIIPTEIDELNSQTLK 128 Query: 110 --GLPLPHMGWNRVY---PQAGNRLFQGIEDGAYFYFVHSYAMPVNPWTIAQCNYGEPFT 164 GLPLPHMGWN++ P + LF G+E G+Y YFVHSY P++ +T+AQC YGE F+ Sbjct: 129 AEGLPLPHMGWNQLTFSNPSQVHPLFAGVEAGSYVYFVHSYRAPLSDYTLAQCRYGEDFS 188 Query: 165 AAVQKDNFYGVQFHPERSGAAGAKLLKNFLEM 196 AA+ KDNF GVQFHPE+S A GA++L NFL+M Sbjct: 189 AAIGKDNFMGVQFHPEKSAAVGAQILGNFLKM 220 Lambda K H 0.322 0.140 0.432 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: 150 Number of extensions: 3 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: 196 Length of database: 221 Length adjustment: 21 Effective length of query: 175 Effective length of database: 200 Effective search space: 35000 Effective search space used: 35000 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 201227 SO2070 (amidotransferase HisH (NCBI ptt file))
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.18006.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-64 203.0 0.0 2.8e-64 202.6 0.0 1.2 1 lcl|FitnessBrowser__MR1:201227 SO2070 amidotransferase HisH (NC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201227 SO2070 amidotransferase HisH (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 202.6 0.0 2.8e-64 2.8e-64 1 198 [] 10 220 .. 10 220 .. 0.90 Alignments for each domain: == domain 1 score: 202.6 bits; conditional E-value: 2.8e-64 TIGR01855 1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvlgiCl 79 +v+id+g++Nl+sv+ a+er+ga++ v++d+ +++ a+++vlPGVG++ +am++l e+ l+e ++ ++pvlg+Cl lcl|FitnessBrowser__MR1:201227 10 VVIIDTGCANLSSVRFAFERLGANVLVTDDKASIKAAKRVVLPGVGSAGAAMASLTEKA---LVELIQGLTQPVLGVCL 85 79*******************************************************77...55888999********* PP TIGR01855 80 GmQllfekseE.gk........evkglglikgkvkkleaek......kvPhiGWnevevvkes...ellkgleeearvY 140 GmQ+l s+E g+ ++k+lg+i+ +++ l++++ ++Ph+GWn++++ + s +l++g+e++++vY lcl|FitnessBrowser__MR1:201227 86 GMQMLTLLSKErGGqaldcqahDCKCLGIIPTEIDELNSQTlkaeglPLPHMGWNQLTFSNPSqvhPLFAGVEAGSYVY 164 *********9964322222222479*************9988999999********98765432339************ PP TIGR01855 141 fvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknflel 198 fvHsY+++l++ ++la++ yge+f aa+ kdn++gvQFHPEkS+++G+++l nfl++ lcl|FitnessBrowser__MR1:201227 165 FVHSYRAPLSD--YTLAQCRYGEDFSAAIGKDNFMGVQFHPEKSAAVGAQILGNFLKM 220 **********7..9*****************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (198 nodes) Target sequences: 1 (221 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 5.43 // [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