Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Synpcc7942_1519 Synpcc7942_1519 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__SynE:Synpcc7942_1519 Length = 434 Score = 278 bits (710), Expect = 6e-79 Identities = 162/407 (39%), Positives = 242/407 (59%), Gaps = 11/407 (2%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPE--EYFEGLTEEMKEALDLSIE 445 V I++ V+ +G++AL+E+T++FDG L L E ++ + +E+ +A+ L+ Sbjct: 34 VREIVQAVQRRGDAALIEFTQEFDGFALQAENLRVSGAELDAAYQQIPKELLDAIRLAHH 93 Query: 446 NVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVA 505 + FH ++P ++ VL R+ P+++ GLY+PGG A PST LM VPA+VA Sbjct: 94 QIEAFHRQRVPKSWVQFGADGEVLGKRYT-PVDRAGLYVPGGRAAYPSTVLMNAVPAKVA 152 Query: 506 QCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKIL 565 + +V +PP DG ++P V+ A++ G +I GGAQA+AA+AYGT TIPKVD I Sbjct: 153 GVERVVITTPPGP-DGSLNPAVLVAAQEAGIEEIYRVGGAQAIAALAYGTATIPKVDVIS 211 Query: 566 GPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDS 625 GPGN +VT AK V ID AGPSEVL+IAD A+ +VA+DLL+QAEH + Sbjct: 212 GPGNIYVTLAKKLVYGTV----GIDSLAGPSEVLIIADRSANPRWVAADLLAQAEHDPLA 267 Query: 626 QVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTI-VLCDGYEEALEMSNQY 684 IL+ +L + ++ V Q PR + K IAH + ++ D E A+++SNQ+ Sbjct: 268 AAILITPDL--ELATQVGFEVERQLQDHPRRLVTEKAIAHYGLAIVVDSLETAVKLSNQF 325 Query: 685 APEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANT 744 APEHL L++ + V+ V +AG++F+G+ TPE+ GDY +G NHTLPT G AR S + Sbjct: 326 APEHLELEVEDPWALVEQVRHAGAIFLGSLTPEAIGDYVAGPNHTLPTSGAARYASALSV 385 Query: 745 ATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKL 791 TF K + T L+ + RAV +A EGL+ H +V++R L Sbjct: 386 ETFLKSSSLIEYTAASLQRVARAVDVLATAEGLESHAESVRLRQQSL 432 Lambda K H 0.315 0.133 0.371 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: 653 Number of extensions: 28 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: 799 Length of database: 434 Length adjustment: 37 Effective length of query: 762 Effective length of database: 397 Effective search space: 302514 Effective search space used: 302514 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 53 (25.0 bits)
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