Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Ga0059261_1281 Ga0059261_1281 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Korea:Ga0059261_1281 Length = 428 Score = 233 bits (593), Expect = 2e-65 Identities = 151/412 (36%), Positives = 227/412 (55%), Gaps = 16/412 (3%) Query: 382 SEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPE--EYFEGLTEEMKEA 439 +++ V I+ +VRD+G++AL +T KFD L+ + F+ L ++++A Sbjct: 27 ADVARDVRTIVASVRDEGDAALHAFTRKFDRHDLNETGWRIEKADCAAAFDALEPKLRDA 86 Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLG 499 L L+ + + +H Q P ++ + GV + +E G+Y+PGG A PS+ LM Sbjct: 87 LQLAADRITAYHEKQKPADS-DTTDAAGVRTGARWQAVEAAGVYVPGGRAAYPSSVLMNA 145 Query: 500 VPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIP 559 +PA+VA +V +P DG+V+P V+ A G +I GGAQA+AA+AYGT I Sbjct: 146 IPAKVAGVDRLVMVTPT--PDGEVNPLVLAAAHIAGVDEIWRVGGAQAIAALAYGTGRIA 203 Query: 560 KVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQA 619 VD I GPGN +V AK + + IDM AGPSE++VIAD D +++A+DLLSQ+ Sbjct: 204 AVDVITGPGNAWVAEAKRQLYG----VVGIDMVAGPSEIVVIADGKNDPEWIAADLLSQS 259 Query: 620 EHGIDSQVILVGVNLSEKKI--QEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEE 676 EH SQ IL L++ I ++ +AV Q L + R+ A+ I+L +E Sbjct: 260 EHDPTSQSIL----LTDDAIFAGKVAEAVDLQIGTLSTKGVARQSWDANGAIILTGSLDE 315 Query: 677 ALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYA 736 A+ + N+ APEHL L + + V +AGSVF+G TPE+ GDY +G NH LPT A Sbjct: 316 AIPLVNKLAPEHLELACDDPDALFARVRHAGSVFLGRMTPEAIGDYVAGPNHVLPTGRRA 375 Query: 737 RQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 R SG + F K + + GL IG A + +A+ EGL H +V +R+ Sbjct: 376 RFASGLSVLDFMKRTSFLALDAAGLAAIGPAAVALAEAEGLPAHARSVSLRL 427 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: 630 Number of extensions: 26 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: 428 Length adjustment: 36 Effective length of query: 763 Effective length of database: 392 Effective search space: 299096 Effective search space used: 299096 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