Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate CCNA_02431 CCNA_02431 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Caulo:CCNA_02431 Length = 428 Score = 226 bits (575), Expect = 3e-63 Identities = 145/402 (36%), Positives = 217/402 (53%), Gaps = 17/402 (4%) Query: 391 IIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTE---EMKEALDLSIENV 447 ++E VR +G ALL+Y+ +FD V L+ + EE G E +++EA+ + + Sbjct: 36 VLEAVRTQGIEALLDYSRRFDKVDLTAETIRVT-AEEIEAGAAETPADVREAIAFAAARI 94 Query: 448 RKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQC 507 R +H+ Q P + + + GV P+E VG+Y+PGG A PST LM VPAQVA Sbjct: 95 RAYHSRQRPADQAWTD-EAGVELGWRWTPLEAVGVYVPGGRAAYPSTVLMNAVPAQVAGV 153 Query: 508 KEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGP 567 I +PP GK+ P V+ A++ G ++I GGAQAVAA+AYG I VDKI+GP Sbjct: 154 DRIAMVTPP----GKLQPAVLAAAKEAGVTEIWRVGGAQAVAALAYGAGPIQPVDKIVGP 209 Query: 568 GNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQV 627 GN +VTAAK + + ID AGPSE++V+AD + D++A+DLLSQAEH +Q Sbjct: 210 GNAYVTAAKRRLYG----VVGIDALAGPSEIVVVADNKNNPDWIAADLLSQAEHDPAAQS 265 Query: 628 ILVGVNLSEKKIQEIQDAVHNQALQLPR-VDIVRKCIAHSTIVLCDGYEEALEMSNQYAP 686 IL+ + E ++ A+ + L D H +++ +E+ + + AP Sbjct: 266 ILITDD--EAFAAAVEQAIAERLKTLATGEDAAASWRDHGAVIIAP-LDESPALVDAIAP 322 Query: 687 EHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTAT 746 EH+ + N V +AG++F+G TPE+ GDY +G+NH LPT AR SG + Sbjct: 323 EHVEFALDNPERLSDRVRHAGAIFLGRVTPEAIGDYVAGSNHVLPTSRAARFQSGLSIYD 382 Query: 747 FQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 F K + P +G + +AK EGL H + +R+ Sbjct: 383 FIKRTSIVKCDPASFAVLGPHTVALAKAEGLPAHALSASVRL 424 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: 26 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: 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