Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013841335.1 DESRU_RS06590 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000215085.1:WP_013841335.1 Length = 432 Score = 301 bits (771), Expect = 5e-86 Identities = 171/434 (39%), Positives = 261/434 (60%), Gaps = 13/434 (2%) Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP 418 + +++ SD G++ L I V I++ VR++G+ AL +T +FDG L+ Sbjct: 2 IKIIEVSDSEGLKALLKGRSGGQEGIASRVAAIMQEVRERGDIALCGFTRRFDGASLTPE 61 Query: 419 VLNAPFPE--EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRP 476 L E + + + +E+ +L L+ + +RK+H QL + E G L + P Sbjct: 62 QLRVTDEEIDQAYSMVDQEVLTSLKLARDRIRKYHQKQLTRSWFDTEPN-GTLLGQLITP 120 Query: 477 IEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGA 536 +++VG+Y+PGGTA PS+ LM VPA+VA ++V +PP +DGK++P + A + G Sbjct: 121 LDRVGVYVPGGTASYPSSVLMNAVPAKVAGVSQVVMVTPPG-ADGKLNPYTLVAAREAGV 179 Query: 537 SKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPS 596 +I AGGAQA+AA+AYGTETI VDKI GPGN FVT AK V IDM AGPS Sbjct: 180 DEIYKAGGAQAIAALAYGTETIAPVDKITGPGNIFVTLAKRMVYGQVD----IDMLAGPS 235 Query: 597 EVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQE-IQDAVHNQALQLPR 655 EVLV+AD A+ ++ A+D+LSQAEH + + +L+ +++ E ++ + Q LPR Sbjct: 236 EVLVVADASANPEYAAADMLSQAEHDVLASAVLL---THHRELAEWVRQELEKQVALLPR 292 Query: 656 VDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAY 714 D+ R+ +A HS +V+ EE+LE++N +APEHL L + ++ + +AG+VF+GA+ Sbjct: 293 QDLAREALANHSALVITGSLEESLELANAFAPEHLELLVEEPFRWLSRIRHAGAVFLGAH 352 Query: 715 TPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKK 774 +PE GDY +G NH LPT G AR YS N TF K + + + E LE +G ++ +A+ Sbjct: 353 SPEPVGDYLAGPNHVLPTGGTARFYSPLNVDTFMKKSSIISFSKENLELLGPDIIRLAEV 412 Query: 775 EGLDGHRNAVKIRM 788 EGL H NAV++R+ Sbjct: 413 EGLQAHANAVRVRL 426 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: 697 Number of extensions: 38 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: 432 Length adjustment: 37 Effective length of query: 762 Effective length of database: 395 Effective search space: 300990 Effective search space used: 300990 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 Jul 25 2024. The underlying query database was built on Jul 25 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