Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate GFF3068 PGA1_c31190 histidinol dehydrogenase HisD
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Phaeo:GFF3068 Length = 433 Score = 261 bits (666), Expect = 7e-74 Identities = 166/439 (37%), Positives = 242/439 (55%), Gaps = 12/439 (2%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 P+ L+ A L + + ++ +V II +VR +G++AL+E T KFD ++L Sbjct: 2 PVFLNASDAGFDQAFATLLGAKREDSPDVDAVVADIIADVRTRGDAALIELTAKFDRLQL 61 Query: 416 SNPVLNAPFPE--EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRF 473 + L E + ++ E + AL+L++E +R +H Q+P + E + G Sbjct: 62 TADQLRISDAEIDAAIQDVSTEERVALELAVERIRAYHLRQMP-QGAEWQDDAGASLGWR 120 Query: 474 PRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEK 533 + GLY+PGG A PS+ LM VPA+VA + + P DG+++P V+ A Sbjct: 121 WSAVSAAGLYVPGGLASYPSSVLMNAVPAKVAGVERLAVVVPT--PDGQINPLVLLAARL 178 Query: 534 VGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPA 593 G +I GGAQAVAA+AYGTE+I VDKI GPGN FV AAK V IDM A Sbjct: 179 SGVDEIYRVGGAQAVAALAYGTESIAPVDKITGPGNAFVAAAKRRVFGKV----GIDMIA 234 Query: 594 GPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQL 653 GPSE+LVIAD+D D D++A DLLSQAEH +Q IL+ + E + + DAV + L Sbjct: 235 GPSEILVIADKDNDPDWIALDLLSQAEHDESAQSILITDD--EAFGRSVADAVEARLQTL 292 Query: 654 PRVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVG 712 R I + +++ + A ++SN+ APEHL L +A+A + +AG++F+G Sbjct: 293 ERSAIAGPSWRDYGAVIVVPDLDVAAQLSNRIAPEHLELCVADARALSEKTIHAGAIFLG 352 Query: 713 AYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVA 772 YTPE+ GDY G NH LPT AR SG + F K T +TP+ L IG A +A Sbjct: 353 QYTPEAIGDYIGGPNHVLPTARSARFSSGLSVMDFLKRTTLSEMTPDALRAIGPAAETLA 412 Query: 773 KKEGLDGHRNAVKIRMSKL 791 K E L+ H +++ R+ +L Sbjct: 413 KSESLEAHGLSIRARLDRL 431 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: 657 Number of extensions: 33 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: 433 Length adjustment: 37 Effective length of query: 762 Effective length of database: 396 Effective search space: 301752 Effective search space used: 301752 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