Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate Ac3H11_4724 Histidinol dehydrogenase (EC 1.1.1.23)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4724 Length = 460 Score = 251 bits (642), Expect = 5e-71 Identities = 158/460 (34%), Positives = 244/460 (53%), Gaps = 28/460 (6%) Query: 351 EKLTGPIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKF 410 + + P +L A + Q+ L + I V I+ +V+ +G++A+LEYT +F Sbjct: 2 KSIAAPAYLSTADADFEKKFQQCLHWSADTDAAIEQRVADILADVQKRGDAAVLEYTARF 61 Query: 411 DGVKLSN----PVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPT--ETLEVET 464 DG+ N + A F + F+ + + ++AL + + VR +H AQ E+ Sbjct: 62 DGLSAPNMAALELTQADF-KAAFDAIPQAQRDALQAAAKRVRSYHEAQKKASGESWSYRD 120 Query: 465 QPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPP-------- 516 + G L + P+++VG+Y+PGG A PS+ LM +PA VA +EI+ P Sbjct: 121 EDGTLLGQKVTPLDRVGIYVPGGKAAYPSSLLMNAIPAHVAGVQEIIMVVPTPVRGSVAT 180 Query: 517 ------RKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQ 570 + G+ + V+ A G ++ GGAQAVAA+AYGT T+PKVDKI GPGN Sbjct: 181 GGTGEGTSTKGERNELVLAAAYVAGVTRAFTIGGAQAVAALAYGTATVPKVDKITGPGNA 240 Query: 571 FVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILV 630 +V +AK V IDM AGPSE+LV+AD D+VA DL SQAEH +Q IL+ Sbjct: 241 YVASAKKRVFGTV----GIDMIAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILL 296 Query: 631 GVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHL 689 + + + +Q + +PR +I+ K + ++L EEA +SN+ APEHL Sbjct: 297 CPDAAY--LDAVQREIDRLLPTMPRAEIIAKSLTGRGALILTKDMEEACAISNRIAPEHL 354 Query: 690 ILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQK 749 + + + + L+ +AG++F+GAYT ES GDY +G NH LPT G AR S FQK Sbjct: 355 EVSSTDPHRWEPLLRHAGAIFLGAYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQK 414 Query: 750 FITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 + ++ G + +G+ +A EGL H A ++R++ Sbjct: 415 RSSLIEVSEAGAQVLGKIAAELAYGEGLQAHAQAAEMRLT 454 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: 725 Number of extensions: 35 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: 460 Length adjustment: 37 Effective length of query: 762 Effective length of database: 423 Effective search space: 322326 Effective search space used: 322326 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