Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 5209745 Shew_2198 histidinol dehydrogenase (RefSeq)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__PV4:5209745 Length = 443 Score = 355 bits (912), Expect = e-102 Identities = 195/422 (46%), Positives = 272/422 (64%), Gaps = 9/422 (2%) Query: 371 QKALSR-PIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 ++ALSR P+ + + V II+ V +G+ AL +++KFD V+L L+ Sbjct: 25 REALSRSPLIGDANLEQQVKAIIDQVASQGDVALKAFSQKFDKVELDALRLSDAAIAAAS 84 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA 489 E +T E+K A++ + +N+ FH AQ + +++ETQ GV C PIEKVGLYIPGG+A Sbjct: 85 ERVTPEIKAAIEQAKQNIETFHQAQA-FKGIDLETQAGVRCELRSEPIEKVGLYIPGGSA 143 Query: 490 ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVA 549 L ST LML +PA++A C++ V SPP D +VY A+ G + I GGAQA+A Sbjct: 144 PLISTVLMLALPAKIAGCEQRVLVSPPPIDDA-----IVYAAKACGITDIYQIGGAQAIA 198 Query: 550 AMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVD 609 A+A GTE++P VDKI GPGN++VT AK V D++ + SIDMPAGPSEVLVIAD +A+ D Sbjct: 199 ALAQGTESVPAVDKIFGPGNRYVTEAKRLVAQDSRCVVSIDMPAGPSEVLVIADNEANPD 258 Query: 610 FVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIV 669 F+A+DLLSQAEHG DSQV+LV S+ + ++ Q +LPR +I + ++ S + Sbjct: 259 FIAADLLSQAEHGPDSQVMLV--TDSQTLADAVNQSLGEQLARLPRAEIAMQALSASRTL 316 Query: 670 LCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHT 729 + + +A E+SN+Y PEHLI+Q + + AGSVF+GAYTPES GDY+SGTNH Sbjct: 317 IVEDMAQAAEVSNRYGPEHLIIQTRAPRKLLSKIRAAGSVFLGAYTPESVGDYASGTNHV 376 Query: 730 LPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 LPTYGY+R S + A F + T Q ++ EGL +G VM +A E LD HRNAV +R++ Sbjct: 377 LPTYGYSRAVSSLSLADFSRRFTVQELSAEGLRGLGECVMTLASAEQLDAHRNAVAVRLA 436 Query: 790 KL 791 L Sbjct: 437 TL 438 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: 659 Number of extensions: 24 Number of successful extensions: 4 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: 443 Length adjustment: 37 Effective length of query: 762 Effective length of database: 406 Effective search space: 309372 Effective search space used: 309372 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