Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 6937801 Sama_1942 histidinol dehydrogenase (RefSeq)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__SB2B:6937801 Length = 435 Score = 360 bits (925), Expect = e-104 Identities = 197/422 (46%), Positives = 273/422 (64%), Gaps = 9/422 (2%) Query: 371 QKALSR-PIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 ++ALSR P+ + V+ I+ NV+ +G+S L+EY +FD ++ L+A Sbjct: 15 RQALSRSPLVGDDSLATSVSDILCNVKRRGDSTLIEYAARFDKAEIDTLALSADEIAAAC 74 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA 489 E ++ E+K+A++ + N+ +FH+AQ +E + +ETQPGV C IEKVGLYIPGG+A Sbjct: 75 ERVSPELKDAINAARTNIARFHSAQQFSE-ISLETQPGVRCELKSEAIEKVGLYIPGGSA 133 Query: 490 ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVA 549 L ST LML VPA +A C + V SPP D ++Y A G + + GGAQA+A Sbjct: 134 PLISTVLMLAVPAAIAGCTKRVLVSPPPIDDA-----ILYAASVCGITDVFQIGGAQAIA 188 Query: 550 AMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVD 609 A+AYGTE++PKVDKI GPGN++VT AK V DTQA +IDMPAGPSEVLVIAD+ A+ + Sbjct: 189 ALAYGTESVPKVDKIFGPGNRYVTEAKAQVARDTQAAVTIDMPAGPSEVLVIADDAANPE 248 Query: 610 FVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIV 669 F+A+DLLSQAEHG DSQVI V S + ++ A+ Q LPR + ++ S I+ Sbjct: 249 FIAADLLSQAEHGSDSQVIF--VTDSRTQANAVEAALERQLTLLPRRETAEGALSCSRII 306 Query: 670 LCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHT 729 + +EA +SN YAPEHLI+Q + + AGSVF+GAYTPES GDY+SGTNH Sbjct: 307 ITATLDEAAIVSNLYAPEHLIIQTREPRALLPRIRAAGSVFLGAYTPESVGDYASGTNHV 366 Query: 730 LPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 LPTYGY++ S + A F + T Q ++ EGL+ +G+ VM +A E LD H+NAVK+R+ Sbjct: 367 LPTYGYSKTVSSLSLADFCRRFTVQELSAEGLKGLGQTVMTLAAAESLDAHKNAVKVRLD 426 Query: 790 KL 791 + Sbjct: 427 AI 428 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: 671 Number of extensions: 22 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: 435 Length adjustment: 37 Effective length of query: 762 Effective length of database: 398 Effective search space: 303276 Effective search space used: 303276 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