Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011032377.1 MM_RS02285 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000007065.1:WP_011032377.1 Length = 433 Score = 338 bits (866), Expect = 5e-97 Identities = 176/418 (42%), Positives = 269/418 (64%), Gaps = 8/418 (1%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 +Q+ +SR +++ V+ ++ +VR KG++AL EYT+KFD V+L+N ++ E+ Sbjct: 17 MQRLISRG-SGLADVGDTVSAVLSDVRMKGDAALREYTKKFDKVELANFEVSEEEFEKAL 75 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA 489 + E+ L ++ EN+R FH AQ+P T +E QPGV+ + P+E VG Y PGG A Sbjct: 76 SEIGSELLGHLRIAAENIRAFHRAQMPETTWFMELQPGVVLGQKATPLESVGAYAPGGRA 135 Query: 490 ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVA 549 PST LM +PA+VA ++++ +PPR +DG V P + A+ GA K+ GG QA+ Sbjct: 136 SYPSTVLMTVIPARVAGVEQVIVCTPPR-ADGSVHPLTLAAAKVAGADKVFKLGGVQAIG 194 Query: 550 AMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVD 609 AMAYGTET+P+VDKI+GPGN FVT+AKM V++ + ID PAGPSEVL+IADE AD Sbjct: 195 AMAYGTETVPRVDKIVGPGNVFVTSAKMQVRD----IAEIDFPAGPSEVLIIADESADAA 250 Query: 610 FVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIV 669 ASD+++QAEH D + V V SE +E++ V QA R +IV+ + ++ ++ Sbjct: 251 MAASDIIAQAEH--DPNAVSVLVTTSETLAEEVEQEVLAQAESTARSEIVKISLENAAVL 308 Query: 670 LCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHT 729 + D ++ ++ SN++APEHL + + +++ + + NAGS+F+G Y P GDY+SGTNH Sbjct: 309 IADSLDQCIDFSNKFAPEHLEIMVEDSDFVLDRIKNAGSIFIGNYAPVPVGDYASGTNHV 368 Query: 730 LPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 LPT GYA+ YSG N F K+ + Q I+ GLE++ V+ +A++EGL H ++++ R Sbjct: 369 LPTAGYAKIYSGLNINHFLKYSSIQKISKSGLESLKETVIALAEEEGLKAHADSIRAR 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: 705 Number of extensions: 30 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: 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 10 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