Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_090447997.1 BLS63_RS22290 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_900100495.1:WP_090447997.1 Length = 439 Score = 257 bits (657), Expect = 8e-73 Identities = 155/447 (34%), Positives = 249/447 (55%), Gaps = 16/447 (3%) Query: 353 LTGPIHLDVVKASDKV---GVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEK 409 +T PI + + A+D+ + LS + V II+ VR++G++AL+E+T++ Sbjct: 1 MTAPIAIRRLNAADQDFARHLDHLLSWESVSDDAVNQRVLDIIQAVRERGDAALVEFTQR 60 Query: 410 FDGVKLSNP---VLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQP 466 FDG++++ +L E +T +EAL+ + E VR +H Q E Sbjct: 61 FDGLQVAGMAELILPRARLELALSRITAAQREALEKAAERVRLYHERQKQDSWTYTEAD- 119 Query: 467 GVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPE 526 G + + P+++ GLY+PGG A PS+ LM +PA+VA E+V P + G+++ Sbjct: 120 GTVLGQQVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVPEVVMVVPTPR--GEINEI 177 Query: 527 VVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQAL 586 V+ A G ++ GGAQAVAA+AYGTE++P VDKI+GPGN +V AK +V Sbjct: 178 VLAAACIAGVDRVFTIGGAQAVAALAYGTESVPPVDKIVGPGNIYVATAKRHVFGKV--- 234 Query: 587 CSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAV 646 IDM AGPSE+LV+ D D D++A DL SQAEH D+Q ILV + + + ++ +++ Sbjct: 235 -GIDMIAGPSEILVVCDGATDPDWIAMDLFSQAEHDEDAQSILVSPDAAF--LDKVAESI 291 Query: 647 HNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDN 705 + R +I+R + A ++ +A+E++N+ APEHL L +A+ + Y+ + + Sbjct: 292 TRLLPSMERAEIIRTSLEARGALIQVADMAQAIEVANRIAPEHLELSVADPDQYLAQIRH 351 Query: 706 AGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIG 765 AG++F+G YT E+ GDY +G NH LPT G AR S FQK + + + EG +G Sbjct: 352 AGAIFMGRYTAEALGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIHCSAEGASELG 411 Query: 766 RAVMCVAKKEGLDGHRNAVKIRMSKLG 792 + +A+ E L H + + R+ G Sbjct: 412 KTASVLARGESLSAHARSAEYRIKGEG 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: 700 Number of extensions: 36 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: 439 Length adjustment: 37 Effective length of query: 762 Effective length of database: 402 Effective search space: 306324 Effective search space used: 306324 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