Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate GFF761 PGA1_c07750 histidinol dehydrogenase HisD
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Phaeo:GFF761 Length = 435 Score = 238 bits (608), Expect = 4e-67 Identities = 152/425 (35%), Positives = 227/425 (53%), Gaps = 12/425 (2%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 ++KA P SE V I++++ G++ LEY KFD + N +L E Sbjct: 6 LKKAALTPKSDASETHKTVQGILDDIEAGGDAKALEYAAKFDRYE-GNVLLTDEEIEAAC 64 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPT-ETLEVETQPGVLCSRFPRPIEKVGLYIPGGT 488 + E++K + S +NVR+F Q T + +E E PG + + P++ G Y+PGG Sbjct: 65 ALVPEKLKADIRFSHDNVRRFAELQKSTMQNVETEICPGFITGQKVIPVDAAGCYVPGGR 124 Query: 489 AILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAV 548 ++A+M A+VA CK I SPPR G V+P +VY A GA KI+ GG Q V Sbjct: 125 YSHIASAIMTVTTAKVAGCKHITACSPPRPGVG-VAPAIVYAAHICGADKIMAMGGVQGV 183 Query: 549 AAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADV 608 AAM +G +PK + ++GPGNQFV AK + IDM AGP++ L++AD AD Sbjct: 184 AAMTFGLFGLPKANILVGPGNQFVAEAKRILFGRV----GIDMIAGPTDSLILADRTADA 239 Query: 609 DFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA---H 665 VA+DL+SQAEHG +S V LV + + +E+ V LP V+ A + Sbjct: 240 HIVATDLVSQAEHGYNSPVWLVTDDRA--LAEEVMRLVPGLIDDLPEVNRENAAAAWRDY 297 Query: 666 STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSG 725 + ++LC EE S+ YAPEHL +Q + + ++ + GS+F+G T S GD ++G Sbjct: 298 AEVILCSDREEMAACSDDYAPEHLTVQAEDLDWWLGQLTCYGSLFLGEETTVSYGDKAAG 357 Query: 726 TNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVK 785 TNH LPT A G + + K +T Q T EG + + A +A+ EG++GH A Sbjct: 358 TNHVLPTSRAASYTGGLSVHKYMKIVTWQRATREGSKAVAEATARIARLEGMEGHARAAD 417 Query: 786 IRMSK 790 +R++K Sbjct: 418 VRLAK 422 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: 27 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: 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