Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_089300773.1 CHB84_RS07515 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_900188115.1:WP_089300773.1 Length = 449 Score = 218 bits (555), Expect = 6e-61 Identities = 142/434 (32%), Positives = 226/434 (52%), Gaps = 23/434 (5%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 ++ L R + + V P++++V ++G A L+YT +FD V+ + + Sbjct: 17 LRACLPRAEVNVDDALRAVRPLVDDVAERGVPAALDYTARFDAVRPGAVRVPRSELDRAL 76 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA 489 L ++ AL+ S+ R HA Q T+ + G + R+ P+ +VGLY PGG A Sbjct: 77 TELAPAVRAALEESVTRARAVHADQRRTDVTTRVAEGGTVTERWV-PVARVGLYAPGGLA 135 Query: 490 ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVS-PEVVYVAEKVGASKIVLAGGAQAV 548 PS+ +M VPAQ A +V +PP+ G + P + A +G ++ GGAQAV Sbjct: 136 AYPSSVVMNVVPAQEAGVGSVVLCTPPQAEFGGLPHPTTLAAAALLGVDEVWAVGGAQAV 195 Query: 549 AAMAYG-TET----IPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIAD 603 A +AYG T+T + VD + GPGN ++TAAK ++ + ID AG +E+ ++AD Sbjct: 196 ALLAYGGTDTDGTELDPVDMVTGPGNVYLTAAKRMLRG----VIGIDSEAGTTEIAILAD 251 Query: 604 EDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI 663 + AD +VASDL+SQAEH + +LV ++ ++ DAV + + V + + Sbjct: 252 DTADPGYVASDLISQAEHDPAAASVLVTPSV------QLADAVDAELARRVPVTKHHERV 305 Query: 664 AH------STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPE 717 A S VL G ++ + + + YA EHL + A+A + V NAG++FVG Y P Sbjct: 306 AEALRGRQSGTVLVSGLDDGVRVVDAYAAEHLEIHTADAREVAARVRNAGAIFVGPYAPV 365 Query: 718 SCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGL 777 S GDY +G+NH LPT G AR +G + TF + I + + + L + V+ +A E L Sbjct: 366 SLGDYCAGSNHVLPTGGSARHSAGLSVQTFLRGIHVVDYSADALREVAGHVVTLADVEDL 425 Query: 778 DGHRNAVKIRMSKL 791 H AV R+ + Sbjct: 426 PAHGEAVLARVGSV 439 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: 665 Number of extensions: 30 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: 449 Length adjustment: 37 Effective length of query: 762 Effective length of database: 412 Effective search space: 313944 Effective search space used: 313944 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