Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_057506748.1 ABB28_RS00530 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_001431535.1:WP_057506748.1 Length = 431 Score = 355 bits (911), Expect = e-102 Identities = 194/418 (46%), Positives = 267/418 (63%), Gaps = 7/418 (1%) Query: 372 KALSRPIQKTS-EIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFE 430 +AL RP+Q + + H V +I VR G++AL E T +FD V+L + + A E + Sbjct: 16 EALQRPVQAVAAQTRHAVAALIAQVRADGDAALREITARFDRVQLDDIEVTAAEFEAAEQ 75 Query: 431 GLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAI 490 + +++ A++ + +R+FH A + ++ VET PGV C R RPI +VGLY+P G+A Sbjct: 76 AVAVDLRAAMEEAAARIRRFHEAGM-SQGYAVETAPGVHCERMIRPIGRVGLYVPAGSAP 134 Query: 491 LPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAA 550 LPSTALMLGVPA +A C ++V +PPR +DG P V+ A G ++ GGAQA+AA Sbjct: 135 LPSTALMLGVPAALAGCPQVVLCTPPR-ADGSADPAVLVAARLTGVQRVFKLGGAQAIAA 193 Query: 551 MAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDF 610 MA+GT ++P DK+ GPGN FVT AK V D +IDMPAGPSEVLVIAD A+ F Sbjct: 194 MAHGTASVPACDKLFGPGNSFVTEAKQQVAQDGSV--AIDMPAGPSEVLVIADAGANAAF 251 Query: 611 VASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVL 670 VA+DLLSQAEHG DSQV+L+ + + ++ ++ V Q LPR I R+ + S ++L Sbjct: 252 VAADLLSQAEHGPDSQVLLLTDDAA--LLEAVEAEVERQVALLPRETIARRALGASRLIL 309 Query: 671 CDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTL 730 D ++A E+SN+YAPEHLIL + ++ V AGSVF+G YTPE+ GDY SGTNH L Sbjct: 310 VDRLQDAFEISNRYAPEHLILALREPRAWLGQVQAAGSVFLGDYTPEALGDYCSGTNHVL 369 Query: 731 PTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 PT G AR +SG + A+FQ I+ Q+ + EG+ IG +A EGLD H AV +RM Sbjct: 370 PTAGAARAWSGVSVASFQNTISVQSASAEGIVAIGGCARILASAEGLDAHERAVALRM 427 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: 652 Number of extensions: 26 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: 431 Length adjustment: 37 Effective length of query: 762 Effective length of database: 394 Effective search space: 300228 Effective search space used: 300228 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