Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_028314173.1 G491_RS0107675 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000429905.1:WP_028314173.1 Length = 433 Score = 246 bits (629), Expect = 1e-69 Identities = 149/410 (36%), Positives = 234/410 (57%), Gaps = 16/410 (3%) Query: 388 VNPIIENVRDKGNSALLEYTEKFD--GVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIE 445 V+ I+E+VR G+ A+++Y+ +FD G+ + + + ++ + + ++A++ S Sbjct: 33 VSKILEDVRKNGDQAVVDYSNRFDAGGMTVESMRVTDQEMKDALAQVDPDFQKAMERSHR 92 Query: 446 NVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGG---TAILPSTALMLGVPA 502 NV FH QLP + + +PG + + RP++ G+Y+PGG + L S+ +M GVPA Sbjct: 93 NVADFHRRQLPKSWITTD-RPGTVLGQMIRPVDAAGVYVPGGQGGSTPLVSSVIMGGVPA 151 Query: 503 QVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVD 562 ++A + ++ +PPR +DG V P ++ A G ++ G A A+AAMA+GTETI VD Sbjct: 152 KIAGVERVIMVTPPR-ADGTVHPYLLAAAHLTGIDEVYKIGSAWAIAAMAFGTETIKAVD 210 Query: 563 KILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHG 622 I+GPGN +VT AK V IDM AGPSEVLVIAD AD D +A+DLLSQAEH Sbjct: 211 VIVGPGNIYVTIAKSLVAGTV----GIDMIAGPSEVLVIADHTADPDCIAADLLSQAEHD 266 Query: 623 IDSQVILVGVNLSEKKIQ-EIQDAVHNQALQLPRVDIVRKCIAHSTIV-LCDGYEEALEM 680 + ILV +++KI + A++ + +L R +I + + + + D + A ++ Sbjct: 267 PMASSILV---TTKRKIALNAKKALYERVAKLSRREIAEASVQKNCVAFVVDDLDAAADL 323 Query: 681 SNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYS 740 SN APEHL L + + Y + +AG++F+G YTPE GDY +G NH LPT G R S Sbjct: 324 SNAIAPEHLELLVEDPFAYFPKIKHAGAMFLGQYTPEPVGDYVAGPNHVLPTQGTGRFSS 383 Query: 741 GANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790 N F K + + + E + ++ +A+ EGL H +VK R+ K Sbjct: 384 ALNVDNFLKKTSLLHYSKETFDEEAEDIIRLAEVEGLTAHAESVKARLKK 433 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: 723 Number of extensions: 31 Number of successful extensions: 7 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