Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012537563.1 AFE_RS13945 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000021485.1:WP_012537563.1 Length = 433 Score = 243 bits (621), Expect = 1e-68 Identities = 154/409 (37%), Positives = 225/409 (55%), Gaps = 13/409 (3%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPV-LNAPFP--EEYFEGLTEEMKEALDLSI 444 V I+ VRD+G++AL EYTE+FDGV ++ L P + GL + AL+ + Sbjct: 33 VREIVTTVRDRGDAALREYTERFDGVTTASAAELEIPRSAWDAALHGLEPTQRVALEEAA 92 Query: 445 ENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQV 504 + +R +H Q E +L R P+ +VG+Y+PGG A PS+ LM +PA V Sbjct: 93 QRIRSYHEHQRSVGWTFTEADGTMLGQRI-LPLARVGIYVPGGKAAYPSSVLMNAIPAHV 151 Query: 505 AQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKI 564 A KEI+ P + G+V+P V+ A G ++ GGAQAVAA+AYGTE++P VDKI Sbjct: 152 AGVKEIIMTVPTPQ--GQVNPWVLAAAAIAGVDRVFCIGGAQAVAALAYGTESVPAVDKI 209 Query: 565 LGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGID 624 +GPGN +V AK V IDM AGPSE+LVI+D A +++A DLLSQAEH Sbjct: 210 VGPGNIYVATAKRMVFGRV----GIDMIAGPSEILVISDGSAPAEWLAWDLLSQAEHDEI 265 Query: 625 SQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQ 683 +Q I + + + I+ + +AV L R I RK A ++ EA ++++ Sbjct: 266 AQSIFI--SWDDAHIESVVNAVDAALDVLDRAPIARKSWADRGAVIRVRDRAEACAIADR 323 Query: 684 YAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGAN 743 APEHL L + N D++ + NAG++F+G ++ E+ GDY +G NH LPT G AR S Sbjct: 324 IAPEHLELAVQNPEDWLADIHNAGAIFMGIHSCEALGDYVAGPNHVLPTGGSARFSSPLG 383 Query: 744 TATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKLG 792 F K + + +P G +G+ +A EGL H + R+ + G Sbjct: 384 VYDFVKRSSLIHSSPAGAARLGQIAERLALGEGLTAHARSAACRIPEAG 432 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: 694 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: 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 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