Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013430204.1 CALKRO_RS06255 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000166775.1:WP_013430204.1 Length = 431 Score = 244 bits (622), Expect = 9e-69 Identities = 157/424 (37%), Positives = 232/424 (54%), Gaps = 14/424 (3%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFD--GVKLSN-PVLNAPFPE 426 ++ A R + EI V II +V+DK + ALL YT FD G+ L+ V+ Sbjct: 14 IETAKIRKWENEEEIEQKVRRIISDVKDKKDEALLYYTRMFDCKGICLNELRVVQEEIER 73 Query: 427 EYFEGLTEE--MKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYI 484 YFE E+ +AL+ + +N+ ++H Q ++ G L + P+EKVG+Y+ Sbjct: 74 AYFECEKEDGDFIDALNAAYKNIYEYHMRQKEESWFYIKN--GSLLGQIIMPLEKVGIYV 131 Query: 485 PGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGG 544 PGG PST LM +PA+VA ++I+ +PP K+ +S + A+ G +I GG Sbjct: 132 PGGKGAYPSTVLMNSIPAKVAGVEKIIMVTPPDKNKS-ISKYTLAAAKICGIDEIYKVGG 190 Query: 545 AQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADE 604 AQAVAA+A+GT+ IPKVDKI+GPGN +V AK + ID AGPSEV+VIADE Sbjct: 191 AQAVAALAFGTQIIPKVDKIVGPGNIYVATAKKLLFG----YVDIDSVAGPSEVMVIADE 246 Query: 605 DADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA 664 A+ ++A+DLLSQAEH ++ ILV +L + QE+ + V + Sbjct: 247 SANPKYIAADLLSQAEHDPMARCILVTTSL--QVAQEVSENVDKMLARFENSVAFEAIEK 304 Query: 665 HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSS 724 + I++ D EA E++N APEHL + +A + + NAG+VFVG Y+PE GDY + Sbjct: 305 NGVIIVVDDLFEAAEIANIIAPEHLEICCNDAEKVLFKIRNAGAVFVGEYSPEPIGDYIA 364 Query: 725 GTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAV 784 G NH LPT G A +S F K ++ + E + +A+KEG H N++ Sbjct: 365 GPNHVLPTSGTASFFSPLGVYDFVKRMSLIKYSKEQFLTDAPHAINIAQKEGFLFHANSL 424 Query: 785 KIRM 788 K+R+ Sbjct: 425 KVRL 428 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: 806 Number of extensions: 55 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 Jul 26 2024. The underlying query database was built on Jul 25 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