Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_029000579.1 H537_RS0128480 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000430725.1:WP_029000579.1 Length = 439 Score = 280 bits (716), Expect = 1e-79 Identities = 168/439 (38%), Positives = 246/439 (56%), Gaps = 14/439 (3%) Query: 358 HLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSN 417 HL A + Q+ L + + I H V IIE VR++G++A+LE+T +FDGV+ + Sbjct: 7 HLSTADADFESAFQRVLHWSAETDAAIEHRVAEIIEAVRERGDAAVLEFTARFDGVQADS 66 Query: 418 PVLNAPFPEEY---FEGLTEEMKEALDLSIENVRKFHAAQLPT--ETLEVETQPGVLCSR 472 EE F+ +T +EAL+ + + VR +H QL ++ + G L + Sbjct: 67 VSALELGREELKAAFDAITPAQREALEFAAQRVRSYHERQLEASGKSWSYRDEDGTLLGQ 126 Query: 473 FPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAE 532 P+++VG+Y+PGG A PS+ LM +PA VA EIV P + G+ +P V+ A Sbjct: 127 KVTPLDRVGIYVPGGKAAYPSSVLMNAIPAHVAGVPEIVMVVPTPR--GEKNPLVLAAAY 184 Query: 533 KVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMP 592 G + GGAQAVAA+AYGT TIP+VDKI GPGN +V +AK V IDM Sbjct: 185 VAGVHRAFTVGGAQAVAALAYGTATIPRVDKITGPGNAYVASAKRRVFGQV----GIDMI 240 Query: 593 AGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQ 652 AGPSE+LV+AD D+VA DL SQAEH +Q IL+ + I ++++A+ Sbjct: 241 AGPSEILVLADGSTPADWVAMDLFSQAEHDELAQSILLCPDAGY--IAQVREAIERLLPG 298 Query: 653 LPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFV 711 +PR D++R + ++ EEA E+SN+ APEHL + + + + L+ +AG++F+ Sbjct: 299 MPRADVIRASLEGRGALIHTRSMEEACEISNRIAPEHLEVSSSEPHRWEPLLRHAGAIFL 358 Query: 712 GAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCV 771 GAYT ES GDY +G NH LPT G AR S T FQK + ++ +G + +GR + Sbjct: 359 GAYTSESLGDYCAGPNHVLPTSGTARFSSPLGTYDFQKRSSLIEVSEQGAQQLGRVAAEL 418 Query: 772 AKKEGLDGHRNAVKIRMSK 790 A EGL H A + R+ K Sbjct: 419 AYGEGLQAHAQAAEFRLKK 437 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: 688 Number of extensions: 34 Number of successful extensions: 6 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: 439 Length adjustment: 37 Effective length of query: 762 Effective length of database: 402 Effective search space: 306324 Effective search space used: 306324 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