Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 (characterized)
to candidate WP_011842331.1 RSPH17029_RS17090 5-dehydro-4-deoxyglucarate dehydratase
Query= SwissProt::Q07607 (292 letters) >NCBI__GCF_000015985.1:WP_011842331.1 Length = 301 Score = 91.7 bits (226), Expect = 2e-23 Identities = 86/291 (29%), Positives = 130/291 (44%), Gaps = 17/291 (5%) Query: 4 GSITALVTPF-ADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEIT 62 G ++ VTPF A++R VEW + L G TGE +L+ E +V Sbjct: 13 GLLSFPVTPFDAENRFAAAPYQKHVEWLSGFDAPVLFAAGGTGEFFSLTPDEIPAIVRAA 72 Query: 63 IKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAID 122 ++A G+ +++G G T A R + AG DG+L++ Y QEG+Y H KA+ Sbjct: 73 KESA-GKTAIVSGCGYG-TEIARGIARSVEAAGGDGILLLPHYLIDAPQEGLYAHVKAVC 130 Query: 123 AASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGN--LLRPSLERMACGED 180 A+ + ++VYN R + +TLAR+ +DCPN+ G KD TG+ L+R +M G+ Sbjct: 131 QATGMGVMVYN---RDNAVLQADTLARLCDDCPNLVGFKDGTGDIGLVRQITAKM--GDR 185 Query: 181 FNLLTGEDGTAL---GYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLM 237 L G L Y+ S N PAL F A GD A + + Sbjct: 186 LTYLGGMPTAELFAEAYLGASFTTYSSAVFNFVPALANKFYAALRAGDRATCESILNSFF 245 Query: 238 PLHRALFLETN---PAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAM 285 L A K ++ +G G +R PL ++ +EEI A+ Sbjct: 246 YPFMELRSRRKGYAVAAVKAGVRLVGFDAGPVRAPLSDLTGE-EEEILKAL 295 Lambda K H 0.319 0.136 0.402 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: 206 Number of extensions: 11 Number of successful extensions: 2 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: 292 Length of database: 301 Length adjustment: 26 Effective length of query: 266 Effective length of database: 275 Effective search space: 73150 Effective search space used: 73150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 16 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