Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SMc03259 SMc03259 hypothetical protein
Query= BRENDA::O67216 (294 letters) >FitnessBrowser__Smeli:SMc03259 Length = 302 Score = 104 bits (259), Expect = 3e-27 Identities = 79/239 (33%), Positives = 116/239 (48%), Gaps = 4/239 (1%) Query: 4 GSIVALITPFKEG-EVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFA 62 G A+ T EG EVD EA + I+ V G ++V GE+ ++T E E +I A Sbjct: 6 GVFPAVTTKLTEGGEVDIEATKDSIDRLVKAGVSGVIVLPMLGENASMTISERETIIREA 65 Query: 63 VKRAAGRIKVIAGTGGNATHEAVHLTAHAKE-VGADGALVVVPYYNKPTQRGLYEHFKTV 121 V AAGRI V++G AT + A E GA G +V K R E ++ + Sbjct: 66 VDVAAGRIPVLSGLA-EATLANAKVNARLYESFGAQGLMVFPSLGYKTDVRETAEWYRGI 124 Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181 A +PI+IYN P V+ +V+ + L + E IV KE + ++ R++++ E F Sbjct: 125 AGASSLPIMIYNNPIAYGVDCTVEVLKDLVNTPE-IVCIKEESGDIRRVTDLYVEFAERF 183 Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLF 240 SV G D L + ALG G +S NV P E EL + + +ARE++ L F Sbjct: 184 SVFCGVDDLIVESSALGVTGWVSGMANVWPSECVELFDLCSQNRYNQARELYQILTPAF 242 Lambda K H 0.318 0.136 0.390 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: 202 Number of extensions: 14 Number of successful extensions: 3 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: 294 Length of database: 302 Length adjustment: 26 Effective length of query: 268 Effective length of database: 276 Effective search space: 73968 Effective search space used: 73968 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 (21.7 bits) S2: 48 (23.1 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