Align serine racemase (EC 5.1.1.18) (characterized)
to candidate Ac3H11_2427 Threonine dehydratase, catabolic (EC 4.3.1.19)
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2427 Length = 334 Score = 384 bits (986), Expect = e-111 Identities = 187/328 (57%), Positives = 250/328 (76%), Gaps = 6/328 (1%) Query: 1 MSDNLVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRG 60 M ++ LPT+DDVA+A+ R+ A+ TPV+ +T+++ A++FFKCEN Q+ GAFKFRG Sbjct: 6 MPPSVSLPTHDDVAAAARRLAGVAHHTPVMRCNTIDERLGAKLFFKCENLQRTGAFKFRG 65 Query: 61 ALNALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYG 120 A NAL+Q ++AQR+ GVLTFS+GNHAQAIALSA++L +PA ++MP DA +K+AAT+ YG Sbjct: 66 AYNALAQFSDAQREHGVLTFSAGNHAQAIALSARLLDMPALVVMPEDAAASKMAATREYG 125 Query: 121 GQVIMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFV 180 QV+ Y+RY +DRE ++++++ G+T+IPP+DHPHV+AGQGTAA EL +EV LD LFV Sbjct: 126 AQVVTYNRYTEDREAISRQLAHERGMTLIPPFDHPHVIAGQGTAALELLQEVPDLDYLFV 185 Query: 181 CLGGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQ 240 CLGGGGLLSGS LAA+ AP C+V GVEPE ND QQS R G IV I P TIADGAQ Sbjct: 186 CLGGGGLLSGSLLAAQALAPRCKVIGVEPETANDAQQSLRAGHIVRIPNPHTIADGAQAP 245 Query: 241 HLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMK----- 295 LG T+ II+E V+DI+TVSD++LI L+F+A RMK+VVEPTG L+FA +A Sbjct: 246 SLGELTYPIIREHVEDIVTVSDQQLIQALRFFAERMKVVVEPTGALAFAGVQAFSGEDDG 305 Query: 296 -EKLKNKRIGIIISGGNVDIERYAHFLS 322 + L+ + +G+I+SGGNVD+ R A FL+ Sbjct: 306 AKLLQGEHVGVIVSGGNVDLPRLARFLA 333 Lambda K H 0.318 0.135 0.384 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: 305 Number of extensions: 10 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: 323 Length of database: 334 Length adjustment: 28 Effective length of query: 295 Effective length of database: 306 Effective search space: 90270 Effective search space used: 90270 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: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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