Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate Synpcc7942_1714 Synpcc7942_1714 hypothetical protein
Query= SwissProt::D0L1T6 (403 letters) >FitnessBrowser__SynE:Synpcc7942_1714 Length = 338 Score = 103 bits (256), Expect = 1e-26 Identities = 104/337 (30%), Positives = 144/337 (42%), Gaps = 41/337 (12%) Query: 33 LDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAETDRKPGWWDSAIGP 92 LDCG LP LVY TYG+LN + SNA+L + H D IG Sbjct: 13 LDCGAVLPEASLVYATYGELNRDRSNAILYPTSYGAQHSTI-------------DWLIGG 59 Query: 93 GKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVKDWVHAQYRLM-QY 151 + +D DR+F+V +N G G + S DPA G + + D V AQ L+ Q Sbjct: 60 DRILDPDRWFIVIVNQFGN--GLSSSPSNDPACGLAEQGFW--FSHWDSVCAQQALLSQV 115 Query: 152 LGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIAFNEVARQAIITD 211 LG+ A + G S+G Q W+I +PD V + + + N F E R A+I D Sbjct: 116 LGIEQLALIYGWSMGAQQAYHWAIAFPDRVQRIAALCGTAKTTEHNRLFLESLRAALIAD 175 Query: 212 PEFYGGRYADHNALPRRGL-MLARMLGHITYLSDDAMRAKFGRELRAG-QVQYGFDVEFQ 269 P + G R+ A P RG AR+ Y S A +A + RAG Q G+ Sbjct: 176 PTWDGQRF---QATPDRGYKAFARI-----YASWAASQAFY----RAGIYRQQGYS---S 220 Query: 270 VESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQ--ASNDDLVAALAEVKAHFLVVSFT 327 +E YL + + D + L M D + A DL AL + A LV+ T Sbjct: 221 LEDYLERGWEANYRQRDPHDLLAMIDTWLRCDVSDRPAFGGDLAKALGSITAQTLVMPST 280 Query: 328 SDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDA 364 +D F+PE + + + Y I S GH A Sbjct: 281 TDLYFTPEDCEAEAQLI----PKAHYCPIPSIWGHRA 313 Lambda K H 0.320 0.135 0.412 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: 324 Number of extensions: 11 Number of successful extensions: 4 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: 403 Length of database: 338 Length adjustment: 30 Effective length of query: 373 Effective length of database: 308 Effective search space: 114884 Effective search space used: 114884 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: 49 (23.5 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