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Table 2 A selected list of protein family/motifs identified by SVD-derived singular triplets (st's). In this summary table, unique example proteins (rsv-gi#) were chosen from the 5 to 40 "top five" proteins identified as members of a given family by as many as 8 distinct right singular vectors. As examples, six individual ras proteins representing six broad categories of ras (highlighted in italics) are defined by a total of 13 right singular vectors, and 18 ribosomal proteins (highlighted in bold) are defined by a total of 65 right singular vectors. The lengths of continuous copep strings identified from the corresponding left singular vectors and their specificities (E-values) as revealed by pairwise BLAST are also provided.

From: An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage

triplet # rsv-gi# Name Protein Description lsv copep string (E-value)
421a 1 11415030 HIST1H4J H4 histone family, member E 62 aa's (1e-54)
417a 2 21166389 HIST1H2BC H2B histone family, member L 75 aa's (4e-67)
413a 1 31560385 Rpl21 ribosomal protein L21 60 aa's (2e-55)
408 1 4501885 ACTB beta actin; beta cytoskeletal actin 42 aa's (9e-38)
405 1 4506661 Rpl7a ribosomal protein 7a 79 aa's (3e-62)
392a 1 5174735 TUBB2 tubulin, beta, 2 45 aa's (7e-41)
389a 2 13569962 RAB1B RAB1B, RAS oncogene family; small GTP-binding 14 aa's (2e-11)
389 3 6677781 Rpl29 ribosomal protein L29 77 aa's (3e-60)
387 3 31981690 Hspa8 heat shock 70kD protein 8 40 aa's (2e-35)
385a 1 11024714 UBB ubiquitin B precursor; polyubiquitin B 77 aa's (2e-68)
378a 5 26051216 CAMK2B calmodulin-dependent protein kinase IIB isoform 7 14 aa's (2e-10)
373a 2 4502201 ARF1 ADP-ribosylation factor 1 86 aa's (1e-41)
371a 3 6679439 Ppia peptidylprolyl isomerase A; cyclophilin A 55 aa's (2e-48)
368a 5 25150942 Tcb-1 transposable element tcb1 transposase (1O615) 88 aa's (7e-74)
363 3 33149310 UBE2D3 ubiquitin-conjugating enzyme E2D 3 isoform 1 138 aa's (7e-91)
354 3 4502549 CALM2 calmodulin 2; phosphorylase kinase delta 40 aa's (1e-19)
352a 4 17105394 RPL23A ribosomal protein L23a 44 aa's (3e-33)
350a 4 9845511 RAC1 ras-related C3 botox sub 1 isoform Rac1, rho 15 aa's (2e-12)
347a 3 51873060 Eef1a1 eukaryotic translation elongation factor 1 alpha 1 24 aa's (4e-19)
345 2 27679110 Rpl17 ribosomal protein L17 (L23) 92 aa's (2e-89)
341a 5 31980772 Ppp1cc protein phosphatase 1, catalytic, gamma isoform 20 aa's (5e-17)
337 5 24648716 mod(mdg4) modifier of mdg4 32 aa's (2e-29)
334 5 24653107 Galpha49B G protein alpha49B 19 aa's (9e-18)
333a 3 4506633 RPL31 ribosomal protein L31 78 aa's (8e-74)
329a 2 34878793 Pcdha13 protocadherin alpha 13 17 aa's (8e-14)
327 3 32307119 PPP2R2B Serine/threonine protein phosphatase 2A, neuronal 23 aa's (7e-20)
324 1 31982919 ZNF430 zinc finger protein 430 18 aa's (3e-11)
322a 3 34871376 LOC287293 similar to high mobility group 1 protein 15 aa's (9e-13)
321a 3 4504445 HNRPA1 heterogeneous nuclear ribonucleoprotein A1 23 aa's (2e-18)
320a 2 25141298 kin-1 cyclic AMP-dependent catalytic subunit (kin-1) 66 aa's (4e-62)
316a 5 22094075 Slc25a5 solute carrier family 25; adenine nucleotide 27 aa's (7e-22)
308a 3 9845502 LAMR1 laminin receptor 1 (67kD, ribosomal protein SA) 68 aa's (1e-60)
304 3 6978809 Eno1 enolase 1, alpha 32 aa's (3e-27)
301 4 27676004 LOC365206 similar to ribosomal protein L9 139 aa's (1e-13)
295 2 31083250 PPP2R5C Ser/threo protein phosphatase 2A, 56 kD regulator, 16 aa's (6e-12)
292 4 31560517 Rpl27a ribosomal protein L27a 58 aa's (7e-56)
291 2 15011936 RPS26 ribosomal protein S26 77 aa's (7e-64)
288 1 22129671 Olfr493 olfactory receptor MOR204–35 12 aa's (3e-08)
287 2 38076430 LOC193565 similar to T-cell receptor alpha chain 16 aa's (2e-12)
285a 3 6754140 H2-Q7 histocompatibility 2, Q region locus 7 19 aa's (5e-16)
280a 5 16418339 Rpl10 ribosomal protein 10 27 aa's (4e-23)
277a 1 15718763 KRAS2 cellular c-Ki-ras2 proto-oncogene 9 aa's (2e-06)
277 2 27689505 Rab5c similar to Rab5c protein 17 aa's (4e-13)
276 4 24580529 M(2)21AB Minute (2) 21AB CG2674-PA 25 aa's (5e-20)
272 1 25742772 Kcna2 potassium voltage-gated channel, shaker-related, 12 aa's (1e-09)
270 4 33186863 Rpl13 ribosomal protein L13 11 aa's (3e-09)
266 4 4506697 RPS20 ribosomal protein S20 54 aa's (2e-49)
256 3 4506597 RPL12 ribosomal protein L12 34 aa's (8e-30)
253a 6 15809016 MRLC2 myosin regulatory light chain MRCL2 19 aa's (7e-16)
247 3 31981515 Rpl7 ribosomal protein L7 10 aa's (4e-08)
240a 5 24639734 Dlc dynein light chain ATPase 22 aa's (4e-21)
237a 4 34865959 gpdh similar to glyceraldehyde-3-phosphate 16 aa's (7e-13)
236a 2 10835049 ARHA Aplysia ras-related homolog 12; oncogene RHO 9 aa's (9e-07)
230 6 15431293 RPL15 ribosomal protein L15 11 aa's (6e-09)
224 5 13592069 Rps10 ribosomal protein S10 81 aa's (1e-78)
197a 2 14249144 Rab11b RAB11B, member RAS oncogene family 15 aa's (4e-12)
190a 6 4506621 RPL26 ribosomal protein L26 16 aa's (8e-14)
183a 5 14277700 RPS12 ribosomal protein S12 13 aa's (1e-10)