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Table 2 Comparisons between experimental and DDBP prediction results*

From: Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins

A   B C D E F G H I J K
I 11058-C7 249 no no 4–190; 1–220; 80–190 no 24%, (7–240/8–268, 288); 26%, (4–240/7–225, 251) (1–249)# 1–249 NP_506406 F20G2.1
I 11048-D3 199 no no 9–199 76–98, 181–181 26%, (5–160/3–164, 208) (1–199)$ 1–199 NP_502315 F35G2.2
I 11011-D8 190 no no 8–36, 47–75, 83–111; 2–107; 148–172, 108–120, 82–92, 49–51 27%, (37–105/1–69, 146) (45–190)& 1–107, 52–190 NP_493641 F23F1.2
I 18-A2 210 no no 29–79; 108–194 no 30%, (75–193/4–115, 135) (74–210)& 75–210 NP_491893 BAG1 (human) homolog family member (bag-1)
I 11033-F3 208 no no 6–74; 128–194; 1–97; 80–207 39–56 31%, (2–207/1–197, 198) (1–208)# 1–208 NP_496863 Glutathione S-Transferase family member (gst-16)
I 11-D11 346 no no 80–317; 55–320; 219–317 19–34, 116–126 31%, (76–334/36–291, 298) (56–346)& 55–346 NP_491872 C55B7.3
I 11104-F4 370 no no 2–221, 1–370 126–143, 348–352, 19–25, 71–82, 292–297, 233–237 34%, (128–347/15–231, 265) (125–370, 1–124)& 1–125, 128–347 NP_001040820 Cell Division Cycle related family member (cdc-37)
I 79-D4 401 no no 65–395; 37–400 66–108, 27–45, 108–125, 217–236, 138–146 35%, (212–395/2– 185, 185) (206–401)# 212–401 NP_491735 C06A5.7b
I 9-H3 212 no no no 19–52, 162–192, 79–89 35%, (86–136/84– 131, 217) (59–212)$ 53–212 NP_493365 Y40B1B.5
I 76-D4 254 no no 2–171; 3–250; 139–167 139–147 36%, (3–251/8–265, 278) (1–254)# 1–254 NP_001021765 Y47G6A.22
I 8-C1 142 no no 4–140 no 46%, (5–141/9–149, 150) (1–142)& 1–142 NP_499813 T12D8.6
I 11-F6 327 no 209– 231, 246– 268 207–227, 246–266 56–95, 19–56, 95–136, 136–161 50%, (141–167/1– 28, 163) (1–182, 1–145)& 1–135 NP_491774 T09B4.5a
I 1-F11 229 no no 148–217; 170–201; 170–212 19–21, 129–134 59%, (135–220/20–107, 113) (135–229)# 135–229 NP_506367 F53F4.3
I 3-H6 431 no no 24–118, 141–234; 254–370; 261–370 397–413, 214–225, 100–107, 123–128 60%, (4–131/20–147, 149); 48%, (4–244/41–280, 280); 40%, (7–408/24–422, 457); 35%, (128–428/22–330, 336); (1–135)# 1–131, 128–244, 245–431 NP_508026 FK506-Binding protein family member (fkb-6)
I 20-H6 496 no no 38–496; 186–261, 293–363, 422–483; 183–272, 275–374, 422–487 120–151, 265–279 66%, (394–496/1– 103, 104) ; 75%, (183–269/1– 87, 90); 75%, (290–366/1– 78, 85) (169–385, 386–496)& 183–272, 290–366, 394–496 NP_001022967 U2AF splicing factor family member (uaf-1)
I 1-D10 206 1–21 no 41–198; 23–77, 85–141, 143–196 no no (23–206)# 22–206 NP_491320 R12E2.13
I 11020-H6** 494 no no 53–225; 337–475; 336–453; 236–494 19–52, 106–145, 215–241, 373–383, 325–330 no (1–237, 238–494) &$ 53–225, 236–494, 331–494 NP_493412 Y37H9A.3
I 70-H8 130 no 107– 129 109–129 19–104 no (1–130)# 1–130 NP_491052 W03D8.3
I 8-C9 183 no no 125–159; no no (1–183)# ; (28–183, 23–183)$ 1–183 NP_510277 BMP receptor Associated protein family member (bra-1)
I 11005-B8 245 no no no 19–20, 129–136, 41–46 no (9–245)# 1–245 NP_740981 R05F9.1b
II 18-F7 288 no no 34–286 19–30, 72–78, 196–202, 66–70 45%, (35–286/21– 274, 276) (32–266)$ 34–286 NP_001021584 EXOnuclease family member (exo-3)
II 4-F5 592 no no 189–269 485–509, 125–142, 19–37, 369–382,99–109, 311–317 35%, (210–269/15–74, 76); (1–144)& 1–124, 143–269 NP_494544 C16C8.16
II 11011-C6 162 no no 4–162; 5–54, 71–132 51–68 no (1–148, 1–124)& 1–162 NP_500324 F42A6.6
II 11058-H2 249 no no 4–190; 4–230; 4–209 no 40%, (5–245/23– 263, 267) (1–222)$ 1–249 NP_506407 F20G2.2
II 76-F10 263 no no 23–130; 33–109 118–126, 20–20 27%, (27–120/6–98, 108) (1–129)& 21–130 T26031 hypothetical protein W01A8.2
II 79-H11 245 no no 2–156, 1–241 144–181, 181–204, 121–144 51%, (2–154/2–154, 155) (1–185)$ 1–156 NP_492567 C03D6.5
II 25–B11 302 no no 23–127; 45–114 203–236, 19–24, 236–248, 146–161, 187–195 no (1–153)& 23–145 NP_492781 B0511.7
II 11-D3 313 no no 28–214; 9–302 151–174, 19–22 no (1–313)# ; (213–313)$ 23–313 NP_001021333 Suppressor of PResenilin defect family member (spr-2)
II 11058-F12 272 no no 40–63; 40–68, 90–124 no 32%, (67–119/3–54, 60); 26%, (40–119/5–84, 87); 31%, (41–114/36– 113, 124) (1–147)& 1–124 NP_503566 F36F12.8
III 20-D7 500 no no 311–395; 41–278; 283–436 387–417, 288–308, 453–469, 481–482 28%, (342–432/68–153, 289) (1–500)# ; (298–500, 388–500, 407–500)$ 1–287, 283–452 NP_491868 lariat DeBRanching enzyme related family member (dbr-1)
III 37-G9 245 no no no 206–227, 19–21 no (1–102, 103–245)& 1–245 NP_507040 F14H3.6
III 70-D2 265 1–25 15–37 69–243 223–247, 195–199 22%, (128–264/13–121, 135) (1–130, 1–174)& 1–265 AAC25860 Hypothetical protein C37C3.3
III 2-B6 316 no no 27–294 225–260, 174–191, 149–163, 296–298, 71–82, 84–84, 219–220 23%, (53–168/46– 180, 201) (71–294)# ; (104–316)$& 1–295 NP_501422 D2096.8
III 10-E5 274 no no 1–80, 108–190 229–246, 193–213 25%, (17–161/32– 166, 196) (65–237, 1–74, 75–274)& 1–192 NP_502380 C25G4.6
III 3-D2 419 no no 95–128, 133–166; 93–197; 133–166 196–217, 41–62, 259–275, 341–351, 19–21 26%, (95–239/13– 144, 166); 32%, (99–197/8–95, 118) (140–309, 290–419)& 93–197, 93–258 NP_495087 C17G10.2
III 113-H8 588 no no 232–342; 241–334 492–515, 19–56, 81–132, 150–185 29%, (234–328/2– 85, 105) (1–345, 34–313)& 232–342 NP_740981 R05F9.1b
III 76-F6 803 no 769– 791 17–250, 558–652; 10–34, 111–148, 382–402 752–767, 19–24, 717–727, 280–281 29%, (62–257/5– 200, 205); 29%, (83–257/1– 175, 181) (1–181)& 25–257 NP_491008 alpha-CaTuliN (catenin/vinculin related) family member (ctn-1)
III 4-A4 569 no no 164–338, 369–527;187–200, 206–222, 263–279, 305–321, 321–335, 506–527; 263–318, 388–452, 511–568 65–97, 19–38,112–139 32%, (154–567/18–397, 402) (334–542, 334–501)&; (1–569)# 154–549 NP_495753 associated with RAN (nuclear import/export) function family member (ran-3)
III 25-H8 339 no no 24–84; 24–75 215–276, 111–169, 187–201, 100–109 41%, (22–75/7–61, 70) (1–152)& 1–99 NP_495652 T09A5.8
III 2-H9 356 no no 22–273; 1–108, 115–297; 13–284 192–215, 303–312, 338 42%, (1–284/1–289, 382) (1–335, 1–356) $& 1–197 NP_497949 T23F11.1
III 18-H1 208 no no 32–124; 36–113; 24–45, 51–68, 131–145, 164–181, 186–205 171–190, 114–171, 19–40 43%, (41–110/10– 76, 90) (1–81)&$ 32–124 NP_510410 HIStone family member (his-24)
III 11049-D6 435 no no 293–433; 270–433 110–152, 234–260, 175–186, 375–381 no (1–156)# ; (9–158, 1–119)$& 261–435 NP_001041025 Y41E3.7a
III 9-G11 250 no no 1–194 228–232 no (35–250)& 1–227 NP_497076 R05H10.1
III 10-E1 251 no no no 158–199 no (1–206)& 1–251 NP_496943 W01G7.4
III 37-F11 230 no no 1–230 106–126, 168–182 no (45–179, 45–230)& 1–230 NP_507024 T10C6.5
III 75-A8 228 no no no 19–44, 125–135 no (1–189)$& 1–228 NP_492509 F46A9.1
III 11048-E2 262 no no 33–178; 61–179 183–198 no (1–262)$ 1–182 NP_501337 MEChanosensory abnormality family member (mec-17)
  1. * column A: Prediction accuracy level (I, accurate; II, basically accurate; III, wrong) and Plate-ID, users could query/search the sequence relative information from the SGCE web site [41]; column B: number of amino acids in the ORF; column C: signal peptide prediction results using SignalP; column D: transmembrane region prediction results using TMHMM; column E: domains/fragments from Interpro/InterProScan analysis; column F: domain linker regions predicted by Domain Linker Finder; column G: PDB-alignment results, including the percentage of sequence identity, query/subject sequence start position and end position, and the length of the subject sequence; column H: experimental results from protein crystal/three-dimensional structures (labeled with #), limited proteolysis (labeled with $) or spontaneous degradation (labeled with &); column I: DDBP prediction results; J: Accession Number, user could obtain sequence relative information from National Center for Biotechnology Information (NCBI) [40]; K: Definition of the protein or ACEID for proteins without known functions.
  2. ** 11020-H6 is corresponding to the region 299–792 of NP_493412.