Topography Prediction of Helical Transmembrane Proteins by a New Modification of the Sliding Window Method

Table 3

Comparison of TMD boundaries calculated upon processing of hydrophobicity functions 𝑓_𝑛(𝑘) at 𝑛=4,5 on 𝐻_𝑁(𝑖) (𝑁=3,5,6) scales for GPCRs with known data from [21].

Protein name, code, length	Data source	Number and boundaries of transmembrane domains
	Scale level	1	2	3	4	5	6	7
S1PR1_; HUMAN P21453; 382 aa	[21], by similarity	47–71	79–107	122–140	160–185	202–222	256–277	294–314
	𝐻5(𝑖),𝑛=5; 𝑢=0.25	48–69	83–107	122–142	160–195	199–223	255–281	293–310
ACM2_; HUMAN P08172; 466 aa	[21], by similarity	23–45	60–80	98–119	140–162	185–207	389–409	424–443
	𝐻3(𝑖),𝑛=5; 𝑢=0.07	21–48	60–85	90–122	142–167	192–208	389–415	422–429
ACM3_; RAT P08483; 589 aa	[21], by similarity	67–90	104–124	142–163	184–206	229–251	492–512	527–546
	𝐻5(𝑖),𝑛=5; 𝑢=0.30	62–92	105–128	137–161	187–208	221–249	492–515	526–541
CXCR1_; HUMAN P25024; 350 aa	[21], potential	40–66	76–96	112–133	155–174	200–220	243–264	286–308
	𝐻3(𝑖),𝑛=4; 𝑢=−0.05	39–67	76–96	102–141	152–175	199–230	241–267	291–308
CCR5_; HUMAN P51681; 352 aa	[21], potential	31–58	69–89	103–124	142–166	199–218	236–260	278–301
	𝐻5(𝑖),𝑛=5; 𝑢=0.25	33–56	68–93	100–136	141–164	196–218	238–264	288–299
HRH1_; HUMAN P35367; 487 aa	[21], potential	30–49	64–83	102–123	146–165	190–210	419–438	451–470
	𝐻5(𝑖),𝑛=5; 𝑢=0.17	25–50	63–93	96–122	147–167	188–212	418–442	449–469
OPRK_; HUMAN P41145; 380 aa	[21], potential	59–85	96–117	133–154	174–196	223–247	276–299	312–333
	𝐻6(𝑖),𝑛=4; 𝑢=0.50	56–83	99–122	143–151	180–195	227–248	277–300	302–320
OPRM_; MOUSE P42866; 398 aa	[21], potential	65–94	104–121	144–163	194–209	235–257	281–303	312–328
	𝐻3(𝑖),𝑛=4; 𝑢=−0.02	68–95	105–114	136–162	187–205	229–262	280–306	317–325
OPRD_; MOUSE P32300; 372 aa	[21], potential	46–75	85–102	125–144	175–190	216–238	262–284	294–310
	𝐻5(𝑖),𝑛=5; 𝑢=0.213	44–74	85–102	112–142	167–187	211–236	263–286	296–319
OPRX_; HUMAN P41146; 370 aa	[21], potential	51–77	88–109	125–146	166–188	212–236	265–288	301–322
	𝐻3(𝑖),𝑛=5; 𝑢=0.011	42–79	90–107	112–130	172–186	212–241	263–284	301–335
NTR1_; RAT P20789; 424 aa	[21], potential	65–87	97–121	144–165	189–210	236–260	309–330	349–372
	𝐻5(𝑖),𝑛=5; 𝑢=0.144	63–86	103–139	154–172	191–208	220–268	306–324	338–374
PAR1_; HUMAN P25116; 425 aa	[21], potential	103–128	138–157	177–198	219–239	269–288	312–334	351–374
	𝐻3(𝑖),𝑛=4; 𝑢=0.100	101–133	136–158	175–208	221–238	270–296	313–338	350–371
O51E1_; HUMAN Q8TCB6; 317 aa	[21], potential	28–48	57–77	102–122	142–162	199–219	239–259	275–295
	𝐻5(𝑖),𝑛=5; ⟨𝑢⟩=0.300	12–49	60–77	80–120	146–166	198–227	243–260	276–292
SMO_; HUMAN Q99835; 787 aa	[21], potential	234–254	263–283	315–335	359–379	403–423	452–472	525–545
	𝐻3(𝑖),𝑛=5; 𝑢=0.00	236–251	264–283	313–340	362–380	403–425	451–473	519–545
GP160_; HUMAN Q9UJ42; 338 aa	[21], potential	24–44	59–79	94–114	137–157	178–198	245–265	269–289
	𝐻5(𝑖),𝑛=5; 𝑢=0.420	26–40	59–81	97–118	139–157	182–202	244–271	274–292
HRH3_; HUMAN Q9Y5N1; 445 aa	[21], potential	40–60	71–91	109–129	157–177	197–217	360–380	396–416
	𝐻3(𝑖),𝑛=5; 𝑢=0.00	33–61	72–95	105–132	155–173	191–222	360–388	395–416
HRH4_; HUMAN Q9H3N8; 390 aa	[21], potential	20–40	53–73	88–108	132–152	173–193	305–325	342–362
	𝐻5(𝑖),𝑛=5; 𝑢=0.25	16–41	55–79	83–107	130–153	169–198	305–331	341–357
RAI3_; HUMAN Q8NFJ5; 357 aa	[21], potential	34–54	69–89	98–118	130–150	177–197	213–233	248–268
	𝐻5(𝑖),𝑛=4; ⟨𝑢⟩=0.195	26–53	68–92	96–118	130–155	178–202	213–233	246–265
VN1R1_; HUMAN Q9GZP7; 353 aa	[21], potential	57–77	85–105	133–153	170–190	227–247	275–295	304–324
	𝐻4(𝑖),𝑛=5; ⟨𝑢⟩=0.754	53–77	90–103	122–145	165–188	222–245	274–301	306–338
APJ_; HUMAN P35414; 380 aa	[21], potential	27–51	67–91	101–125	145–166	201–221	245–271	285–308
	𝐻3(𝑖),𝑛=5; 𝑢=−0.090	30–52	67–85	98–135	147–167	208–228	246–; 246–266	−312; 292–312