Query 044908
Match_columns 275
No_of_seqs 223 out of 1504
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 07:58:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01657 Stress-antifung: Salt 99.9 5.5E-26 1.2E-30 177.0 7.5 100 12-112 1-106 (106)
2 PF01657 Stress-antifung: Salt 99.9 4.7E-23 1E-27 160.4 6.7 85 134-218 16-106 (106)
3 PF08693 SKG6: Transmembrane a 97.3 0.0002 4.3E-09 45.3 2.5 26 244-269 14-39 (40)
4 PF01102 Glycophorin_A: Glycop 95.5 0.0042 9E-08 49.4 0.3 22 238-259 60-81 (122)
5 PTZ00382 Variant-specific surf 95.4 0.017 3.7E-07 44.0 3.3 22 237-258 61-82 (96)
6 PF04478 Mid2: Mid2 like cell 94.2 0.069 1.5E-06 43.8 4.2 31 242-272 49-81 (154)
7 PF14610 DUF4448: Protein of u 93.4 0.11 2.4E-06 44.3 4.3 27 241-267 156-182 (189)
8 PF02439 Adeno_E3_CR2: Adenovi 93.0 0.069 1.5E-06 33.3 1.7 16 244-259 5-20 (38)
9 PF02009 Rifin_STEVOR: Rifin/s 92.7 0.023 5.1E-07 52.0 -0.9 15 29-43 35-49 (299)
10 PF15102 TMEM154: TMEM154 prot 90.7 0.17 3.8E-06 41.2 2.2 12 244-255 58-69 (146)
11 PF06697 DUF1191: Protein of u 89.8 0.29 6.2E-06 44.3 3.0 20 236-255 207-227 (278)
12 PF03302 VSP: Giardia variant- 89.8 0.35 7.5E-06 46.2 3.8 30 237-266 362-391 (397)
13 PF12877 DUF3827: Domain of un 88.6 0.53 1.1E-05 47.0 4.1 29 58-86 78-106 (684)
14 PF02439 Adeno_E3_CR2: Adenovi 87.9 0.18 3.9E-06 31.5 0.3 28 243-270 7-34 (38)
15 PTZ00046 rifin; Provisional 87.6 0.17 3.6E-06 47.3 -0.0 15 29-43 55-69 (358)
16 TIGR01477 RIFIN variant surfac 87.0 0.19 4.1E-06 46.8 -0.0 15 29-43 58-72 (353)
17 PF05454 DAG1: Dystroglycan (D 84.8 0.28 6.2E-06 44.7 0.0 28 244-271 150-177 (290)
18 PF15345 TMEM51: Transmembrane 84.6 3.3 7.1E-05 36.4 6.4 29 243-271 58-87 (233)
19 PF08693 SKG6: Transmembrane a 83.9 0.93 2E-05 28.8 2.0 33 241-273 7-40 (40)
20 PF01034 Syndecan: Syndecan do 83.8 0.35 7.7E-06 33.8 0.1 6 262-267 31-36 (64)
21 PF08374 Protocadherin: Protoc 83.5 1.6 3.5E-05 37.9 4.0 17 239-255 35-51 (221)
22 PF02480 Herpes_gE: Alphaherpe 82.0 0.43 9.3E-06 46.1 0.0 13 169-181 238-250 (439)
23 PF13908 Shisa: Wnt and FGF in 80.5 0.9 1.9E-05 38.3 1.4 15 241-255 78-92 (179)
24 PF04689 S1FA: DNA binding pro 80.3 4.4 9.4E-05 28.3 4.5 23 236-258 7-29 (69)
25 TIGR01478 STEVOR variant surfa 79.2 0.75 1.6E-05 41.6 0.6 13 28-40 57-69 (295)
26 PTZ00370 STEVOR; Provisional 78.4 0.82 1.8E-05 41.4 0.5 13 28-40 56-68 (296)
27 PF11857 DUF3377: Domain of un 77.3 3.2 6.9E-05 29.9 3.2 21 239-259 26-46 (74)
28 PF01102 Glycophorin_A: Glycop 77.3 0.59 1.3E-05 37.2 -0.6 21 239-260 65-85 (122)
29 PF05568 ASFV_J13L: African sw 74.0 1.6 3.6E-05 35.5 1.2 9 247-255 34-42 (189)
30 PF01034 Syndecan: Syndecan do 73.0 1 2.2E-05 31.5 -0.2 26 242-267 13-39 (64)
31 PHA03265 envelope glycoprotein 70.0 5.1 0.00011 37.4 3.5 10 260-269 367-376 (402)
32 PF05808 Podoplanin: Podoplani 68.7 1.6 3.5E-05 36.2 0.0 24 236-259 123-146 (162)
33 PF06365 CD34_antigen: CD34/Po 66.4 7.2 0.00016 33.7 3.5 26 243-268 101-128 (202)
34 PF15012 DUF4519: Domain of un 63.9 3.2 7E-05 28.2 0.7 22 243-264 29-50 (56)
35 PTZ00382 Variant-specific surf 61.8 3.5 7.6E-05 31.3 0.7 20 239-258 67-86 (96)
36 PF12191 stn_TNFRSF12A: Tumour 60.8 2.8 6.1E-05 33.3 0.0 13 261-273 97-109 (129)
37 PF01299 Lamp: Lysosome-associ 59.7 3.3 7.2E-05 37.9 0.3 28 242-269 270-299 (306)
38 PF02480 Herpes_gE: Alphaherpe 58.3 3.3 7.1E-05 40.1 0.0 12 244-255 354-365 (439)
39 PF04478 Mid2: Mid2 like cell 56.7 2.1 4.5E-05 35.3 -1.4 10 246-255 49-58 (154)
40 COG3889 Predicted solute bindi 52.7 18 0.00039 37.3 4.1 25 243-267 845-870 (872)
41 PLN03150 hypothetical protein; 51.4 15 0.00033 37.1 3.5 15 241-255 543-557 (623)
42 PF05568 ASFV_J13L: African sw 51.0 4 8.7E-05 33.3 -0.6 18 243-260 34-51 (189)
43 PTZ00046 rifin; Provisional 48.6 3.3 7.2E-05 38.8 -1.6 28 244-271 317-344 (358)
44 PF13908 Shisa: Wnt and FGF in 48.5 17 0.00036 30.5 2.8 19 241-259 74-92 (179)
45 TIGR01477 RIFIN variant surfac 48.3 3.4 7.5E-05 38.6 -1.5 28 244-271 312-339 (353)
46 PF00558 Vpu: Vpu protein; In 47.4 3.9 8.4E-05 30.1 -1.1 8 265-272 30-37 (81)
47 PF01708 Gemini_mov: Geminivir 46.2 1.1E+02 0.0024 23.0 6.4 16 240-255 33-48 (91)
48 PTZ00208 65 kDa invariant surf 44.8 3.7 8E-05 39.0 -1.9 22 185-208 305-326 (436)
49 PF13268 DUF4059: Protein of u 44.6 27 0.00058 25.0 2.8 15 260-274 25-39 (72)
50 PTZ00087 thrombosponding-relat 43.9 26 0.00056 31.7 3.3 19 237-255 291-309 (340)
51 PF12768 Rax2: Cortical protei 43.4 37 0.00079 30.9 4.3 17 237-253 222-238 (281)
52 PF05545 FixQ: Cbb3-type cytoc 43.0 18 0.0004 23.6 1.7 7 264-270 29-35 (49)
53 PF02009 Rifin_STEVOR: Rifin/s 42.9 7.2 0.00016 35.8 -0.3 29 244-272 258-286 (299)
54 PF07010 Endomucin: Endomucin; 42.4 15 0.00033 32.3 1.6 12 261-272 207-218 (259)
55 KOG3653 Transforming growth fa 40.9 46 0.00099 32.7 4.7 8 207-214 123-130 (534)
56 TIGR02976 phageshock_pspB phag 40.9 20 0.00043 26.0 1.8 12 247-258 6-17 (75)
57 PF05337 CSF-1: Macrophage col 39.5 9.8 0.00021 34.4 0.0 27 244-270 227-253 (285)
58 PF03229 Alpha_GJ: Alphavirus 38.9 36 0.00077 26.8 3.0 20 241-260 82-101 (126)
59 PF07204 Orthoreo_P10: Orthore 38.5 16 0.00035 27.5 1.0 15 244-258 44-58 (98)
60 PF10873 DUF2668: Protein of u 38.1 52 0.0011 26.9 3.9 13 243-255 62-74 (155)
61 PF05393 Hum_adeno_E3A: Human 37.4 37 0.0008 25.3 2.7 6 266-271 57-62 (94)
62 COG3197 FixS Uncharacterized p 35.0 47 0.001 22.8 2.7 22 244-265 3-24 (58)
63 PHA03290 envelope glycoprotein 34.5 69 0.0015 29.9 4.6 11 59-69 50-60 (357)
64 PF07297 DPM2: Dolichol phosph 34.3 22 0.00047 26.0 1.1 27 245-271 46-77 (78)
65 PF15102 TMEM154: TMEM154 prot 34.2 7.1 0.00015 32.0 -1.6 7 241-247 58-64 (146)
66 PF14914 LRRC37AB_C: LRRC37A/B 34.1 24 0.00052 28.9 1.4 24 241-264 119-142 (154)
67 PF14991 MLANA: Protein melan- 33.9 8.8 0.00019 30.0 -1.0 11 257-267 40-50 (118)
68 PF11884 DUF3404: Domain of un 32.7 13 0.00028 33.4 -0.3 12 206-217 210-221 (262)
69 PF12877 DUF3827: Domain of un 32.4 48 0.001 33.6 3.4 24 236-259 264-287 (684)
70 PF12606 RELT: Tumour necrosis 32.0 47 0.001 22.1 2.3 15 245-259 3-17 (50)
71 PF05795 Plasmodium_Vir: Plasm 30.4 77 0.0017 28.8 4.4 6 103-108 116-121 (354)
72 KOG1094 Discoidin domain recep 29.6 25 0.00054 35.5 1.0 10 246-255 395-404 (807)
73 PRK01844 hypothetical protein; 28.6 15 0.00033 26.4 -0.5 21 247-267 7-27 (72)
74 PHA03283 envelope glycoprotein 28.4 45 0.00099 32.9 2.5 6 209-214 332-337 (542)
75 PF15361 RIC3: Resistance to i 26.7 80 0.0017 26.0 3.4 31 241-271 78-108 (152)
76 PF05624 LSR: Lipolysis stimul 25.7 39 0.00084 22.1 1.0 17 245-261 6-22 (49)
77 PF04971 Lysis_S: Lysis protei 25.2 25 0.00054 25.0 0.1 26 242-267 33-58 (68)
78 PF05283 MGC-24: Multi-glycosy 24.8 1.2E+02 0.0026 25.9 4.2 16 250-265 166-181 (186)
79 PF13974 YebO: YebO-like prote 24.6 78 0.0017 23.2 2.6 16 251-266 5-20 (80)
80 PF05083 LST1: LST-1 protein; 24.0 85 0.0018 22.4 2.6 15 255-269 9-23 (74)
81 PF15013 CCSMST1: CCSMST1 fami 23.6 70 0.0015 23.3 2.2 20 248-267 33-52 (77)
82 PRK00523 hypothetical protein; 23.4 17 0.00037 26.1 -1.0 21 247-267 8-28 (72)
83 PF06667 PspB: Phage shock pro 23.0 60 0.0013 23.5 1.8 8 248-255 7-14 (75)
84 PF00974 Rhabdo_glycop: Rhabdo 22.7 28 0.00061 34.3 0.0 15 164-178 340-354 (501)
85 PF00558 Vpu: Vpu protein; In 22.6 37 0.0008 25.0 0.6 11 261-271 23-33 (81)
86 KOG1226 Integrin beta subunit 22.4 84 0.0018 32.5 3.2 18 243-260 712-729 (783)
87 PF01299 Lamp: Lysosome-associ 22.4 10 0.00023 34.6 -2.9 28 246-273 270-300 (306)
88 PHA03291 envelope glycoprotein 22.0 52 0.0011 30.9 1.6 11 59-69 51-61 (401)
89 PF15065 NCU-G1: Lysosomal tra 21.4 12 0.00026 35.1 -2.7 21 92-112 155-175 (350)
90 KOG3488 Dolichol phosphate-man 21.4 76 0.0016 22.7 1.9 11 245-255 48-58 (81)
91 PF03597 CcoS: Cytochrome oxid 21.4 70 0.0015 20.7 1.7 20 245-264 3-22 (45)
92 TIGR03154 sulfolob_CbsA cytoch 20.5 64 0.0014 30.3 1.8 19 242-260 440-458 (465)
93 PRK10884 SH3 domain-containing 20.3 71 0.0015 27.7 2.0 8 268-275 197-204 (206)
No 1
>PF01657 Stress-antifung: Salt stress response/antifungal; InterPro: IPR002902 This domain is found in plants and has no known function. The structure of this domain is known and it is thought to be involved in antifungal responses in plants []. Two copies of this domain are also found together in cysteine-rich protein kinases and cysteine-rich repeat secretory proteins. The domain contains four conserved cysteines.; PDB: 3A2E_D.
Probab=99.93 E-value=5.5e-26 Score=176.97 Aligned_cols=100 Identities=31% Similarity=0.584 Sum_probs=76.3
Q ss_pred ccccc-c-cccc-CCCchHHHHHHHHHHHhcccCCC---CCceeeecCCCCCCcEEEEEecCCCCCccchHHHHHHhhHH
Q 044908 12 YKNCS-S-QTLA-GSNESHSKSLHSLFQELVPQSSK---SKFFKATAGDDPSAAVSGFFQCRGDLSNKDCFDCVNTLPDL 85 (275)
Q Consensus 12 ~~~C~-~-~~~~-~~~s~y~~nl~~ll~~L~~~~~~---~~f~~~~~g~~~~~~vygl~~CrgD~s~~~C~~Cl~~a~~~ 85 (275)
|+.|+ + .+++ +.+++|+.||+.||+.|..+++. .+|+++..| .+++++|||+||++|+++++|+.||+.|..+
T Consensus 1 ~~~Cs~~~~~~~~~~~~~f~~~l~~ll~~l~~~a~~~~~~~f~~~~~~-~~~~~vYgl~qC~~Dls~~dC~~Cl~~a~~~ 79 (106)
T PF01657_consen 1 WHFCSSNTNNNYTTDNSTFEQNLNSLLSSLVSNAASSSSKGFATGSAG-SGPDTVYGLAQCRGDLSPSDCRACLADAVAN 79 (106)
T ss_dssp ---E---SSB----TT-THHHHHHHHHHHHHHHGGGTT-TEEEEEE---ST---EEEEEEE-TTS-HHHHHHHHHHHHCC
T ss_pred CCcCCCCCCCCcCCCCchHHHHHHHHHHHHHHHHhhccccCcEEeecC-CCCCeEEEEEEcCCCCChhhhHHHHHHHHHH
Confidence 78899 3 3445 57888999999999999988653 379998888 8899999999999999999999999999999
Q ss_pred hhhcCcCCceeEEEeCceEEEEecCcc
Q 044908 86 SNSLCNKAVAGRIQLHGCYFYYETDEF 112 (275)
Q Consensus 86 ~~~~C~~~~~a~i~~d~C~lRYs~~~f 112 (275)
+.+.|+..++++||++.|+||||+++|
T Consensus 80 ~~~~C~~~~g~~v~~~~C~lRY~~~~F 106 (106)
T PF01657_consen 80 ISSCCPGSRGGRVWYDSCFLRYENYPF 106 (106)
T ss_dssp HHHHTTSBSSEEEEESSEEEEEESS--
T ss_pred HHHhCCCCceEEEECCCEEEEEECCCC
Confidence 999999999999999999999999988
No 2
>PF01657 Stress-antifung: Salt stress response/antifungal; InterPro: IPR002902 This domain is found in plants and has no known function. The structure of this domain is known and it is thought to be involved in antifungal responses in plants []. Two copies of this domain are also found together in cysteine-rich protein kinases and cysteine-rich repeat secretory proteins. The domain contains four conserved cysteines.; PDB: 3A2E_D.
Probab=99.88 E-value=4.7e-23 Score=160.42 Aligned_cols=85 Identities=34% Similarity=0.741 Sum_probs=69.4
Q ss_pred chhHHHHHHHHHHhhhcccCCC--CccccC----CCCcEEEEEEcCCCCCcchhHHHHHHHHHHHHhhCCCCcceEEEcc
Q 044908 134 DSSFEGQRDKAFETMESGVIDG--KGFYSG----DYESVHAMAQCEGDLIDCDCGECVSNAVQIAQEECVGSVSGQIYLD 207 (275)
Q Consensus 134 ~~~F~~~~~~~~~~l~~~~~~~--~~f~~~----~~~~vYgLaQCt~DLs~~dC~~CL~~a~~~i~~~C~~~~ggrv~~~ 207 (275)
+..|++++..++..|.+.++.+ .+|+++ +.++||||+||++||++++|+.||+.++.+++++|++++||+|+++
T Consensus 16 ~~~f~~~l~~ll~~l~~~a~~~~~~~f~~~~~~~~~~~vYgl~qC~~Dls~~dC~~Cl~~a~~~~~~~C~~~~g~~v~~~ 95 (106)
T PF01657_consen 16 NSTFEQNLNSLLSSLVSNAASSSSKGFATGSAGSGPDTVYGLAQCRGDLSPSDCRACLADAVANISSCCPGSRGGRVWYD 95 (106)
T ss_dssp T-THHHHHHHHHHHHHHHGGGTT-TEEEEEE--ST---EEEEEEE-TTS-HHHHHHHHHHHHCCHHHHTTSBSSEEEEES
T ss_pred CchHHHHHHHHHHHHHHHHhhccccCcEEeecCCCCCeEEEEEEcCCCCChhhhHHHHHHHHHHHHHhCCCCceEEEECC
Confidence 4569999999999988775432 477764 4789999999999999999999999999999999999999999999
Q ss_pred eeEEEEecccC
Q 044908 208 RCFISYSYFPH 218 (275)
Q Consensus 208 ~C~lRYe~~~F 218 (275)
+|+||||+|+|
T Consensus 96 ~C~lRY~~~~F 106 (106)
T PF01657_consen 96 SCFLRYENYPF 106 (106)
T ss_dssp SEEEEEESS--
T ss_pred CEEEEEECCCC
Confidence 99999999998
No 3
>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]. This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].
Probab=97.30 E-value=0.0002 Score=45.34 Aligned_cols=26 Identities=19% Similarity=0.085 Sum_probs=15.3
Q ss_pred EEEEeehHHHHHHHHHHHHHHHHhhC
Q 044908 244 TVAIVLGGVAALALGFIFLSFLRSCG 269 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~r~~~ 269 (275)
.+++++|++++++++++++++||||+
T Consensus 14 a~~VvVPV~vI~~vl~~~l~~~~rR~ 39 (40)
T PF08693_consen 14 AVGVVVPVGVIIIVLGAFLFFWYRRK 39 (40)
T ss_pred EEEEEechHHHHHHHHHHhheEEecc
Confidence 45677887766655555555555443
No 4
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=95.51 E-value=0.0042 Score=49.35 Aligned_cols=22 Identities=14% Similarity=0.134 Sum_probs=14.3
Q ss_pred CCCCCcEEEEeehHHHHHHHHH
Q 044908 238 DSNTGKTVAIVLGGVAALALGF 259 (275)
Q Consensus 238 ~~~~~~iiaivv~~v~~v~~~~ 259 (275)
+...+.|+.|++++++.+++++
T Consensus 60 ~fs~~~i~~Ii~gv~aGvIg~I 81 (122)
T PF01102_consen 60 RFSEPAIIGIIFGVMAGVIGII 81 (122)
T ss_dssp SSS-TCHHHHHHHHHHHHHHHH
T ss_pred CccccceeehhHHHHHHHHHHH
Confidence 3445568888888888774444
No 5
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=95.38 E-value=0.017 Score=44.03 Aligned_cols=22 Identities=23% Similarity=0.145 Sum_probs=15.2
Q ss_pred CCCCCCcEEEEeehHHHHHHHH
Q 044908 237 GDSNTGKTVAIVLGGVAALALG 258 (275)
Q Consensus 237 ~~~~~~~iiaivv~~v~~v~~~ 258 (275)
++.+++.|++|+|++++++.+|
T Consensus 61 ~~ls~gaiagi~vg~~~~v~~l 82 (96)
T PTZ00382 61 SGLSTGAIAGISVAVVAVVGGL 82 (96)
T ss_pred CCcccccEEEEEeehhhHHHHH
Confidence 4456778999999877666333
No 6
>PF04478 Mid2: Mid2 like cell wall stress sensor; InterPro: IPR007567 This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway [].
Probab=94.18 E-value=0.069 Score=43.83 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=15.9
Q ss_pred CcEEEEeehHHHHHHHHH--HHHHHHHhhCCCC
Q 044908 242 GKTVAIVLGGVAALALGF--IFLSFLRSCGDKD 272 (275)
Q Consensus 242 ~~iiaivv~~v~~v~~~~--~~~~~~r~~~~~~ 272 (275)
.+||++||++-++++|++ +.|+|++|+||++
T Consensus 49 nIVIGvVVGVGg~ill~il~lvf~~c~r~kktd 81 (154)
T PF04478_consen 49 NIVIGVVVGVGGPILLGILALVFIFCIRRKKTD 81 (154)
T ss_pred cEEEEEEecccHHHHHHHHHhheeEEEecccCc
Confidence 457888988644443332 3333334444444
No 7
>PF14610 DUF4448: Protein of unknown function (DUF4448)
Probab=93.40 E-value=0.11 Score=44.34 Aligned_cols=27 Identities=19% Similarity=0.150 Sum_probs=17.9
Q ss_pred CCcEEEEeehHHHHHHHHHHHHHHHHh
Q 044908 241 TGKTVAIVLGGVAALALGFIFLSFLRS 267 (275)
Q Consensus 241 ~~~iiaivv~~v~~v~~~~~~~~~~r~ 267 (275)
....++|+||+++++++++++++++++
T Consensus 156 ~~~~laI~lPvvv~~~~~~~~~~~~~~ 182 (189)
T PF14610_consen 156 GKYALAIALPVVVVVLALIMYGFFFWN 182 (189)
T ss_pred cceeEEEEccHHHHHHHHHHHhhheee
Confidence 455889999998877555544444443
No 8
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=92.98 E-value=0.069 Score=33.33 Aligned_cols=16 Identities=31% Similarity=0.472 Sum_probs=10.1
Q ss_pred EEEEeehHHHHHHHHH
Q 044908 244 TVAIVLGGVAALALGF 259 (275)
Q Consensus 244 iiaivv~~v~~v~~~~ 259 (275)
+|+|++++++.+++++
T Consensus 5 ~IaIIv~V~vg~~iii 20 (38)
T PF02439_consen 5 TIAIIVAVVVGMAIII 20 (38)
T ss_pred hhhHHHHHHHHHHHHH
Confidence 5777777766654443
No 9
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=92.74 E-value=0.023 Score=51.97 Aligned_cols=15 Identities=20% Similarity=0.352 Sum_probs=10.6
Q ss_pred HHHHHHHHHhcccCC
Q 044908 29 KSLHSLFQELVPQSS 43 (275)
Q Consensus 29 ~nl~~ll~~L~~~~~ 43 (275)
+-|..+++.+-..++
T Consensus 35 PeMK~Vme~F~rqTs 49 (299)
T PF02009_consen 35 PEMKSVMENFDRQTS 49 (299)
T ss_pred HHHHHHHHHHHHHHH
Confidence 578888888865554
No 10
>PF15102 TMEM154: TMEM154 protein family
Probab=90.71 E-value=0.17 Score=41.21 Aligned_cols=12 Identities=17% Similarity=0.166 Sum_probs=8.3
Q ss_pred EEEEeehHHHHH
Q 044908 244 TVAIVLGGVAAL 255 (275)
Q Consensus 244 iiaivv~~v~~v 255 (275)
++.|+||.|+++
T Consensus 58 iLmIlIP~VLLv 69 (146)
T PF15102_consen 58 ILMILIPLVLLV 69 (146)
T ss_pred EEEEeHHHHHHH
Confidence 778888855543
No 11
>PF06697 DUF1191: Protein of unknown function (DUF1191); InterPro: IPR010605 This family contains hypothetical plant proteins of unknown function.
Probab=89.81 E-value=0.29 Score=44.26 Aligned_cols=20 Identities=30% Similarity=-0.177 Sum_probs=10.6
Q ss_pred CCCCCCCcEEEE-eehHHHHH
Q 044908 236 GGDSNTGKTVAI-VLGGVAAL 255 (275)
Q Consensus 236 ~~~~~~~~iiai-vv~~v~~v 255 (275)
+++...|++|+- ++++++++
T Consensus 207 ~~~~~~W~iv~g~~~G~~~L~ 227 (278)
T PF06697_consen 207 RKRSWWWKIVVGVVGGVVLLG 227 (278)
T ss_pred CCcceeEEEEEEehHHHHHHH
Confidence 555566765543 55554433
No 12
>PF03302 VSP: Giardia variant-specific surface protein; InterPro: IPR005127 During infection, the intestinal protozoan parasite Giardia lamblia virus undergoes continuous antigenic variation which is determined by diversification of the parasite's major surface antigen, named VSP (variant surface protein).
Probab=89.80 E-value=0.35 Score=46.17 Aligned_cols=30 Identities=20% Similarity=0.152 Sum_probs=19.4
Q ss_pred CCCCCCcEEEEeehHHHHHHHHHHHHHHHH
Q 044908 237 GDSNTGKTVAIVLGGVAALALGFIFLSFLR 266 (275)
Q Consensus 237 ~~~~~~~iiaivv~~v~~v~~~~~~~~~~r 266 (275)
++-+++.|..|.|++|++|.-||-+|+||.
T Consensus 362 s~LstgaIaGIsvavvvvVgglvGfLcWwf 391 (397)
T PF03302_consen 362 SGLSTGAIAGISVAVVVVVGGLVGFLCWWF 391 (397)
T ss_pred ccccccceeeeeehhHHHHHHHHHHHhhhe
Confidence 344677799999998887744443344443
No 13
>PF12877 DUF3827: Domain of unknown function (DUF3827); InterPro: IPR024606 The function of the proteins in this entry is not currently known, but one of the human proteins (Q9HCM3 from SWISSPROT) has been implicated in pilocytic astrocytomas [, , ]. In the majority of cases of pilocytic astrocytomas a tandem duplication produces an in-frame fusion of the gene encoding this protein and the BRAF oncogene. The resulting fusion protein has constitutive BRAF kinase activity and is capable of transforming cells.
Probab=88.56 E-value=0.53 Score=46.99 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=20.6
Q ss_pred CcEEEEEecCCCCCccchHHHHHHhhHHh
Q 044908 58 AAVSGFFQCRGDLSNKDCFDCVNTLPDLS 86 (275)
Q Consensus 58 ~~vygl~~CrgD~s~~~C~~Cl~~a~~~~ 86 (275)
+-+|+.--=+|-++.++=+.=|.+.....
T Consensus 78 ~i~~aVr~~~~~LnGt~~S~lL~~Ls~~~ 106 (684)
T PF12877_consen 78 SITYAVRNGSGFLNGTEVSELLRQLSAVE 106 (684)
T ss_pred EEEEEEecCceeeccHHHHHHHHhhhhhh
Confidence 57898888888888888666555544443
No 14
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=87.91 E-value=0.18 Score=31.46 Aligned_cols=28 Identities=11% Similarity=0.195 Sum_probs=14.8
Q ss_pred cEEEEeehHHHHHHHHHHHHHHHHhhCC
Q 044908 243 KTVAIVLGGVAALALGFIFLSFLRSCGD 270 (275)
Q Consensus 243 ~iiaivv~~v~~v~~~~~~~~~~r~~~~ 270 (275)
.||+.|+..++.+++.++++.+.+||.+
T Consensus 7 aIIv~V~vg~~iiii~~~~YaCcykk~~ 34 (38)
T PF02439_consen 7 AIIVAVVVGMAIIIICMFYYACCYKKHR 34 (38)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence 3444444445556567666655444443
No 15
>PTZ00046 rifin; Provisional
Probab=87.60 E-value=0.17 Score=47.29 Aligned_cols=15 Identities=20% Similarity=0.352 Sum_probs=8.9
Q ss_pred HHHHHHHHHhcccCC
Q 044908 29 KSLHSLFQELVPQSS 43 (275)
Q Consensus 29 ~nl~~ll~~L~~~~~ 43 (275)
+-+..++...-..++
T Consensus 55 PeMK~Vme~F~rqTs 69 (358)
T PTZ00046 55 PEMKSVMENFDRQTS 69 (358)
T ss_pred HHHHHHHHHHhHHHH
Confidence 456677766654444
No 16
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=86.98 E-value=0.19 Score=46.82 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=8.9
Q ss_pred HHHHHHHHHhcccCC
Q 044908 29 KSLHSLFQELVPQSS 43 (275)
Q Consensus 29 ~nl~~ll~~L~~~~~ 43 (275)
+-++.++...-..++
T Consensus 58 PeMK~Vm~nF~rqTs 72 (353)
T TIGR01477 58 PEMKSVMEQFDRQTS 72 (353)
T ss_pred HHHHHHHHHHhHHHH
Confidence 456667666654444
No 17
>PF05454 DAG1: Dystroglycan (Dystrophin-associated glycoprotein 1); InterPro: IPR008465 Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5.5 kb transcript in Homo sapiens. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in Mus musculus brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear [].; PDB: 1EG4_P.
Probab=84.79 E-value=0.28 Score=44.68 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=0.0
Q ss_pred EEEEeehHHHHHHHHHHHHHHHHhhCCC
Q 044908 244 TVAIVLGGVAALALGFIFLSFLRSCGDK 271 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~r~~~~~ 271 (275)
|+++||.++++++.+++|+|++|||+-|
T Consensus 150 IpaVVI~~iLLIA~iIa~icyrrkR~GK 177 (290)
T PF05454_consen 150 IPAVVIAAILLIAGIIACICYRRKRKGK 177 (290)
T ss_dssp ----------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhccc
Confidence 3444444444443344555554444433
No 18
>PF15345 TMEM51: Transmembrane protein 51
Probab=84.55 E-value=3.3 Score=36.43 Aligned_cols=29 Identities=34% Similarity=0.236 Sum_probs=16.1
Q ss_pred cEEEEeehHHHH-HHHHHHHHHHHHhhCCC
Q 044908 243 KTVAIVLGGVAA-LALGFIFLSFLRSCGDK 271 (275)
Q Consensus 243 ~iiaivv~~v~~-v~~~~~~~~~~r~~~~~ 271 (275)
-+||.|+-.+.+ ++||.+|+.++.|||++
T Consensus 58 ~SVAyVLVG~Gv~LLLLSICL~IR~KRr~r 87 (233)
T PF15345_consen 58 FSVAYVLVGSGVALLLLSICLSIRDKRRRR 87 (233)
T ss_pred EEEEEehhhHHHHHHHHHHHHHHHHHHHHh
Confidence 356666544333 35556788776554443
No 19
>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]. This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].
Probab=83.91 E-value=0.93 Score=28.75 Aligned_cols=33 Identities=24% Similarity=0.288 Sum_probs=23.6
Q ss_pred CCcEEEEeehHHHHHHHH-HHHHHHHHhhCCCCC
Q 044908 241 TGKTVAIVLGGVAALALG-FIFLSFLRSCGDKDS 273 (275)
Q Consensus 241 ~~~iiaivv~~v~~v~~~-~~~~~~~r~~~~~~~ 273 (275)
....++|.+++++.++.+ ++..+++...+||++
T Consensus 7 ~~~~vaIa~~VvVPV~vI~~vl~~~l~~~~rR~k 40 (40)
T PF08693_consen 7 NSNTVAIAVGVVVPVGVIIIVLGAFLFFWYRRKK 40 (40)
T ss_pred CCceEEEEEEEEechHHHHHHHHHHhheEEeccC
Confidence 456799999998887444 455566777787764
No 20
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=83.82 E-value=0.35 Score=33.80 Aligned_cols=6 Identities=17% Similarity=0.235 Sum_probs=0.0
Q ss_pred HHHHHh
Q 044908 262 LSFLRS 267 (275)
Q Consensus 262 ~~~~r~ 267 (275)
|+.+|.
T Consensus 31 f~iyR~ 36 (64)
T PF01034_consen 31 FLIYRM 36 (64)
T ss_dssp ------
T ss_pred HHHHHH
Confidence 344454
No 21
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=83.49 E-value=1.6 Score=37.89 Aligned_cols=17 Identities=24% Similarity=0.280 Sum_probs=10.5
Q ss_pred CCCCcEEEEeehHHHHH
Q 044908 239 SNTGKTVAIVLGGVAAL 255 (275)
Q Consensus 239 ~~~~~iiaivv~~v~~v 255 (275)
....++||||.++++++
T Consensus 35 d~~~I~iaiVAG~~tVI 51 (221)
T PF08374_consen 35 DYVKIMIAIVAGIMTVI 51 (221)
T ss_pred cceeeeeeeecchhhhH
Confidence 34555677777766555
No 22
>PF02480 Herpes_gE: Alphaherpesvirus glycoprotein E; InterPro: IPR003404 Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation [].; GO: 0016020 membrane; PDB: 2GJ7_F 2GIY_B.
Probab=82.03 E-value=0.43 Score=46.14 Aligned_cols=13 Identities=23% Similarity=0.401 Sum_probs=8.8
Q ss_pred EEEcCCCCCcchh
Q 044908 169 MAQCEGDLIDCDC 181 (275)
Q Consensus 169 LaQCt~DLs~~dC 181 (275)
+..|.++....+|
T Consensus 238 y~~C~~~~~~~~C 250 (439)
T PF02480_consen 238 YANCSPSGWPRRC 250 (439)
T ss_dssp EEEEBTTC-TTTT
T ss_pred hcCCCCCCCcCCC
Confidence 4579887766666
No 23
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=80.47 E-value=0.9 Score=38.29 Aligned_cols=15 Identities=33% Similarity=0.552 Sum_probs=7.1
Q ss_pred CCcEEEEeehHHHHH
Q 044908 241 TGKTVAIVLGGVAAL 255 (275)
Q Consensus 241 ~~~iiaivv~~v~~v 255 (275)
.++|++||+++|++|
T Consensus 78 ~~iivgvi~~Vi~Iv 92 (179)
T PF13908_consen 78 TGIIVGVICGVIAIV 92 (179)
T ss_pred eeeeeehhhHHHHHH
Confidence 334455555544444
No 24
>PF04689 S1FA: DNA binding protein S1FA; InterPro: IPR006779 S1FA is an unusual small plant peptide of only 70 amino acids with a basic domain which contains a nuclear localization signal and a putative DNA binding helix. S1FA is highly conserved between dicotyledonous and monocotyledonous plants and may be a DNA-binding protein that specifically recognises the negative promoter element S1F [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=80.32 E-value=4.4 Score=28.33 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=16.7
Q ss_pred CCCCCCCcEEEEeehHHHHHHHH
Q 044908 236 GGDSNTGKTVAIVLGGVAALALG 258 (275)
Q Consensus 236 ~~~~~~~~iiaivv~~v~~v~~~ 258 (275)
.++-+.+.|+.|||+.+++++|+
T Consensus 7 ~KGlnPGlIVLlvV~g~ll~flv 29 (69)
T PF04689_consen 7 AKGLNPGLIVLLVVAGLLLVFLV 29 (69)
T ss_pred ccCCCCCeEEeehHHHHHHHHHH
Confidence 45667888999988877666444
No 25
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=79.23 E-value=0.75 Score=41.59 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=8.5
Q ss_pred HHHHHHHHHHhcc
Q 044908 28 SKSLHSLFQELVP 40 (275)
Q Consensus 28 ~~nl~~ll~~L~~ 40 (275)
++-|+.+++.+-.
T Consensus 57 DpEmK~iid~~n~ 69 (295)
T TIGR01478 57 DPELKEIIDKLNE 69 (295)
T ss_pred cHHHHHHHHHHhH
Confidence 3567777777755
No 26
>PTZ00370 STEVOR; Provisional
Probab=78.39 E-value=0.82 Score=41.41 Aligned_cols=13 Identities=8% Similarity=0.281 Sum_probs=8.7
Q ss_pred HHHHHHHHHHhcc
Q 044908 28 SKSLHSLFQELVP 40 (275)
Q Consensus 28 ~~nl~~ll~~L~~ 40 (275)
++-|+.+++.+-.
T Consensus 56 DpemK~i~d~~n~ 68 (296)
T PTZ00370 56 DPELKEIIDKMNE 68 (296)
T ss_pred cHHHHHHHHHHhH
Confidence 4567777777765
No 27
>PF11857 DUF3377: Domain of unknown function (DUF3377); InterPro: IPR021805 This domain is functionally uncharacterised and found at the C terminus of peptidases belonging to MEROPS peptidase family M10A, membrane-type matrix metallopeptidases (clan MA). ; GO: 0004222 metalloendopeptidase activity
Probab=77.27 E-value=3.2 Score=29.90 Aligned_cols=21 Identities=29% Similarity=0.232 Sum_probs=14.7
Q ss_pred CCCCcEEEEeehHHHHHHHHH
Q 044908 239 SNTGKTVAIVLGGVAALALGF 259 (275)
Q Consensus 239 ~~~~~iiaivv~~v~~v~~~~ 259 (275)
.++..+++||||.++++.+++
T Consensus 26 ~~~~~avaVviPl~L~LCiLv 46 (74)
T PF11857_consen 26 GGTVNAVAVVIPLVLLLCILV 46 (74)
T ss_pred CCceeEEEEeHHHHHHHHHHH
Confidence 445668899999887764443
No 28
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=77.25 E-value=0.59 Score=37.15 Aligned_cols=21 Identities=14% Similarity=0.215 Sum_probs=12.1
Q ss_pred CCCCcEEEEeehHHHHHHHHHH
Q 044908 239 SNTGKTVAIVLGGVAALALGFI 260 (275)
Q Consensus 239 ~~~~~iiaivv~~v~~v~~~~~ 260 (275)
.-.++|++++.++++.+ |+++
T Consensus 65 ~i~~Ii~gv~aGvIg~I-lli~ 85 (122)
T PF01102_consen 65 AIIGIIFGVMAGVIGII-LLIS 85 (122)
T ss_dssp CHHHHHHHHHHHHHHHH-HHHH
T ss_pred ceeehhHHHHHHHHHHH-HHHH
Confidence 44566667666665544 4444
No 29
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=74.04 E-value=1.6 Score=35.53 Aligned_cols=9 Identities=22% Similarity=0.360 Sum_probs=3.7
Q ss_pred EeehHHHHH
Q 044908 247 IVLGGVAAL 255 (275)
Q Consensus 247 ivv~~v~~v 255 (275)
|+|++|+.+
T Consensus 34 ILiaIvVli 42 (189)
T PF05568_consen 34 ILIAIVVLI 42 (189)
T ss_pred HHHHHHHHH
Confidence 344444433
No 30
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=73.00 E-value=1 Score=31.54 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=0.7
Q ss_pred CcEEEEeehHHHHH-HHHHHHHHHHHh
Q 044908 242 GKTVAIVLGGVAAL-ALGFIFLSFLRS 267 (275)
Q Consensus 242 ~~iiaivv~~v~~v-~~~~~~~~~~r~ 267 (275)
+.|.++|++++.++ +++++++.+++|
T Consensus 13 avIaG~Vvgll~ailLIlf~iyR~rkk 39 (64)
T PF01034_consen 13 AVIAGGVVGLLFAILLILFLIYRMRKK 39 (64)
T ss_dssp ------------------------S--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33444555544433 444566776665
No 31
>PHA03265 envelope glycoprotein D; Provisional
Probab=69.99 E-value=5.1 Score=37.37 Aligned_cols=10 Identities=30% Similarity=0.295 Sum_probs=4.8
Q ss_pred HHHHHHHhhC
Q 044908 260 IFLSFLRSCG 269 (275)
Q Consensus 260 ~~~~~~r~~~ 269 (275)
|.|++|||||
T Consensus 367 il~~~~rr~k 376 (402)
T PHA03265 367 ILYVCLRRKK 376 (402)
T ss_pred HHHHHhhhhh
Confidence 4444555544
No 32
>PF05808 Podoplanin: Podoplanin; InterPro: IPR008783 This family consists of several mammalian podoplanin-like proteins which are thought to control specifically the unique shape of podocytes [].; GO: 0016021 integral to membrane; PDB: 3IET_X.
Probab=68.68 E-value=1.6 Score=36.23 Aligned_cols=24 Identities=21% Similarity=0.149 Sum_probs=0.0
Q ss_pred CCCCCCCcEEEEeehHHHHHHHHH
Q 044908 236 GGDSNTGKTVAIVLGGVAALALGF 259 (275)
Q Consensus 236 ~~~~~~~~iiaivv~~v~~v~~~~ 259 (275)
+.+-.+..++.|||++++++.|+.
T Consensus 123 k~GL~T~tLVGIIVGVLlaIG~ig 146 (162)
T PF05808_consen 123 KDGLSTVTLVGIIVGVLLAIGFIG 146 (162)
T ss_dssp ------------------------
T ss_pred cCCcceeeeeeehhhHHHHHHHHh
Confidence 344456678899999888775553
No 33
>PF06365 CD34_antigen: CD34/Podocalyxin family; InterPro: IPR013836 This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation [, ]. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion [].
Probab=66.39 E-value=7.2 Score=33.74 Aligned_cols=26 Identities=15% Similarity=-0.017 Sum_probs=12.4
Q ss_pred cEEEEeehH--HHHHHHHHHHHHHHHhh
Q 044908 243 KTVAIVLGG--VAALALGFIFLSFLRSC 268 (275)
Q Consensus 243 ~iiaivv~~--v~~v~~~~~~~~~~r~~ 268 (275)
.+|+||+.. ++++++++..|+++.||
T Consensus 101 ~lI~lv~~g~~lLla~~~~~~Y~~~~Rr 128 (202)
T PF06365_consen 101 TLIALVTSGSFLLLAILLGAGYCCHQRR 128 (202)
T ss_pred EEEehHHhhHHHHHHHHHHHHHHhhhhc
Confidence 667776544 22233333444554443
No 34
>PF15012 DUF4519: Domain of unknown function (DUF4519)
Probab=63.93 E-value=3.2 Score=28.21 Aligned_cols=22 Identities=27% Similarity=0.409 Sum_probs=15.1
Q ss_pred cEEEEeehHHHHHHHHHHHHHH
Q 044908 243 KTVAIVLGGVAALALGFIFLSF 264 (275)
Q Consensus 243 ~iiaivv~~v~~v~~~~~~~~~ 264 (275)
.+.-||+|++++++++++.|.+
T Consensus 29 kv~tVVlP~l~~~~~~Ivv~vy 50 (56)
T PF15012_consen 29 KVFTVVLPTLAAVFLFIVVFVY 50 (56)
T ss_pred hheeEehhHHHHHHHHHhheeE
Confidence 3778899998877555554433
No 35
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=61.78 E-value=3.5 Score=31.32 Aligned_cols=20 Identities=20% Similarity=0.091 Sum_probs=9.6
Q ss_pred CCCCcEEEEeehHHHHHHHH
Q 044908 239 SNTGKTVAIVLGGVAALALG 258 (275)
Q Consensus 239 ~~~~~iiaivv~~v~~v~~~ 258 (275)
.-.++.|++++.+.+++.|+
T Consensus 67 aiagi~vg~~~~v~~lv~~l 86 (96)
T PTZ00382 67 AIAGISVAVVAVVGGLVGFL 86 (96)
T ss_pred cEEEEEeehhhHHHHHHHHH
Confidence 34455666555444444343
No 36
>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins. Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.
Probab=60.76 E-value=2.8 Score=33.35 Aligned_cols=13 Identities=15% Similarity=0.368 Sum_probs=0.0
Q ss_pred HHHHHHhhCCCCC
Q 044908 261 FLSFLRSCGDKDS 273 (275)
Q Consensus 261 ~~~~~r~~~~~~~ 273 (275)
.++.|||.|+|++
T Consensus 97 g~lv~rrcrrr~~ 109 (129)
T PF12191_consen 97 GFLVWRRCRRREK 109 (129)
T ss_dssp -------------
T ss_pred HHHHHhhhhcccc
Confidence 3444555555554
No 37
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=59.73 E-value=3.3 Score=37.93 Aligned_cols=28 Identities=25% Similarity=0.143 Sum_probs=14.1
Q ss_pred CcEEEEeehHHHHH-HHHH-HHHHHHHhhC
Q 044908 242 GKTVAIVLGGVAAL-ALGF-IFLSFLRSCG 269 (275)
Q Consensus 242 ~~iiaivv~~v~~v-~~~~-~~~~~~r~~~ 269 (275)
..+|-|+||+++++ +|++ +.|++.|||.
T Consensus 270 ~~~vPIaVG~~La~lvlivLiaYli~Rrr~ 299 (306)
T PF01299_consen 270 SDLVPIAVGAALAGLVLIVLIAYLIGRRRS 299 (306)
T ss_pred cchHHHHHHHHHHHHHHHHHHhheeEeccc
Confidence 45677777765543 2232 3344444433
No 38
>PF02480 Herpes_gE: Alphaherpesvirus glycoprotein E; InterPro: IPR003404 Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation [].; GO: 0016020 membrane; PDB: 2GJ7_F 2GIY_B.
Probab=58.29 E-value=3.3 Score=40.13 Aligned_cols=12 Identities=25% Similarity=0.462 Sum_probs=0.0
Q ss_pred EEEEeehHHHHH
Q 044908 244 TVAIVLGGVAAL 255 (275)
Q Consensus 244 iiaivv~~v~~v 255 (275)
++++|+++++++
T Consensus 354 ~l~vVlgvavli 365 (439)
T PF02480_consen 354 LLGVVLGVAVLI 365 (439)
T ss_dssp ------------
T ss_pred hHHHHHHHHHHH
Confidence 444444444433
No 39
>PF04478 Mid2: Mid2 like cell wall stress sensor; InterPro: IPR007567 This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway [].
Probab=56.67 E-value=2.1 Score=35.29 Aligned_cols=10 Identities=40% Similarity=0.634 Sum_probs=4.4
Q ss_pred EEeehHHHHH
Q 044908 246 AIVLGGVAAL 255 (275)
Q Consensus 246 aivv~~v~~v 255 (275)
.||+++|+.|
T Consensus 49 nIVIGvVVGV 58 (154)
T PF04478_consen 49 NIVIGVVVGV 58 (154)
T ss_pred cEEEEEEecc
Confidence 4444444443
No 40
>COG3889 Predicted solute binding protein [General function prediction only]
Probab=52.72 E-value=18 Score=37.26 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=11.7
Q ss_pred cEEEEeehHHHHH-HHHHHHHHHHHh
Q 044908 243 KTVAIVLGGVAAL-ALGFIFLSFLRS 267 (275)
Q Consensus 243 ~iiaivv~~v~~v-~~~~~~~~~~r~ 267 (275)
++.+-|++.++++ +|.++-++++||
T Consensus 845 tt~~~i~g~i~iiv~LaAla~lLrRR 870 (872)
T COG3889 845 TTGGGICGPIVIIVGLAALALLLRRR 870 (872)
T ss_pred ccccccchHHHHHHHHHHHHHHHHhh
Confidence 3455555555333 444444544443
No 41
>PLN03150 hypothetical protein; Provisional
Probab=51.43 E-value=15 Score=37.06 Aligned_cols=15 Identities=27% Similarity=0.508 Sum_probs=9.0
Q ss_pred CCcEEEEeehHHHHH
Q 044908 241 TGKTVAIVLGGVAAL 255 (275)
Q Consensus 241 ~~~iiaivv~~v~~v 255 (275)
.+.++++++++++++
T Consensus 543 ~~~~i~~~~~~~~~~ 557 (623)
T PLN03150 543 VGAKIGIAFGVSVAF 557 (623)
T ss_pred CceEEEEEhHHHHHH
Confidence 445667777666544
No 42
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=51.03 E-value=4 Score=33.32 Aligned_cols=18 Identities=22% Similarity=0.264 Sum_probs=12.1
Q ss_pred cEEEEeehHHHHHHHHHH
Q 044908 243 KTVAIVLGGVAALALGFI 260 (275)
Q Consensus 243 ~iiaivv~~v~~v~~~~~ 260 (275)
+.|+|||+++++++++.+
T Consensus 34 ILiaIvVliiiiivli~l 51 (189)
T PF05568_consen 34 ILIAIVVLIIIIIVLIYL 51 (189)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 367888888776655433
No 43
>PTZ00046 rifin; Provisional
Probab=48.61 E-value=3.3 Score=38.80 Aligned_cols=28 Identities=21% Similarity=0.215 Sum_probs=12.6
Q ss_pred EEEEeehHHHHHHHHHHHHHHHHhhCCC
Q 044908 244 TVAIVLGGVAALALGFIFLSFLRSCGDK 271 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~r~~~~~ 271 (275)
|++-||++|++|+++++.|+.+|-||||
T Consensus 317 IiaSiiAIvVIVLIMvIIYLILRYRRKK 344 (358)
T PTZ00046 317 IIASIVAIVVIVLIMVIIYLILRYRRKK 344 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4444445544443344444444444433
No 44
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=48.47 E-value=17 Score=30.51 Aligned_cols=19 Identities=11% Similarity=0.067 Sum_probs=12.6
Q ss_pred CCcEEEEeehHHHHHHHHH
Q 044908 241 TGKTVAIVLGGVAALALGF 259 (275)
Q Consensus 241 ~~~iiaivv~~v~~v~~~~ 259 (275)
+..++.|+|++|++|++++
T Consensus 74 ~~~~~~iivgvi~~Vi~Iv 92 (179)
T PF13908_consen 74 IYFITGIIVGVICGVIAIV 92 (179)
T ss_pred ccceeeeeeehhhHHHHHH
Confidence 3457778888877664443
No 45
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=48.25 E-value=3.4 Score=38.61 Aligned_cols=28 Identities=18% Similarity=0.197 Sum_probs=12.2
Q ss_pred EEEEeehHHHHHHHHHHHHHHHHhhCCC
Q 044908 244 TVAIVLGGVAALALGFIFLSFLRSCGDK 271 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~r~~~~~ 271 (275)
|++-||++|++|+++++.|+.+|-||||
T Consensus 312 IiaSiIAIvvIVLIMvIIYLILRYRRKK 339 (353)
T TIGR01477 312 IIASIIAILIIVLIMVIIYLILRYRRKK 339 (353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 3444444444443334444444444433
No 46
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=47.44 E-value=3.9 Score=30.10 Aligned_cols=8 Identities=13% Similarity=0.148 Sum_probs=0.0
Q ss_pred HHhhCCCC
Q 044908 265 LRSCGDKD 272 (275)
Q Consensus 265 ~r~~~~~~ 272 (275)
+|+.+|.+
T Consensus 30 Yrk~~rqr 37 (81)
T PF00558_consen 30 YRKIKRQR 37 (81)
T ss_dssp --------
T ss_pred HHHHHHHH
Confidence 45444433
No 47
>PF01708 Gemini_mov: Geminivirus putative movement protein ; InterPro: IPR002621 This family consists of putative movement proteins from Maize streak virus and Wheat dwarf virus [].; GO: 0046740 spread of virus in host, cell to cell, 0016021 integral to membrane
Probab=46.23 E-value=1.1e+02 Score=22.98 Aligned_cols=16 Identities=13% Similarity=0.167 Sum_probs=7.3
Q ss_pred CCCcEEEEeehHHHHH
Q 044908 240 NTGKTVAIVLGGVAAL 255 (275)
Q Consensus 240 ~~~~iiaivv~~v~~v 255 (275)
..++++.|++.++++|
T Consensus 33 ~ws~vv~v~i~~lvaV 48 (91)
T PF01708_consen 33 PWSRVVEVAIFTLVAV 48 (91)
T ss_pred cceeEeeeeehHHHHH
Confidence 3444544444444444
No 48
>PTZ00208 65 kDa invariant surface glycoprotein; Provisional
Probab=44.76 E-value=3.7 Score=38.95 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=14.0
Q ss_pred HHHHHHHHHhhCCCCcceEEEcce
Q 044908 185 VSNAVQIAQEECVGSVSGQIYLDR 208 (275)
Q Consensus 185 L~~a~~~i~~~C~~~~ggrv~~~~ 208 (275)
|...+..... .+++|+.|..|.
T Consensus 305 lsevi~~ak~--a~~kgak~~~p~ 326 (436)
T PTZ00208 305 LSEVIVAAKE--AGKKGAKIIIPA 326 (436)
T ss_pred HHHHHHHHHH--hcccCceeecCC
Confidence 4556655543 468888887653
No 49
>PF13268 DUF4059: Protein of unknown function (DUF4059)
Probab=44.62 E-value=27 Score=24.99 Aligned_cols=15 Identities=20% Similarity=0.147 Sum_probs=9.1
Q ss_pred HHHHHHHhhCCCCCC
Q 044908 260 IFLSFLRSCGDKDSI 274 (275)
Q Consensus 260 ~~~~~~r~~~~~~~~ 274 (275)
..+.+||.++|||+-
T Consensus 25 ~~wi~~Ra~~~~DKT 39 (72)
T PF13268_consen 25 GIWILWRALRKKDKT 39 (72)
T ss_pred HHHHHHHHHHcCCCc
Confidence 334556777777763
No 50
>PTZ00087 thrombosponding-related protein; Provisional
Probab=43.94 E-value=26 Score=31.67 Aligned_cols=19 Identities=32% Similarity=0.238 Sum_probs=14.0
Q ss_pred CCCCCCcEEEEeehHHHHH
Q 044908 237 GDSNTGKTVAIVLGGVAAL 255 (275)
Q Consensus 237 ~~~~~~~iiaivv~~v~~v 255 (275)
+.+++-+|+.|++|+|+++
T Consensus 291 ~~sst~~i~~i~~piv~vi 309 (340)
T PTZ00087 291 KESSTFKILIILLPIVLII 309 (340)
T ss_pred CCCCcceEeeeehhHHHHH
Confidence 3455667888889988766
No 51
>PF12768 Rax2: Cortical protein marker for cell polarity
Probab=43.45 E-value=37 Score=30.91 Aligned_cols=17 Identities=24% Similarity=0.108 Sum_probs=8.9
Q ss_pred CCCCCCcEEEEeehHHH
Q 044908 237 GDSNTGKTVAIVLGGVA 253 (275)
Q Consensus 237 ~~~~~~~iiaivv~~v~ 253 (275)
++-..+.+|.|-+++.+
T Consensus 222 ~~l~~G~VVlIslAiAL 238 (281)
T PF12768_consen 222 KKLSRGFVVLISLAIAL 238 (281)
T ss_pred ccccceEEEEEehHHHH
Confidence 33445556666555433
No 52
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=42.98 E-value=18 Score=23.57 Aligned_cols=7 Identities=14% Similarity=0.074 Sum_probs=2.7
Q ss_pred HHHhhCC
Q 044908 264 FLRSCGD 270 (275)
Q Consensus 264 ~~r~~~~ 270 (275)
.+|+++|
T Consensus 29 ~~~~~~k 35 (49)
T PF05545_consen 29 AYRPRNK 35 (49)
T ss_pred HHcccch
Confidence 3344333
No 53
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=42.89 E-value=7.2 Score=35.85 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=14.6
Q ss_pred EEEEeehHHHHHHHHHHHHHHHHhhCCCC
Q 044908 244 TVAIVLGGVAALALGFIFLSFLRSCGDKD 272 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~r~~~~~~ 272 (275)
|++.+++++++|+++++.++.||.||||+
T Consensus 258 I~aSiiaIliIVLIMvIIYLILRYRRKKK 286 (299)
T PF02009_consen 258 IIASIIAILIIVLIMVIIYLILRYRRKKK 286 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45555555555544444455555555333
No 54
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=42.37 E-value=15 Score=32.25 Aligned_cols=12 Identities=25% Similarity=0.620 Sum_probs=5.9
Q ss_pred HHHHHHhhCCCC
Q 044908 261 FLSFLRSCGDKD 272 (275)
Q Consensus 261 ~~~~~r~~~~~~ 272 (275)
.+-|+|..+|++
T Consensus 207 LvgLyr~C~k~d 218 (259)
T PF07010_consen 207 LVGLYRMCWKTD 218 (259)
T ss_pred HHHHHHHhhcCC
Confidence 344455555544
No 55
>KOG3653 consensus Transforming growth factor beta/activin receptor subfamily of serine/threonine kinases [Signal transduction mechanisms]
Probab=40.92 E-value=46 Score=32.68 Aligned_cols=8 Identities=38% Similarity=0.721 Sum_probs=5.0
Q ss_pred ceeEEEEe
Q 044908 207 DRCFISYS 214 (275)
Q Consensus 207 ~~C~lRYe 214 (275)
+-|+..|+
T Consensus 123 ~~CN~n~s 130 (534)
T KOG3653|consen 123 DFCNANFS 130 (534)
T ss_pred CcccCCcc
Confidence 35777665
No 56
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=40.92 E-value=20 Score=25.98 Aligned_cols=12 Identities=0% Similarity=-0.014 Sum_probs=6.0
Q ss_pred EeehHHHHHHHH
Q 044908 247 IVLGGVAALALG 258 (275)
Q Consensus 247 ivv~~v~~v~~~ 258 (275)
+++|+++.++++
T Consensus 6 l~~Pliif~ifV 17 (75)
T TIGR02976 6 LAIPLIIFVIFV 17 (75)
T ss_pred HHHHHHHHHHHH
Confidence 455655554343
No 57
>PF05337 CSF-1: Macrophage colony stimulating factor-1 (CSF-1); InterPro: IPR008001 Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility [] and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption [].; GO: 0005125 cytokine activity, 0008083 growth factor activity, 0016021 integral to membrane; PDB: 3EJJ_A.
Probab=39.54 E-value=9.8 Score=34.39 Aligned_cols=27 Identities=15% Similarity=0.121 Sum_probs=0.0
Q ss_pred EEEEeehHHHHHHHHHHHHHHHHhhCC
Q 044908 244 TVAIVLGGVAALALGFIFLSFLRSCGD 270 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~r~~~~ 270 (275)
+.-+.||.|++|+|-+..++|+|+|+|
T Consensus 227 vf~lLVPSiILVLLaVGGLLfYr~rrR 253 (285)
T PF05337_consen 227 VFYLLVPSIILVLLAVGGLLFYRRRRR 253 (285)
T ss_dssp ---------------------------
T ss_pred cccccccchhhhhhhccceeeeccccc
Confidence 334455555555444445666555443
No 58
>PF03229 Alpha_GJ: Alphavirus glycoprotein J; InterPro: IPR004913 The exact function of the herpesvirus glycoprotein J is unknown, but it appears to play a role in the inhibition of apotosis of the host cell [].; GO: 0019050 suppression by virus of host apoptosis
Probab=38.88 E-value=36 Score=26.78 Aligned_cols=20 Identities=30% Similarity=0.595 Sum_probs=12.6
Q ss_pred CCcEEEEeehHHHHHHHHHH
Q 044908 241 TGKTVAIVLGGVAALALGFI 260 (275)
Q Consensus 241 ~~~iiaivv~~v~~v~~~~~ 260 (275)
...++-.||+.+.+++|.++
T Consensus 82 ~d~aLp~VIGGLcaL~Laam 101 (126)
T PF03229_consen 82 VDFALPLVIGGLCALTLAAM 101 (126)
T ss_pred cccchhhhhhHHHHHHHHHH
Confidence 44577777877666655543
No 59
>PF07204 Orthoreo_P10: Orthoreovirus membrane fusion protein p10; InterPro: IPR009854 This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction [].
Probab=38.49 E-value=16 Score=27.55 Aligned_cols=15 Identities=20% Similarity=-0.029 Sum_probs=6.0
Q ss_pred EEEEeehHHHHHHHH
Q 044908 244 TVAIVLGGVAALALG 258 (275)
Q Consensus 244 iiaivv~~v~~v~~~ 258 (275)
.+|.--+++++++++
T Consensus 44 yLA~GGG~iLilIii 58 (98)
T PF07204_consen 44 YLAAGGGLILILIII 58 (98)
T ss_pred HhhccchhhhHHHHH
Confidence 344433444444333
No 60
>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known [].
Probab=38.08 E-value=52 Score=26.95 Aligned_cols=13 Identities=31% Similarity=0.365 Sum_probs=8.3
Q ss_pred cEEEEeehHHHHH
Q 044908 243 KTVAIVLGGVAAL 255 (275)
Q Consensus 243 ~iiaivv~~v~~v 255 (275)
.|.+||+++|.++
T Consensus 62 AIaGIVfgiVfim 74 (155)
T PF10873_consen 62 AIAGIVFGIVFIM 74 (155)
T ss_pred eeeeeehhhHHHH
Confidence 4557777776654
No 61
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=37.44 E-value=37 Score=25.35 Aligned_cols=6 Identities=0% Similarity=0.108 Sum_probs=2.2
Q ss_pred HhhCCC
Q 044908 266 RSCGDK 271 (275)
Q Consensus 266 r~~~~~ 271 (275)
+|+|.+
T Consensus 57 kRkrsR 62 (94)
T PF05393_consen 57 KRKRSR 62 (94)
T ss_pred Hhhhcc
Confidence 333333
No 62
>COG3197 FixS Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]
Probab=34.95 E-value=47 Score=22.76 Aligned_cols=22 Identities=9% Similarity=-0.158 Sum_probs=11.5
Q ss_pred EEEEeehHHHHHHHHHHHHHHH
Q 044908 244 TVAIVLGGVAALALGFIFLSFL 265 (275)
Q Consensus 244 iiaivv~~v~~v~~~~~~~~~~ 265 (275)
++.+.+|+.++++++++..++|
T Consensus 3 ~l~~Lipvsi~l~~v~l~~flW 24 (58)
T COG3197 3 ILYILIPVSILLGAVGLGAFLW 24 (58)
T ss_pred eeeeHHHHHHHHHHHHHHHHHH
Confidence 5666677655554444433343
No 63
>PHA03290 envelope glycoprotein I; Provisional
Probab=34.48 E-value=69 Score=29.85 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=7.9
Q ss_pred cEEEEEecCCC
Q 044908 59 AVSGFFQCRGD 69 (275)
Q Consensus 59 ~vygl~~CrgD 69 (275)
.+||-.+=.||
T Consensus 50 ~V~G~LlFLGd 60 (357)
T PHA03290 50 EIKGQFLFIGD 60 (357)
T ss_pred EEEeEEEecCC
Confidence 57777777777
No 64
>PF07297 DPM2: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2); InterPro: IPR009914 This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2 [].; GO: 0009059 macromolecule biosynthetic process, 0030176 integral to endoplasmic reticulum membrane
Probab=34.33 E-value=22 Score=25.99 Aligned_cols=27 Identities=26% Similarity=0.134 Sum_probs=13.5
Q ss_pred EEEeehHHHHHHHH-----HHHHHHHHhhCCC
Q 044908 245 VAIVLGGVAALALG-----FIFLSFLRSCGDK 271 (275)
Q Consensus 245 iaivv~~v~~v~~~-----~~~~~~~r~~~~~ 271 (275)
.||.+|+++.++++ ++.+.++|.+|||
T Consensus 46 yAi~lP~~lll~~~~~vg~f~g~vmik~~~kk 77 (78)
T PF07297_consen 46 YAIILPIFLLLLGLSGVGTFLGYVMIKSKKKK 77 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Confidence 56777776554222 1234445554544
No 65
>PF15102 TMEM154: TMEM154 protein family
Probab=34.25 E-value=7.1 Score=31.96 Aligned_cols=7 Identities=0% Similarity=-0.406 Sum_probs=3.0
Q ss_pred CCcEEEE
Q 044908 241 TGKTVAI 247 (275)
Q Consensus 241 ~~~iiai 247 (275)
-..|+.-
T Consensus 58 iLmIlIP 64 (146)
T PF15102_consen 58 ILMILIP 64 (146)
T ss_pred EEEEeHH
Confidence 3444433
No 66
>PF14914 LRRC37AB_C: LRRC37A/B like protein 1 C-terminal domain
Probab=34.10 E-value=24 Score=28.95 Aligned_cols=24 Identities=17% Similarity=0.051 Sum_probs=13.0
Q ss_pred CCcEEEEeehHHHHHHHHHHHHHH
Q 044908 241 TGKTVAIVLGGVAALALGFIFLSF 264 (275)
Q Consensus 241 ~~~iiaivv~~v~~v~~~~~~~~~ 264 (275)
...|+||.|.+|+.++++++|+.-
T Consensus 119 nklilaisvtvv~~iliii~CLie 142 (154)
T PF14914_consen 119 NKLILAISVTVVVMILIIIFCLIE 142 (154)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHH
Confidence 345777766555444444555443
No 67
>PF14991 MLANA: Protein melan-A; PDB: 2GTZ_F 2GT9_F 3MRO_P 2GUO_C 3MRQ_P 2GTW_C 3L6F_C 3MRP_P.
Probab=33.90 E-value=8.8 Score=30.01 Aligned_cols=11 Identities=18% Similarity=-0.170 Sum_probs=0.0
Q ss_pred HHHHHHHHHHh
Q 044908 257 LGFIFLSFLRS 267 (275)
Q Consensus 257 ~~~~~~~~~r~ 267 (275)
|++.|+++.||
T Consensus 40 LliGCWYckRR 50 (118)
T PF14991_consen 40 LLIGCWYCKRR 50 (118)
T ss_dssp -----------
T ss_pred HHHhheeeeec
Confidence 33445444444
No 68
>PF11884 DUF3404: Domain of unknown function (DUF3404); InterPro: IPR021821 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 260 amino acids in length. This domain is found associated with PF02518 from PFAM, PF00512 from PFAM.
Probab=32.73 E-value=13 Score=33.44 Aligned_cols=12 Identities=25% Similarity=0.686 Sum_probs=9.1
Q ss_pred cceeEEEEeccc
Q 044908 206 LDRCFISYSYFP 217 (275)
Q Consensus 206 ~~~C~lRYe~~~ 217 (275)
+.+|++||.+-=
T Consensus 210 ~~sC~~r~gNlC 221 (262)
T PF11884_consen 210 GNSCFVRYGNLC 221 (262)
T ss_pred CCcccceeccee
Confidence 578999998543
No 69
>PF12877 DUF3827: Domain of unknown function (DUF3827); InterPro: IPR024606 The function of the proteins in this entry is not currently known, but one of the human proteins (Q9HCM3 from SWISSPROT) has been implicated in pilocytic astrocytomas [, , ]. In the majority of cases of pilocytic astrocytomas a tandem duplication produces an in-frame fusion of the gene encoding this protein and the BRAF oncogene. The resulting fusion protein has constitutive BRAF kinase activity and is capable of transforming cells.
Probab=32.41 E-value=48 Score=33.63 Aligned_cols=24 Identities=8% Similarity=0.020 Sum_probs=16.8
Q ss_pred CCCCCCCcEEEEeehHHHHHHHHH
Q 044908 236 GGDSNTGKTVAIVLGGVAALALGF 259 (275)
Q Consensus 236 ~~~~~~~~iiaivv~~v~~v~~~~ 259 (275)
...++.|+|+++++|+++++++++
T Consensus 264 s~~~NlWII~gVlvPv~vV~~Iii 287 (684)
T PF12877_consen 264 SPPNNLWIIAGVLVPVLVVLLIII 287 (684)
T ss_pred CCCCCeEEEehHhHHHHHHHHHHH
Confidence 345778999999888776654433
No 70
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=32.03 E-value=47 Score=22.12 Aligned_cols=15 Identities=7% Similarity=-0.031 Sum_probs=7.8
Q ss_pred EEEeehHHHHHHHHH
Q 044908 245 VAIVLGGVAALALGF 259 (275)
Q Consensus 245 iaivv~~v~~v~~~~ 259 (275)
+.++|+++.+++++.
T Consensus 3 ~~~iV~i~iv~~lLg 17 (50)
T PF12606_consen 3 AFLIVSIFIVMGLLG 17 (50)
T ss_pred ehHHHHHHHHHHHHH
Confidence 344566665554443
No 71
>PF05795 Plasmodium_Vir: Plasmodium vivax Vir protein; InterPro: IPR008780 This family consists of several Vir proteins specific to the genus Plasmodium and Plasmodium vivax in particular. The vir genes are present at about 600-1,000 copies per haploid genome and encode proteins that are immunovariant in natural infections, indicating that they may have a functional role in establishing chronic infection through antigenic variation [].
Probab=30.43 E-value=77 Score=28.78 Aligned_cols=6 Identities=50% Similarity=1.242 Sum_probs=2.5
Q ss_pred eEEEEe
Q 044908 103 CYFYYE 108 (275)
Q Consensus 103 C~lRYs 108 (275)
|..-|.
T Consensus 116 C~~~~~ 121 (354)
T PF05795_consen 116 CKPYYK 121 (354)
T ss_pred Cccccc
Confidence 544333
No 72
>KOG1094 consensus Discoidin domain receptor DDR1 [Signal transduction mechanisms]
Probab=29.64 E-value=25 Score=35.54 Aligned_cols=10 Identities=10% Similarity=0.036 Sum_probs=4.3
Q ss_pred EEeehHHHHH
Q 044908 246 AIVLGGVAAL 255 (275)
Q Consensus 246 aivv~~v~~v 255 (275)
.|.|.++++|
T Consensus 395 ~~f~~if~iv 404 (807)
T KOG1094|consen 395 IIFVAIFLIV 404 (807)
T ss_pred HHHHHHHHHH
Confidence 3344444444
No 73
>PRK01844 hypothetical protein; Provisional
Probab=28.57 E-value=15 Score=26.36 Aligned_cols=21 Identities=29% Similarity=0.178 Sum_probs=9.1
Q ss_pred EeehHHHHHHHHHHHHHHHHh
Q 044908 247 IVLGGVAALALGFIFLSFLRS 267 (275)
Q Consensus 247 ivv~~v~~v~~~~~~~~~~r~ 267 (275)
|+++++++++-+++.|++.|+
T Consensus 7 I~l~I~~li~G~~~Gff~ark 27 (72)
T PRK01844 7 ILVGVVALVAGVALGFFIARK 27 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444444333444555444
No 74
>PHA03283 envelope glycoprotein E; Provisional
Probab=28.40 E-value=45 Score=32.89 Aligned_cols=6 Identities=17% Similarity=0.484 Sum_probs=3.5
Q ss_pred eEEEEe
Q 044908 209 CFISYS 214 (275)
Q Consensus 209 C~lRYe 214 (275)
|.++|.
T Consensus 332 fVv~yN 337 (542)
T PHA03283 332 FVLLYN 337 (542)
T ss_pred EEEEEC
Confidence 556664
No 75
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=26.66 E-value=80 Score=25.98 Aligned_cols=31 Identities=10% Similarity=0.062 Sum_probs=16.3
Q ss_pred CCcEEEEeehHHHHHHHHHHHHHHHHhhCCC
Q 044908 241 TGKTVAIVLGGVAALALGFIFLSFLRSCGDK 271 (275)
Q Consensus 241 ~~~iiaivv~~v~~v~~~~~~~~~~r~~~~~ 271 (275)
.....++++|+=.+-|++++.|.+++..++|
T Consensus 78 ~~g~~~~imPlYtiGI~~f~lY~l~Ki~~~k 108 (152)
T PF15361_consen 78 GKGLMGQIMPLYTIGIVLFILYTLFKIKKKK 108 (152)
T ss_pred CCchhhhHhHHHHHHHHHHHHHHHHHHHhcC
Confidence 3446777888744433444445555543333
No 76
>PF05624 LSR: Lipolysis stimulated receptor (LSR); InterPro: IPR008664 This domain consists of mammalian LISCH7 protein homologues. LISCH7 is a liver-specific BHLH-ZIP transcription factor.
Probab=25.73 E-value=39 Score=22.07 Aligned_cols=17 Identities=41% Similarity=0.395 Sum_probs=6.9
Q ss_pred EEEeehHHHHHHHHHHH
Q 044908 245 VAIVLGGVAALALGFIF 261 (275)
Q Consensus 245 iaivv~~v~~v~~~~~~ 261 (275)
+.|+++.+..++|+.+|
T Consensus 6 ~~iilg~~ll~~LigiC 22 (49)
T PF05624_consen 6 VLIILGALLLLLLIGIC 22 (49)
T ss_pred eHHHHHHHHHHHHHHHH
Confidence 34444444333333343
No 77
>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].
Probab=25.21 E-value=25 Score=24.95 Aligned_cols=26 Identities=15% Similarity=0.034 Sum_probs=12.1
Q ss_pred CcEEEEeehHHHHHHHHHHHHHHHHh
Q 044908 242 GKTVAIVLGGVAALALGFIFLSFLRS 267 (275)
Q Consensus 242 ~~iiaivv~~v~~v~~~~~~~~~~r~ 267 (275)
+..|+++.+++..++-++.-+.|.+|
T Consensus 33 W~aIGvi~gi~~~~lt~ltN~YFK~k 58 (68)
T PF04971_consen 33 WAAIGVIGGIFFGLLTYLTNLYFKIK 58 (68)
T ss_pred chhHHHHHHHHHHHHHHHhHhhhhhh
Confidence 44455555554444333344555443
No 78
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=24.75 E-value=1.2e+02 Score=25.89 Aligned_cols=16 Identities=25% Similarity=0.225 Sum_probs=6.8
Q ss_pred hHHHHHHHHHHHHHHH
Q 044908 250 GGVAALALGFIFLSFL 265 (275)
Q Consensus 250 ~~v~~v~~~~~~~~~~ 265 (275)
|||+++.++.|.|+++
T Consensus 166 GIVL~LGv~aI~ff~~ 181 (186)
T PF05283_consen 166 GIVLTLGVLAIIFFLY 181 (186)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4444444444444443
No 79
>PF13974 YebO: YebO-like protein
Probab=24.59 E-value=78 Score=23.24 Aligned_cols=16 Identities=13% Similarity=0.032 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHHHH
Q 044908 251 GVAALALGFIFLSFLR 266 (275)
Q Consensus 251 ~v~~v~~~~~~~~~~r 266 (275)
++++++.++++|+.-|
T Consensus 5 ~~~~lv~livWFFVnR 20 (80)
T PF13974_consen 5 VLVLLVGLIVWFFVNR 20 (80)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333434444444433
No 80
>PF05083 LST1: LST-1 protein; InterPro: IPR007775 B144/LST1 is a gene encoded in the human major histocompatibility complex that produces multiple forms of alternatively spliced mRNA and encodes peptides fewer than 100 amino acids in length. B144/LST1 is strongly expressed in dendritic cells. Transfection of B144/LST1 into a variety of cells induces morphologic changes including the production of long, thin filopodia []. A possible role in modulating immune responses. Induces morphological changes including production of filopodia and microspikes when overexpressed in a variety of cell types and may be involved in dendritic cell maturation. Isoform 1 and isoform 2 have an inhibitory effect on lymphocyte proliferation [, ]. ; GO: 0000902 cell morphogenesis, 0006955 immune response, 0016020 membrane
Probab=23.97 E-value=85 Score=22.40 Aligned_cols=15 Identities=20% Similarity=-0.084 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHhhC
Q 044908 255 LALGFIFLSFLRSCG 269 (275)
Q Consensus 255 v~~~~~~~~~~r~~~ 269 (275)
|+++.+|++...||.
T Consensus 9 vvll~~clC~lsrRv 23 (74)
T PF05083_consen 9 VVLLSACLCRLSRRV 23 (74)
T ss_pred HHHHHHHHHHHHhhh
Confidence 345556776654433
No 81
>PF15013 CCSMST1: CCSMST1 family
Probab=23.62 E-value=70 Score=23.31 Aligned_cols=20 Identities=35% Similarity=0.423 Sum_probs=9.2
Q ss_pred eehHHHHHHHHHHHHHHHHh
Q 044908 248 VLGGVAALALGFIFLSFLRS 267 (275)
Q Consensus 248 vv~~v~~v~~~~~~~~~~r~ 267 (275)
+.++.+.++++++.||++|.
T Consensus 33 ~~~is~sl~~fliyFC~lRe 52 (77)
T PF15013_consen 33 VYPISLSLAAFLIYFCFLRE 52 (77)
T ss_pred eehhHHHHHHHHHHHhhccc
Confidence 33444444344445555553
No 82
>PRK00523 hypothetical protein; Provisional
Probab=23.43 E-value=17 Score=26.08 Aligned_cols=21 Identities=19% Similarity=0.070 Sum_probs=8.4
Q ss_pred EeehHHHHHHHHHHHHHHHHh
Q 044908 247 IVLGGVAALALGFIFLSFLRS 267 (275)
Q Consensus 247 ivv~~v~~v~~~~~~~~~~r~ 267 (275)
|.+.++++++-+++.|++.|+
T Consensus 8 I~l~i~~li~G~~~Gffiark 28 (72)
T PRK00523 8 LGLGIPLLIVGGIIGYFVSKK 28 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333333333233344555444
No 83
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=23.00 E-value=60 Score=23.48 Aligned_cols=8 Identities=0% Similarity=-0.014 Sum_probs=3.4
Q ss_pred eehHHHHH
Q 044908 248 VLGGVAAL 255 (275)
Q Consensus 248 vv~~v~~v 255 (275)
++|+++.+
T Consensus 7 ~~plivf~ 14 (75)
T PF06667_consen 7 FVPLIVFM 14 (75)
T ss_pred HHHHHHHH
Confidence 34444443
No 84
>PF00974 Rhabdo_glycop: Rhabdovirus spike glycoprotein; InterPro: IPR001903 Different families of ssRNA negative-strand viruses contain glycoproteins responsible for forming spikes on the surface of the virion. The glycoprotein spike is made up of a trimer of glycoproteins. These proteins are frequently abbreviated to G protein. Channel formed by glycoprotein spike is thought to function in a similar manner to Influenza virus M2 protein channel, thus allowing a signal to pass across the viral membrane to signal for viral uncoating [, ].; GO: 0019031 viral envelope; PDB: 2CMZ_C 2J6J_A 3EGD_D.
Probab=22.74 E-value=28 Score=34.33 Aligned_cols=15 Identities=13% Similarity=0.125 Sum_probs=10.2
Q ss_pred CcEEEEEEcCCCCCc
Q 044908 164 ESVHAMAQCEGDLID 178 (275)
Q Consensus 164 ~~vYgLaQCt~DLs~ 178 (275)
...|--+-+..+..+
T Consensus 340 ~~~Y~~V~~~~~i~~ 354 (501)
T PF00974_consen 340 DTHYKRVDIWGPIIP 354 (501)
T ss_dssp EEEEEEEEESSSEES
T ss_pred EEEEEEEeccCcccc
Confidence 567777777776644
No 85
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=22.65 E-value=37 Score=24.99 Aligned_cols=11 Identities=0% Similarity=-0.139 Sum_probs=1.4
Q ss_pred HHHHHHhhCCC
Q 044908 261 FLSFLRSCGDK 271 (275)
Q Consensus 261 ~~~~~r~~~~~ 271 (275)
+...++.-||.
T Consensus 23 W~iv~ieYrk~ 33 (81)
T PF00558_consen 23 WTIVYIEYRKI 33 (81)
T ss_dssp HHHH-------
T ss_pred HHHHHHHHHHH
Confidence 33334444443
No 86
>KOG1226 consensus Integrin beta subunit (N-terminal portion of extracellular region) [Signal transduction mechanisms; Extracellular structures]
Probab=22.41 E-value=84 Score=32.50 Aligned_cols=18 Identities=44% Similarity=0.471 Sum_probs=12.5
Q ss_pred cEEEEeehHHHHHHHHHH
Q 044908 243 KTVAIVLGGVAALALGFI 260 (275)
Q Consensus 243 ~iiaivv~~v~~v~~~~~ 260 (275)
.|++|++++|++++++.+
T Consensus 712 ~~~~i~lgvv~~ivligl 729 (783)
T KOG1226|consen 712 NILAIVLGVVAGIVLIGL 729 (783)
T ss_pred cEeeehHHHHHHHHHHHH
Confidence 478888888777655543
No 87
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=22.36 E-value=10 Score=34.65 Aligned_cols=28 Identities=11% Similarity=-0.034 Sum_probs=16.9
Q ss_pred EEeehHHHHHHHHHHHHHH---HHhhCCCCC
Q 044908 246 AIVLGGVAALALGFIFLSF---LRSCGDKDS 273 (275)
Q Consensus 246 aivv~~v~~v~~~~~~~~~---~r~~~~~~~ 273 (275)
-++|||++.++|.+++++. +.-.|||.+
T Consensus 270 ~~~vPIaVG~~La~lvlivLiaYli~Rrr~~ 300 (306)
T PF01299_consen 270 SDLVPIAVGAALAGLVLIVLIAYLIGRRRSR 300 (306)
T ss_pred cchHHHHHHHHHHHHHHHHHHhheeEecccc
Confidence 6788887777666543333 344566654
No 88
>PHA03291 envelope glycoprotein I; Provisional
Probab=21.98 E-value=52 Score=30.88 Aligned_cols=11 Identities=27% Similarity=0.383 Sum_probs=6.7
Q ss_pred cEEEEEecCCC
Q 044908 59 AVSGFFQCRGD 69 (275)
Q Consensus 59 ~vygl~~CrgD 69 (275)
.|+|-.+=.||
T Consensus 51 ~V~G~LlFLG~ 61 (401)
T PHA03291 51 EVPGELHFLGP 61 (401)
T ss_pred EEeeEEEEecC
Confidence 56666665555
No 89
>PF15065 NCU-G1: Lysosomal transcription factor, NCU-G1
Probab=21.42 E-value=12 Score=35.13 Aligned_cols=21 Identities=14% Similarity=0.137 Sum_probs=11.3
Q ss_pred CCceeEEEeCceEEEEecCcc
Q 044908 92 KAVAGRIQLHGCYFYYETDEF 112 (275)
Q Consensus 92 ~~~~a~i~~d~C~lRYs~~~f 112 (275)
+...-.++.++..-|..+..|
T Consensus 155 NStq~dv~L~~~~~~~n~SRF 175 (350)
T PF15065_consen 155 NSTQVDVVLDGVTPRGNNSRF 175 (350)
T ss_pred CceEEEEEEeCcEecCCCcce
Confidence 444555566666666544444
No 90
>KOG3488 consensus Dolichol phosphate-mannose regulatory protein (DPM2) [Posttranslational modification, protein turnover, chaperones]
Probab=21.42 E-value=76 Score=22.70 Aligned_cols=11 Identities=36% Similarity=0.311 Sum_probs=6.7
Q ss_pred EEEeehHHHHH
Q 044908 245 VAIVLGGVAAL 255 (275)
Q Consensus 245 iaivv~~v~~v 255 (275)
.||.+|+.+.+
T Consensus 48 yAi~iPvaagl 58 (81)
T KOG3488|consen 48 YAITIPVAAGL 58 (81)
T ss_pred HHhhhHHHHHH
Confidence 46667766554
No 91
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=21.41 E-value=70 Score=20.72 Aligned_cols=20 Identities=15% Similarity=0.011 Sum_probs=8.5
Q ss_pred EEEeehHHHHHHHHHHHHHH
Q 044908 245 VAIVLGGVAALALGFIFLSF 264 (275)
Q Consensus 245 iaivv~~v~~v~~~~~~~~~ 264 (275)
+.+.+|+.++++++++..++
T Consensus 3 l~~lip~sl~l~~~~l~~f~ 22 (45)
T PF03597_consen 3 LYILIPVSLILGLIALAAFL 22 (45)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 34445554444333333333
No 92
>TIGR03154 sulfolob_CbsA cytochrome b558/566, subunit A. Members of this protein family are CbsA, one subunit of a highly glycosylated, heterodimeric, mono-heme cytochrome b558/566, found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota.
Probab=20.55 E-value=64 Score=30.34 Aligned_cols=19 Identities=21% Similarity=0.207 Sum_probs=9.8
Q ss_pred CcEEEEeehHHHHHHHHHH
Q 044908 242 GKTVAIVLGGVAALALGFI 260 (275)
Q Consensus 242 ~~iiaivv~~v~~v~~~~~ 260 (275)
..|...|++++++++.+++
T Consensus 440 tTIlwTVaGVvIAiVALV~ 458 (465)
T TIGR03154 440 TTLYVTIIGVVIAIVALVI 458 (465)
T ss_pred eeEEEEeehhHHHHHHHhh
Confidence 3355556666555544433
No 93
>PRK10884 SH3 domain-containing protein; Provisional
Probab=20.35 E-value=71 Score=27.69 Aligned_cols=8 Identities=13% Similarity=0.534 Sum_probs=3.8
Q ss_pred hCCCCCCC
Q 044908 268 CGDKDSIW 275 (275)
Q Consensus 268 ~~~~~~~~ 275 (275)
||||++-|
T Consensus 197 rRkr~~~W 204 (206)
T PRK10884 197 RRKRKDRW 204 (206)
T ss_pred cccccccc
Confidence 34444546
Done!