Query 011697
Match_columns 479
No_of_seqs 172 out of 307
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:14:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1087 Cytosolic sorting prot 100.0 2.4E-30 5.2E-35 270.8 22.6 141 1-141 131-277 (470)
2 PF03127 GAT: GAT domain; Int 99.9 2.5E-23 5.5E-28 176.3 12.0 87 58-144 10-96 (100)
3 KOG1086 Cytosolic sorting prot 99.6 3.8E-15 8.2E-20 155.1 8.9 107 45-151 200-310 (594)
4 KOG2199 Signal transducing ada 94.1 0.17 3.6E-06 54.2 7.8 77 61-140 290-366 (462)
5 PF12210 Hrs_helical: Hepatocy 79.4 6.5 0.00014 34.9 6.3 70 61-132 4-73 (96)
6 PF07106 TBPIP: Tat binding pr 77.3 43 0.00093 31.0 11.5 82 58-139 85-168 (169)
7 PF14523 Syntaxin_2: Syntaxin- 76.1 45 0.00098 27.9 10.8 78 60-140 4-92 (102)
8 KOG0307 Vesicle coat complex C 74.5 1E+02 0.0022 37.3 15.8 44 321-367 783-826 (1049)
9 PF04740 LXG: LXG domain of WX 73.7 34 0.00073 32.1 10.0 81 60-140 69-166 (204)
10 PF05400 FliT: Flagellar prote 65.3 22 0.00047 28.3 5.9 52 86-137 8-65 (84)
11 PF02203 TarH: Tar ligand bind 64.7 59 0.0013 28.8 9.1 77 59-136 82-161 (171)
12 smart00503 SynN Syntaxin N-ter 64.5 87 0.0019 26.4 10.8 82 58-139 14-109 (117)
13 cd00179 SynN Syntaxin N-termin 63.0 1.1E+02 0.0023 27.2 10.4 82 58-139 12-108 (151)
14 PF10168 Nup88: Nuclear pore c 62.0 55 0.0012 37.8 10.4 47 92-138 610-658 (717)
15 PF03670 UPF0184: Uncharacteri 61.5 28 0.0006 30.3 6.1 59 55-115 22-80 (83)
16 PF14735 HAUS4: HAUS augmin-li 59.3 1.1E+02 0.0023 31.0 10.7 78 61-138 112-193 (238)
17 PRK09458 pspB phage shock prot 51.2 22 0.00047 30.4 3.7 25 84-108 37-61 (75)
18 PF13801 Metal_resist: Heavy-m 51.1 1E+02 0.0022 25.4 7.7 64 43-109 40-107 (125)
19 COG5278 Predicted periplasmic 50.7 1.1E+02 0.0023 30.5 9.0 73 59-132 45-120 (207)
20 KOG1656 Protein involved in gl 50.0 2.9E+02 0.0063 28.0 13.0 64 59-124 92-169 (221)
21 PF07200 Mod_r: Modifier of ru 48.9 1.1E+02 0.0024 27.7 8.2 80 54-138 2-88 (150)
22 PF06667 PspB: Phage shock pro 47.7 27 0.00058 29.7 3.8 27 83-109 36-62 (75)
23 PF01895 PhoU: PhoU domain; I 47.7 1.1E+02 0.0023 23.8 7.1 17 64-80 5-21 (88)
24 PF01544 CorA: CorA-like Mg2+ 47.6 1.3E+02 0.0027 28.9 8.9 78 58-137 157-239 (292)
25 KOG0307 Vesicle coat complex C 46.6 4.8E+02 0.01 32.0 14.7 11 92-102 559-569 (1049)
26 PF12729 4HB_MCP_1: Four helix 44.7 2E+02 0.0042 24.7 8.8 47 64-110 84-130 (181)
27 PRK11546 zraP zinc resistance 41.7 1.4E+02 0.0029 28.3 7.8 63 43-107 42-107 (143)
28 PRK06863 single-stranded DNA-b 41.0 24 0.00053 33.7 2.9 10 358-367 144-153 (168)
29 TIGR02976 phageshock_pspB phag 41.0 34 0.00073 29.0 3.4 27 84-110 37-63 (75)
30 PF04961 FTCD_C: Formiminotran 40.8 99 0.0022 29.6 7.0 41 71-111 33-74 (184)
31 TIGR00153 conserved hypothetic 40.3 1.6E+02 0.0034 28.3 8.3 82 59-140 18-102 (216)
32 PF13324 GCIP: Grap2 and cycli 39.6 3.4E+02 0.0075 27.2 10.8 48 86-133 222-273 (275)
33 PF00512 HisKA: His Kinase A ( 38.4 1.6E+02 0.0035 22.3 6.6 49 59-109 11-60 (68)
34 PF04156 IncA: IncA protein; 38.1 2.7E+02 0.0058 25.9 9.3 21 89-109 130-150 (191)
35 TIGR03582 EF_0829 PRD domain p 37.6 81 0.0018 28.4 5.4 48 69-116 45-93 (107)
36 TIGR00383 corA magnesium Mg(2+ 37.5 3.1E+02 0.0066 27.4 10.1 77 58-136 181-262 (318)
37 PF00015 MCPsignal: Methyl-acc 37.4 85 0.0018 28.7 5.8 19 117-135 192-210 (213)
38 PF14555 UBA_4: UBA-like domai 37.2 65 0.0014 23.7 4.1 34 104-137 3-38 (43)
39 PF05508 Ran-binding: RanGTP-b 37.0 90 0.002 32.8 6.4 52 87-138 82-137 (302)
40 PRK09269 chorismate mutase; Pr 36.8 2.7E+02 0.0059 27.3 9.3 60 88-147 90-158 (193)
41 PF10112 Halogen_Hydrol: 5-bro 36.2 2.1E+02 0.0045 27.2 8.3 73 60-140 76-150 (199)
42 cd05132 RasGAP_GAPA GAPA is an 36.1 80 0.0017 32.7 5.9 65 63-127 203-270 (331)
43 PF04156 IncA: IncA protein; 35.8 2.5E+02 0.0053 26.2 8.6 14 89-102 137-150 (191)
44 PLN03229 acetyl-coenzyme A car 35.5 3.2E+02 0.0069 32.3 10.9 88 46-134 506-619 (762)
45 PF06798 PrkA: PrkA serine pro 35.4 1.5E+02 0.0033 30.0 7.6 76 64-140 39-129 (254)
46 KOG3192 Mitochondrial J-type c 35.2 82 0.0018 30.6 5.3 63 69-131 36-111 (168)
47 KOG1899 LAR transmembrane tyro 34.8 4.3E+02 0.0094 31.0 11.5 28 117-144 282-316 (861)
48 PF07106 TBPIP: Tat binding pr 34.7 1.6E+02 0.0034 27.3 7.1 53 91-143 88-140 (169)
49 KOG2199 Signal transducing ada 34.7 1.5E+02 0.0033 32.7 7.8 10 317-326 399-408 (462)
50 KOG4603 TBP-1 interacting prot 33.9 91 0.002 30.8 5.5 46 59-111 100-145 (201)
51 PF12917 HD_2: HD containing h 33.8 1.2E+02 0.0025 30.6 6.4 44 101-144 112-155 (215)
52 PTZ00446 vacuolar sorting prot 33.6 2.8E+02 0.006 27.4 8.8 66 58-125 97-174 (191)
53 PF04184 ST7: ST7 protein; In 32.7 47 0.001 37.3 3.8 20 59-78 270-289 (539)
54 cd05392 RasGAP_Neurofibromin_l 32.7 89 0.0019 32.0 5.6 54 62-115 201-254 (323)
55 cd09235 V_Alix Middle V-domain 32.4 96 0.0021 32.2 5.8 45 58-102 20-66 (339)
56 PF05667 DUF812: Protein of un 32.2 1.9E+02 0.0042 32.8 8.5 53 86-138 465-531 (594)
57 PF12309 KBP_C: KIF-1 binding 32.2 1.6E+02 0.0034 31.4 7.5 81 60-140 194-277 (371)
58 PF06246 Isy1: Isy1-like splic 32.1 77 0.0017 32.4 4.9 43 95-137 42-89 (255)
59 COG1344 FlgL Flagellin and rel 30.3 4.2E+02 0.0092 27.6 10.1 67 59-134 57-127 (360)
60 PF10211 Ax_dynein_light: Axon 30.2 2.5E+02 0.0053 27.2 7.8 63 69-141 40-106 (189)
61 TIGR02263 benz_CoA_red_C benzo 30.1 3.7E+02 0.0081 28.3 9.7 55 91-145 137-191 (380)
62 PF10735 DUF2526: Protein of u 29.9 2.1E+02 0.0045 24.6 6.3 27 47-79 5-31 (77)
63 PF09361 Phasin_2: Phasin prot 29.9 68 0.0015 26.0 3.5 65 51-115 24-92 (102)
64 cd04519 RasGAP RasGAP: Ras-GTP 29.6 2.3E+02 0.005 27.7 7.6 53 62-114 205-257 (318)
65 PF05816 TelA: Toxic anion res 29.1 1.9E+02 0.0041 30.0 7.3 51 92-142 87-139 (333)
66 cd00176 SPEC Spectrin repeats, 28.4 4.2E+02 0.009 23.4 8.7 42 60-105 8-49 (213)
67 PHA02334 hypothetical protein 28.1 1.9E+02 0.0042 24.0 5.6 36 85-120 21-56 (64)
68 TIGR02916 PEP_his_kin putative 28.0 1.5E+02 0.0032 33.0 6.7 50 88-137 507-558 (679)
69 PF08020 DUF1706: Protein of u 27.8 69 0.0015 30.5 3.6 30 91-120 101-130 (166)
70 cd05133 RasGAP_IQGAP1 IQGAP1 i 27.7 2.2E+02 0.0048 30.4 7.6 52 64-115 209-260 (360)
71 COG5394 Uncharacterized protei 27.7 99 0.0022 30.3 4.6 47 62-108 140-193 (193)
72 PF07568 HisKA_2: Histidine ki 27.4 2.6E+02 0.0056 22.9 6.4 39 63-101 5-43 (76)
73 KOG3091 Nuclear pore complex, 27.2 2.7E+02 0.0058 31.4 8.2 50 59-110 348-397 (508)
74 COG4010 Uncharacterized protei 27.0 3.1E+02 0.0066 26.7 7.6 57 62-121 24-80 (170)
75 COG2822 Predicted periplasmic 26.8 2E+02 0.0044 30.8 6.9 76 62-137 260-337 (376)
76 PF02252 PA28_beta: Proteasome 26.7 2.6E+02 0.0057 26.4 7.1 26 90-115 21-46 (150)
77 PF05769 DUF837: Protein of un 26.7 4E+02 0.0086 25.8 8.5 74 61-137 9-91 (181)
78 PRK12292 hisZ ATP phosphoribos 26.2 2.5E+02 0.0055 29.5 7.7 76 61-138 156-245 (391)
79 KOG1103 Predicted coiled-coil 25.9 1.6E+02 0.0034 32.2 6.1 57 52-108 51-108 (561)
80 PF03962 Mnd1: Mnd1 family; I 25.9 6.1E+02 0.013 24.5 10.7 69 52-123 70-142 (188)
81 PF00435 Spectrin: Spectrin re 25.7 3.2E+02 0.007 21.3 9.6 24 85-108 30-53 (105)
82 PF09727 CortBP2: Cortactin-bi 25.6 1.4E+02 0.0031 29.5 5.3 47 88-134 83-141 (192)
83 cd09234 V_HD-PTP_like Protein- 25.6 3.2E+02 0.0069 28.3 8.2 46 58-103 20-69 (337)
84 cd08063 MPN_CSN6 Mpr1p, Pad1p 25.2 5.9E+02 0.013 25.9 9.9 81 58-139 192-280 (288)
85 PF07267 Nucleo_P87: Nucleopol 25.2 2.5E+02 0.0054 32.4 7.7 46 65-110 36-86 (654)
86 KOG1086 Cytosolic sorting prot 24.8 2.4E+02 0.0052 31.7 7.3 22 89-110 216-237 (594)
87 PRK00411 cdc6 cell division co 24.6 4.7E+02 0.01 26.7 9.1 76 64-141 248-331 (394)
88 COG5002 VicK Signal transducti 24.4 3E+02 0.0065 30.3 7.8 74 68-143 240-321 (459)
89 PLN03196 MOC1-like protein; Pr 24.0 97 0.0021 34.0 4.3 40 98-139 372-416 (487)
90 PF12729 4HB_MCP_1: Four helix 24.0 4.6E+02 0.0099 22.4 11.0 27 87-113 110-136 (181)
91 PF09726 Macoilin: Transmembra 23.9 2.8E+02 0.006 32.2 8.0 63 51-116 425-487 (697)
92 PRK05431 seryl-tRNA synthetase 23.9 4.2E+02 0.0091 28.6 9.0 76 60-139 3-93 (425)
93 PF08899 DUF1844: Domain of un 23.8 1.3E+02 0.0029 25.5 4.1 40 59-99 32-71 (74)
94 COG3879 Uncharacterized protei 23.7 4.9E+02 0.011 26.8 8.8 81 67-148 27-114 (247)
95 smart00323 RasGAP GTPase-activ 23.7 1.9E+02 0.0042 29.7 6.2 52 63-114 228-279 (344)
96 KOG0804 Cytoplasmic Zn-finger 23.6 3.6E+02 0.0078 30.2 8.4 71 55-128 343-414 (493)
97 PF05397 Med15_fungi: Mediator 23.4 3.2E+02 0.0069 24.6 6.8 55 85-142 31-89 (115)
98 cd05127 RasGAP_IQGAP_related T 23.2 1.7E+02 0.0036 30.1 5.6 52 63-114 202-253 (325)
99 PRK02793 phi X174 lysis protei 23.2 4.4E+02 0.0095 21.9 7.3 35 65-108 21-55 (72)
100 PF11744 ALMT: Aluminium activ 23.1 7.9E+02 0.017 26.8 10.8 50 58-107 294-344 (406)
101 PF03273 Baculo_gp64: Baculovi 23.1 2.1E+02 0.0046 32.0 6.5 33 91-123 305-339 (498)
102 PF10157 DUF2365: Uncharacteri 22.9 6.6E+02 0.014 23.9 13.5 87 45-140 49-137 (149)
103 PRK04325 hypothetical protein; 22.7 4.5E+02 0.0099 21.9 7.3 36 65-109 22-57 (74)
104 TIGR01010 BexC_CtrB_KpsE polys 22.7 6.4E+02 0.014 26.0 9.7 56 59-114 177-239 (362)
105 PF07729 FCD: FCD domain; Int 22.6 3.3E+02 0.0073 21.8 6.3 18 60-77 1-18 (125)
106 KOG4603 TBP-1 interacting prot 22.5 3.4E+02 0.0074 27.0 7.2 55 89-143 93-147 (201)
107 PRK14148 heat shock protein Gr 22.3 5.8E+02 0.013 25.2 8.8 66 59-133 40-108 (195)
108 TIGR00019 prfA peptide chain r 22.3 6.8E+02 0.015 27.0 10.0 30 107-137 67-96 (360)
109 KOG1960 Predicted RNA-binding 22.1 1.1E+03 0.024 26.4 11.5 22 434-456 486-507 (531)
110 PF05633 DUF793: Protein of un 22.0 1.6E+02 0.0034 32.1 5.3 52 58-109 314-368 (389)
111 cd08334 DED_Caspase_8_10_repea 21.9 1.8E+02 0.0038 24.8 4.6 49 56-110 31-79 (83)
112 COG1340 Uncharacterized archae 21.8 6.3E+02 0.014 26.7 9.4 84 58-147 199-283 (294)
113 cd00176 SPEC Spectrin repeats, 21.8 5.6E+02 0.012 22.6 8.1 29 49-78 38-66 (213)
114 PF05527 DUF758: Domain of unk 21.7 3.6E+02 0.0079 26.6 7.3 74 62-135 58-134 (186)
115 PLN03122 Poly [ADP-ribose] pol 21.7 1.5E+02 0.0033 34.9 5.5 86 53-140 488-591 (815)
116 PF08893 DUF1839: Domain of un 21.7 2.9E+02 0.0062 29.5 6.9 76 59-134 238-318 (319)
117 COG2352 Ppc Phosphoenolpyruvat 21.6 2.6E+02 0.0056 33.5 7.1 78 61-142 6-96 (910)
118 PF05384 DegS: Sensor protein 21.5 2.8E+02 0.006 26.6 6.3 51 89-139 2-54 (159)
119 PRK10378 inactive ferrous ion 21.2 3.8E+02 0.0081 29.0 7.9 76 62-137 259-336 (375)
120 PF01025 GrpE: GrpE; InterPro 21.1 2.4E+02 0.0051 25.7 5.6 49 87-136 60-109 (165)
121 KOG4460 Nuclear pore complex, 21.0 5.1E+02 0.011 30.0 9.0 78 59-138 602-681 (741)
122 KOG4515 Uncharacterized conser 21.0 2.1E+02 0.0046 28.6 5.5 40 92-131 116-163 (217)
123 PF08429 PLU-1: PLU-1-like pro 20.9 2.7E+02 0.0058 28.3 6.5 43 86-128 103-147 (335)
124 PF04728 LPP: Lipoprotein leuc 20.8 2.6E+02 0.0057 22.8 5.1 47 91-137 5-56 (56)
125 KOG1465 Translation initiation 20.8 2.4E+02 0.0051 30.3 6.1 49 59-111 25-86 (353)
126 PF07851 TMPIT: TMPIT-like pro 20.8 3.4E+02 0.0074 28.9 7.3 47 59-106 39-85 (330)
127 PF03904 DUF334: Domain of unk 20.8 6.3E+02 0.014 25.9 8.8 61 56-116 40-113 (230)
128 PRK00846 hypothetical protein; 20.5 5.5E+02 0.012 22.0 7.2 21 89-109 41-61 (77)
129 PHA03373 tegument protein; Pro 20.4 4.2E+02 0.0091 27.3 7.5 67 55-135 49-142 (247)
130 PF04102 SlyX: SlyX; InterPro 20.3 4.4E+02 0.0095 21.5 6.4 40 61-109 13-52 (69)
131 cd09238 V_Alix_like_1 Protein- 20.2 9.8E+02 0.021 24.9 10.5 12 117-128 266-277 (339)
132 cd08915 V_Alix_like Protein-in 20.1 8.1E+02 0.017 25.2 9.8 22 58-79 20-42 (342)
133 PF05739 SNARE: SNARE domain; 20.0 2.5E+02 0.0054 21.4 4.8 45 60-106 5-49 (63)
No 1
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=2.4e-30 Score=270.76 Aligned_cols=141 Identities=45% Similarity=0.651 Sum_probs=110.1
Q ss_pred CccccccCCCCCCCC-CCCCCCCCCCCCCCCC-cc---CCCCCCCCCCCCChhHH-HhhhhhcHHHHHHHHHHHHHHHHH
Q 011697 1 MQRYGVQFPKRSPDA-APIFTPPVSHPTLGQA-QA---SYGMPSNSSRRLDETMA-TEVETLSFSSLDSMRDVMELLSDM 74 (479)
Q Consensus 1 LKrkGVeFP~rd~da-aPIfTPp~TvP~~~~~-~~---~~~~ps~s~~~l~peq~-sklekLS~sELevVrnNVkVLsEM 74 (479)
||+|||+||+|++++ ++|.+|.+..+..... +. .+..+.-......+.+. .+...++++||++|+++|+||+||
T Consensus 131 l~~~G~~FP~r~~~sl~~~~pp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~seLe~~~~~~~ll~em 210 (470)
T KOG1087|consen 131 LRRKGVEFPQRDEESLAVLTPPAVLRPAPEPQEQSGPPNEANASMKSMAGYPTEATPEVSTLSLSELESVKGKADLLSEM 210 (470)
T ss_pred HHHcCCcCCCCccccccccCCCCCCCCCCCchhhcCCccccccccccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 678999999999988 5554454444432211 00 00111111111222222 244555589999999999999999
Q ss_pred HHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHHHhhC
Q 011697 75 LQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASG 141 (479)
Q Consensus 75 L~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr~~kG 141 (479)
|++++|+++++.++|||++|+++||.||+|||+||++++||++|+++|++||+|++||.|||+|.+|
T Consensus 211 L~~v~p~~~e~~~~el~~~L~~qcr~~q~rv~~Li~~~~DE~ll~~lL~lND~L~~vL~~ye~~~~g 277 (470)
T KOG1087|consen 211 LNAVDPSDEEAAKDELLVDLVEQCRSKQRRVMHLIEETSDEELLCELLKLNDELQRVLERYERIASG 277 (470)
T ss_pred HhccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999
No 2
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=99.90 E-value=2.5e-23 Score=176.32 Aligned_cols=87 Identities=29% Similarity=0.525 Sum_probs=82.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr 137 (479)
++||++|++|++||+|||++++|++....+.|+|+|||++||+||+||++||..+.|||+|++||++||+|++||.||++
T Consensus 10 ~~~l~~v~~~~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r~~i~~li~~~~dee~l~~lL~~ND~L~~~l~~Y~~ 89 (100)
T PF03127_consen 10 RSELEKVKNNAKLLNEMLDNYDPGEESSSDNELIQELYESCKSMRPRIQRLIEEVEDEELLGELLQANDELNQALERYDR 89 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999998888889999999999999999999999999999999999999999999999999
Q ss_pred HhhCCCC
Q 011697 138 IASGLPI 144 (479)
Q Consensus 138 ~~kG~~~ 144 (479)
|++|+..
T Consensus 90 l~~~~~~ 96 (100)
T PF03127_consen 90 LVKGQQR 96 (100)
T ss_dssp HHCCC--
T ss_pred HHcCccc
Confidence 9998875
No 3
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.58 E-value=3.8e-15 Score=155.15 Aligned_cols=107 Identities=18% Similarity=0.284 Sum_probs=93.0
Q ss_pred CChhHHHhhhhhcH--HHHHHHHHHHHHHHHHHHhhCC-CCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH-HHHH
Q 011697 45 LDETMATEVETLSF--SSLDSMRDVMELLSDMLQAVNP-SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE-LLGR 120 (479)
Q Consensus 45 l~peq~sklekLS~--sELevVrnNVkVLsEML~e~~P-g~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE-lL~E 120 (479)
+..+..+|++|+++ ..||.|+|||++|.|||-.+.- |+..++...+|++||++|+++|+.+++|+++++|+| .|+|
T Consensus 200 lVkeee~k~eKiskR~~aleev~n~vk~l~em~l~~s~eg~a~pd~E~~lq~v~~~ce~lr~tlfrlaset~dnD~aL~e 279 (594)
T KOG1086|consen 200 LVKEEEHKLEKISKRVKALEEVNNNVKLLEEMLLDYSQEGNASPDNELLLQEVYNRCEQLRPTLFRLASETEDNDPALAE 279 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCcHHHHHHHHHHHHHHHHHHHHHhhcccccCcHHHHH
Confidence 33456688999987 7899999999999999998864 444444444999999999999999999999998877 9999
Q ss_pred HHHhhhHHHHHHHHHHHHhhCCCCCCcccCC
Q 011697 121 GLELNDILQNLLAKHDAIASGLPIPTEVTNL 151 (479)
Q Consensus 121 LL~lNDdLNnVL~RYdr~~kG~~~~~e~~~~ 151 (479)
+|++||.|++|+..|+.++.|+...+++...
T Consensus 280 ILqanD~ltrvi~~ykt~~~G~~~~g~a~t~ 310 (594)
T KOG1086|consen 280 ILQANDNLTRVINLYKTPKEGNVANGSARTQ 310 (594)
T ss_pred HHhhhhhHHhhhhhcccccccccccccceec
Confidence 9999999999999999999999999886543
No 4
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=94.11 E-value=0.17 Score=54.20 Aligned_cols=77 Identities=17% Similarity=0.178 Sum_probs=63.0
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHHHhh
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIAS 140 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr~~k 140 (479)
..+....|+-|-.||.+.+|.++. .|++-|.+|+..|..|++.|-++++.+.-. =++|++||-.|-.++..|+.++.
T Consensus 290 vfi~e~~iDrlL~~L~~~dPtd~~-~D~~~l~~le~~~~~mgPlid~~Le~idrk--~~eL~~Ln~~l~~Al~lY~kLm~ 366 (462)
T KOG2199|consen 290 VFIDEDKIDRLLQVLHEADPTDEV-QDDDDLLDLEAAVHQMGPLIDRKLEKIDRK--HEELSQLNVKLLDALRLYNKLMN 366 (462)
T ss_pred eeccHHHHHHHHHHHhhcCCCCcc-CCCHHHHHHHHHHHHhhhHHHHHHHHHHhh--HHHHHHHHHHHHHHHHHHHHHHh
Confidence 344566788888999999997664 556777899999999999999999987533 24568899999999999999984
No 5
>PF12210 Hrs_helical: Hepatocyte growth factor-regulated tyrosine kinase substrate; InterPro: IPR024641 This domain comprises the helical region of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). It is approximately 100 amino acids in length. Hrs, together with signal transducing adaptor molecule (STAM), forms the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation []. ; PDB: 3F1I_H.
Probab=79.37 E-value=6.5 Score=34.89 Aligned_cols=70 Identities=14% Similarity=0.336 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHH
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLL 132 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL 132 (479)
+...+..|++|..=+....-.+.....|.-++.|+.+.-.|+++|++.|.+..|.-.=.|.| .|.|..+=
T Consensus 4 ~~~l~~~v~if~nRmksns~RGrsIanDsaVqsLF~~lt~mH~~LL~~i~~~ee~R~~~E~l--QdkL~qi~ 73 (96)
T PF12210_consen 4 CNTLRSSVEIFVNRMKSNSSRGRSIANDSAVQSLFQTLTAMHPQLLKYIQEQEEKRVYYEGL--QDKLAQIK 73 (96)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--GGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHhcCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH
Confidence 56677888888777766655566678889999999999999999999999987665444433 46665553
No 6
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=77.26 E-value=43 Score=31.03 Aligned_cols=82 Identities=13% Similarity=0.096 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcC--ChHHHHHHHHhhhHHHHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG--DEELLGRGLELNDILQNLLAKH 135 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~--DEElL~ELL~lNDdLNnVL~RY 135 (479)
+.+|...+.-++-|..=|..+.-.-....=.+.|.+|-..|+.++.||..|-.... +++.+.++..-...+.+...+.
T Consensus 85 ~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~k~w~kR 164 (169)
T PF07106_consen 85 REELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYKKWRKEWKKR 164 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 68899999999999999999963222222235677899999999999999988433 3445555555555555555555
Q ss_pred HHHh
Q 011697 136 DAIA 139 (479)
Q Consensus 136 dr~~ 139 (479)
.++.
T Consensus 165 Kri~ 168 (169)
T PF07106_consen 165 KRIC 168 (169)
T ss_pred HHHh
Confidence 5543
No 7
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=76.06 E-value=45 Score=27.88 Aligned_cols=78 Identities=12% Similarity=0.160 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhh---HHHHHHHHHHHHHHHHHHHHhhhc------CChH--HHHHHHHhhhHH
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKD---EVIVDLVSRCRSNQKKLMQMLTTT------GDEE--LLGRGLELNDIL 128 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~---ELlqEL~eqCRsmQ~RI~~LIs~t------~DEE--lL~ELL~lNDdL 128 (479)
-|..+.+++.-|.-|+..+- ... +.. +-|.++...|+.+-..+-++|..+ .+.+ .-...=.|..++
T Consensus 4 ~l~~in~~v~~l~k~~~~lG--t~~-Ds~~lR~~i~~~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df 80 (102)
T PF14523_consen 4 NLFKINQNVSQLEKLVNQLG--TPR-DSQELREKIHQLIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDF 80 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHH---SSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhC--Ccc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHH
Confidence 47888999999999999993 221 222 333555666666665555544432 2222 334555677888
Q ss_pred HHHHHHHHHHhh
Q 011697 129 QNLLAKHDAIAS 140 (479)
Q Consensus 129 NnVL~RYdr~~k 140 (479)
..++.+|.++.+
T Consensus 81 ~~~l~~fq~~q~ 92 (102)
T PF14523_consen 81 KEALQEFQKAQR 92 (102)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 888888887753
No 8
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.46 E-value=1e+02 Score=37.32 Aligned_cols=44 Identities=39% Similarity=0.590 Sum_probs=24.8
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 011697 321 PYNNYVAPWAQPQSQPLPQSQPQFQPGVQPQYPHYSSAYPPPPWAPT 367 (479)
Q Consensus 321 ~~n~yv~pwaq~~~~~q~~~~~q~~~~~~~q~~~~~s~yP~PpWa~~ 367 (479)
|||.+-+| +....+.+++-.+......+-++ +.+-||+|+|.+-
T Consensus 783 p~~p~p~p--~~~~~p~~~s~~~p~~~stP~~~-~~~~~P~~~~~~~ 826 (1049)
T KOG0307|consen 783 PYNPSPAP--QPSYTPAPQSNARPNSASTPTPP-AFSFTPPPSSGAA 826 (1049)
T ss_pred CCCCCCCC--CCCCCCCCcCCCCCCCCCCCCCC-CcCCCCCCccccc
Confidence 66666666 44334444443343433333344 7778888888873
No 9
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=73.68 E-value=34 Score=32.07 Aligned_cols=81 Identities=12% Similarity=0.264 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhhHHHH-HHHHHHHHHHHHHHHHhhhc-------C---------ChHHHHHHH
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIV-DLVSRCRSNQKKLMQMLTTT-------G---------DEELLGRGL 122 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlq-EL~eqCRsmQ~RI~~LIs~t-------~---------DEElL~ELL 122 (479)
=++.+...++.+.+-+..+++....-.+.++|+ ||...+++....+..+...+ . ...+...+.
T Consensus 69 ~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~~~~~~~~~~~~~~~~~~~vsdiv~~~~~~~~~~~~~~~ 148 (204)
T PF04740_consen 69 LLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQLKEQIEDLQDEINSILSSVSDIVSLPKPSSSSFIDSLE 148 (204)
T ss_pred HHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccchHHHHhhccchHHHHHHHHH
Confidence 356666667777887888876444446778887 88777777776666554443 1 123566677
Q ss_pred HhhhHHHHHHHHHHHHhh
Q 011697 123 ELNDILQNLLAKHDAIAS 140 (479)
Q Consensus 123 ~lNDdLNnVL~RYdr~~k 140 (479)
.+.+.|+.++++...|-.
T Consensus 149 ~~~~~l~~~lekL~~fd~ 166 (204)
T PF04740_consen 149 KAKKKLQETLEKLRAFDQ 166 (204)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 788888999999988864
No 10
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=65.35 E-value=22 Score=28.29 Aligned_cols=52 Identities=27% Similarity=0.350 Sum_probs=37.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHH---Hhh-hcCCh--HHHHHHHHhhhHHHHHHHHHHH
Q 011697 86 VKDEVIVDLVSRCRSNQKKLMQ---MLT-TTGDE--ELLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 86 ~d~ELlqEL~eqCRsmQ~RI~~---LIs-~t~DE--ElL~ELL~lNDdLNnVL~RYdr 137 (479)
.|.|-+.+|.+.|...-.+|+. .+. ....+ ++|.++|.++..|...+.....
T Consensus 8 ~dWe~l~~l~~~R~~ll~~l~~~~~~~~~~~~~~~~~~l~~Il~~d~~i~~ll~~~~~ 65 (84)
T PF05400_consen 8 GDWEELEELLDERQELLERLFEEQAALSPPEQEELRELLRRILELDQEIRALLQARRD 65 (84)
T ss_dssp T-HHHHHHHHHHHHHHHHHHHHCHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHHhhccccCChhhHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 4678899999999998888887 122 11222 3888899999999888876544
No 11
>PF02203 TarH: Tar ligand binding domain homologue; InterPro: IPR003122 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors.; GO: 0004888 transmembrane signaling receptor activity, 0006935 chemotaxis, 0007165 signal transduction, 0016020 membrane; PDB: 2ASR_A 3ATP_A 2D4U_A 2LIG_A 1VLS_A 1LIH_A 1WAT_B 1VLT_B 1WAS_A 1JMW_A.
Probab=64.70 E-value=59 Score=28.82 Aligned_cols=77 Identities=14% Similarity=0.181 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccc-hhhHHHHHHHHHHHH-HHHHHHHHhhhcCChHHHHHHHHh-hhHHHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREA-VKDEVIVDLVSRCRS-NQKKLMQMLTTTGDEELLGRGLEL-NDILQNLLAKH 135 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~-~d~ELlqEL~eqCRs-mQ~RI~~LIs~t~DEElL~ELL~l-NDdLNnVL~RY 135 (479)
..|+.++..++-..+.+..+.-..... .+.+++++|.+.-+. ++..|..++......| +.+.+.+ +..++..|..|
T Consensus 82 ~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~al~~~d-~~~~~~~~~~~~~~~~~~~ 160 (171)
T PF02203_consen 82 ELLARAEQNLEQAEQAFDAFKALPHASPEERALADELEASFDAYLQQALDPLLAALRAGD-IAAFMQLPNEKIQPLFDAF 160 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCS---GTGGHHHHHHHHHHHHH-HHHHHHHHHHHHHTT--HHHHHHSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHCCC-HHHHHHHHHHhcchhHHHH
Confidence 456666666666666666664322222 455677777777776 5566666666554443 1222222 44455555444
Q ss_pred H
Q 011697 136 D 136 (479)
Q Consensus 136 d 136 (479)
.
T Consensus 161 ~ 161 (171)
T PF02203_consen 161 T 161 (171)
T ss_dssp H
T ss_pred H
Confidence 4
No 12
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=64.49 E-value=87 Score=26.41 Aligned_cols=82 Identities=9% Similarity=0.159 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCC-CccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC-----------hH--HHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPS-DREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD-----------EE--LLGRGLE 123 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg-~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D-----------EE--lL~ELL~ 123 (479)
..+|..+++||+=|..+...+--. +....-.+-|.+|.+.++..-..|-.+|..+.. ++ .....=.
T Consensus 14 ~~~I~~i~~~v~~l~~l~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~lk~l~~~~~~~~~~~~~~~r~~~~q~~~ 93 (117)
T smart00503 14 RANIQKISQNVAELQKLHEELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRASGSASDRTRKAQTEK 93 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcccCCHhhhHHHHHHHH
Confidence 678999999999888888887421 111111233444444444444444444332211 12 2334445
Q ss_pred hhhHHHHHHHHHHHHh
Q 011697 124 LNDILQNLLAKHDAIA 139 (479)
Q Consensus 124 lNDdLNnVL~RYdr~~ 139 (479)
|-.+|..+|.+|..+-
T Consensus 94 L~~~f~~~m~~fq~~Q 109 (117)
T smart00503 94 LRKKFKEVMNEFQRLQ 109 (117)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6778888999998763
No 13
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=62.99 E-value=1.1e+02 Score=27.21 Aligned_cols=82 Identities=11% Similarity=0.163 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCC-CccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC------------hH--HHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPS-DREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD------------EE--LLGRGL 122 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg-~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D------------EE--lL~ELL 122 (479)
+.+|..++.+++-|..+...+--. +....-.+-|.+|.+.+..+...|-.+|..+.. ++ .-.+.=
T Consensus 12 ~~~i~~i~~~v~~l~~l~~~~~t~~~~~~~~~~~l~~~~~~~~~~~~~ik~~lk~l~~~~~~~~~~~~s~~~r~~~~q~~ 91 (151)
T cd00179 12 RGNIDKISEDVEELQKLHSQLLTAPDADPELKQELESLVQEIKKLAKEIKGKLKELEESNEQNEALNGSSVDRIRKTQHS 91 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHH
Confidence 577888888888888887777321 101111233444444444444444444443321 11 123444
Q ss_pred HhhhHHHHHHHHHHHHh
Q 011697 123 ELNDILQNLLAKHDAIA 139 (479)
Q Consensus 123 ~lNDdLNnVL~RYdr~~ 139 (479)
.|..++..+|.+|..+-
T Consensus 92 ~L~~~f~~~m~~fq~~Q 108 (151)
T cd00179 92 GLSKKFVEVMTEFNKAQ 108 (151)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 57889999999998873
No 14
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=62.02 E-value=55 Score=37.76 Aligned_cols=47 Identities=21% Similarity=0.213 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCChH--HHHHHHHhhhHHHHHHHHHHHH
Q 011697 92 VDLVSRCRSNQKKLMQMLTTTGDEE--LLGRGLELNDILQNLLAKHDAI 138 (479)
Q Consensus 92 qEL~eqCRsmQ~RI~~LIs~t~DEE--lL~ELL~lNDdLNnVL~RYdr~ 138 (479)
+.|.++|+.+-.++..-....++.| ...||-.+++.|+..=.+-+.+
T Consensus 610 e~L~~R~~~vl~~l~~~~P~LS~AEr~~~~EL~~~~~~l~~l~~si~~l 658 (717)
T PF10168_consen 610 EKLMKRVDRVLQLLNSQLPVLSEAEREFKKELERMKDQLQDLKASIEQL 658 (717)
T ss_pred HHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555544444455545 7778888998887765555554
No 15
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=61.47 E-value=28 Score=30.28 Aligned_cols=59 Identities=12% Similarity=0.238 Sum_probs=43.8
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCCh
Q 011697 55 TLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDE 115 (479)
Q Consensus 55 kLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DE 115 (479)
.....|+..+...++-|+--|+++. ++...=..-|++|.+.||+.|..+.+.......+
T Consensus 22 e~~~~E~~~ins~LD~Lns~LD~LE--~rnD~l~~~L~~LLesnrq~R~e~~~~~~~~~~~ 80 (83)
T PF03670_consen 22 EFDEEEYAAINSMLDQLNSCLDHLE--QRNDHLHAQLQELLESNRQIRLEFQEQLSKAPSE 80 (83)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHH--HhhhHHHHHHHHHHHHHHHHHHHHHHHhccCCcc
Confidence 3345688889999999999999884 3332223557899999999999998887766543
No 16
>PF14735 HAUS4: HAUS augmin-like complex subunit 4
Probab=59.35 E-value=1.1e+02 Score=31.03 Aligned_cols=78 Identities=14% Similarity=0.205 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHH----HHhhhcCChHHHHHHHHhhhHHHHHHHHHH
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLM----QMLTTTGDEELLGRGLELNDILQNLLAKHD 136 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~----~LIs~t~DEElL~ELL~lNDdLNnVL~RYd 136 (479)
..+....+.+|..||..+.-+.....|.--.+-|...|+.|.-||. +|+.+|=..|.+.-+=.+-|.|..++.+-+
T Consensus 112 ~~vL~~cl~~L~~li~~~rl~~q~~~d~~~~~~L~~kceam~lKLr~~~~~iL~~TYTpe~v~Al~~Ir~~L~~~~~~~e 191 (238)
T PF14735_consen 112 YQVLLQCLQLLQKLIEKHRLGTQAELDKIKAEYLEAKCEAMILKLRVLELEILSDTYTPETVPALRKIRDHLEEAIEELE 191 (238)
T ss_pred HHHHHHHHHHHHHHHHHHhhcchHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHhHHHHHHHHHHHHHHHHHHH
Confidence 6777888999999999998776666666778899999999998874 466666667766666667888888777665
Q ss_pred HH
Q 011697 137 AI 138 (479)
Q Consensus 137 r~ 138 (479)
.=
T Consensus 192 ~~ 193 (238)
T PF14735_consen 192 QE 193 (238)
T ss_pred HH
Confidence 43
No 17
>PRK09458 pspB phage shock protein B; Provisional
Probab=51.24 E-value=22 Score=30.41 Aligned_cols=25 Identities=4% Similarity=0.254 Sum_probs=21.7
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHH
Q 011697 84 EAVKDEVIVDLVSRCRSNQKKLMQM 108 (479)
Q Consensus 84 e~~d~ELlqEL~eqCRsmQ~RI~~L 108 (479)
+..|.+.+++|+++.++|+.||.-|
T Consensus 37 s~~d~~~L~~L~~~A~rm~~RI~tL 61 (75)
T PRK09458 37 SQEEQQRLAQLTEKAERMRERIQAL 61 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4467889999999999999999765
No 18
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=51.06 E-value=1e+02 Score=25.39 Aligned_cols=64 Identities=14% Similarity=0.180 Sum_probs=34.7
Q ss_pred CCCChhHHHhhhhhcH---HHHHHHHHHHHHHH-HHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHh
Q 011697 43 RRLDETMATEVETLSF---SSLDSMRDVMELLS-DMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 43 ~~l~peq~sklekLS~---sELevVrnNVkVLs-EML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LI 109 (479)
..|+++|..++..+-. .++...+..+.-+. ||...+. .+..|.+-|..|.+.+...+..+.+..
T Consensus 40 l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~---~~~~D~~~i~a~~~~~~~~~~~l~~~~ 107 (125)
T PF13801_consen 40 LNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLA---APPPDEAAIEALLEEIREAQAELRQER 107 (125)
T ss_dssp S-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---CSSS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678888888866633 34555555554443 3444442 123445566666666666665555443
No 19
>COG5278 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=50.73 E-value=1.1e+02 Score=30.47 Aligned_cols=73 Identities=19% Similarity=0.172 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCc---cchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDR---EAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLL 132 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~---e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL 132 (479)
+.-++.+.-.+|++.|++..+- .. --.++++++..++.-+.+.+++-+|-.-+.||+...+.|..+..++..+
T Consensus 45 ~t~~~~~a~~~l~s~~~~~esg-qRGYLLTG~~~yL~py~~a~~~~~~~~~~l~~l~~d~p~~~~~l~~l~~~i~~~ 120 (207)
T COG5278 45 ETQQVLAAALDLLSAVSDAESG-QRGYLLTGNDEYLEPYEEATEELDQKLEELRALTADDPELLESLDDLEPLIQWK 120 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc-CcceeecCCHhhhhHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 3456677778888999988752 22 2247899999999999999999999999989877777777777655544
No 20
>KOG1656 consensus Protein involved in glucose derepression and pre-vacuolar endosome protein sorting [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.96 E-value=2.9e+02 Score=27.98 Aligned_cols=64 Identities=19% Similarity=0.279 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhC------CC-CccchhhHHHHHHHHHHHHHHHHHHHHhhh-c-----CChH-HHHHHHHh
Q 011697 59 SSLDSMRDVMELLSDMLQAVN------PS-DREAVKDEVIVDLVSRCRSNQKKLMQMLTT-T-----GDEE-LLGRGLEL 124 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~------Pg-~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~-t-----~DEE-lL~ELL~l 124 (479)
.-|+.|.-|.+||.-|=.... -+ +- +.-+++|.|+.++..-++ -|.+.|+. + -||| ++.||=+|
T Consensus 92 ~alEnA~~n~Evl~~m~~~A~AmK~~h~~mDi-DkVdd~MdeI~eQqe~a~-eIseAiS~Pvg~~a~~DEDEL~~ELdeL 169 (221)
T KOG1656|consen 92 EALENANTNTEVLDAMGSAAKAMKAAHKNMDI-DKVDDLMDEIAEQQEVAE-EISEAISAPVGFGADFDEDELMAELDEL 169 (221)
T ss_pred HHHHcccccHHHHHHHHHHHHHHHHHHhccCh-hHHHHHHHHHHHHHHHHH-HHHHHHhCccccccccCHHHHHHHHHHH
Confidence 457777777777776644221 01 11 122488888888866554 35555542 2 2444 77777444
No 21
>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.
Probab=48.92 E-value=1.1e+02 Score=27.66 Aligned_cols=80 Identities=16% Similarity=0.168 Sum_probs=41.5
Q ss_pred hhhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHH-------HHHHHHhhhcCChHHHHHHHHhhh
Q 011697 54 ETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQ-------KKLMQMLTTTGDEELLGRGLELND 126 (479)
Q Consensus 54 ekLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ-------~RI~~LIs~t~DEElL~ELL~lND 126 (479)
..+|.+||...-++=+.|.+++..+..-.. =.+.+.+|...++.+- ++|-++-..+. +.+.++=.+..
T Consensus 2 ~~lS~~eL~~Ll~d~~~l~~~v~~l~~~~~---~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~--~~~~~~~~L~~ 76 (150)
T PF07200_consen 2 QDLSTEELQELLSDEEKLDAFVKSLPQVQE---LQQEREELLAENEELAEQNLSLEPELEELRSQLQ--ELYEELKELES 76 (150)
T ss_dssp GS-TTHHHHHHHHH-HHHHHHGGGGS--HH---HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH--HHHHHHHHHHH
T ss_pred CcCCHHHHHHHHcCHHHHHHHHHcCHHHHH---HHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHH--HHHHHHHHHHH
Confidence 457788999999999999999998854211 1123333333443333 33333333332 34444444455
Q ss_pred HHHHHHHHHHHH
Q 011697 127 ILQNLLAKHDAI 138 (479)
Q Consensus 127 dLNnVL~RYdr~ 138 (479)
.......+|+.+
T Consensus 77 ~~~~k~~~~~~l 88 (150)
T PF07200_consen 77 EYQEKEQQQDEL 88 (150)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 555555555554
No 22
>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=47.66 E-value=27 Score=29.67 Aligned_cols=27 Identities=4% Similarity=0.156 Sum_probs=22.5
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHh
Q 011697 83 REAVKDEVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 83 ~e~~d~ELlqEL~eqCRsmQ~RI~~LI 109 (479)
-+..|.+.|++|+++.++|+.||.-|=
T Consensus 36 Ls~~d~~~L~~L~~~a~rm~eRI~tLE 62 (75)
T PF06667_consen 36 LSEEDEQRLQELYEQAERMEERIETLE 62 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999997653
No 23
>PF01895 PhoU: PhoU domain; InterPro: IPR008170 This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle []. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect; suggesting that the protein has some secondary function []. ; PDB: 2I0M_A 1T72_B 1T8B_A 1SUM_B 1VCT_A 2BKN_A 2BKP_A 2BKO_A.
Probab=47.65 E-value=1.1e+02 Score=23.80 Aligned_cols=17 Identities=29% Similarity=0.327 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHhhCC
Q 011697 64 MRDVMELLSDMLQAVNP 80 (479)
Q Consensus 64 VrnNVkVLsEML~e~~P 80 (479)
.+...++|.+++..+.-
T Consensus 5 ~~~~~~~l~~~~~~~~~ 21 (88)
T PF01895_consen 5 GELVEEMLDDAIEAFEE 21 (88)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 34455666666666643
No 24
>PF01544 CorA: CorA-like Mg2+ transporter protein; InterPro: IPR002523 The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli [, ]. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. Transporter ZntB mediates efflux of zinc ions [].; GO: 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 2HN1_A 3NWI_D 3NVO_B 3CK6_A 2IUB_E 2BBJ_E 2HN2_A 2BBH_A.
Probab=47.64 E-value=1.3e+02 Score=28.94 Aligned_cols=78 Identities=14% Similarity=0.161 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhh-C---CCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH-HHHHHHHhhhHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAV-N---PSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE-LLGRGLELNDILQNLL 132 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~-~---Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE-lL~ELL~lNDdLNnVL 132 (479)
+.+|...+..+.-+.++|..+ . .........+.+.+|.+.|+.+..++..+.+.+.+-. ...- .++.++|+++
T Consensus 157 ~~~l~~l~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~n~~m 234 (292)
T PF01544_consen 157 RRELSRLRRSLSPLREVLQRLLRRDDSPFISDEDKEYLRDLLDRIERLLERAESLRERLESLQDLYQS--KLSNRQNRVM 234 (292)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCCCSTTSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHTCHHHHHH
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Confidence 455666666666666666322 2 1122223345688898888888888887777665543 2222 3455577776
Q ss_pred HHHHH
Q 011697 133 AKHDA 137 (479)
Q Consensus 133 ~RYdr 137 (479)
.+.-.
T Consensus 235 ~~LT~ 239 (292)
T PF01544_consen 235 KVLTI 239 (292)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 66543
No 25
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.58 E-value=4.8e+02 Score=31.97 Aligned_cols=11 Identities=36% Similarity=0.594 Sum_probs=7.7
Q ss_pred HHHHHHHHHHH
Q 011697 92 VDLVSRCRSNQ 102 (479)
Q Consensus 92 qEL~eqCRsmQ 102 (479)
++++++|..++
T Consensus 559 ~~~ve~~~~k~ 569 (1049)
T KOG0307|consen 559 DDYVETCEVKQ 569 (1049)
T ss_pred HHHHhhcchhh
Confidence 46777777776
No 26
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=44.73 E-value=2e+02 Score=24.65 Aligned_cols=47 Identities=6% Similarity=0.114 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhh
Q 011697 64 MRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLT 110 (479)
Q Consensus 64 VrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs 110 (479)
++...+-+.+.|..+........+.+++.++.+..+.+.....+++.
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~ 130 (181)
T PF12729_consen 84 IDEARAEIDEALEEYEKLILSPEEKQLLEEFKEAWKAYRKLRDQVIE 130 (181)
T ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444433222333455666555555555443333333
No 27
>PRK11546 zraP zinc resistance protein; Provisional
Probab=41.66 E-value=1.4e+02 Score=28.34 Aligned_cols=63 Identities=8% Similarity=0.044 Sum_probs=41.0
Q ss_pred CCCChhHHHhhhhhcH---HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHH
Q 011697 43 RRLDETMATEVETLSF---SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQ 107 (479)
Q Consensus 43 ~~l~peq~sklekLS~---sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~ 107 (479)
..|++||..+++++=. .+....|..+-.-..=|+++- .....|.+-|..|......+|.+|.+
T Consensus 42 ~~LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl--~~~~pD~~kI~aL~kEI~~Lr~kL~e 107 (143)
T PRK11546 42 APLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALL--TANPPDSSKINAVAKEMENLRQSLDE 107 (143)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999988732 456666666666555566552 22234566677777777777766654
No 28
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=41.02 E-value=24 Score=33.69 Aligned_cols=10 Identities=30% Similarity=0.491 Sum_probs=8.4
Q ss_pred CCCCCCCCCC
Q 011697 358 AYPPPPWAPT 367 (479)
Q Consensus 358 ~yP~PpWa~~ 367 (479)
.||+|.|+++
T Consensus 144 ~~~~~~~~~~ 153 (168)
T PRK06863 144 SRPAPQQAAP 153 (168)
T ss_pred cccCcccccc
Confidence 5889999877
No 29
>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=40.98 E-value=34 Score=28.98 Aligned_cols=27 Identities=4% Similarity=0.175 Sum_probs=22.7
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHhh
Q 011697 84 EAVKDEVIVDLVSRCRSNQKKLMQMLT 110 (479)
Q Consensus 84 e~~d~ELlqEL~eqCRsmQ~RI~~LIs 110 (479)
...|.+.+++|+++.++|+.||.-|=.
T Consensus 37 s~~d~~~L~~L~~~a~rm~eRI~tLE~ 63 (75)
T TIGR02976 37 STDDQALLQELYAKADRLEERIDTLER 63 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999976543
No 30
>PF04961 FTCD_C: Formiminotransferase-cyclodeaminase; InterPro: IPR007044 Enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate [],as shown in reaction (2) (1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3) (2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase-cyclodeaminase []. The eukaryotic enzyme is a circular tetramer of homodimers [], while the prokaryotic enzyme is a dimer [, ]. The crystal structure of the cyclodeaminase enzyme (Q9X1P6 from SWISSPROT) from Thermaotogoa maritima has been studied []. It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.; GO: 0003824 catalytic activity, 0044237 cellular metabolic process; PDB: 2PFD_C 1O5H_B.
Probab=40.85 E-value=99 Score=29.65 Aligned_cols=41 Identities=10% Similarity=0.302 Sum_probs=31.9
Q ss_pred HHHHHHhhCCCCcc-chhhHHHHHHHHHHHHHHHHHHHHhhh
Q 011697 71 LSDMLQAVNPSDRE-AVKDEVIVDLVSRCRSNQKKLMQMLTT 111 (479)
Q Consensus 71 LsEML~e~~Pg~~e-~~d~ELlqEL~eqCRsmQ~RI~~LIs~ 111 (479)
|..|.-.+.-+.+. ..-.+.++++.++|++.+.++.+|+.+
T Consensus 33 L~~Mv~~lT~gkk~~~~~~~~~~~~~~~~~~~~~~ll~l~d~ 74 (184)
T PF04961_consen 33 LGSMVANLTLGKKKYEDVEEELKEIIEKLEELREELLDLADE 74 (184)
T ss_dssp HHHHHHHCTTTSTTSGGGHHHHHHHHHHHHHHHHHHHCHHHH
T ss_pred HHHHHHHHhCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66788888766543 334578999999999999999988863
No 31
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=40.29 E-value=1.6e+02 Score=28.29 Aligned_cols=82 Identities=13% Similarity=0.216 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccc--hhhHHHHHHHHHHHHHHHHHHHHhhhcC-ChHHHHHHHHhhhHHHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREA--VKDEVIVDLVSRCRSNQKKLMQMLTTTG-DEELLGRGLELNDILQNLLAKH 135 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~--~d~ELlqEL~eqCRsmQ~RI~~LIs~t~-DEElL~ELL~lNDdLNnVL~RY 135 (479)
+-.+.+...+.+|.+|+..+.-++-+. ....-|.+|-..|...+.+|...+.++. -.-.=..++.+.+.|.+|+..=
T Consensus 18 ~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~I~~lE~eaD~i~~~i~~~L~~~fitP~dReDi~~L~~~lD~I~D~i 97 (216)
T TIGR00153 18 QHIEKVGECVQLLIKSFELLKSGNNEKDEELRKEIIEIEHEADEIKREIRLNLEKGAFLPNDRRDLLELAELLDEILDSL 97 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccCcCcHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999985333221 2345567888899999999999887642 1112223456666666666666
Q ss_pred HHHhh
Q 011697 136 DAIAS 140 (479)
Q Consensus 136 dr~~k 140 (479)
+....
T Consensus 98 ~~~a~ 102 (216)
T TIGR00153 98 EHAAM 102 (216)
T ss_pred HHHHH
Confidence 66543
No 32
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=39.58 E-value=3.4e+02 Score=27.17 Aligned_cols=48 Identities=13% Similarity=0.263 Sum_probs=35.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhhcC---ChH-HHHHHHHhhhHHHHHHH
Q 011697 86 VKDEVIVDLVSRCRSNQKKLMQMLTTTG---DEE-LLGRGLELNDILQNLLA 133 (479)
Q Consensus 86 ~d~ELlqEL~eqCRsmQ~RI~~LIs~t~---DEE-lL~ELL~lNDdLNnVL~ 133 (479)
...+-|.+|++.|++...+|=+|+..+= |.+ +-..+-.++.-|.+++.
T Consensus 222 ~~v~~Ld~L~~~~~~i~~~VDel~~slYpP~d~~~v~~~~~~L~~~l~~~l~ 273 (275)
T PF13324_consen 222 EQVAQLDKLLDLCQEISPSVDELASSLYPPQDPDEVRAAAAKLSSVLKKMLK 273 (275)
T ss_dssp T-HHHHHHHHHHHHHHHHHHHHHHHHHSSS--HHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHhhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4457789999999999999999999873 444 55566677777776654
No 33
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=38.40 E-value=1.6e+02 Score=22.25 Aligned_cols=49 Identities=14% Similarity=0.144 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchh-hHHHHHHHHHHHHHHHHHHHHh
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVK-DEVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d-~ELlqEL~eqCRsmQ~RI~~LI 109 (479)
.||..--+.+..+.++|... ......+ .+++..+...|+.|..-|-+|+
T Consensus 11 Helr~PL~~i~~~~~~l~~~--~~~~~~~~~~~l~~i~~~~~~l~~li~~ll 60 (68)
T PF00512_consen 11 HELRNPLTAIRGYLELLERD--SDLDPEQLREYLDRIRSAADRLNELINDLL 60 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHCS--SCC-HHHCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHc--cCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444442 1222222 4555555555555555544443
No 34
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=38.08 E-value=2.7e+02 Score=25.93 Aligned_cols=21 Identities=14% Similarity=0.192 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 011697 89 EVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 89 ELlqEL~eqCRsmQ~RI~~LI 109 (479)
+-++.|-+.|+.+..++.+|.
T Consensus 130 ~~l~~l~~~~~~~~~e~~~l~ 150 (191)
T PF04156_consen 130 ERLDSLDESIKELEKEIRELQ 150 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444445555555555544
No 35
>TIGR03582 EF_0829 PRD domain protein EF_0829/AHA_3910. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. This protein contains a PRD domain (see pfam00874). The function is unknown.
Probab=37.61 E-value=81 Score=28.41 Aligned_cols=48 Identities=10% Similarity=0.184 Sum_probs=37.7
Q ss_pred HHHHHHHHhhCCCCcc-chhhHHHHHHHHHHHHHHHHHHHHhhhcCChH
Q 011697 69 ELLSDMLQAVNPSDRE-AVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE 116 (479)
Q Consensus 69 kVLsEML~e~~Pg~~e-~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE 116 (479)
.=|..||.-..-|+.- ..|.+|+.|+.....++-+.|+..+....++|
T Consensus 45 THlaaml~Rs~~GE~lp~vD~~Lf~EIs~~sl~la~~v~~~f~~L~~~E 93 (107)
T TIGR03582 45 SHLNAMVYRSTTGETLPEVDRSLFDEISKESIKLAEEVVAALGNLAEDE 93 (107)
T ss_pred HHHHHHHHHHHcCCcCCccCHHHHHHHHHHHHHHHHHHHHHhcCCChhh
Confidence 3466677777666553 47899999999988888899999988887777
No 36
>TIGR00383 corA magnesium Mg(2+) and cobalt Co(2+) transport protein (corA). The article in Microb Comp Genomics 1998;3(3):151-69 (Medline:98448512) discusses this family and suggests that some members may have functions other than Mg2+ transport.
Probab=37.52 E-value=3.1e+02 Score=27.44 Aligned_cols=77 Identities=13% Similarity=0.075 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCc-c---chhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHH-HHHhhhHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPSDR-E---AVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGR-GLELNDILQNLL 132 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg~~-e---~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~E-LL~lNDdLNnVL 132 (479)
+.+|-..|..+.-+.++|..+..... . ....+.+.++++..+++...+..+-+.+.. ++.. +=.+|.++|+++
T Consensus 181 ~~~l~~l~~~l~~~~~vl~~l~~~~~~~~~~~~~~~~~~dv~~~~~~l~~~~~~~~e~l~~--l~d~~~~~~s~~~N~~m 258 (318)
T TIGR00383 181 RTELLALRRSLWPLRDVLNFLLRKTHLPIQTEEVREYLRDIYDHILSLLEMIETYRELLSS--LMDLYLSLVNNKMNEIM 258 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHH
Confidence 45677777777777777777643221 1 223345556555554444443333222211 1110 112455666666
Q ss_pred HHHH
Q 011697 133 AKHD 136 (479)
Q Consensus 133 ~RYd 136 (479)
.+.-
T Consensus 259 k~LT 262 (318)
T TIGR00383 259 KILT 262 (318)
T ss_pred HHHH
Confidence 5543
No 37
>PF00015 MCPsignal: Methyl-accepting chemotaxis protein (MCP) signalling domain; InterPro: IPR004089 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the signalling domain found in several methyl-accepting chemotaxis proteins. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016020 membrane; PDB: 2CH7_A 3ZX6_B 1QU7_A 3G6B_B 3UR1_C 3G67_B.
Probab=37.43 E-value=85 Score=28.70 Aligned_cols=19 Identities=21% Similarity=0.135 Sum_probs=10.1
Q ss_pred HHHHHHHhhhHHHHHHHHH
Q 011697 117 LLGRGLELNDILQNLLAKH 135 (479)
Q Consensus 117 lL~ELL~lNDdLNnVL~RY 135 (479)
.+.++..+-++|+..+.||
T Consensus 192 ~~~~l~~~a~~L~~~v~~F 210 (213)
T PF00015_consen 192 AAEELSESAEELQELVDRF 210 (213)
T ss_dssp HHHHHHHHHCCCCHHCHHH
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 4445555555555555555
No 38
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=37.21 E-value=65 Score=23.72 Aligned_cols=34 Identities=29% Similarity=0.334 Sum_probs=22.4
Q ss_pred HHHHHhhhcC-ChHHHHHHHHhhh-HHHHHHHHHHH
Q 011697 104 KLMQMLTTTG-DEELLGRGLELND-ILQNLLAKHDA 137 (479)
Q Consensus 104 RI~~LIs~t~-DEElL~ELL~lND-dLNnVL~RYdr 137 (479)
+|.++++-++ +++.-.++|+.|+ +|+.++..|=.
T Consensus 3 ~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~ 38 (43)
T PF14555_consen 3 KIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFD 38 (43)
T ss_dssp HHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4444444332 5567778888888 99999998843
No 39
>PF05508 Ran-binding: RanGTP-binding protein; InterPro: IPR008812 The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The Saccharomyces cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with S. cerevisiae RanBP1 (Yrb1p) for binding to the GTP-bound form of S. cerevisiae Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins [].
Probab=36.97 E-value=90 Score=32.82 Aligned_cols=52 Identities=17% Similarity=0.154 Sum_probs=43.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhc----CChHHHHHHHHhhhHHHHHHHHHHHH
Q 011697 87 KDEVIVDLVSRCRSNQKKLMQMLTTT----GDEELLGRGLELNDILQNLLAKHDAI 138 (479)
Q Consensus 87 d~ELlqEL~eqCRsmQ~RI~~LIs~t----~DEElL~ELL~lNDdLNnVL~RYdr~ 138 (479)
-.+|+++|.......-.||-++.... ..+..-.++..+..++..+|.|-|+.
T Consensus 82 al~L~~~L~~eI~~f~~~l~~~~~~~e~~~~~~~~~~~i~~V~~~ik~LL~rId~a 137 (302)
T PF05508_consen 82 ALPLTKDLRREIDSFDERLEEAAEKEELSKSSENQKESIKKVERYIKDLLARIDDA 137 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhccCcchhHHHHHHHHHHHHHHHHHHHhh
Confidence 46899999999999999999998833 34446667889999999999999876
No 40
>PRK09269 chorismate mutase; Provisional
Probab=36.75 E-value=2.7e+02 Score=27.31 Aligned_cols=60 Identities=18% Similarity=0.135 Sum_probs=46.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhc-C-------Ch-HHHHHHHHhhhHHHHHHHHHHHHhhCCCCCCc
Q 011697 88 DEVIVDLVSRCRSNQKKLMQMLTTT-G-------DE-ELLGRGLELNDILQNLLAKHDAIASGLPIPTE 147 (479)
Q Consensus 88 ~ELlqEL~eqCRsmQ~RI~~LIs~t-~-------DE-ElL~ELL~lNDdLNnVL~RYdr~~kG~~~~~e 147 (479)
.+++.++.+.||..|.+++..-... . |= ++=-+|.+||++|-..|..+..+..+..|...
T Consensus 90 ~~iF~~~I~aSk~iQ~~~~a~W~~~~~~~~~~~~dL~~~Rp~l~~L~~~il~~l~~~~~~r~~~~C~~~ 158 (193)
T PRK09269 90 RRFFRDQIEANKLVQYALLARWRLAGAAPPGPRPDLASIRPRLDRLQQELLDALADVAPLRSAPDCPAR 158 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcHHH
Confidence 4788899999999999998843322 1 11 23348999999999999999999888777644
No 41
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=36.19 E-value=2.1e+02 Score=27.22 Aligned_cols=73 Identities=11% Similarity=0.149 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCCh-HHHHHHHHh-hhHHHHHHHHHHH
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDE-ELLGRGLEL-NDILQNLLAKHDA 137 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DE-ElL~ELL~l-NDdLNnVL~RYdr 137 (479)
.|+.++..++-|.+.+... .+.++.+.+.+-|+-.+ +|++.|.+-... ..+.+.|.. =|.+.+++++|..
T Consensus 76 ~l~ea~~~i~~i~~~~~~i-------~~~~~~~~~~~~~~~~~-~I~~~v~~~P~~l~~a~~Fl~~yLp~~~~l~~kY~~ 147 (199)
T PF10112_consen 76 ILEEAKEKIRRIEKAIKRI-------RDLEMIEKVSRIEKIAR-RIFKYVEKDPERLTQARKFLYYYLPTAVKLLEKYAE 147 (199)
T ss_pred HHHHHHHHHHHHHHHHHHc-------CCHHHHHHHHHHHHHHH-HHHHHHHHCHHhHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 3444555555555444444 23345555444444433 334444332111 122222222 1678889999999
Q ss_pred Hhh
Q 011697 138 IAS 140 (479)
Q Consensus 138 ~~k 140 (479)
+.+
T Consensus 148 l~~ 150 (199)
T PF10112_consen 148 LES 150 (199)
T ss_pred HHh
Confidence 876
No 42
>cd05132 RasGAP_GAPA GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests that there are both similarities and differences in their function.
Probab=36.07 E-value=80 Score=32.73 Aligned_cols=65 Identities=20% Similarity=0.194 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcC---ChHHHHHHHHhhhH
Q 011697 63 SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG---DEELLGRGLELNDI 127 (479)
Q Consensus 63 vVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~---DEElL~ELL~lNDd 127 (479)
.+|.|+.+++-||.++--+.....+...|+-|..-+++...|+.+++.++. |-|.-.++-.-||-
T Consensus 203 ~~rrnL~lIaKvLQ~lan~~~f~~ke~~m~pLn~fi~~~~~~~~~fl~~l~~v~~~e~~~~~d~y~dl 270 (331)
T cd05132 203 TARKNLTLIAKMLQNLANKPSFGDKEKWMVPLNPWIDENKEKVNNFLEELTEVGDPEEYLQVDKYMAL 270 (331)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHhcCHhHHHHH
Confidence 578899999999999966555555667788888777777777777776554 43333333333443
No 43
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=35.83 E-value=2.5e+02 Score=26.17 Aligned_cols=14 Identities=36% Similarity=0.328 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHH
Q 011697 89 EVIVDLVSRCRSNQ 102 (479)
Q Consensus 89 ELlqEL~eqCRsmQ 102 (479)
+.++++.+.|+.++
T Consensus 137 ~~~~~~~~e~~~l~ 150 (191)
T PF04156_consen 137 ESIKELEKEIRELQ 150 (191)
T ss_pred HHHHHHHHHHHHHH
Confidence 44444444444444
No 44
>PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional
Probab=35.55 E-value=3.2e+02 Score=32.29 Aligned_cols=88 Identities=13% Similarity=0.260 Sum_probs=47.3
Q ss_pred ChhHHHhhhhhcHHHHH----------HHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHH------HHHHHHHHh
Q 011697 46 DETMATEVETLSFSSLD----------SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRS------NQKKLMQML 109 (479)
Q Consensus 46 ~peq~sklekLS~sELe----------vVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRs------mQ~RI~~LI 109 (479)
++....|+++| +.||+ .++..+++|+++..+-.-.+....-.+|=+||.+...+ ++.++--+.
T Consensus 506 ~~~L~eK~~kL-k~Efnkkl~ea~n~p~lk~Kle~Lk~~~~~~~~s~g~~~a~~Lk~ei~kki~e~~~~~~~kek~ea~~ 584 (762)
T PLN03229 506 HPVLMEKIEKL-KDEFNKRLSRAPNYLSLKYKLDMLNEFSRAKALSEKKSKAEKLKAEINKKFKEVMDRPEIKEKMEALK 584 (762)
T ss_pred cHHHHHHHHHH-HHHHHHhhhcccccHHHHHHHHHHHHHHHhhhhcccchhhhhhhHHHHHHHHHhcccHHHHHHHHHHH
Confidence 34445556666 54543 57777877777765211111100122333444444444 444433222
Q ss_pred h----------hcCChHHHHHHHHhhhHHHHHHHH
Q 011697 110 T----------TTGDEELLGRGLELNDILQNLLAK 134 (479)
Q Consensus 110 s----------~t~DEElL~ELL~lNDdLNnVL~R 134 (479)
. ..-|+++-.++..+|.+++.-|+.
T Consensus 585 aev~~~g~s~~~~~~~~lkeki~~~~~Ei~~eie~ 619 (762)
T PLN03229 585 AEVASSGASSGDELDDDLKEKVEKMKKEIELELAG 619 (762)
T ss_pred HHHHhcCccccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 2 134667899999999988866654
No 45
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=35.39 E-value=1.5e+02 Score=30.02 Aligned_cols=76 Identities=16% Similarity=0.169 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHH-------HHHHHHHHhh-------hcCChHHHHHHHHhhhH-H
Q 011697 64 MRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRS-------NQKKLMQMLT-------TTGDEELLGRGLELNDI-L 128 (479)
Q Consensus 64 VrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRs-------mQ~RI~~LIs-------~t~DEElL~ELL~lNDd-L 128 (479)
.|-.+++|++.|... +...-..-.+||..|.+.|+. -+.+.+.+|. +.-..|+..-++..+++ +
T Consensus 39 ~R~~~~~ls~a~~~~-~~~~~i~p~~vl~~L~~~l~~~~~i~~e~~~~y~~~l~~v~~~Y~~~v~~EV~~A~~~~~ee~~ 117 (254)
T PF06798_consen 39 PRFVIKILSNALSSD-SEEDCINPLDVLNELEEGLKDHPSISEEERERYLEFLKSVRKEYDERVEKEVQEAFYYSYEEQI 117 (254)
T ss_pred HhHHHHHHHHHHHhC-cccceecHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHH
Confidence 455677777777773 233334556777777777776 2334333433 33345666666656776 9
Q ss_pred HHHHHHHHHHhh
Q 011697 129 QNLLAKHDAIAS 140 (479)
Q Consensus 129 NnVL~RYdr~~k 140 (479)
++.|.+|=..+.
T Consensus 118 ~~l~~nYl~~v~ 129 (254)
T PF06798_consen 118 QNLFENYLDHVE 129 (254)
T ss_pred HHHHHHHHHHHH
Confidence 999999977643
No 46
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=35.16 E-value=82 Score=30.60 Aligned_cols=63 Identities=14% Similarity=0.145 Sum_probs=37.8
Q ss_pred HHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHH------Hhh-------hcCChHHHHHHHHhhhHHHHH
Q 011697 69 ELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQ------MLT-------TTGDEELLGRGLELNDILQNL 131 (479)
Q Consensus 69 kVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~------LIs-------~t~DEElL~ELL~lNDdLNnV 131 (479)
+=|..|+..+.-......-.|-..+|.+.|+.+..+|-| |-. .+.|.++|.|+|+++++|...
T Consensus 36 kkL~~d~~~~~~~~~~d~a~eqSa~lnkAY~TLk~pL~RA~Yilkl~g~e~~sne~stDpe~Lmevle~~E~IS~~ 111 (168)
T KOG3192|consen 36 KKLHPDRPGLSFAGDTDQASEQSAELNKAYDTLKDPLARARYLLKLKGQEQTSNELSTDPEFLMEVLEYHEAISEM 111 (168)
T ss_pred HhhCcccccccccccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCCchhhhccCHHHHHHHHHHHHHHHhc
Confidence 445666655532111112335567888888888766543 333 223667888998888887653
No 47
>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]
Probab=34.81 E-value=4.3e+02 Score=30.98 Aligned_cols=28 Identities=29% Similarity=0.242 Sum_probs=22.2
Q ss_pred HHHHHHHhh-------hHHHHHHHHHHHHhhCCCC
Q 011697 117 LLGRGLELN-------DILQNLLAKHDAIASGLPI 144 (479)
Q Consensus 117 lL~ELL~lN-------DdLNnVL~RYdr~~kG~~~ 144 (479)
.|+.++..| .+|.+.+++|+..+.-..+
T Consensus 282 a~eslm~ane~kdr~ie~lr~~ln~y~k~~~iv~i 316 (861)
T KOG1899|consen 282 ALESLMRANEQKDRFIESLRNYLNNYDKNAQIVRI 316 (861)
T ss_pred HHHHHHhhchhhhhHHHHHHHHhhhhhhhhhhhhh
Confidence 677899999 6799999999988654443
No 48
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=34.74 E-value=1.6e+02 Score=27.34 Aligned_cols=53 Identities=23% Similarity=0.303 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHHHhhCCC
Q 011697 91 IVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLP 143 (479)
Q Consensus 91 lqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr~~kG~~ 143 (479)
+.+|-..|+.++..|-.|....+++|+..++=++-.++..+-.|-+.+.++..
T Consensus 88 l~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~ 140 (169)
T PF07106_consen 88 LAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSK 140 (169)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 45667778888888888899999999999999999999999999999886443
No 49
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=34.70 E-value=1.5e+02 Score=32.67 Aligned_cols=10 Identities=30% Similarity=0.590 Sum_probs=5.7
Q ss_pred CCCCCCCccc
Q 011697 317 QGQVPYNNYV 326 (479)
Q Consensus 317 ~~~~~~n~yv 326 (479)
.++.+-|.|-
T Consensus 399 ~~q~~~q~ys 408 (462)
T KOG2199|consen 399 RAQYPSQSYS 408 (462)
T ss_pred ccccCcccCC
Confidence 4455556665
No 50
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=33.92 E-value=91 Score=30.80 Aligned_cols=46 Identities=15% Similarity=0.165 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhh
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTT 111 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~ 111 (479)
.++.-|..-+++|+.||+-- .=.|-|++|-.-|+.|+.||..|-.-
T Consensus 100 ~t~s~veaEik~L~s~Lt~e-------emQe~i~~L~kev~~~~erl~~~k~g 145 (201)
T KOG4603|consen 100 QTCSYVEAEIKELSSALTTE-------EMQEEIQELKKEVAGYRERLKNIKAG 145 (201)
T ss_pred HHHHHHHHHHHHHHHhcChH-------HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56778888888898888743 12466889999999999999987663
No 51
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=33.76 E-value=1.2e+02 Score=30.62 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=32.9
Q ss_pred HHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHHHhhCCCC
Q 011697 101 NQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLPI 144 (479)
Q Consensus 101 mQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr~~kG~~~ 144 (479)
+|..-.+++.+.-||.+-+++|.+-|.|...++.+..+.+|..-
T Consensus 112 ~q~~Y~~~l~E~KDdt~EG~Iv~~ADkidal~e~~~Ei~~GN~E 155 (215)
T PF12917_consen 112 FQEAYRRRLKEGKDDTLEGQIVKAADKIDALYECFGEIQKGNPE 155 (215)
T ss_dssp GHHHHHHHHS---SSSHHHHHHHHHHHHHHHHHHHHHHHTT-S-
T ss_pred HHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 45555556666666679999999999999999999999999876
No 52
>PTZ00446 vacuolar sorting protein SNF7-like; Provisional
Probab=33.62 E-value=2.8e+02 Score=27.35 Aligned_cols=66 Identities=15% Similarity=0.108 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHHHH------hhCCCCccc-hhhHHHHHHHHHHHHHHHHHHHHhhhc----CCh-HHHHHHHHhh
Q 011697 58 FSSLDSMRDVMELLSDMLQ------AVNPSDREA-VKDEVIVDLVSRCRSNQKKLMQMLTTT----GDE-ELLGRGLELN 125 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~------e~~Pg~~e~-~d~ELlqEL~eqCRsmQ~RI~~LIs~t----~DE-ElL~ELL~lN 125 (479)
...|+.++.|.+|+.-|-. .+.- .-+. .=++|+.|+-++|. ++..|.++++.- .|| |+.+||=++-
T Consensus 97 ~~~iE~a~~~~ev~~aLk~g~~aLK~~~k-~~~idkVd~lmDei~E~~e-~~~EIseaLs~~~~~~~DEdELe~ELe~Le 174 (191)
T PTZ00446 97 MINLENMHLHKIAVNALSYAANTHKKLNN-EINTQKVEKIIDTIQENKD-IQEEINQALSFNLLNNVDDDEIDKELDLLK 174 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHH-HHHHHHHHHcCCCCCCCCHHHHHHHHHHHH
Confidence 3567777777777776633 2221 1111 12366677776665 456677766632 244 4777765553
No 53
>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
Probab=32.73 E-value=47 Score=37.26 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHhh
Q 011697 59 SSLDSMRDVMELLSDMLQAV 78 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~ 78 (479)
-.|...+.-|++|.|||.++
T Consensus 270 rklGr~~EAIk~~rdLlke~ 289 (539)
T PF04184_consen 270 RKLGRLREAIKMFRDLLKEF 289 (539)
T ss_pred HHhCChHHHHHHHHHHHhhC
Confidence 45667777788888888776
No 54
>cd05392 RasGAP_Neurofibromin_like Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In yeast Ras proteins are activated by GEFs, and inhibited by two GAPs, Ira1 and Ira2. Ras proteins activate the cAMP/protein kinase A (PKA) pathway, which controls metabolism, stress resistance, growth, and meiosis. Recent studies showed that the kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with Ira1 and Ira2. Gpb1/2 bind to a conserved C-terminal domain of Ira1/2, and loss of Gpb1/2 results in a destabilization of Ira1 and Ira2, leading to elevated levels of Ras2-GTP and uninhibited cAMP-PKA signaling. Since the Gpb1/2 binding domain on Ira1/2 is conserved in the human neurofibromin prote
Probab=32.70 E-value=89 Score=31.97 Aligned_cols=54 Identities=20% Similarity=0.298 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCCh
Q 011697 62 DSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDE 115 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DE 115 (479)
..+|.|+-+++-||.++--+.....++..|+-|.+-.++...||.+++.++.+.
T Consensus 201 ~~~rr~L~~iaKvLQ~lan~~~f~~ke~~m~~ln~fi~~~~~~~~~fl~~i~~~ 254 (323)
T cd05392 201 PKARRSLILLAKVLQNIANGVLFSIKEPFMESLNDFLKSNSDKIFDFLKEISSD 254 (323)
T ss_pred hhhchhHHHHHHHHHHHhCcCcCCCCchHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 456888999999999886555555577788888888888888888888776543
No 55
>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the
Probab=32.43 E-value=96 Score=32.18 Aligned_cols=45 Identities=24% Similarity=0.415 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhC-CCCccchhh-HHHHHHHHHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVN-PSDREAVKD-EVIVDLVSRCRSNQ 102 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~-Pg~~e~~d~-ELlqEL~eqCRsmQ 102 (479)
+.+++.++..-..|+.+|.+++ |+.-+..+. .|=..|.+.|..++
T Consensus 20 ~~~~~~l~~~~~~l~~~L~slnLP~sl~~l~~~~lP~sl~~~~~~i~ 66 (339)
T cd09235 20 NREIGKLREATQLLNGVLASLNLPAAIEDVSGDTVPQSLLEKSRTVI 66 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcHHHHHhcCCCCCHHHHHHHHHHH
Confidence 6789999999999999999997 443222222 35567777777774
No 56
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=32.25 E-value=1.9e+02 Score=32.84 Aligned_cols=53 Identities=23% Similarity=0.365 Sum_probs=39.0
Q ss_pred hhhHHHHHHHHHHHHHH---------HHHHHHhhhc--CChH---HHHHHHHhhhHHHHHHHHHHHH
Q 011697 86 VKDEVIVDLVSRCRSNQ---------KKLMQMLTTT--GDEE---LLGRGLELNDILQNLLAKHDAI 138 (479)
Q Consensus 86 ~d~ELlqEL~eqCRsmQ---------~RI~~LIs~t--~DEE---lL~ELL~lNDdLNnVL~RYdr~ 138 (479)
.++|++.+|....+.|- .||+++|..+ .++| +|.+--.|..+||.+-.|-+|-
T Consensus 465 ~Kee~~~qL~~e~e~~~k~~~Rs~Yt~RIlEIv~NI~KQk~eI~KIl~DTr~lQkeiN~l~gkL~Rt 531 (594)
T PF05667_consen 465 QKEELYKQLVKELEKLPKDVNRSAYTRRILEIVKNIRKQKEEIEKILSDTRELQKEINSLTGKLDRT 531 (594)
T ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 45677777777766543 7999999977 3444 7777778888888887777764
No 57
>PF12309 KBP_C: KIF-1 binding protein C terminal; InterPro: IPR022083 This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 365 and 621 amino acids in length. There is a conserved LLP sequence motif. KBP is a binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a type of kinesin interacting protein.
Probab=32.22 E-value=1.6e+02 Score=31.39 Aligned_cols=81 Identities=11% Similarity=0.107 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcC--ChH-HHHHHHHhhhHHHHHHHHHH
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG--DEE-LLGRGLELNDILQNLLAKHD 136 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~--DEE-lL~ELL~lNDdLNnVL~RYd 136 (479)
-+-+-+..+++|..+|..++|..-...-.+|.-||.+++..|-.--++...... .+. .-..+-.+|.-+.+++.-|.
T Consensus 194 ~~kmhkRR~d~Le~~~~~Ln~~~y~~~~rql~fElae~~~~i~dlk~~~~~~~~~~~~~~~~~~~~kin~l~~~ai~~y~ 273 (371)
T PF12309_consen 194 QIKMHKRRADLLEPLLKELNPQYYLNLCRQLWFELAEIYSEIMDLKLEKLDEPQNDNEPPDDHALKKINQLCSKAIKYYQ 273 (371)
T ss_pred HHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccCCCCChHHHHHHHHHHHHHHHHHH
Confidence 366778889999999999998544445566777777777776655444444211 111 22234459999999999999
Q ss_pred HHhh
Q 011697 137 AIAS 140 (479)
Q Consensus 137 r~~k 140 (479)
.|..
T Consensus 274 ~fl~ 277 (371)
T PF12309_consen 274 KFLD 277 (371)
T ss_pred HHHH
Confidence 9975
No 58
>PF06246 Isy1: Isy1-like splicing family; InterPro: IPR009360 Isy1 protein is important in the optimisation of splicing [].; PDB: 1X4T_A.
Probab=32.10 E-value=77 Score=32.37 Aligned_cols=43 Identities=12% Similarity=0.184 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHhh----hcCChH-HHHHHHHhhhHHHHHHHHHHH
Q 011697 95 VSRCRSNQKKLMQMLT----TTGDEE-LLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 95 ~eqCRsmQ~RI~~LIs----~t~DEE-lL~ELL~lNDdLNnVL~RYdr 137 (479)
+..|+..+..|++=|+ .+.|.- -=.++=.|||+||++|.....
T Consensus 42 l~~ae~WR~~ii~EIs~kv~~Iqd~~L~E~~IRdLNDeINkL~rEK~~ 89 (255)
T PF06246_consen 42 LPEAEKWRRQIIKEISRKVTRIQDPSLGEFQIRDLNDEINKLIREKRH 89 (255)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH--S-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777776444 344544 334778899999999976543
No 59
>COG1344 FlgL Flagellin and related hook-associated proteins [Cell motility and secretion]
Probab=30.30 E-value=4.2e+02 Score=27.61 Aligned_cols=67 Identities=15% Similarity=0.103 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC-hH---HHHHHHHhhhHHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD-EE---LLGRGLELNDILQNLLAK 134 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D-EE---lL~ELL~lNDdLNnVL~R 134 (479)
..|+.+..|+..--.||... +-.|.+..+..++||.+++.....+-. +| +-.|+-++-|+|.++..-
T Consensus 57 ~~L~q~~~n~~~g~s~lqta---------e~aL~~~~~~lqrirelavqaan~t~s~~dr~~iq~Ei~~l~~el~~iant 127 (360)
T COG1344 57 RGLSQAKDNAQDGISKLQTA---------EGALSEISKILQRIKELAVQAANGTLSDADRAAIQKEIEQLLDELDNIANT 127 (360)
T ss_pred HhhHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 55888888888888888776 466899999999999999999986543 33 333677777777777654
No 60
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=30.19 E-value=2.5e+02 Score=27.17 Aligned_cols=63 Identities=22% Similarity=0.251 Sum_probs=44.5
Q ss_pred HHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH----HHHHHHHhhhHHHHHHHHHHHHhhC
Q 011697 69 ELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE----LLGRGLELNDILQNLLAKHDAIASG 141 (479)
Q Consensus 69 kVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE----lL~ELL~lNDdLNnVL~RYdr~~kG 141 (479)
+.|..||....- ...+. -.+..+||.+|= -+||..++=+. +| |+.|=|++..+|.+|..+.+.
T Consensus 40 e~Ld~~L~~~~a-r~~gI-cpvr~~ly~~~F------~ELIRQVTi~C~ERGlL--L~rvrde~~~~l~~y~~l~~s 106 (189)
T PF10211_consen 40 EWLDKMLQQRQA-RETGI-CPVREELYSQCF------DELIRQVTIDCPERGLL--LLRVRDEYRMTLDAYQTLYES 106 (189)
T ss_pred HHHHHHHHHhcC-Ccccc-cHHHHHHHHHHH------HHHHHHHHhCcHHHhHH--HHHHHHHHHHHHHHHHHHHHH
Confidence 456777777642 33333 567789999994 56888765432 44 588899999999999888654
No 61
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=30.14 E-value=3.7e+02 Score=28.32 Aligned_cols=55 Identities=5% Similarity=-0.024 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHHHhhCCCCC
Q 011697 91 IVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLPIP 145 (479)
Q Consensus 91 lqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr~~kG~~~~ 145 (479)
++=+.++++.+..+|-++....-++|.|.+.+++-.+..+.+.++-.+.+..+.+
T Consensus 137 ~~Y~~~el~~l~~~LE~~~G~~it~e~L~~aI~~~N~~R~~~~~l~~l~~~~p~p 191 (380)
T TIGR02263 137 GEFYTAELNELCEGLEHLSGKKITDDAIRASIAVFNDNRKLIQALYGLRADEPWK 191 (380)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCC
Confidence 7778888888888988888888889999999999999999998877777665543
No 62
>PF10735 DUF2526: Protein of unknown function (DUF2526) ; InterPro: IPR019671 This entry represents proteins with unknown function and is a highly conserved sequence, it is restricted to Enterobacteriaceae.
Probab=29.90 E-value=2.1e+02 Score=24.65 Aligned_cols=27 Identities=11% Similarity=0.309 Sum_probs=21.7
Q ss_pred hhHHHhhhhhcHHHHHHHHHHHHHHHHHHHhhC
Q 011697 47 ETMATEVETLSFSSLDSMRDVMELLSDMLQAVN 79 (479)
Q Consensus 47 peq~sklekLS~sELevVrnNVkVLsEML~e~~ 79 (479)
++.+.++ +.-++.+.+.-|||||-++.
T Consensus 5 devi~rV------d~~iae~vI~~MNELLi~LS 31 (77)
T PF10735_consen 5 DEVIARV------DAAIAENVIAHMNELLIELS 31 (77)
T ss_pred HHHHHHH------HHHHHHhHHHHHHHHHHHHc
Confidence 3455555 77789999999999999994
No 63
>PF09361 Phasin_2: Phasin protein; InterPro: IPR018968 Phasins (or granule-associate proteins) are surface proteins found covering Polyhydroxyalkanoate (PHA) storage granules in bacteria. Polyhydroxyalkanoates are linear polyesters produced by bacterial fermentation of sugar or lipids for the purpose of storing carbon and energy, and are accumulated as intracellular granules by many bacteria under unfavorable conditions, enhancing their fitness and stress resistance []. The layer of phasins stabilises the granules and prevents coalescence of separated granules in the cytoplasm and nonspecific binding of other proteins to the hydrophobic surfaces of the granules. For example, in Ralstonia eutropha (strain ATCC 17699/H16/DSM 428/Stanier 337) (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)), the major surface protein of polyhydroxybutyrate (PHB) granules is phasin PhaP1(Reu), which occurs along with three homologues (PhaP2, PhaP3, and PhaP4) that have the capacity to bind to PHB granules but are present at minor levels [, ]. These four phasins lack a highly conserved domain but share homologous hydrophobic regions. This entry describes a group of phasins that associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB).
Probab=29.88 E-value=68 Score=26.00 Aligned_cols=65 Identities=20% Similarity=0.267 Sum_probs=41.8
Q ss_pred HhhhhhcHHHHHHHHHHHHHHHHHHHhhC----CCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCCh
Q 011697 51 TEVETLSFSSLDSMRDVMELLSDMLQAVN----PSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDE 115 (479)
Q Consensus 51 sklekLS~sELevVrnNVkVLsEML~e~~----Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DE 115 (479)
.-+++|...-++.++.+++--.+.+..+. |.+--....++++++++++-..-.+|.+++.++..|
T Consensus 24 ~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~a~~~~e~~~~Q~~~~~~~~e~~~~~~~~~~e~~~~~~~e 92 (102)
T PF09361_consen 24 EGAEALAALNLEAARQNVEEAFAQAQQLASAKDPQELVALQSEFAQEQFERLASYARELAEIASKAQEE 92 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555567777777776666665553 222222356777888888888888888888776554
No 64
>cd04519 RasGAP RasGAP: Ras-GTPase Activating Domain. RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a myriad of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGap domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator.
Probab=29.56 E-value=2.3e+02 Score=27.71 Aligned_cols=53 Identities=17% Similarity=0.219 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 011697 62 DSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD 114 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D 114 (479)
..+|.|+.++.-+|.++--+.....++..+..|.+-.+....++.+++.++.+
T Consensus 205 ~~~~r~L~~iakvlq~lan~~~~~~k~~~~~~ln~~i~~~~~~~~~fl~~i~~ 257 (318)
T cd04519 205 PKARRNLTLIAKVLQNLANGKLFSGKEPYMEPLNDFIKENKDKFKDFLDEISS 257 (318)
T ss_pred HhhhhHHHHHHHHHHHHhCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 45778888888888888655444456788888888888888888888877654
No 65
>PF05816 TelA: Toxic anion resistance protein (TelA); InterPro: IPR008863 This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance [] and plasmid fertility inhibition [].
Probab=29.07 E-value=1.9e+02 Score=30.01 Aligned_cols=51 Identities=10% Similarity=0.161 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCChH--HHHHHHHhhhHHHHHHHHHHHHhhCC
Q 011697 92 VDLVSRCRSNQKKLMQMLTTTGDEE--LLGRGLELNDILQNLLAKHDAIASGL 142 (479)
Q Consensus 92 qEL~eqCRsmQ~RI~~LIs~t~DEE--lL~ELL~lNDdLNnVL~RYdr~~kG~ 142 (479)
+.+..+-+.++..|=+++..+...+ ++...-.+........+-|..+..-.
T Consensus 87 ~~~~~ky~sv~~qId~I~~~L~~~~~~L~~d~~~L~~l~~~n~~~~~~L~~~I 139 (333)
T PF05816_consen 87 ERYFAKYQSVQSQIDKIIAELESGQDELLRDNAMLDQLYEKNWEYYQELEKYI 139 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555555555555554332 55555555555555555555555433
No 66
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=28.35 E-value=4.2e+02 Score=23.39 Aligned_cols=42 Identities=14% Similarity=0.241 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHH
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKL 105 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI 105 (479)
+++.+..=++-..++|....++. +.+-++++.++++.++.-|
T Consensus 8 ~~~~l~~Wl~~~e~~l~~~~~~~----d~~~~~~~l~~~~~~~~e~ 49 (213)
T cd00176 8 DADELEAWLSEKEELLSSTDYGD----DLESVEALLKKHEALEAEL 49 (213)
T ss_pred hHHHHHHHHHHHHHHhcCcccCC----CHHHHHHHHHHHHHHHHHH
Confidence 33334444444444444443322 3334444444444444333
No 67
>PHA02334 hypothetical protein
Probab=28.11 E-value=1.9e+02 Score=24.01 Aligned_cols=36 Identities=25% Similarity=0.266 Sum_probs=30.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHH
Q 011697 85 AVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGR 120 (479)
Q Consensus 85 ~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~E 120 (479)
+.+.||-..|++-|-..-.+.++|-.+.-|++++..
T Consensus 21 Pd~~elgeklieici~il~kaVklT~TdmDD~ll~~ 56 (64)
T PHA02334 21 PDDEELGEKLIEICLLILGKAVKLTKTDMDDELLEV 56 (64)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHhccCcchHHHHHH
Confidence 567799999999999999999999888778876653
No 68
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=27.95 E-value=1.5e+02 Score=33.05 Aligned_cols=50 Identities=16% Similarity=0.234 Sum_probs=23.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhcCChH--HHHHHHHhhhHHHHHHHHHHH
Q 011697 88 DEVIVDLVSRCRSNQKKLMQMLTTTGDEE--LLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 88 ~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE--lL~ELL~lNDdLNnVL~RYdr 137 (479)
.+..+++.++.+..-.|+.+|+....+.. .-.+.+.+++-+..++..+..
T Consensus 507 ~~~~~~~l~~i~~~~~rl~~ll~~l~~~~~~~~~~~~~l~~ll~~~~~~~~~ 558 (679)
T TIGR02916 507 PEFQDDMLETVENAVNRMKKLLAQLRSKGLEEEKLCVDLVDLLRRAIASKRA 558 (679)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCCccccHHHHHHHHHHHhhh
Confidence 34444555555555555555554443211 111234455556666665543
No 69
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=27.82 E-value=69 Score=30.53 Aligned_cols=30 Identities=20% Similarity=0.469 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCChHHHHH
Q 011697 91 IVDLVSRCRSNQKKLMQMLTTTGDEELLGR 120 (479)
Q Consensus 91 lqEL~eqCRsmQ~RI~~LIs~t~DEElL~E 120 (479)
+.||.+..++.+.+|+.||+..+|||+...
T Consensus 101 l~e~~~~l~~s~~~v~~lI~~~sdeeLf~~ 130 (166)
T PF08020_consen 101 LEELKALLKESHQKVIALIESFSDEELFEK 130 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCcchhhccc
Confidence 346677778888999999999999987643
No 70
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=27.67 E-value=2.2e+02 Score=30.41 Aligned_cols=52 Identities=10% Similarity=0.089 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCCh
Q 011697 64 MRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDE 115 (479)
Q Consensus 64 VrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DE 115 (479)
.|.|+.++.-||.++--+..-..+...|+-|..-..++..|+.+++.++.|-
T Consensus 209 ~rrnL~~iaKvLQ~lan~~~f~~~e~~m~pLN~fI~~~~~~~~~fl~~~~~V 260 (360)
T cd05133 209 QRRNLGSIAKMLQHAASNKMFLGDNAHLSIINEYLSQSYQKFRRFFQSACEV 260 (360)
T ss_pred HHhhHHHHHHHHHHHHcCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 6889999999999886555444454578888887777777887777765443
No 71
>COG5394 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.66 E-value=99 Score=30.34 Aligned_cols=47 Identities=21% Similarity=0.355 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCCcc-------chhhHHHHHHHHHHHHHHHHHHHH
Q 011697 62 DSMRDVMELLSDMLQAVNPSDRE-------AVKDEVIVDLVSRCRSNQKKLMQM 108 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e-------~~d~ELlqEL~eqCRsmQ~RI~~L 108 (479)
+-+|.|++++.-|+..+.|-... ....+-+++|..+.+.||++|-+|
T Consensus 140 eq~rrn~~mf~~aM~~f~pf~~~pa~~~~~~~~~~d~~~lk~ql~a~Q~kldkl 193 (193)
T COG5394 140 EQIRRNMEMFQQAMQMFSPFAKAPAPKEAPKPMSDDLDELKGQLRAMQPKLDKL 193 (193)
T ss_pred HHHHHhHHHHHHHHHhcCcccCCCCccccCccchhHHHHHHHHHHHhhhhhccC
Confidence 45899999999999887663222 112223999999999999998543
No 72
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=27.44 E-value=2.6e+02 Score=22.95 Aligned_cols=39 Identities=13% Similarity=0.286 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHH
Q 011697 63 SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSN 101 (479)
Q Consensus 63 vVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsm 101 (479)
.|+||+-++..||.--.....+..-.+.+.++..+.+.|
T Consensus 5 RVkNnLq~i~sll~lq~~~~~~~e~~~~L~~~~~RI~ai 43 (76)
T PF07568_consen 5 RVKNNLQIISSLLRLQARRSEDPEAREALEDAQNRIQAI 43 (76)
T ss_pred hHHhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 589999999999986643222222234455555444444
No 73
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.21 E-value=2.7e+02 Score=31.41 Aligned_cols=50 Identities=8% Similarity=0.155 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhh
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLT 110 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs 110 (479)
.++.-.|-.|+-+.|=|.+++ ...++---=|.++-++..++..||+|++-
T Consensus 348 q~~~~~r~ri~~i~e~v~eLq--k~~ad~~~KI~~~k~r~~~Ls~RiLRv~i 397 (508)
T KOG3091|consen 348 QEVKQHRIRINAIGERVTELQ--KHHADAVAKIEEAKNRHVELSHRILRVMI 397 (508)
T ss_pred HHHHHHHHHHHHHHHHHHHHH--hhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666777777777777775 33333334467888888889999999765
No 74
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.02 E-value=3.1e+02 Score=26.65 Aligned_cols=57 Identities=16% Similarity=0.161 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHH
Q 011697 62 DSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRG 121 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~EL 121 (479)
..|-.|+.+-+-.|+.+.- ++... ...|...++-....|..|++|++++.+ |+.++-
T Consensus 24 ~~V~E~lRlar~~l~~Y~~-DPh~s-~~~L~~~~~~Ln~~Q~~L~~lcet~~~-~l~e~~ 80 (170)
T COG4010 24 TSVTEDLRLARTSLNFYKS-DPHNS-MKELKRINDMLNSIQEELLELCETVSS-DLPEQW 80 (170)
T ss_pred HHHHHHHHHHHHHHHHhcc-CCcch-HHHHHHHHHHHHHHHHHHHHHHhcCch-hhhHHH
Confidence 4577888999999999853 33222 566777788888899999999999887 455443
No 75
>COG2822 Predicted periplasmic lipoprotein involved in iron transport [Inorganic ion transport and metabolism]
Probab=26.78 E-value=2e+02 Score=30.83 Aligned_cols=76 Identities=14% Similarity=0.161 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhc--CChHHHHHHHHhhhHHHHHHHHHHH
Q 011697 62 DSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT--GDEELLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t--~DEElL~ELL~lNDdLNnVL~RYdr 137 (479)
.+|.|.++||+|+-..---|+++.=-.--|.+|....+-.|.-+.-+..-+ .|.+++.++=.-=+.++.+|.+|..
T Consensus 260 ~vv~GA~eLi~Eva~SKItGEEerYShtDL~Df~ANVeGsqki~dl~rp~Lek~dk~L~~kid~nF~kv~~~LakYkt 337 (376)
T COG2822 260 KVVGGAAELIEEVATSKISGEEDRYSHTDLWDFQANVEGSQKIVDLFRPALEKKDKDLLDKIDANFKKVNTILAKYRT 337 (376)
T ss_pred hhhhhHHHHHHHHHhccCCcchhhcccccHHHHhccchhHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHhcc
Confidence 478999999999988776666653322234566666666665444444433 4556777766666788888888864
No 76
>PF02252 PA28_beta: Proteasome activator pa28 beta subunit; InterPro: IPR003186 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the beta subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_N.
Probab=26.68 E-value=2.6e+02 Score=26.38 Aligned_cols=26 Identities=15% Similarity=0.373 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCh
Q 011697 90 VIVDLVSRCRSNQKKLMQMLTTTGDE 115 (479)
Q Consensus 90 LlqEL~eqCRsmQ~RI~~LIs~t~DE 115 (479)
-+.+|.+.|...+.=|+-+|..++|.
T Consensus 21 ei~~l~e~~~~vk~WI~l~IPkiEDG 46 (150)
T PF02252_consen 21 EIRELIEKCNTVKMWIQLLIPKIEDG 46 (150)
T ss_dssp HHHHHHHHHHHHHHHHHHT-----SS
T ss_pred HHHHHHHHHHHHHHHHHHhCcccccC
Confidence 36788888888888888888888764
No 77
>PF05769 DUF837: Protein of unknown function (DUF837); InterPro: IPR008555 This family consists of several eukaryotic proteins of unknown function. One of the family members (O02197 from SWISSPROT) is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke) [].
Probab=26.68 E-value=4e+02 Score=25.83 Aligned_cols=74 Identities=16% Similarity=0.221 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcC---------ChHHHHHHHHhhhHHHHH
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG---------DEELLGRGLELNDILQNL 131 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~---------DEElL~ELL~lNDdLNnV 131 (479)
|..|+.-++-|++...+.+ .--.+-+.+..-+..|+++|.-|..|=.-+. ++.-+.+|+.=|.+|...
T Consensus 9 l~dak~L~~rL~~~d~~ad---~Ll~qa~~l~~~i~sm~~y~eei~~l~~~~~~~~~~~l~~En~qi~~Lq~EN~eL~~~ 85 (181)
T PF05769_consen 9 LADAKRLVERLKDHDNAAD---SLLSQAEALNKQIESMRQYQEEIQELNELSKNRPRAGLQQENRQIRQLQQENRELRQS 85 (181)
T ss_pred HHHHHHHHHHHHHhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHhhHHHHHHHHHHHHHHHH
Confidence 4445555555555444442 1122334555566777777777665432211 334678888999999888
Q ss_pred HHHHHH
Q 011697 132 LAKHDA 137 (479)
Q Consensus 132 L~RYdr 137 (479)
|..|..
T Consensus 86 leEhq~ 91 (181)
T PF05769_consen 86 LEEHQS 91 (181)
T ss_pred HHHHHH
Confidence 877764
No 78
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=26.16 E-value=2.5e+02 Score=29.47 Aligned_cols=76 Identities=16% Similarity=0.170 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHH-----------HHH-HHHHHHHHHHHHhhhcCChHHHHHHH--Hhhh
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVD-----------LVS-RCRSNQKKLMQMLTTTGDEELLGRGL--ELND 126 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqE-----------L~e-qCRsmQ~RI~~LIs~t~DEElL~ELL--~lND 126 (479)
+.+.=|++.+|..+|..+.- .+....+++.- +.. -|.....+|.+|+.--++++++.++. ..|+
T Consensus 156 ~~i~i~~~~i~~~il~~~~~--~~~~~~~l~~~l~~~~~~~~~~~~~~l~~~~~~~l~~l~~~~g~~~~l~~~~~~~~~~ 233 (391)
T PRK12292 156 FTLDLGHVGLFRALLEAAGL--SEELEEVLRRALANKDYVALEELVLDLSEELRDALLALPRLRGGREVLEEARKLLPSL 233 (391)
T ss_pred eEEEeccHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHHHhcCCHHHHHHHHHhccCh
Confidence 33445778888888887632 11111222222 211 23344556667766555666665443 2344
Q ss_pred HHHHHHHHHHHH
Q 011697 127 ILQNLLAKHDAI 138 (479)
Q Consensus 127 dLNnVL~RYdr~ 138 (479)
.+...++..+.+
T Consensus 234 ~~~~~l~~L~~l 245 (391)
T PRK12292 234 PIKRALDELEAL 245 (391)
T ss_pred HHHHHHHHHHHH
Confidence 444455554444
No 79
>KOG1103 consensus Predicted coiled-coil protein [Function unknown]
Probab=25.91 E-value=1.6e+02 Score=32.18 Aligned_cols=57 Identities=7% Similarity=0.271 Sum_probs=34.5
Q ss_pred hhhhhcHHH-HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHH
Q 011697 52 EVETLSFSS-LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQM 108 (479)
Q Consensus 52 klekLS~sE-LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~L 108 (479)
+..|+..++ |-..+.-..+|.|-.++-+--.......++++.+..+|+.||.+..-|
T Consensus 51 kYGK~NinDP~~ALqRDf~~l~Ek~D~EK~p~ct~spl~iL~~mM~qcKnmQe~~~s~ 108 (561)
T KOG1103|consen 51 KYGKLNINDPFAALQRDFAILGEKIDEEKIPQCTESPLDILDKMMAQCKNMQENAASL 108 (561)
T ss_pred hhcccccCChHHHHHHHHHHHhccccccccceeccChhHHHHHHHHHHHHHHHHHHHH
Confidence 344443333 444455555555555544333333456788999999999999776543
No 80
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=25.86 E-value=6.1e+02 Score=24.51 Aligned_cols=69 Identities=17% Similarity=0.258 Sum_probs=42.2
Q ss_pred hhhhhcHHHHHHHHHHHHHHHHHHHhhCCCCccch-h---hHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHH
Q 011697 52 EVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAV-K---DEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLE 123 (479)
Q Consensus 52 klekLS~sELevVrnNVkVLsEML~e~~Pg~~e~~-d---~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~ 123 (479)
++++| ..+++.++..+.-|.+-|....-+..+.. . .+-+.+|-..|++++..|..+.. .|.+.+.++-+
T Consensus 70 ~~~~l-~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~~~--~Dp~~i~~~~~ 142 (188)
T PF03962_consen 70 KLEKL-QKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELEKYSE--NDPEKIEKLKE 142 (188)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCHHHHHHHHH
Confidence 34444 68899999999999999998865544331 2 23344566666666666663332 34444444433
No 81
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=25.72 E-value=3.2e+02 Score=21.27 Aligned_cols=24 Identities=8% Similarity=0.104 Sum_probs=15.7
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHH
Q 011697 85 AVKDEVIVDLVSRCRSNQKKLMQM 108 (479)
Q Consensus 85 ~~d~ELlqEL~eqCRsmQ~RI~~L 108 (479)
..+.+-+.++...|+.++..|...
T Consensus 30 ~~~~~~~~~~~~~~~~~~~ei~~~ 53 (105)
T PF00435_consen 30 GSDLEELEEQLKKHKELQEEIESR 53 (105)
T ss_dssp SSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhhhhhHHHHH
Confidence 445666777777777777655543
No 82
>PF09727 CortBP2: Cortactin-binding protein-2; InterPro: IPR019131 This entry represents a N-terminal domain found in cortactin-binding protein 2 and in filamin A interacting protein 1 (Filip1). In addition to being a positional candidate for autism, cortactin-binding protein 2 is expressed at highest levels in the brain in humans. Towards the C-terminal end of this protein are a series of proline-rich regions which are likely to be the points of interaction with the SH3 domain of cortactin. The human protein has six associated ankyrin repeat domains (IPR002110 from INTERPRO) towards the C terminus of the protein which act as protein-protein interaction domains []. Filip1 controls the start of neocortical cell migration from the ventricular zone by acting through a filamin-A/F-actin axis. It may be able to induce the degradation of Filamin A [, ].
Probab=25.58 E-value=1.4e+02 Score=29.50 Aligned_cols=47 Identities=19% Similarity=0.310 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhcC-----------ChH-HHHHHHHhhhHHHHHHHH
Q 011697 88 DEVIVDLVSRCRSNQKKLMQMLTTTG-----------DEE-LLGRGLELNDILQNLLAK 134 (479)
Q Consensus 88 ~ELlqEL~eqCRsmQ~RI~~LIs~t~-----------DEE-lL~ELL~lNDdLNnVL~R 134 (479)
...+.-|+..||.||.|+...+-.++ +|. -=.+...=-||+.+.|++
T Consensus 83 l~~Le~l~~~qk~~q~Rm~~qL~~aE~rhrr~i~eLe~EKrkh~~~~aqgDD~t~lLEk 141 (192)
T PF09727_consen 83 LAELEKLMEHQKKMQRRMLEQLAAAEKRHRRTIQELEEEKRKHAEDMAQGDDFTNLLEK 141 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHH
Confidence 46788999999999999988654433 222 233344456777766654
No 83
>cd09234 V_HD-PTP_like Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains. This family contains the V-shaped (V) domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23) and related domains. It belongs to the V_Alix_like superfamily which includes the V domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X/ also known as apoptosis-linked gene-2 interacting protein 1, AIP1), and related domains. HD_PTP interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in cell migration and endosomal trafficking. The related Alix V-domain (belonging to a different family in this superfamily) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. In addi
Probab=25.56 E-value=3.2e+02 Score=28.33 Aligned_cols=46 Identities=22% Similarity=0.214 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhC-CCCccch-h--hHHHHHHHHHHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVN-PSDREAV-K--DEVIVDLVSRCRSNQK 103 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~-Pg~~e~~-d--~ELlqEL~eqCRsmQ~ 103 (479)
+.+++.++..-+.|+..|.+++ |+.-... + ..|=.+|.+.|..++.
T Consensus 20 r~~~~~~e~~~~~l~~~L~slnLP~~~~~~~~~~~~lP~~l~~~~~~i~~ 69 (337)
T cd09234 20 REVVSEIEDKDEELDQFLSSLQLDPLNVMDMDGQFELPQDLVERCAALSV 69 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCChhhhhccCCCCCCCHHHHHHHHHHhc
Confidence 5779999999999999999987 4421121 2 1355677777777773
No 84
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=25.24 E-value=5.9e+02 Score=25.89 Aligned_cols=81 Identities=14% Similarity=0.219 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHH----HHHHHhhhcCChH----HHHHHHHhhhHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQK----KLMQMLTTTGDEE----LLGRGLELNDILQ 129 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~----RI~~LIs~t~DEE----lL~ELL~lNDdLN 129 (479)
.+.|......++++.+-|..+..|+. ..|.+++..|.+.|...-. ++-+.+..--+|- .|..+.+.--.|+
T Consensus 192 ~~al~~L~~rl~~i~~Yl~~V~~g~~-~~d~~ilR~l~~~~~~lP~~~~~~~~~~~~~~~~D~lmv~yLs~lt~~~~~l~ 270 (288)
T cd08063 192 HNAIKMLNSRVELILEYLKAVPVGEV-PPDHSILRSISALCSRLPVLKSEAFREELLAEYNDVLLVAYLATLTKGCNTLN 270 (288)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCC-CCCHHHHHHHHHHHHhCccCChHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 34566667777777777777765544 6778999999999965432 3333333322222 3344445555566
Q ss_pred HHHHHHHHHh
Q 011697 130 NLLAKHDAIA 139 (479)
Q Consensus 130 nVL~RYdr~~ 139 (479)
.++.||....
T Consensus 271 ~~~~k~~~~~ 280 (288)
T cd08063 271 ELVDKFNVVY 280 (288)
T ss_pred HHHHHHhhhh
Confidence 6666665543
No 85
>PF07267 Nucleo_P87: Nucleopolyhedrovirus capsid protein P87; InterPro: IPR009893 This family consists of several Nucleopolyhedrovirus capsid protein P87 sequences. P87 is expressed late in infection and concentrated in infected cell nuclei [].; GO: 0019028 viral capsid
Probab=25.15 E-value=2.5e+02 Score=32.45 Aligned_cols=46 Identities=13% Similarity=0.237 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhhCCCCccchh--hHHH---HHHHHHHHHHHHHHHHHhh
Q 011697 65 RDVMELLSDMLQAVNPSDREAVK--DEVI---VDLVSRCRSNQKKLMQMLT 110 (479)
Q Consensus 65 rnNVkVLsEML~e~~Pg~~e~~d--~ELl---qEL~eqCRsmQ~RI~~LIs 110 (479)
...++-|.+|..++.++.....+ ..++ -.|+.+-+.||.|+.+++-
T Consensus 36 ~qKlD~l~~mv~s~~~~~~~~~~~~~~~~~~NS~l~~qd~~lR~~vl~~Av 86 (654)
T PF07267_consen 36 NQKLDALTSMVDSMPPGGPSPANLRAAEIQNNSILIAQDYVLRYRVLQTAV 86 (654)
T ss_pred HHHHHHHHHHHHhcCCCCCCCchhhHHHHhhhhhHhhhhHHHHHHHHHHHH
Confidence 45778899999999988755444 2233 3678888999999988654
No 86
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.82 E-value=2.4e+02 Score=31.66 Aligned_cols=22 Identities=5% Similarity=0.157 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 011697 89 EVIVDLVSRCRSNQKKLMQMLT 110 (479)
Q Consensus 89 ELlqEL~eqCRsmQ~RI~~LIs 110 (479)
.-++|....||..+.-++.-..
T Consensus 216 ~aleev~n~vk~l~em~l~~s~ 237 (594)
T KOG1086|consen 216 KALEEVNNNVKLLEEMLLDYSQ 237 (594)
T ss_pred HHHHHHHHHHHHHHHHHHhhcc
Confidence 3445556666666555555443
No 87
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=24.58 E-value=4.7e+02 Score=26.71 Aligned_cols=76 Identities=16% Similarity=0.134 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH--HHHHHHHhhh------HHHHHHHHH
Q 011697 64 MRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE--LLGRGLELND------ILQNLLAKH 135 (479)
Q Consensus 64 VrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE--lL~ELL~lND------dLNnVL~RY 135 (479)
+|--+++|...+....-......+.+.+.+-.+... ...+.+.+......+ +|.-+....+ .+..++.+|
T Consensus 248 ~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~--~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y 325 (394)
T PRK00411 248 ARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE--IVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEY 325 (394)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH--HHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence 344445555544333211222234344433333331 233455677777766 4444444433 688999999
Q ss_pred HHHhhC
Q 011697 136 DAIASG 141 (479)
Q Consensus 136 dr~~kG 141 (479)
..+.+.
T Consensus 326 ~~l~~~ 331 (394)
T PRK00411 326 KELCEE 331 (394)
T ss_pred HHHHHH
Confidence 999753
No 88
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=24.45 E-value=3e+02 Score=30.30 Aligned_cols=74 Identities=8% Similarity=0.223 Sum_probs=52.3
Q ss_pred HHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhc------CChH--HHHHHHHhhhHHHHHHHHHHHHh
Q 011697 68 MELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT------GDEE--LLGRGLELNDILQNLLAKHDAIA 139 (479)
Q Consensus 68 VkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t------~DEE--lL~ELL~lNDdLNnVL~RYdr~~ 139 (479)
+.-|...|.++.-|- ..|.|+-...+.....--.|+++||+++ .+.. +=.|.+.++.=|+..|.|||.++
T Consensus 240 ltsmksyLEALe~ga--~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~~~~qln~e~inft~fl~~ii~R~e~~~ 317 (459)
T COG5002 240 LTSMKSYLEALEEGA--WEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDNARYQLNKEWINFTAFLNEIINRFEMIL 317 (459)
T ss_pred hHHHHHHHHHHhcCC--ccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcchhhhhhHHHHHhHHHHHHHHHHHHHHH
Confidence 344566666774332 2456777777777777778888888864 2222 55699999999999999999996
Q ss_pred hCCC
Q 011697 140 SGLP 143 (479)
Q Consensus 140 kG~~ 143 (479)
+...
T Consensus 318 ~~e~ 321 (459)
T COG5002 318 KKET 321 (459)
T ss_pred hhHH
Confidence 5443
No 89
>PLN03196 MOC1-like protein; Provisional
Probab=24.02 E-value=97 Score=33.99 Aligned_cols=40 Identities=13% Similarity=0.054 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhhhcCC--hHHHH--HHHHhhhHH-HHHHHHHHHHh
Q 011697 98 CRSNQKKLMQMLTTTGD--EELLG--RGLELNDIL-QNLLAKHDAIA 139 (479)
Q Consensus 98 CRsmQ~RI~~LIs~t~D--EElL~--ELL~lNDdL-NnVL~RYdr~~ 139 (479)
.+.+++++-=|+++.+- ++++. .+|. =.| .++.-||+.++
T Consensus 372 ~~~l~~k~dFlvneMg~~~~~Iv~fP~~Ls--ySLEkRI~PR~~~L~ 416 (487)
T PLN03196 372 LEIMKPSLEFFKKEMKRPLKELVEFPAYFT--YGLESRIKPRYERVA 416 (487)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHhChHHhc--cChhhhhHHHHHHHH
Confidence 36666666666666542 23333 2332 233 36666676653
No 90
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=23.95 E-value=4.6e+02 Score=22.37 Aligned_cols=27 Identities=7% Similarity=0.080 Sum_probs=12.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhcC
Q 011697 87 KDEVIVDLVSRCRSNQKKLMQMLTTTG 113 (479)
Q Consensus 87 d~ELlqEL~eqCRsmQ~RI~~LIs~t~ 113 (479)
..+-+++..+.-+....+++.++..-.
T Consensus 110 ~~~~~~~~~~~y~~~~~~~~~~~~~~~ 136 (181)
T PF12729_consen 110 LLEEFKEAWKAYRKLRDQVIELAKSGD 136 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 334444444444444445555444433
No 91
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=23.91 E-value=2.8e+02 Score=32.24 Aligned_cols=63 Identities=17% Similarity=0.268 Sum_probs=48.9
Q ss_pred HhhhhhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH
Q 011697 51 TEVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE 116 (479)
Q Consensus 51 sklekLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE 116 (479)
.++.+| +.||...|..=.=|+-.|..+.-++. .-..-|..|-..|+.+|.||..|+..-.-|-
T Consensus 425 ~dvkkL-raeLq~~Rq~E~ELRsqis~l~~~Er--~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DK 487 (697)
T PF09726_consen 425 ADVKKL-RAELQSSRQSEQELRSQISSLTNNER--SLKSELSQLRQENEQLQNKLQNLVQARQQDK 487 (697)
T ss_pred HHHHHH-HHHHHhhhhhHHHHHHHHhhccccch--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566 89999999999999999998864333 3335578899999999999999999765443
No 92
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=23.87 E-value=4.2e+02 Score=28.60 Aligned_cols=76 Identities=20% Similarity=0.285 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHH----------hhh---c-CC-hHHHHHHHHh
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQM----------LTT---T-GD-EELLGRGLEL 124 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~L----------Is~---t-~D-EElL~ELL~l 124 (479)
||..+|.|.+++.+.|..=. - ..+.|-+.+|+...|+.+.+|-.| |.. . .+ ++++.++-++
T Consensus 3 D~k~ir~n~~~v~~~l~~R~--~--~~~vd~i~~ld~~~r~l~~~~~~lr~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l 78 (425)
T PRK05431 3 DIKLIRENPEAVKEALAKRG--F--PLDVDELLELDEERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKEL 78 (425)
T ss_pred CHHHHHhCHHHHHHHHHhcC--C--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHH
Confidence 46667778888877777652 1 123566667777777766555443 221 1 12 2477788888
Q ss_pred hhHHHHHHHHHHHHh
Q 011697 125 NDILQNLLAKHDAIA 139 (479)
Q Consensus 125 NDdLNnVL~RYdr~~ 139 (479)
+++|..+-.+.+.+.
T Consensus 79 ~~~~~~~~~~~~~~~ 93 (425)
T PRK05431 79 KEEIKALEAELDELE 93 (425)
T ss_pred HHHHHHHHHHHHHHH
Confidence 888888877776664
No 93
>PF08899 DUF1844: Domain of unknown function (DUF1844); InterPro: IPR014995 This group of proteins are functionally uncharacterised.
Probab=23.77 E-value=1.3e+02 Score=25.55 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCR 99 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCR 99 (479)
.+|..||..+++| +||.+=.-|+-+..+.++++.++...|
T Consensus 32 ~dl~~Ak~tID~L-~mL~eKTkGNL~~~E~~lL~~~L~eLR 71 (74)
T PF08899_consen 32 VDLELAKQTIDLL-AMLQEKTKGNLDEEEERLLESALYELR 71 (74)
T ss_pred CCHHHHHHHHHHH-HHHHHHHccCCCHHHHHHHHHHHHHHh
Confidence 3788899999998 578877778888888899988877665
No 94
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.67 E-value=4.9e+02 Score=26.84 Aligned_cols=81 Identities=28% Similarity=0.283 Sum_probs=51.6
Q ss_pred HHHHHHHHHHhhC--CCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH-HHHHH----HHhhhHHHHHHHHHHHHh
Q 011697 67 VMELLSDMLQAVN--PSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE-LLGRG----LELNDILQNLLAKHDAIA 139 (479)
Q Consensus 67 NVkVLsEML~e~~--Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE-lL~EL----L~lNDdLNnVL~RYdr~~ 139 (479)
++.+..-|+.... -+.++..+.+.+ +|.+-.++.|+++.+|..++.+=+ .+... +..+-.|++-++++....
T Consensus 27 ~~~l~~~~~a~~~q~~k~~~~~~~r~~-~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~a 105 (247)
T COG3879 27 AMLLAGVMLAAVFQTSKGESVRRARDL-DLVKELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLA 105 (247)
T ss_pred HHHHHHHHHHHHHhhccCcchhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHh
Confidence 3444444554432 234444555555 899999999999999999887654 44433 466666666667777666
Q ss_pred hCCCCCCcc
Q 011697 140 SGLPIPTEV 148 (479)
Q Consensus 140 kG~~~~~e~ 148 (479)
.-..+.|++
T Consensus 106 G~v~V~G~G 114 (247)
T COG3879 106 GSVPVTGPG 114 (247)
T ss_pred ccCCCcCCc
Confidence 655555544
No 95
>smart00323 RasGAP GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
Probab=23.66 E-value=1.9e+02 Score=29.72 Aligned_cols=52 Identities=15% Similarity=0.207 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 011697 63 SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD 114 (479)
Q Consensus 63 vVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D 114 (479)
.+|.|+.++.-+|.++--+.....++..|.-|.+-.++...+|.+++.++.+
T Consensus 228 ~~rr~L~liaKvLQ~lan~~~f~~ke~~m~~ln~fi~~~~~~~~~fl~~i~~ 279 (344)
T smart00323 228 TTRRTLTLIAKVLQNLANLSEFGSKEPWMEPLNDFLLSHKDRVKDFLDELSS 279 (344)
T ss_pred hhhhhHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 4788999999999988655555567789999999999999999998887654
No 96
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=23.65 E-value=3.6e+02 Score=30.21 Aligned_cols=71 Identities=18% Similarity=0.121 Sum_probs=47.1
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHH-HHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHH
Q 011697 55 TLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVI-VDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDIL 128 (479)
Q Consensus 55 kLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELl-qEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdL 128 (479)
++.+++|+..+.-.+++..-+.++.- +..+.+-. +-+.++|.+.|.||-++..+..++.-+.+.|.-|-++
T Consensus 343 e~~qsqlen~k~~~e~~~~e~~~l~~---~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~E~n~~l~knq~v 414 (493)
T KOG0804|consen 343 EYEQSQLENQKQYYELLITEADSLKQ---ESSDLEAEKKIVERKLQQLQTKLKKCQKELKEEREENKKLIKNQDV 414 (493)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHhhhh---hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 33346788888877777777776632 22333333 3455679999999999999887777666666655443
No 97
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.39 E-value=3.2e+02 Score=24.62 Aligned_cols=55 Identities=15% Similarity=0.195 Sum_probs=37.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhhh----cCChHHHHHHHHhhhHHHHHHHHHHHHhhCC
Q 011697 85 AVKDEVIVDLVSRCRSNQKKLMQMLTT----TGDEELLGRGLELNDILQNLLAKHDAIASGL 142 (479)
Q Consensus 85 ~~d~ELlqEL~eqCRsmQ~RI~~LIs~----t~DEElL~ELL~lNDdLNnVL~RYdr~~kG~ 142 (479)
+.+...|.+....|..|-.||=.||.. +.+|+.+.+||++.--|-+.| |....|.
T Consensus 31 ~eeK~~i~~~l~~~~~m~~~vd~li~~f~~lt~ne~~~k~LlqMr~~~~~q~---e~~~~~~ 89 (115)
T PF05397_consen 31 PEEKAAIRQQLQEIQDMLARVDSLIPWFYKLTKNEENTKRLLQMRIMLKEQF---EWLPQGQ 89 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHH---hhhhcCc
Confidence 445666777777777777777777764 367778888888877776666 4444443
No 98
>cd05127 RasGAP_IQGAP_related This family represents IQ motif containing GTPase activating protein (IQGAP) which associated with the Ras GTP-binding protein. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% indentity. IQGAPs are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP is an essential regulator of cytoskeletal function. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity, the protein actually lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite of their similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGA
Probab=23.16 E-value=1.7e+02 Score=30.07 Aligned_cols=52 Identities=12% Similarity=0.121 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 011697 63 SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD 114 (479)
Q Consensus 63 vVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D 114 (479)
.+|.|+.++.-||.++--+.....++..++-|.+=.++...++.+++.++.+
T Consensus 202 ~~rrnL~~iaKvLq~lan~~~f~~ke~~m~~LN~fi~~~~~~~~~fl~~l~~ 253 (325)
T cd05127 202 DQRRNLGEVAKVLQQAASNKPFGGENGYLSPLNDYISESKPRFRDFLKELID 253 (325)
T ss_pred HHHhhHHHHHHHHHHHHCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHHcC
Confidence 4788889999999888655554446677777777777777777777766543
No 99
>PRK02793 phi X174 lysis protein; Provisional
Probab=23.15 E-value=4.4e+02 Score=21.89 Aligned_cols=35 Identities=20% Similarity=0.116 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHH
Q 011697 65 RDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQM 108 (479)
Q Consensus 65 rnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~L 108 (479)
...++-||++|... ...|..|-.+|+.+..||..+
T Consensus 21 e~tIe~Ln~~v~~Q---------q~~I~~L~~~l~~L~~rl~~~ 55 (72)
T PRK02793 21 EITIEELNVTVTAH---------EMEMAKLRDHLRLLTEKLKAS 55 (72)
T ss_pred HHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHhh
Confidence 44555566665554 234556666666666666554
No 100
>PF11744 ALMT: Aluminium activated malate transporter; InterPro: IPR020966 This entry represents an malate transporter which has been is identified as being critical for aluminium tolerance in Arabidopsis thaliana [].; GO: 0010044 response to aluminum ion
Probab=23.09 E-value=7.9e+02 Score=26.81 Aligned_cols=50 Identities=12% Similarity=0.217 Sum_probs=37.2
Q ss_pred HHHHHHH-HHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHH
Q 011697 58 FSSLDSM-RDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQ 107 (479)
Q Consensus 58 ~sELevV-rnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~ 107 (479)
++++..+ ....++|+|+=+.++--.+...-++++.++.+.+++.|..|-.
T Consensus 294 ~~~~~~~~~e~~kvLrel~~~ik~m~~~~~~~~~~~~~~~A~~~Lq~~l~~ 344 (406)
T PF11744_consen 294 QEECTRVSSESAKVLRELSNSIKTMTKSSSIDDHVANLKEAAEDLQSKLDS 344 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCCCchhHHHHHHHHHHHHHHHHHh
Confidence 4565444 8889999999888864344333368899999999999998854
No 101
>PF03273 Baculo_gp64: Baculovirus gp64 envelope glycoprotein family; InterPro: IPR004955 Gp64 is the major envelope fusion glycoprotein in some, though not all, baculoviruses [, ]. It is found on the surface of both infected cells and budded virions as a homotrimer, and by determining the viral receptor preferences it defines the host range and infection efficiency. Baculovirus enters its host cells by endocytosis followed by a low-pH-induced fusion of the viral envelope with the endosomal membrane, allowing viral entrance into the cell cytoplasm. This membrane fusion, and also the efficient budding of virions from the infected cell, is dependent on Gp64. Gp75 is a homologous envelope glycoprotein from Thogotoviruses that, like Gp64, forms homotrimers and is involved in both binding and entering the host cell [].; GO: 0019048 virus-host interaction, 0019031 viral envelope; PDB: 3DUZ_A.
Probab=23.08 E-value=2.1e+02 Score=32.02 Aligned_cols=33 Identities=21% Similarity=0.348 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcC--ChHHHHHHHH
Q 011697 91 IVDLVSRCRSNQKKLMQMLTTTG--DEELLGRGLE 123 (479)
Q Consensus 91 lqEL~eqCRsmQ~RI~~LIs~t~--DEElL~ELL~ 123 (479)
+..|+.+-++|..++-+||..+. ||+|++.||.
T Consensus 305 l~~L~~~~~~l~~~l~~vI~SvaKiDeRLIG~L~~ 339 (498)
T PF03273_consen 305 LEQLHAHFNKLSNMLNTVIQSVAKIDERLIGRLMG 339 (498)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTT-TTHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhc
Confidence 56788888888888888888875 6779998885
No 102
>PF10157 DUF2365: Uncharacterized conserved protein (DUF2365); InterPro: IPR019314 This entry is found in a highly conserved family of proteins which have no known function.
Probab=22.94 E-value=6.6e+02 Score=23.86 Aligned_cols=87 Identities=15% Similarity=0.215 Sum_probs=53.2
Q ss_pred CChhHHHhhhhhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcC--ChHHHHHHH
Q 011697 45 LDETMATEVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG--DEELLGRGL 122 (479)
Q Consensus 45 l~peq~sklekLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~--DEElL~ELL 122 (479)
+++..+.+||+- -..++.+-..||..+=..+. .--.+..|..+.+|..-.++-+=+...- ...+|+++.
T Consensus 49 id~~~L~~LE~~---a~~ia~svd~ll~~L~~~L~------~mS~~Tv~~~~~y~~sv~~~cdsvD~sik~~y~liakce 119 (149)
T PF10157_consen 49 IDPAVLHDLERD---AQAIAESVDSLLRSLRSSLH------SMSAITVEHMETYKDSVDKLCDSVDASIKSMYTLIAKCE 119 (149)
T ss_pred ccHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666444 23333333333333333331 1246677777777777666666554322 224899999
Q ss_pred HhhhHHHHHHHHHHHHhh
Q 011697 123 ELNDILQNLLAKHDAIAS 140 (479)
Q Consensus 123 ~lNDdLNnVL~RYdr~~k 140 (479)
+||+++..|-.-..+|+.
T Consensus 120 ELn~~M~~v~~La~qIK~ 137 (149)
T PF10157_consen 120 ELNESMKPVYKLAQQIKD 137 (149)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999888888763
No 103
>PRK04325 hypothetical protein; Provisional
Probab=22.72 E-value=4.5e+02 Score=21.91 Aligned_cols=36 Identities=11% Similarity=0.118 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHh
Q 011697 65 RDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 65 rnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LI 109 (479)
...|+-||++|..- ...|..|-.+|+.+..||..+-
T Consensus 22 E~tIe~LN~vv~~Q---------q~~I~~L~~ql~~L~~rl~~~~ 57 (74)
T PRK04325 22 EDLIDGLNATVARQ---------QQTLDLLQAQLRLLYQQMRDAN 57 (74)
T ss_pred HHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHhc
Confidence 44555666666554 2345666667777766666543
No 104
>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family. This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.
Probab=22.68 E-value=6.4e+02 Score=25.98 Aligned_cols=56 Identities=13% Similarity=0.118 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCC-------ccchhhHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSD-------REAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD 114 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~-------~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~D 114 (479)
.+|+.++..++-...-|.++.-.+ ......+++.+|-.++-+.+-++..|-....+
T Consensus 177 ~ql~~~~~~l~~ae~~l~~fr~~~~~~d~~~~~~~~~~~i~~L~~~l~~~~~~l~~l~~~~~~ 239 (362)
T TIGR01010 177 NEVKEAEQRLNATKAELLKYQIKNKVFDPKAQSSAQLSLISTLEGELIRVQAQLAQLRSITPE 239 (362)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 556777777777666666654221 11123456777777777777777766554444
No 105
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=22.56 E-value=3.3e+02 Score=21.78 Aligned_cols=18 Identities=22% Similarity=0.361 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 011697 60 SLDSMRDVMELLSDMLQA 77 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e 77 (479)
||=.+|..++.+--.+..
T Consensus 1 ei~~~R~~Le~~~~~~a~ 18 (125)
T PF07729_consen 1 EIYEVRELLEPAAARLAA 18 (125)
T ss_dssp HHHHHHHHHHHHHHHHHG
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 344556655554444443
No 106
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=22.49 E-value=3.4e+02 Score=26.96 Aligned_cols=55 Identities=16% Similarity=0.230 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHHHHHHHHHHHhhCCC
Q 011697 89 EVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLP 143 (479)
Q Consensus 89 ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr~~kG~~ 143 (479)
|-+++|-.+|+.|.--|..|-+.++-+++-.++-.|-.++-.-=+|-+.|++|+.
T Consensus 93 ek~q~l~~t~s~veaEik~L~s~Lt~eemQe~i~~L~kev~~~~erl~~~k~g~~ 147 (201)
T KOG4603|consen 93 EKVQSLQQTCSYVEAEIKELSSALTTEEMQEEIQELKKEVAGYRERLKNIKAGTN 147 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4457888999999999999999999999888888888888877788888887654
No 107
>PRK14148 heat shock protein GrpE; Provisional
Probab=22.34 E-value=5.8e+02 Score=25.19 Aligned_cols=66 Identities=15% Similarity=0.218 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhc---CChHHHHHHHHhhhHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 133 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t---~DEElL~ELL~lNDdLNnVL~ 133 (479)
.+++..+.-++-|.+=+..+ .+-+.-|..-++-++.|+.+=+... .-+.++.+||-+=|+|.++|.
T Consensus 40 ~e~~~l~~~l~~l~~e~~el---------kd~~lR~~Ae~eN~rKR~~rE~e~~~~~a~~~~~~~LLpV~DnlerAl~ 108 (195)
T PRK14148 40 EQLERAKDTIKELEDSCDQF---------KDEALRAKAEMENIRKRAERDVSNARKFGIEKFAKELLPVIDSIEQALK 108 (195)
T ss_pred hHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 34555555555555555444 2334456666777777777766554 345588899999999988875
No 108
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=22.33 E-value=6.8e+02 Score=27.01 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=18.4
Q ss_pred HHhhhcCChHHHHHHHHhhhHHHHHHHHHHH
Q 011697 107 QMLTTTGDEELLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 107 ~LIs~t~DEElL~ELL~lNDdLNnVL~RYdr 137 (479)
+|+.+ .|+|++.++..-..+|..-+.+++.
T Consensus 67 el~~~-~D~e~~~~a~~e~~~l~~~~~~~e~ 96 (360)
T TIGR00019 67 EILEE-SDPEMREMAKEELEELEEKIEELEE 96 (360)
T ss_pred HHHhc-cCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34434 5666766666666666666666664
No 109
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=22.06 E-value=1.1e+03 Score=26.45 Aligned_cols=22 Identities=14% Similarity=-0.179 Sum_probs=14.9
Q ss_pred CCCCCCcccccccccccccccCc
Q 011697 434 KPFIPSYRLFEDLNVLGSADARL 456 (479)
Q Consensus 434 ~p~~p~~~lf~dln~~~~~~g~~ 456 (479)
+|.+|-- -|---.|+--+||++
T Consensus 486 ~~~~~~p-~~~~~gi~~~~~~~n 507 (531)
T KOG1960|consen 486 APGTGTP-GLTTPGVDPAAYGYN 507 (531)
T ss_pred CCCCCCC-CCccCCcCchhcccc
Confidence 4555555 455567888888875
No 110
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This entry includes Protein BYPASS 1 which is required for normal root and shoot development. Prevents constitutive production of a root mobile carotenoid-derived signaling compound that is capable of arresting shoot and leaf development [, ].
Probab=22.00 E-value=1.6e+02 Score=32.06 Aligned_cols=52 Identities=13% Similarity=0.233 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCccch---hhHHHHHHHHHHHHHHHHHHHHh
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPSDREAV---KDEVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg~~e~~---d~ELlqEL~eqCRsmQ~RI~~LI 109 (479)
+.||+.|.-.++-|.|++..+.-...+.. =.+.++||...|+.|..=|--|.
T Consensus 314 LkEl~~ve~~vr~L~el~d~~~~p~~~e~~~ev~~~V~EL~~~~~~L~~GLdpLe 368 (389)
T PF05633_consen 314 LKELQQVEASVRELHELIDSFQFPLEEEKEEEVREAVEELARVCEALSQGLDPLE 368 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHHHHHHHHHcccHHHH
Confidence 58999999999999999998852222111 12455678888887775554443
No 111
>cd08334 DED_Caspase_8_10_repeat2 Death effector domain, repeat 2, of initator caspases 8 and 10. Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis, and they play partially redundant roles. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. They contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains foun
Probab=21.86 E-value=1.8e+02 Score=24.77 Aligned_cols=49 Identities=14% Similarity=0.209 Sum_probs=31.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhh
Q 011697 56 LSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLT 110 (479)
Q Consensus 56 LS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs 110 (479)
+.+..++.++.-++|+.+|-..-.-+ ..+.+++.+|..++ ++.+.+.|.
T Consensus 31 ip~~kle~~~s~ldlf~~Lek~~~l~---~~nl~~L~elL~~i---r~dLl~~I~ 79 (83)
T cd08334 31 LPRSKLEDNKTLLDVFVEMEKQGLLG---EDNLDELKRILKSL---DKKLAKKIE 79 (83)
T ss_pred cchhhhhccCCHHHHHHHHHHcCCCC---CccHHHHHHHHHHH---HHHHHHHHH
Confidence 34456777778888888887765443 23556777776665 566666554
No 112
>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]
Probab=21.77 E-value=6.3e+02 Score=26.71 Aligned_cols=84 Identities=17% Similarity=0.192 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChHHHHHHHHhhhHHH-HHHHHHH
Q 011697 58 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQ-NLLAKHD 136 (479)
Q Consensus 58 ~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEElL~ELL~lNDdLN-nVL~RYd 136 (479)
..++|.+|--++-|.+++-.+. .....-.+-+..+....+.+..+|+.|...--+-.. ...=++|+ +.=.-|+
T Consensus 199 ~~~~De~Rkeade~he~~ve~~--~~~~e~~ee~~~~~~elre~~k~ik~l~~~~~~~~~----~~~~ee~kera~ei~E 272 (294)
T COG1340 199 FEEADELRKEADELHEEFVELS--KKIDELHEEFRNLQNELRELEKKIKALRAKEKAAKR----REKREELKERAEEIYE 272 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 4778888888888988888873 222233455666777777777777766654322222 22222455 7777899
Q ss_pred HHhhCCCCCCc
Q 011697 137 AIASGLPIPTE 147 (479)
Q Consensus 137 r~~kG~~~~~e 147 (479)
+|+.|..++.+
T Consensus 273 Kfk~GekLt~E 283 (294)
T COG1340 273 KFKRGEKLTTE 283 (294)
T ss_pred HHhCCCCCCHH
Confidence 99999887643
No 113
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=21.76 E-value=5.6e+02 Score=22.57 Aligned_cols=29 Identities=17% Similarity=0.282 Sum_probs=14.7
Q ss_pred HHHhhhhhcHHHHHHHHHHHHHHHHHHHhh
Q 011697 49 MATEVETLSFSSLDSMRDVMELLSDMLQAV 78 (479)
Q Consensus 49 q~sklekLS~sELevVrnNVkVLsEML~e~ 78 (479)
++.++..+ ..||+.-...++-|+..-..+
T Consensus 38 ~l~~~~~~-~~e~~~~~~~~~~l~~~~~~L 66 (213)
T cd00176 38 LLKKHEAL-EAELAAHEERVEALNELGEQL 66 (213)
T ss_pred HHHHHHHH-HHHHHHCHHHHHHHHHHHHHH
Confidence 34444444 456655555555555444444
No 114
>PF05527 DUF758: Domain of unknown function (DUF758) ; InterPro: IPR008477 This is a family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.; PDB: 3F4M_A.
Probab=21.74 E-value=3.6e+02 Score=26.58 Aligned_cols=74 Identities=11% Similarity=0.117 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhh--hcCChH-HHHHHHHhhhHHHHHHHHH
Q 011697 62 DSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLT--TTGDEE-LLGRGLELNDILQNLLAKH 135 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs--~t~DEE-lL~ELL~lNDdLNnVL~RY 135 (479)
.++++-|++.--+---++-++-+..+..++.++.+.|+..--+++.+-+ -+-|-. +..-+.+..|.|..++.+|
T Consensus 58 ki~KniIKi~vKigvl~rn~qf~~eEl~~~~~fr~k~~~~amt~iSF~eV~fTfD~~~L~~~L~ec~~~L~~lv~~H 134 (186)
T PF05527_consen 58 KIIKNIIKIVVKIGVLYRNNQFSDEELALAEKFRKKFHQLAMTAISFYEVDFTFDRNYLSKLLKECRDLLHQLVEPH 134 (186)
T ss_dssp HHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHHHHHHTSTTS---HHHHHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHhheeeecCCCCHHHHHHHHHHHHHHHHHHHHHhhhcccchhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455555555444333333455667888899999999988888888766 245666 4445567888888888776
No 115
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=21.70 E-value=1.5e+02 Score=34.94 Aligned_cols=86 Identities=12% Similarity=0.117 Sum_probs=52.6
Q ss_pred hhhhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHH---------------HHHHHHHHHHHHHhhhcCChHH
Q 011697 53 VETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLV---------------SRCRSNQKKLMQMLTTTGDEEL 117 (479)
Q Consensus 53 lekLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~---------------eqCRsmQ~RI~~LIs~t~DEEl 117 (479)
|+|||+..|...-..++=|.|+|....- ........+.+|- ++-+.++.++++|++.+.|=++
T Consensus 488 LGKLSk~qI~~g~~vL~ei~~~l~~~~~--~~~~~~~~~~dlSnrfYTlIPh~~ppvi~~~~~lk~k~~~mLe~L~DIei 565 (815)
T PLN03122 488 MGMLSDFHLKRCEEVLLEFAEFVKSEKE--TGQKAEAMWLDFSNKWFSLVHSTRPFVIRDIDELADHAASALETVRDINV 565 (815)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHhcccc--ccchhHHHHHHHhccceeccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3778888888877777777777764321 1111123344433 3345566666788888887776
Q ss_pred HHHHHHh---hhHHHHHHHHHHHHhh
Q 011697 118 LGRGLEL---NDILQNLLAKHDAIAS 140 (479)
Q Consensus 118 L~ELL~l---NDdLNnVL~RYdr~~k 140 (479)
-.+||.- +++.+-+-.+|+.+.-
T Consensus 566 A~~ll~~~~~~~~~~pLd~~Y~~L~~ 591 (815)
T PLN03122 566 ASRLIGDMTGSTLDDPLSDRYKKLGC 591 (815)
T ss_pred HHHHHhhccccccCCchHHHHHhcCc
Confidence 6666643 4456777777877753
No 116
>PF08893 DUF1839: Domain of unknown function (DUF1839); InterPro: IPR014989 This group of proteins are functionally uncharacterised.
Probab=21.65 E-value=2.9e+02 Score=29.47 Aligned_cols=76 Identities=17% Similarity=0.155 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccch--hhHHHHHHHHHHHHHHHHHHHHhhhcCCh---HHHHHHHHhhhHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAV--KDEVIVDLVSRCRSNQKKLMQMLTTTGDE---ELLGRGLELNDILQNLLA 133 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~--d~ELlqEL~eqCRsmQ~RI~~LIs~t~DE---ElL~ELL~lNDdLNnVL~ 133 (479)
+.|.-.--|.|||...|.-+.-...... -.+-...+.+.||.||-||.+-|.+--.+ +.|..+-..-|.+-..|.
T Consensus 238 ntlRQlGAnfEL~a~~l~WL~~~g~~~~~~aa~a~~~ias~Ak~~QFrLARAv~r~r~~~~~~~Ld~~~~ay~~~~~~L~ 317 (319)
T PF08893_consen 238 NTLRQLGANFELLASYLRWLDAQGFSGPAEAAEACRTIASEAKVVQFRLARAVARGRFDDCEDCLDPMEAAYDRAMDGLA 317 (319)
T ss_pred hhHHhccccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHHHHHHHh
Confidence 6677777899999999998865443322 34667789999999999999987654332 256655555555555554
Q ss_pred H
Q 011697 134 K 134 (479)
Q Consensus 134 R 134 (479)
+
T Consensus 318 ~ 318 (319)
T PF08893_consen 318 R 318 (319)
T ss_pred c
Confidence 4
No 117
>COG2352 Ppc Phosphoenolpyruvate carboxylase [Energy production and conversion]
Probab=21.61 E-value=2.6e+02 Score=33.53 Aligned_cols=78 Identities=19% Similarity=0.286 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHH-----------HHHHHHHhhhcCChH--HHHHHHHhhhH
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSN-----------QKKLMQMLTTTGDEE--LLGRGLELNDI 127 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsm-----------Q~RI~~LIs~t~DEE--lL~ELL~lNDd 127 (479)
-+.+++||.+|.++|.+.--.. ..+.+-|++++.|+. .+-|.+++..+++++ -+..+-..=..
T Consensus 6 ~~~lr~~v~~Lg~lLge~i~e~----~g~~~~e~ve~ir~~s~~~r~~~~~~~~~L~~~l~~Ls~~~~~~vaRaFs~f~~ 81 (910)
T COG2352 6 YSALRSDVSMLGRLLGETIREA----EGEAILELVETIRKLSKESRAGDQADRQELEATLANLSNDEAIPVARAFSQFLL 81 (910)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH----hhHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHcCCCHhhhhHHHHHHHHHhh
Confidence 3578999999999998874322 233344444444433 345666777777887 45555566667
Q ss_pred HHHHHHHHHHHhhCC
Q 011697 128 LQNLLAKHDAIASGL 142 (479)
Q Consensus 128 LNnVL~RYdr~~kG~ 142 (479)
|-|+-+.|+.+.+.+
T Consensus 82 L~NiaEd~~~~~r~~ 96 (910)
T COG2352 82 LANIAEDYHRIRRRQ 96 (910)
T ss_pred hhhHHHHhhhHhhhh
Confidence 888888888887654
No 118
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=21.46 E-value=2.8e+02 Score=26.55 Aligned_cols=51 Identities=12% Similarity=0.253 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCChH--HHHHHHHhhhHHHHHHHHHHHHh
Q 011697 89 EVIVDLVSRCRSNQKKLMQMLTTTGDEE--LLGRGLELNDILQNLLAKHDAIA 139 (479)
Q Consensus 89 ELlqEL~eqCRsmQ~RI~~LIs~t~DEE--lL~ELL~lNDdLNnVL~RYdr~~ 139 (479)
.+|+..+++....+..||.+.+..-.|- +..+|-.+..++..++..=|.+.
T Consensus 2 ~Ii~~ti~~ie~sK~qIf~I~E~~R~E~~~l~~EL~evk~~v~~~I~evD~Le 54 (159)
T PF05384_consen 2 KIIKKTIDTIESSKEQIFEIAEQARQEYERLRKELEEVKEEVSEVIEEVDKLE 54 (159)
T ss_pred hHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666666666666666554442 55566666666666666666553
No 119
>PRK10378 inactive ferrous ion transporter periplasmic protein EfeO; Provisional
Probab=21.17 E-value=3.8e+02 Score=29.03 Aligned_cols=76 Identities=13% Similarity=0.146 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhh--hcCChHHHHHHHHhhhHHHHHHHHHHH
Q 011697 62 DSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLT--TTGDEELLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 62 evVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs--~t~DEElL~ELL~lNDdLNnVL~RYdr 137 (479)
+++.+-.+||+|++..--.|+++.--.--|.++.-..+-.|.-+--|-. +-.|.+++.++-.-=+.|+.+|.+|.+
T Consensus 259 ~l~~gA~~lleeva~~kitGeEe~yShtDL~Df~ANveGa~~~~~~l~P~l~~~dp~l~~~id~~f~~v~~lL~~~~~ 336 (375)
T PRK10378 259 KVVGGAAGLIEEVAASKISGEEDRYSHTDLWDFQANVDGSQKIVDLLRPLLEKANPELLAKVDANFKKVDTILAKYRT 336 (375)
T ss_pred HHHHHHHHHHHHHHhcccCCcccccccCCHHHHHHHHHHHHHHHHHhhhhhhhcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 6889999999999997666666544333355666666665543332333 234567888888888999999999976
No 120
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=21.11 E-value=2.4e+02 Score=25.71 Aligned_cols=49 Identities=20% Similarity=0.251 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhcCChH-HHHHHHHhhhHHHHHHHHHH
Q 011697 87 KDEVIVDLVSRCRSNQKKLMQMLTTTGDEE-LLGRGLELNDILQNLLAKHD 136 (479)
Q Consensus 87 d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE-lL~ELL~lNDdLNnVL~RYd 136 (479)
...++.+|..-|..+..-+..+- ...+.+ ++.-+-.+-+.|.++|.+|.
T Consensus 60 ~~~~~~~ll~v~D~l~~a~~~~~-~~~~~~~~~~g~~~~~~~l~~~L~~~G 109 (165)
T PF01025_consen 60 LEKFLKDLLPVLDNLERALEAAK-SNEEEESLLEGLEMILKQLEDILEKNG 109 (165)
T ss_dssp HHHHHHHHHHHHHHHHHHHCC-S-HHCTCHHHHHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhh-ccchHHHHHHHHHHHHHHHHHHHHHCC
Confidence 34666666666664332222221 223333 44444445577777777663
No 121
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.01 E-value=5.1e+02 Score=30.01 Aligned_cols=78 Identities=21% Similarity=0.214 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhhcCChH--HHHHHHHhhhHHHHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEE--LLGRGLELNDILQNLLAKHD 136 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~t~DEE--lL~ELL~lNDdLNnVL~RYd 136 (479)
.+|..++...+.++||-..+. +.-..-.|--..|.+.|+++..+---=..-..+-| .-.|+..+||.++.+-.--|
T Consensus 602 Q~l~~~~eer~~i~e~a~~La--~R~eea~e~qe~L~~~~~~L~~~~~~~lp~l~~AErdFk~Elq~~~~~~~~L~~~iE 679 (741)
T KOG4460|consen 602 QDLSYCREERKSLREMAERLA--DRYEEAKEKQEDLMNRMKKLLHSFHSELPVLSDAERDFKKELQLIPDQLRHLGNAIE 679 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhHHHHHHHHHHHHhcccccCCcchhHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 567777777777777766662 11111112223455555544433322222233333 66688899988776554444
Q ss_pred HH
Q 011697 137 AI 138 (479)
Q Consensus 137 r~ 138 (479)
-.
T Consensus 680 T~ 681 (741)
T KOG4460|consen 680 TV 681 (741)
T ss_pred HH
Confidence 33
No 122
>KOG4515 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.00 E-value=2.1e+02 Score=28.64 Aligned_cols=40 Identities=28% Similarity=0.439 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCh--------HHHHHHHHhhhHHHHH
Q 011697 92 VDLVSRCRSNQKKLMQMLTTTGDE--------ELLGRGLELNDILQNL 131 (479)
Q Consensus 92 qEL~eqCRsmQ~RI~~LIs~t~DE--------ElL~ELL~lNDdLNnV 131 (479)
..|+++||.|.-.|..|++.+.+- |.+.++=++.|+|-++
T Consensus 116 n~lv~r~K~v~~s~~tLf~~~~~~qk~ya~yaeq~~k~n~ls~~l~ri 163 (217)
T KOG4515|consen 116 NKLVARCKSVEASMITLFEETRAHQKQYAGYAEQLSKLNQLSDDLCRI 163 (217)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999987653 2344444455555444
No 123
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=20.89 E-value=2.7e+02 Score=28.26 Aligned_cols=43 Identities=16% Similarity=0.157 Sum_probs=30.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhh--cCChHHHHHHHHhhhHH
Q 011697 86 VKDEVIVDLVSRCRSNQKKLMQMLTT--TGDEELLGRGLELNDIL 128 (479)
Q Consensus 86 ~d~ELlqEL~eqCRsmQ~RI~~LIs~--t~DEElL~ELL~lNDdL 128 (479)
.+.+.|++|.+.++..|.+...++.. ..+-+-+.+||..-+.|
T Consensus 103 pEi~~L~~l~~~ve~f~~~a~~~L~~~~~~~~~~le~Ll~~g~s~ 147 (335)
T PF08429_consen 103 PEIDQLKELLEEVEEFQSRAQEALSDPESPSLEELEELLEEGESF 147 (335)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHhcccC
Confidence 45788999999999999999999976 33334555555554433
No 124
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=20.81 E-value=2.6e+02 Score=22.79 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCC-----hHHHHHHHHhhhHHHHHHHHHHH
Q 011697 91 IVDLVSRCRSNQKKLMQMLTTTGD-----EELLGRGLELNDILQNLLAKHDA 137 (479)
Q Consensus 91 lqEL~eqCRsmQ~RI~~LIs~t~D-----EElL~ELL~lNDdLNnVL~RYdr 137 (479)
|.+|-.....+..+|-+|-.++.. ..+-.|+-++|..|.+....|.+
T Consensus 5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN~a~sY~K 56 (56)
T PF04728_consen 5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDNIAQSYKK 56 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhccC
Confidence 344445555555555555444321 12556889999999999988863
No 125
>KOG1465 consensus Translation initiation factor 2B, beta subunit (eIF-2Bbeta/GCD7) [Translation, ribosomal structure and biogenesis]
Probab=20.78 E-value=2.4e+02 Score=30.30 Aligned_cols=49 Identities=10% Similarity=0.252 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHH-------------HHHHHHhhh
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQ-------------KKLMQMLTT 111 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ-------------~RI~~LIs~ 111 (479)
.-..+++.-+.||.-++..-+...- ++||+.+.+.|++++ .||.+||.+
T Consensus 25 gS~aiA~eTl~llr~iIs~~rw~~~----n~Li~~vr~~g~~L~~A~psE~~~gNiirrIlkliRe 86 (353)
T KOG1465|consen 25 GSYAIAIETLNLLRQIISRERWSTA----NDLIESVRDVGKKLHAAQPSELSCGNIIRRILKLIRE 86 (353)
T ss_pred CcHHHHHHHHHHHHHHHHhhCcccH----HHHHHHHHHHHHHhhhcCCchhhhhHHHHHHHHHHHH
Confidence 3477889999999999999877543 499999999999987 677777763
No 126
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=20.78 E-value=3.4e+02 Score=28.95 Aligned_cols=47 Identities=21% Similarity=0.262 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHH
Q 011697 59 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLM 106 (479)
Q Consensus 59 sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~ 106 (479)
+.|+.-+..++-|.+.|..+.++ ....+.+.+++|-+..++.+.++.
T Consensus 39 ssI~~QkkrLk~L~~sLk~~~~~-~~~e~~~~i~~L~~~Ik~r~~~l~ 85 (330)
T PF07851_consen 39 SSISHQKKRLKELKKSLKRCKKS-LSAEERELIEKLEEDIKERRCQLF 85 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC-CChhHHHHHHHHHHHHHHHHhhHH
Confidence 33444444444555555555432 222334444444444444444433
No 127
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=20.75 E-value=6.3e+02 Score=25.91 Aligned_cols=61 Identities=13% Similarity=0.235 Sum_probs=35.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHhhCCCCc--cchhhHHHHHHHHH-------HHHHHHHHHHH----hhhcCChH
Q 011697 56 LSFSSLDSMRDVMELLSDMLQAVNPSDR--EAVKDEVIVDLVSR-------CRSNQKKLMQM----LTTTGDEE 116 (479)
Q Consensus 56 LS~sELevVrnNVkVLsEML~e~~Pg~~--e~~d~ELlqEL~eq-------CRsmQ~RI~~L----Is~t~DEE 116 (479)
|+.+|++..+.+-+|+--+|++++-... +-..+++...|-++ ....+.+++++ +.++.+|+
T Consensus 40 l~nee~~eLk~qnkli~K~l~ei~~~qd~reK~~~~I~ssL~eTtkdf~~~~~k~~~dF~~~Lq~~Lk~V~tde 113 (230)
T PF03904_consen 40 LENEEIQELKRQNKLIIKYLSEIEEKQDIREKNLKEIKSSLEETTKDFIDKTEKVHNDFQDILQDELKDVDTDE 113 (230)
T ss_pred HhHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchHH
Confidence 5567888889999988888888853211 12234555555443 33444444443 44565555
No 128
>PRK00846 hypothetical protein; Provisional
Probab=20.46 E-value=5.5e+02 Score=22.01 Aligned_cols=21 Identities=10% Similarity=-0.164 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 011697 89 EVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 89 ELlqEL~eqCRsmQ~RI~~LI 109 (479)
..|..|-.+|+.|..||..+.
T Consensus 41 ~~I~~L~~ql~~L~~rL~~~~ 61 (77)
T PRK00846 41 LTGARNAELIRHLLEDLGKVR 61 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 344455555555555555443
No 129
>PHA03373 tegument protein; Provisional
Probab=20.43 E-value=4.2e+02 Score=27.27 Aligned_cols=67 Identities=22% Similarity=0.370 Sum_probs=0.0
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHhhh-----------cCChH--HHHHH
Q 011697 55 TLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTT-----------TGDEE--LLGRG 121 (479)
Q Consensus 55 kLS~sELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LIs~-----------t~DEE--lL~EL 121 (479)
+++..||.....+-+|..-||.=+ | +|.+|+.-...|++.+.. ++--. -+-|.
T Consensus 49 Git~~Di~~~~rDtEv~khLL~LL-P-------------~Yk~c~~r~~~L~r~L~~~C~pH~r~AaevEc~KsqrIlea 114 (247)
T PHA03373 49 GITQADIRSLSRDTEVVKHLLQLL-P-------------IYKQCKSRYTFLERCLANGCPPHVRPAAEVECMKSKRILEA 114 (247)
T ss_pred CcCHHHHHHHhhhhHHHHHHHHHh-H-------------HHHHHHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHH
Q ss_pred HHh--------------hhHHHHHHHHH
Q 011697 122 LEL--------------NDILQNLLAKH 135 (479)
Q Consensus 122 L~l--------------NDdLNnVL~RY 135 (479)
|.| -|.|+++|+||
T Consensus 115 LDVvilKl~vGEFtmse~dsle~LL~KF 142 (247)
T PHA03373 115 LDVVILKLLVGEFTMSETDSLNRLLEKF 142 (247)
T ss_pred HHHHHHHHHHhccccCcchHHHHHHHHh
No 130
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=20.34 E-value=4.4e+02 Score=21.48 Aligned_cols=40 Identities=23% Similarity=0.266 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHHHHh
Q 011697 61 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQML 109 (479)
Q Consensus 61 LevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~~LI 109 (479)
|--...-++-||+++... ..-|..|-.+|+.+..||..+-
T Consensus 13 la~qe~~ie~Ln~~v~~Q---------q~~I~~L~~~l~~L~~rl~~~~ 52 (69)
T PF04102_consen 13 LAFQEDTIEELNDVVTEQ---------QRQIDRLQRQLRLLRERLRELE 52 (69)
T ss_dssp HHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHT-----
T ss_pred HHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHhc
Confidence 333445566666666655 4557788888888888888775
No 131
>cd09238 V_Alix_like_1 Protein-interacting V-domain of an uncharacterized family of the V_Alix_like superfamily. This domain family is comprised of uncharacterized plant proteins. It belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), (His-Domain) type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Alix, HD-PTP, Bro1, a
Probab=20.19 E-value=9.8e+02 Score=24.91 Aligned_cols=12 Identities=42% Similarity=0.470 Sum_probs=7.8
Q ss_pred HHHHHHHhhhHH
Q 011697 117 LLGRGLELNDIL 128 (479)
Q Consensus 117 lL~ELL~lNDdL 128 (479)
+|.++-.+|+++
T Consensus 266 ll~~i~~~n~~f 277 (339)
T cd09238 266 LLSRLRALNEKF 277 (339)
T ss_pred HHHHHHHHHHHH
Confidence 666666666654
No 132
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=20.09 E-value=8.1e+02 Score=25.19 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=18.4
Q ss_pred HHHH-HHHHHHHHHHHHHHHhhC
Q 011697 58 FSSL-DSMRDVMELLSDMLQAVN 79 (479)
Q Consensus 58 ~sEL-evVrnNVkVLsEML~e~~ 79 (479)
+.++ +.++.--+.|++.|..++
T Consensus 20 r~e~~~~~e~~~~~l~~~L~sln 42 (342)
T cd08915 20 REHIVEPIEALNKLLNSFLAERN 42 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC
Confidence 5778 888888888888888886
No 133
>PF05739 SNARE: SNARE domain; InterPro: IPR000727 The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes [, ]. Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion. The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (IPR000928 from INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure []. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related []. This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.; GO: 0005515 protein binding; PDB: 1URQ_B 3RL0_R 1HVV_B 1SFC_B 1N7S_B 3IPD_B 3C98_B 3HD7_F 3RK2_B 1KIL_B ....
Probab=20.00 E-value=2.5e+02 Score=21.41 Aligned_cols=45 Identities=16% Similarity=0.333 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCccchhhHHHHHHHHHHHHHHHHHH
Q 011697 60 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLM 106 (479)
Q Consensus 60 ELevVrnNVkVLsEML~e~~Pg~~e~~d~ELlqEL~eqCRsmQ~RI~ 106 (479)
+|+.+...|.-|.+|...+ +..-....++|..|-..+.....+|.
T Consensus 5 ~l~~l~~~i~~l~~~~~~i--~~ev~~Q~~~ld~i~~~vd~~~~~l~ 49 (63)
T PF05739_consen 5 ELDELEQSIQELKQMFQDI--GEEVEEQNEMLDRIEDNVDRANENLK 49 (63)
T ss_dssp HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH--HHHHHHCHhhHHHHHHHHHHHHHHHH
Confidence 4666666666666666666 23323345666666665555554443
Done!