Query 035101
Match_columns 73
No_of_seqs 81 out of 83
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:12:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00302 GED Dynamin GTPase 99.8 5E-21 1.1E-25 122.1 8.4 63 9-73 3-65 (92)
2 PF02212 GED: Dynamin GTPase e 99.7 1.5E-17 3.3E-22 105.2 6.8 63 9-73 3-65 (92)
3 KOG0446 Vacuolar sorting prote 99.5 3.3E-14 7.2E-19 116.1 8.9 67 6-73 560-626 (657)
4 PRK14126 cell division protein 79.2 13 0.00029 23.4 7.3 61 5-72 22-83 (85)
5 PRK09636 RNA polymerase sigma 79.1 3.1 6.7E-05 30.2 3.6 54 17-73 146-199 (293)
6 TIGR02957 SigX4 RNA polymerase 75.9 4.2 9E-05 29.6 3.6 54 17-73 139-192 (281)
7 PF09660 DUF2397: Protein of u 71.9 25 0.00055 28.4 7.4 61 10-71 154-214 (486)
8 PRK09635 sigI RNA polymerase s 71.3 6 0.00013 29.3 3.5 54 17-73 149-202 (290)
9 cd09240 BRO1_Alix Protein-inte 67.6 36 0.00078 25.9 7.1 60 9-68 208-273 (346)
10 cd00781 ketosteroid_isomerase 67.6 10 0.00022 23.2 3.4 29 45-73 3-31 (122)
11 TIGR02960 SigX5 RNA polymerase 62.7 12 0.00025 27.2 3.5 56 18-73 174-232 (324)
12 TIGR02677 conserved hypothetic 61.4 41 0.0009 27.5 6.7 61 9-70 151-211 (494)
13 COG3951 Rod binding protein [C 56.4 48 0.001 24.1 5.7 53 6-63 25-78 (166)
14 PF07817 GLE1: GLE1-like prote 52.7 86 0.0019 22.9 6.7 67 6-72 167-255 (256)
15 TIGR02246 conserved hypothetic 51.3 34 0.00073 20.6 3.8 29 45-73 4-32 (128)
16 PF09355 Phage_Gp19: Phage pro 51.1 26 0.00056 23.3 3.4 29 2-35 1-29 (116)
17 COG3027 zapA Cell division pro 50.1 26 0.00057 23.1 3.3 43 4-46 17-67 (105)
18 PF08349 DUF1722: Protein of u 48.5 70 0.0015 20.7 5.1 62 10-71 10-79 (117)
19 PRK08241 RNA polymerase factor 48.2 28 0.0006 25.6 3.5 55 17-73 184-242 (339)
20 PF05164 ZapA: Cell division p 48.2 49 0.0011 19.6 4.1 44 5-48 16-60 (89)
21 TIGR02698 CopY_TcrY copper tra 46.5 40 0.00087 22.3 3.8 27 46-72 88-116 (130)
22 cd09244 BRO1_Rhophilin Protein 44.4 1.1E+02 0.0025 23.8 6.5 53 12-64 200-258 (350)
23 PF03965 Penicillinase_R: Peni 41.3 58 0.0013 20.6 3.8 26 47-72 88-115 (115)
24 PF14002 YniB: YniB-like prote 40.8 59 0.0013 23.6 4.2 25 36-60 94-118 (166)
25 PF07923 N1221: N1221-like pro 40.1 1.5E+02 0.0033 21.9 7.6 57 7-63 97-192 (293)
26 cd09246 BRO1_Alix_like_1 Prote 38.1 1.8E+02 0.0039 22.2 6.8 59 9-67 200-264 (353)
27 PHA02754 hypothetical protein; 37.9 67 0.0015 20.1 3.6 25 31-55 4-28 (67)
28 PF12731 Mating_N: Mating-type 37.5 70 0.0015 20.3 3.8 24 41-64 12-35 (95)
29 COG0699 Predicted GTPases (dyn 35.9 1.9E+02 0.0042 21.9 8.1 31 12-43 462-492 (546)
30 COG1937 Uncharacterized protei 35.8 69 0.0015 20.8 3.5 28 44-73 5-32 (89)
31 TIGR02096 conserved hypothetic 34.4 57 0.0012 19.8 2.9 25 49-73 2-26 (129)
32 KOG2176 Exocyst complex, subun 34.2 2.3E+02 0.0051 25.2 7.4 58 5-66 625-682 (800)
33 PRK11426 hypothetical protein; 34.0 71 0.0015 22.2 3.6 37 4-40 59-103 (132)
34 PF02583 Trns_repr_metal: Meta 33.7 79 0.0017 19.6 3.5 27 45-73 2-28 (85)
35 cd09239 BRO1_HD-PTP_like Prote 33.7 2.3E+02 0.0049 22.0 7.4 59 9-67 200-269 (361)
36 PF03937 Sdh5: Flavinator of s 33.3 54 0.0012 19.9 2.6 24 50-73 24-47 (74)
37 cd07608 BAR_ArfGAP_fungi The B 33.2 79 0.0017 23.1 3.9 28 9-36 57-84 (192)
38 PF13228 DUF4037: Domain of un 32.2 60 0.0013 20.8 2.8 25 6-30 19-43 (100)
39 KOG2956 CLIP-associating prote 32.1 41 0.00088 28.3 2.4 17 27-43 457-473 (516)
40 PF00159 Hormone_3: Pancreatic 32.1 92 0.002 17.2 3.2 18 9-26 14-31 (36)
41 PRK10564 maltose regulon perip 31.1 1.9E+02 0.004 22.7 5.8 46 5-61 251-302 (303)
42 COG3242 Uncharacterized protei 30.8 30 0.00066 21.5 1.2 10 8-17 38-47 (62)
43 PF08111 Pea-VEAacid: Pea-VEAa 30.7 8.8 0.00019 17.8 -0.9 9 16-24 6-14 (15)
44 PF15178 TOM_sub5: Mitochondri 30.5 68 0.0015 19.2 2.6 17 5-21 10-26 (51)
45 COG3682 Predicted transcriptio 30.2 46 0.001 22.9 2.1 25 48-72 92-118 (123)
46 TIGR02977 phageshock_pspA phag 30.0 1.6E+02 0.0034 21.0 4.9 38 10-49 2-39 (219)
47 PRK07217 replication factor A; 29.5 1.5E+02 0.0033 23.3 5.0 55 7-61 3-60 (311)
48 PF08360 TetR_C_5: QacR-like p 29.1 83 0.0018 21.0 3.2 54 18-72 22-76 (131)
49 PF10664 NdhM: Cyanobacterial 28.5 56 0.0012 22.3 2.3 19 9-27 65-83 (108)
50 PF11960 DUF3474: Domain of un 26.4 52 0.0011 23.2 1.9 27 27-57 101-127 (136)
51 PF10025 DUF2267: Uncharacteri 26.4 1.6E+02 0.0036 19.0 4.2 34 6-39 69-110 (125)
52 PRK10878 hypothetical protein; 26.1 61 0.0013 20.1 2.0 23 51-73 12-34 (72)
53 PF09769 ApoO: Apolipoprotein 25.5 2.1E+02 0.0046 19.2 4.7 31 8-38 43-73 (158)
54 PF04012 PspA_IM30: PspA/IM30 24.9 2.4E+02 0.0053 19.6 5.1 37 11-49 2-38 (221)
55 PF08945 Bclx_interact: Bcl-x 24.9 74 0.0016 18.3 2.0 11 11-21 23-33 (40)
56 PF12767 SAGA-Tad1: Transcript 24.8 2.2E+02 0.0048 20.6 5.0 51 12-62 19-74 (252)
57 PF04091 Sec15: Exocyst comple 24.8 2.3E+02 0.0049 21.5 5.2 57 6-66 175-231 (311)
58 smart00309 PAH Pancreatic horm 24.7 1.3E+02 0.0028 16.7 2.9 17 10-26 15-31 (36)
59 cd00126 PAH Pancreatic Hormone 24.7 1.3E+02 0.0028 16.7 2.9 18 9-26 14-31 (36)
60 PF02288 Dehydratase_MU: Dehyd 24.5 92 0.002 20.7 2.7 20 5-24 88-107 (112)
61 cd09034 BRO1_Alix_like Protein 24.5 2.9E+02 0.0064 20.3 7.8 56 8-63 201-264 (345)
62 PF15335 CAAP1: Caspase activi 24.5 71 0.0015 19.8 2.0 17 47-63 12-28 (64)
63 PHA02604 rI.-1 hypothetical pr 24.0 2.6E+02 0.0056 19.5 5.8 44 6-62 81-124 (126)
64 cd06943 NR_LBD_RXR_like The li 23.1 1.6E+02 0.0035 20.1 3.8 29 42-70 155-186 (207)
65 KOG1753 40S ribosomal protein 22.8 1.8E+02 0.0039 20.8 4.0 26 30-55 83-112 (145)
66 KOG4215 Hepatocyte nuclear fac 22.7 1.9E+02 0.0041 23.9 4.6 27 36-62 262-301 (432)
67 PF15508 NAAA-beta: beta subun 22.6 2E+02 0.0044 17.8 6.5 62 7-69 13-78 (95)
68 cd09242 BRO1_ScBro1_like Prote 22.6 3.5E+02 0.0077 20.6 6.7 58 9-66 195-260 (348)
69 COG1728 Uncharacterized protei 22.1 1.7E+02 0.0038 21.0 3.9 49 17-66 70-133 (151)
70 PF03489 SapB_2: Saposin-like 22.1 1.3E+02 0.0027 15.2 2.8 22 17-38 6-28 (35)
71 PF05794 Tcp11: T-complex prot 22.1 3.7E+02 0.008 20.6 6.0 52 17-72 31-83 (441)
72 cd09249 BRO1_Rhophilin_2 Prote 22.0 3.5E+02 0.0077 21.8 6.0 46 12-57 199-250 (385)
73 PF12449 DUF3684: Protein of u 21.7 62 0.0013 29.5 1.8 26 45-73 1039-1064(1093)
74 PF10408 Ufd2P_core: Ubiquitin 21.4 2.3E+02 0.005 23.2 4.9 58 9-66 488-551 (629)
75 PF02637 GatB_Yqey: GatB domai 21.1 1.5E+02 0.0032 19.6 3.2 20 22-43 2-21 (148)
76 PF10188 Oscp1: Organic solute 20.9 1.8E+02 0.0039 21.0 3.8 37 29-66 105-141 (173)
77 PLN00131 hypothetical protein; 20.8 80 0.0017 23.5 2.0 24 42-65 167-190 (218)
78 PRK15039 transcriptional repre 20.7 1.7E+02 0.0037 18.8 3.3 27 45-73 6-32 (90)
79 PF13474 SnoaL_3: SnoaL-like d 20.3 1.1E+02 0.0025 17.9 2.3 26 48-73 2-27 (121)
80 cd09241 BRO1_ScRim20-like Prot 20.3 4E+02 0.0086 20.3 8.1 60 9-68 193-255 (355)
No 1
>smart00302 GED Dynamin GTPase effector domain.
Probab=99.85 E-value=5e-21 Score=122.11 Aligned_cols=63 Identities=35% Similarity=0.528 Sum_probs=60.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
+.+++.|++++.|||++|+++++|+|||||+||+|+.++++|+++|+++||+.+. +++||+||
T Consensus 3 ~~~~~~i~~lv~sYf~iv~k~i~D~VPKaI~~~lv~~~~~~lq~~L~~~L~~~~~--~~~LL~E~ 65 (92)
T smart00302 3 DSELEEIKSLVKSYFTIVSKTLADQVPKAIMYLLVNESKDSLQNELLALLYKEEL--LDELLEED 65 (92)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHhCccc--HHHHHcCC
Confidence 4688999999999999999999999999999999999999999999999999877 99999997
No 2
>PF02212 GED: Dynamin GTPase effector domain; InterPro: IPR003130 Dynamin GTPase effector domain found in proteins related to dynamin. Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3ZYS_B 3SZR_A 3LJB_B 3T35_C 3T34_A 2X2F_D 2X2E_D 3SNH_A 3ZYC_D 3ZVR_A.
Probab=99.72 E-value=1.5e-17 Score=105.16 Aligned_cols=63 Identities=33% Similarity=0.491 Sum_probs=58.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
+.+.+.|...+.||+++|++++.|+|||||+||+|+.+++.|+++++++++..+. +++||.||
T Consensus 3 ~~~~~~i~~~l~aY~~ia~kr~~D~Vpk~I~~~lv~~~~~~L~~~l~~~l~~~~~--~~~Ll~Ed 65 (92)
T PF02212_consen 3 QREVEEIKALLRAYFEIARKRFIDSVPKAIMHFLVNKSKEQLQSELLNELYDEED--LEELLQED 65 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGG--CCCCT--G
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHhccchHH--HHHHHCCC
Confidence 3578899999999999999999999999999999999999999999999999998 89999997
No 3
>KOG0446 consensus Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport; General function prediction only]
Probab=99.53 E-value=3.3e-14 Score=116.09 Aligned_cols=67 Identities=30% Similarity=0.360 Sum_probs=62.4
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 6 ADPEEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 6 ~~~d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
.+.+.|.++|++++.+|++||+++|+|+||||||||||+.+|++|++.|+++|++ ..++++.||+||
T Consensus 560 ~~~~~~~~~i~~~~~sY~~iv~~~i~d~vpk~i~~~lv~~~k~~l~~~l~~~L~~-~~~~~~~ll~E~ 626 (657)
T KOG0446|consen 560 KRECKETEEISSCPESYLNIVSDKLVDTVPKALNHELLNEFKDDLPNELDQRLYA-GDEQLESLLKED 626 (657)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-chhHHHHHHccC
Confidence 3455699999999999999999999999999999999999999999999999999 477799999997
No 4
>PRK14126 cell division protein ZapA; Provisional
Probab=79.24 E-value=13 Score=23.40 Aligned_cols=61 Identities=11% Similarity=0.148 Sum_probs=42.3
Q ss_pred cCCChHHHHHHHHHHHHHHHHHHHHH-HHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhcc
Q 035101 5 LADPEEELRWISQKVSGYVEAVLNSL-AANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQE 72 (73)
Q Consensus 5 ~~~~d~~lr~i~~~V~sYv~~V~~tL-~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~E 72 (73)
+.++++|++.+++.|..-+.-+++.- .-+..++.|.+-+|=|- .++.. +++...|.+.|+|
T Consensus 22 ~~e~ee~l~~vA~~vd~km~ei~~~~~~ls~~~iAVLaALNia~-----El~k~--~~~~~~l~~~~~~ 83 (85)
T PRK14126 22 GDESTSHIRMVAAIVDDKMRELNEKNPSLDTSKLAVLTAVNVIH-----DYIKL--KEEYEKLKESMTK 83 (85)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH-----HHHHH--HHHHHHHHHHHhc
Confidence 56789999999999999999888764 35667888887775443 33332 3444446666554
No 5
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=79.09 E-value=3.1 Score=30.23 Aligned_cols=54 Identities=9% Similarity=0.208 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 17 QKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
..|.+.+.--++.|+...|... ...+..+.+++.|+..+.....+.|.+||.||
T Consensus 146 ~tVk~~l~RAr~~Lr~~~~~~~---~~~~~~~~~v~~f~~A~~~gD~~~l~~Lla~D 199 (293)
T PRK09636 146 AACRQLASRARKHVRAARPRFP---VSDEEGAELVEAFFAALASGDLDALVALLAPD 199 (293)
T ss_pred HHHHHHHHHHHHHHHhhCCCCC---CCchHHHHHHHHHHHHHHhCCHHHHHHHHhhC
Confidence 4566777777777777766421 12234567899999999999999999999987
No 6
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=75.88 E-value=4.2 Score=29.58 Aligned_cols=54 Identities=20% Similarity=0.263 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 17 QKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
..|.+.+.-.++.|++..|...+ -....+.+++.|...+.+.+...|.+||.||
T Consensus 139 ~tVr~~l~RAr~~Lr~~~~~~~~---~~~~~~~~~~~f~~a~~~gD~~~l~~lL~~d 192 (281)
T TIGR02957 139 ANCRQLVSRARRHLDARRPRFEV---SREESRQLLERFVEAAQTGDLDGLLELLAED 192 (281)
T ss_pred HHHHHHHHHHHHHHHhhCCCCCC---ChHHHHHHHHHHHHHHHhCCHHHHHHHHhhc
Confidence 45666777777777776653111 1235678999999999999999999999997
No 7
>PF09660 DUF2397: Protein of unknown function (DUF2397); InterPro: IPR013493 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=71.93 E-value=25 Score=28.39 Aligned_cols=61 Identities=13% Similarity=0.199 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhc
Q 035101 10 EELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQ 71 (73)
Q Consensus 10 ~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ 71 (73)
++|+.+.+|...|+......+....++.-.+-..+.+--.-|+.|...|..... +++.+|.
T Consensus 154 ~~f~~L~~na~df~~~L~~~~~~~~~~~e~Fl~yKd~Li~YL~~Fv~~L~r~~~-~I~~~l~ 214 (486)
T PF09660_consen 154 EDFERLAQNAQDFYASLQSVKAEEDMDTEAFLAYKDALIDYLRRFVQDLQRRAP-RIAAALR 214 (486)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhccChhHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 588999999999999999999999999999888888888999999999987765 5666554
No 8
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=71.31 E-value=6 Score=29.34 Aligned_cols=54 Identities=6% Similarity=0.007 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 17 QKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
..|.+.+.--++.|++..|..- ...+..+.|++.|.+.....+...|.+||.||
T Consensus 149 ~tVr~~l~RAr~~Lr~~~~~~~---~~~~~~~~~~~~f~~a~~~gd~~~l~~ll~~d 202 (290)
T PRK09635 149 STCRQLAHRARRKINESRIAAS---VEPAQHRVVTRAFIEACSNGDLDTLLEVLDPG 202 (290)
T ss_pred HHHHHHHHHHHHHHHhhCCCCC---CChHHHHHHHHHHHHHHHhCCHHHHHHHhhhh
Confidence 4556666666667776555311 11235678999999999999999999999987
No 9
>cd09240 BRO1_Alix Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains. This family contains the N-terminal, Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), also called apoptosis-linked gene-2 interacting protein 1 (AIP1). It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix 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 f
Probab=67.61 E-value=36 Score=25.93 Aligned_cols=60 Identities=13% Similarity=0.190 Sum_probs=46.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHh-----HHHHHH-HHHHHhHHHHHHHHHHHHHhhhcHHHHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAAN-----VPKAIV-LCQVEKAKEDMLNQLYSSVNAQSTAMIEE 68 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~s-----VPKAiV-hcqV~~aKr~Ll~~l~~~l~~~e~~ql~~ 68 (73)
++-+-+++..++.|++.+.+.+... +||-+. ||++..+-=.-+-++|..+...+..+.++
T Consensus 208 ~~liAKLa~qv~~~Y~~a~~~l~~~~~~~~~~~~W~~~~~~K~~~f~a~A~y~~a~~~~e~~k~Ge 273 (346)
T cd09240 208 DAIIAKLAAQAADYYGDAFKQCQREDVRSLLPKDWIPVLAGKQAYFHALAEYHQSLVAKAQKKFGE 273 (346)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcchhccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchHHH
Confidence 4677899999999999999988764 678776 88888777777788888877666655443
No 10
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=67.59 E-value=10 Score=23.16 Aligned_cols=29 Identities=21% Similarity=0.295 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 45 KAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 45 ~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
++-+.+++.|+..+.+.....+.+|+.||
T Consensus 3 ~~~~~~v~~~~~a~~~~D~~~~~~l~aed 31 (122)
T cd00781 3 QEMKAAVQRYVEAVNAGDPEGIVALFADD 31 (122)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHcCCC
Confidence 35567889999999999999999999887
No 11
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=62.67 E-value=12 Score=27.16 Aligned_cols=56 Identities=18% Similarity=0.216 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHH---HHHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 18 KVSGYVEAVLNSLAANVPKAIVLC---QVEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 18 ~V~sYv~~V~~tL~~sVPKAiVhc---qV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
.|.+.+.-.++.|+..++..-=-+ ......+.+++.||..+...+.+.+.+||.||
T Consensus 174 tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD~~~l~~Lla~D 232 (324)
T TIGR02960 174 SVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYDLDALTALLHED 232 (324)
T ss_pred HHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCCHHHHHHHhcCC
Confidence 445555555566665555320000 12235668899999999999999999999987
No 12
>TIGR02677 conserved hypothetical protein TIGR02677. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).
Probab=61.39 E-value=41 Score=27.47 Aligned_cols=61 Identities=10% Similarity=0.124 Sum_probs=50.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhh
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELL 70 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL 70 (73)
.++|..+..|...|+..+...+.....+.--+-..++.--.-|+.|+..|..... +|+..|
T Consensus 151 ~~~f~~L~~na~df~~~L~~~~~~~~~~~e~Fl~yKd~Li~YL~~Fv~~L~~~~~-~I~~~l 211 (494)
T TIGR02677 151 YGSFESLADNAQAFMADLQRHRPLEVADYEAFLAYKDRLIAYLQDFIVRLVDRSE-QIAQLL 211 (494)
T ss_pred HHHHHHHHHHHHHHHHHHcccchhhhcChhHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 4688999999999999999999988888887777877777888889988886655 565555
No 13
>COG3951 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=56.38 E-value=48 Score=24.13 Aligned_cols=53 Identities=25% Similarity=0.430 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHH-HHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcH
Q 035101 6 ADPEEELRWISQKVSG-YVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQST 63 (73)
Q Consensus 6 ~~~d~~lr~i~~~V~s-Yv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~ 63 (73)
.||..+|+..+..+-+ +++|..++++.+.||---- --++=..++|+++|-+..
T Consensus 25 ~d~~~~l~~~ArqfE~vFv~mMLKSMR~Al~~~~~d-----l~~S~q~rlYtdmyDqql 78 (166)
T COG3951 25 RDPAANLRQVARQFEGVFVQMMLKSMREALPKDGAD-----LFNSQQTRLYTDMYDQQL 78 (166)
T ss_pred cCcHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcch-----hccchhHHHHHHHHHHHH
Confidence 4999999999999876 7899999999999986421 122334566666665443
No 14
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=52.68 E-value=86 Score=22.95 Aligned_cols=67 Identities=7% Similarity=0.100 Sum_probs=36.6
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHH----------------------HhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcH
Q 035101 6 ADPEEELRWISQKVSGYVEAVLNSLA----------------------ANVPKAIVLCQVEKAKEDMLNQLYSSVNAQST 63 (73)
Q Consensus 6 ~~~d~~lr~i~~~V~sYv~~V~~tL~----------------------~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~ 63 (73)
-+.|.|+.||+-.++-|..|+..... |.-|-.-+|+-|-.+==+.--+.+-++|+...
T Consensus 167 E~~~~y~~Rm~Gi~~lyaAi~~~~~~~~~~~~~p~~~~~~W~wlAr~lN~~p~~~~~~~lL~~~Le~ag~~l~~~Yg~Qf 246 (256)
T PF07817_consen 167 ESEDQYLKRMTGIIRLYAAIIQTPPPKGQKTSNPHGLEHGWRWLARILNLPPAPNITATLLHSFLEVAGFRLLQIYGRQF 246 (256)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHS---CCCCTT-SS-THHHHHHHHHHHCS-CC-HHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred cchHHHHHHHHHHHHHHHHHHhccCCcCCCCCCCCCcHHHHHHHHHHhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999875433 33343445554443333333344445555555
Q ss_pred HHHHHhhcc
Q 035101 64 AMIEELLQE 72 (73)
Q Consensus 64 ~ql~~LL~E 72 (73)
..+-+++.|
T Consensus 247 ~Kll~~i~~ 255 (256)
T PF07817_consen 247 VKLLQLISE 255 (256)
T ss_dssp HHHHHHHHT
T ss_pred HHHHHHHhc
Confidence 444454444
No 15
>TIGR02246 conserved hypothetical protein. This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown.
Probab=51.34 E-value=34 Score=20.57 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=23.5
Q ss_pred hHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 45 KAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 45 ~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
++-+.|++.++..+...+...+.++..||
T Consensus 4 ~~i~~l~~~~~~a~~~~D~~~~~~~~~~D 32 (128)
T TIGR02246 4 RAIRALVATWEAAWAAGDAEGFADLFTPD 32 (128)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHhhCCC
Confidence 45567888899999998888888887775
No 16
>PF09355 Phage_Gp19: Phage protein Gp19/Gp15/Gp42; InterPro: IPR018963 This entry is represented by Mycobacteriophage D29, Gp19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=51.11 E-value=26 Score=23.35 Aligned_cols=29 Identities=21% Similarity=0.396 Sum_probs=24.1
Q ss_pred ccccCCChHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 035101 2 ARRLADPEEELRWISQKVSGYVEAVLNSLAANVP 35 (73)
Q Consensus 2 ~~~~~~~d~~lr~i~~~V~sYv~~V~~tL~~sVP 35 (73)
+-||.+||+. ..+......+...|+..+|
T Consensus 1 l~R~Lt~~E~-----~~a~~LL~~As~~Ir~~~~ 29 (116)
T PF09355_consen 1 LWRPLTPEEQ-----ARAEALLEDASDLIRDRIP 29 (116)
T ss_pred CCCCCCHHHH-----HHHHHHHHHHHHHHHHhhh
Confidence 3588999988 6777888888999999888
No 17
>COG3027 zapA Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]
Probab=50.11 E-value=26 Score=23.12 Aligned_cols=43 Identities=16% Similarity=0.098 Sum_probs=30.2
Q ss_pred ccCCChHHHHHHHHHHHHHHHHHHHH------HHHhHHH--HHHHHHHHhH
Q 035101 4 RLADPEEELRWISQKVSGYVEAVLNS------LAANVPK--AIVLCQVEKA 46 (73)
Q Consensus 4 ~~~~~d~~lr~i~~~V~sYv~~V~~t------L~~sVPK--AiVhcqV~~a 46 (73)
=|.+-++||+.++..+..|+..++.+ .+-.|== -|+||++..-
T Consensus 17 c~~~qee~L~~~A~~lD~kv~eik~~~~~~~~~rl~vmaAlNv~~eL~~l~ 67 (105)
T COG3027 17 CPEEQEEHLRQAARLLDDKVRELKESNGVLDTERLAVMAALNVMHELLKLK 67 (105)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHHHHHHH
Confidence 37788999999999999999987653 2222222 2678877443
No 18
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=48.54 E-value=70 Score=20.66 Aligned_cols=62 Identities=10% Similarity=0.148 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHH----HHHHHHHHHHhHHHHHHH----HHHHhHHHHHHHHHHHHHhhhcHHHHHHhhc
Q 035101 10 EELRWISQKVSGY----VEAVLNSLAANVPKAIVL----CQVEKAKEDMLNQLYSSVNAQSTAMIEELLQ 71 (73)
Q Consensus 10 ~~lr~i~~~V~sY----v~~V~~tL~~sVPKAiVh----cqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ 71 (73)
...|.||+.|.+- ++.+.+.....+-+|.-+ -....|-..+.-.|=..+...|.+.|.++++
T Consensus 10 ~~y~~lg~~va~~~~~~~~~~~~~Y~~~l~~al~~~~~~~~~~Nvl~Hi~Gyfk~~ls~~EK~~~~~~i~ 79 (117)
T PF08349_consen 10 KIYRELGRLVANAGKRPLEEVFEEYEELLMEALSKPPTRGSHINVLQHIFGYFKKKLSSEEKQHFLDLIE 79 (117)
T ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 4567777766652 233333333333333222 2333455566777778888888888888875
No 19
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=48.23 E-value=28 Score=25.56 Aligned_cols=55 Identities=20% Similarity=0.253 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHH----HHhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 17 QKVSGYVEAVLNSLAANVPKAIVLCQ----VEKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sVPKAiVhcq----V~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
..|.+.+.-.++.|+..-|++. |. -.+....+...||..+.+.+...+.+||.||
T Consensus 184 ~tVk~~l~RAr~~Lr~~~~~~~--~~~~~~~~~~~~~~v~~~~~A~~~gD~~~l~~lla~D 242 (339)
T PRK08241 184 AAVNSALQRARATLAERGPSAA--DTLREPDDPEERALLARYVAAFEAYDVDALVALLTED 242 (339)
T ss_pred HHHHHHHHHHHHHHhhcCCCcc--cccCCCCChHHHHHHHHHHHHHhcCCHHHHHHHhcCC
Confidence 4455666666667777555311 10 1144567788999999999999999999987
No 20
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=48.23 E-value=49 Score=19.60 Aligned_cols=44 Identities=18% Similarity=0.218 Sum_probs=31.3
Q ss_pred cCCChHHHHHHHHHHHHHHHHHHHHH-HHhHHHHHHHHHHHhHHH
Q 035101 5 LADPEEELRWISQKVSGYVEAVLNSL-AANVPKAIVLCQVEKAKE 48 (73)
Q Consensus 5 ~~~~d~~lr~i~~~V~sYv~~V~~tL-~~sVPKAiVhcqV~~aKr 48 (73)
|.++++++++++..|...++-+.+.- ..+.-++.+.+.++-|-+
T Consensus 16 ~~~~ee~l~~~a~~i~~~i~~~~~~~~~~~~~~~~vlaaLnla~e 60 (89)
T PF05164_consen 16 PDEDEEYLRKAAELINEKINEIKKKYPKLSPERLAVLAALNLADE 60 (89)
T ss_dssp TGCGHHHHHHHHHHHHHHHHHHCTTCCTSSHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 67889999999999999999888764 233445555555554443
No 21
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=46.49 E-value=40 Score=22.33 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=20.3
Q ss_pred HHHHHHHHHHH--HHhhhcHHHHHHhhcc
Q 035101 46 AKEDMLNQLYS--SVNAQSTAMIEELLQE 72 (73)
Q Consensus 46 aKr~Ll~~l~~--~l~~~e~~ql~~LL~E 72 (73)
+-..++.+|+. ++..+|.++|.++|++
T Consensus 88 s~~~ll~~l~~~~~ls~eele~L~~li~~ 116 (130)
T TIGR02698 88 KVGAVIADLIEESPLSQTDIEKLEKLLSE 116 (130)
T ss_pred CHHHHHHHHHhcCCCCHHHHHHHHHHHHh
Confidence 33456677766 7888899999998876
No 22
>cd09244 BRO1_Rhophilin Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin and related domains. This family contains the Bro1-like domain of RhoA-binding proteins, Rhophilin-1 and -2, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-1 and -2, contain an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Their PDZ domains have limited homology. Rhophilin-1 and -2 have different ac
Probab=44.36 E-value=1.1e+02 Score=23.80 Aligned_cols=53 Identities=17% Similarity=0.208 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----hHHHHH-HHHHHHhHHHHHHHHHHHHHhhhcHH
Q 035101 12 LRWISQKVSGYVEAVLNSLAA-----NVPKAI-VLCQVEKAKEDMLNQLYSSVNAQSTA 64 (73)
Q Consensus 12 lr~i~~~V~sYv~~V~~tL~~-----sVPKAi-VhcqV~~aKr~Ll~~l~~~l~~~e~~ 64 (73)
+-+++..|+.|++.+.+.+.. .+|+.+ -|+++...-=.=+-++|..+.-.+.+
T Consensus 200 lAklA~qv~~~Y~~a~~~~~~~~~~~~i~~~W~~~v~~K~~~f~AlA~y~~a~~l~~~~ 258 (350)
T cd09244 200 LAQEAAQVSDCYSEVHKLMNQEPVKDYIPYSWISLVEVKSEHYKALAHYYAAMGLLLEE 258 (350)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 677899999999999998653 378765 56777766555566667666444433
No 23
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=41.32 E-value=58 Score=20.60 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=17.7
Q ss_pred HHHHHHHHHHH--HhhhcHHHHHHhhcc
Q 035101 47 KEDMLNQLYSS--VNAQSTAMIEELLQE 72 (73)
Q Consensus 47 Kr~Ll~~l~~~--l~~~e~~ql~~LL~E 72 (73)
-..++.+|+.+ +..++.++|+++|+|
T Consensus 88 ~~~l~~~l~~~~~ls~~el~~L~~li~e 115 (115)
T PF03965_consen 88 IPQLVAALVESEELSPEELEELRKLIDE 115 (115)
T ss_dssp HHHHHHHHHHCT-S-HHHHHHHHHHHH-
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHcC
Confidence 33556666665 888888899998876
No 24
>PF14002 YniB: YniB-like protein
Probab=40.79 E-value=59 Score=23.62 Aligned_cols=25 Identities=24% Similarity=0.130 Sum_probs=22.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHhh
Q 035101 36 KAIVLCQVEKAKEDMLNQLYSSVNA 60 (73)
Q Consensus 36 KAiVhcqV~~aKr~Ll~~l~~~l~~ 60 (73)
=|=|.|||+.-++++.|+++-+-.+
T Consensus 94 G~rm~rqvk~ire~IEdqlIlE~ak 118 (166)
T PF14002_consen 94 GARMSRQVKFIREGIEDQLILEQAK 118 (166)
T ss_pred hhHHHHHHHHHHHhHHHHHHHHHhc
Confidence 3568899999999999999988777
No 25
>PF07923 N1221: N1221-like protein; InterPro: IPR012486 The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome (P53917 from SWISSPROT). This encodes an acidic polypeptide with several possible transmembrane regions [].
Probab=40.10 E-value=1.5e+02 Score=21.93 Aligned_cols=57 Identities=25% Similarity=0.396 Sum_probs=38.1
Q ss_pred CChHHHHHHHHHHHHHHH-----HHHHHHHHhHHH--------------------------HHHHHHHHhHHHH------
Q 035101 7 DPEEELRWISQKVSGYVE-----AVLNSLAANVPK--------------------------AIVLCQVEKAKED------ 49 (73)
Q Consensus 7 ~~d~~lr~i~~~V~sYv~-----~V~~tL~~sVPK--------------------------AiVhcqV~~aKr~------ 49 (73)
..++++.||..|+.--++ .+.+.|...+=+ .|+|++|.-+.++
T Consensus 97 s~~~ql~~i~~N~~lL~~~g~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~el~~~LTilY~~vev~r~~~~~~~~ 176 (293)
T PF07923_consen 97 SEEEQLQWIRRNVFLLYECGGFPALWELLKMFIENSWSCDDQDSNLPAVSLADSTELRVLLTILYFMVEVARRDRDSPEW 176 (293)
T ss_pred CHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhccccccccccccccccchHHHHHHHHHHHHHHHHHHHhccccchh
Confidence 567899999988865554 555444433322 3788888887777
Q ss_pred --HHHHHHHHHhhhcH
Q 035101 50 --MLNQLYSSVNAQST 63 (73)
Q Consensus 50 --Ll~~l~~~l~~~e~ 63 (73)
..+.|...|+....
T Consensus 177 ~~~~~~~~~~L~~p~l 192 (293)
T PF07923_consen 177 MAIVREFIMELEEPNL 192 (293)
T ss_pred hHHHHHHHHHhcCCcH
Confidence 66777777766554
No 26
>cd09246 BRO1_Alix_like_1 Protein-interacting, N-terminal, Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily. This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix 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 and Bro
Probab=38.14 E-value=1.8e+02 Score=22.23 Aligned_cols=59 Identities=14% Similarity=0.140 Sum_probs=44.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH-----hHHHH-HHHHHHHhHHHHHHHHHHHHHhhhcHHHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAA-----NVPKA-IVLCQVEKAKEDMLNQLYSSVNAQSTAMIE 67 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~-----sVPKA-iVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~ 67 (73)
++-+-+++..|+.|++.+.+.+.. .+|+. +-||++..+-=.-+-++|....-.+..+.+
T Consensus 200 ~sliAKLa~qv~~~Y~~a~~~l~~~~~~~~~~~~W~~~~~~K~~~f~A~A~~~~a~~~~~~~k~G 264 (353)
T cd09246 200 PAVCSKLAKQARSYYEEALEALDSPPLKGHFDKSWVAHVQLKAAYFRAEALYRAAKDLHEKEDIG 264 (353)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcchH
Confidence 356778999999999999988764 35776 578998887777777777777665554443
No 27
>PHA02754 hypothetical protein; Provisional
Probab=37.85 E-value=67 Score=20.14 Aligned_cols=25 Identities=28% Similarity=0.404 Sum_probs=20.0
Q ss_pred HHhHHHHHHHHHHHhHHHHHHHHHH
Q 035101 31 AANVPKAIVLCQVEKAKEDMLNQLY 55 (73)
Q Consensus 31 ~~sVPKAiVhcqV~~aKr~Ll~~l~ 55 (73)
+.-+|||+|---..++.|+|-+.|-
T Consensus 4 AeEi~k~i~eK~Fke~MRelkD~LS 28 (67)
T PHA02754 4 AEEIPKAIMEKDFKEAMRELKDILS 28 (67)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHh
Confidence 4568999999888888888776653
No 28
>PF12731 Mating_N: Mating-type protein beta 1; InterPro: IPR024333 This entry represents a group of homeodomain-containing transcription factor proteins involved in mating [].
Probab=37.47 E-value=70 Score=20.31 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=20.2
Q ss_pred HHHHhHHHHHHHHHHHHHhhhcHH
Q 035101 41 CQVEKAKEDMLNQLYSSVNAQSTA 64 (73)
Q Consensus 41 cqV~~aKr~Ll~~l~~~l~~~e~~ 64 (73)
+.|+.+-..+...|++.|.+.+..
T Consensus 12 ~~I~~~L~~~e~~fl~sL~~g~~~ 35 (95)
T PF12731_consen 12 ADIRQALQALEADFLSSLRGGSDA 35 (95)
T ss_pred HHHHHHHHHHHHHHHHHHhCChHH
Confidence 577888889999999999988853
No 29
>COG0699 Predicted GTPases (dynamin-related) [General function prediction only]
Probab=35.88 E-value=1.9e+02 Score=21.87 Aligned_cols=31 Identities=16% Similarity=0.079 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 035101 12 LRWISQKVSGYVEAVLNSLAANVPKAIVLCQV 43 (73)
Q Consensus 12 lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV 43 (73)
.+.|.+.+++| .++...+++.+++++..-..
T Consensus 462 ~~~i~~l~~~~-~~~~~~~~~~~~~~~~~~~~ 492 (546)
T COG0699 462 KQLIKSLLESL-LILAQKIRDSVLKAIFELLK 492 (546)
T ss_pred hHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 46678999999 99999999999999887543
No 30
>COG1937 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.85 E-value=69 Score=20.76 Aligned_cols=28 Identities=32% Similarity=0.430 Sum_probs=23.2
Q ss_pred HhHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 44 EKAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 44 ~~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
.+.|+.|+++|=+-=|.-++ ++.|++||
T Consensus 5 ~~~kkkl~~RlrRi~GQv~g--I~rMlEe~ 32 (89)
T COG1937 5 IEEKKKLLNRLRRIEGQVRG--IERMLEED 32 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHH--HHHHHhCC
Confidence 35688889999888888888 89999886
No 31
>TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
Probab=34.42 E-value=57 Score=19.79 Aligned_cols=25 Identities=20% Similarity=0.318 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 49 DMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 49 ~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
.+...||..+.+...+.+.+++.+|
T Consensus 2 ~iv~~~~~a~~~~d~~~~~~~~~~d 26 (129)
T TIGR02096 2 ELAQHWIEAFNRGDMDAVLALLAED 26 (129)
T ss_pred HHHHHHHHHHHCCCHHHHHHhcCCC
Confidence 3567788889888888888888876
No 32
>KOG2176 consensus Exocyst complex, subunit SEC15 [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.17 E-value=2.3e+02 Score=25.17 Aligned_cols=58 Identities=14% Similarity=0.187 Sum_probs=46.6
Q ss_pred cCCChHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHH
Q 035101 5 LADPEEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMI 66 (73)
Q Consensus 5 ~~~~d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql 66 (73)
|-||++++ ..+..|.+++-.+-....|+-|-.-.-..+-.+|-..++.=+...+.+|+
T Consensus 625 pq~~~~~i----~e~~~yLet~~~s~~q~LP~~v~~~v~~~~~~his~~iv~llldd~ik~i 682 (800)
T KOG2176|consen 625 PQGPSEYI----NEMLIYLETMFSSALQILPYKVAQLVCLRELDHISTSIVGLLLDDSIKQI 682 (800)
T ss_pred CCCccHHH----HHHHHHHHHHHHHHHhhCcHHHHHHHHHHHHHHHHHHHHHHHhCchHHHH
Confidence 66777775 67888999999999999999888877777777777777777777777766
No 33
>PRK11426 hypothetical protein; Provisional
Probab=33.99 E-value=71 Score=22.19 Aligned_cols=37 Identities=22% Similarity=0.197 Sum_probs=27.9
Q ss_pred ccCCChH--------HHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 035101 4 RLADPEE--------ELRWISQKVSGYVEAVLNSLAANVPKAIVL 40 (73)
Q Consensus 4 ~~~~~d~--------~lr~i~~~V~sYv~~V~~tL~~sVPKAiVh 40 (73)
.|++||. -+..+++.+--=-+.+.+.|+...|++|=+
T Consensus 59 ~pIs~~ql~~~lG~d~i~~lA~q~Gl~~~~~~~~LA~~LP~~VDk 103 (132)
T PRK11426 59 QSVSGEQLESALGTNAVSDLGQKLGVDTSTASSLLAEQLPKIIDA 103 (132)
T ss_pred CCCCHHHHHHHhChHHHHHHHHHHCcCHHHHHHHHHHHhHHHHhc
Confidence 4666664 566667766666788999999999998754
No 34
>PF02583 Trns_repr_metal: Metal-sensitive transcriptional repressor; InterPro: IPR003735 This entry describes proteins of unknown function.; PDB: 2HH7_A 3AAI_A 4ADZ_B.
Probab=33.69 E-value=79 Score=19.64 Aligned_cols=27 Identities=33% Similarity=0.508 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 45 KAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 45 ~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
+.|+.++++|-+--|.-.+ +..|++||
T Consensus 2 ~~k~~ll~RL~rIeGQv~g--I~~Miee~ 28 (85)
T PF02583_consen 2 EDKKDLLNRLKRIEGQVRG--IERMIEED 28 (85)
T ss_dssp HHHHHHHHHHHHHHHHHHH--HHHHHHTT
T ss_pred chHHHHHHHHHHHHHHHHH--HHHHHhCC
Confidence 3567788888888777777 88888765
No 35
>cd09239 BRO1_HD-PTP_like Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains. This family contains the N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP) and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. HD-PTP participates in cell migration and endosomal trafficking. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-l
Probab=33.65 E-value=2.3e+02 Score=21.98 Aligned_cols=59 Identities=17% Similarity=0.178 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH----------hHHHHH-HHHHHHhHHHHHHHHHHHHHhhhcHHHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAA----------NVPKAI-VLCQVEKAKEDMLNQLYSSVNAQSTAMIE 67 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~----------sVPKAi-VhcqV~~aKr~Ll~~l~~~l~~~e~~ql~ 67 (73)
++-+-+++..++.|++-+.+.+.. .+||.+ -||++..+-=.-+-++|..+...+..+.+
T Consensus 200 ~sliAKLA~q~~~~Y~~a~~~l~~~~~~~~~~~~~i~~~W~~~v~~K~~~f~A~A~y~~a~~~~~~~k~G 269 (361)
T cd09239 200 SHITAKVSAQVVEYYKEALRALENWESNSKIILGKIQKEWRKLVQMKIAYYASIAHLHMGKQSEEQQKMG 269 (361)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhcccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 355779999999999999988663 477754 67888877767777888877766665554
No 36
>PF03937 Sdh5: Flavinator of succinate dehydrogenase; InterPro: IPR005631 This entry represents a group of uncharacterised small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [] and YgfY from Escherichia coli []. YgfY may be involved in transcriptional regulation. The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. ; PDB: 2LM4_A 1PUZ_A 2JR5_A 1X6I_A 1X6J_A.
Probab=33.25 E-value=54 Score=19.89 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=17.6
Q ss_pred HHHHHHHHHhhhcHHHHHHhhccC
Q 035101 50 MLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 50 Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
-+++.|.++...+..+|+.||+.+
T Consensus 24 f~~~~~~~l~~~el~~fe~lL~~~ 47 (74)
T PF03937_consen 24 FADAHLDSLSEEELDAFERLLDLE 47 (74)
T ss_dssp HHHHHHHHS-HHHHHHHHHHHTS-
T ss_pred HHHHHHhhCCHHHHHHHHHHHcCC
Confidence 345667888899999999999763
No 37
>cd07608 BAR_ArfGAP_fungi The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized fungal Arf GAP proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of uncharacterized fungal proteins containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, and an Arf GTPase Activating Protein (GAP) domain. These proteins may play roles in Arf-mediated functions involving membrane dynamics. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=33.20 E-value=79 Score=23.14 Aligned_cols=28 Identities=7% Similarity=0.039 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAANVPK 36 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~sVPK 36 (73)
|+++..+..++..|...+|..+...|=-
T Consensus 57 ~~yf~~~~~~~~~~~~~~~~~lq~~~ie 84 (192)
T cd07608 57 DSYFDPFLLNLAFFLRDVCQDLQLKKIE 84 (192)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999999998876533
No 38
>PF13228 DUF4037: Domain of unknown function (DUF4037)
Probab=32.21 E-value=60 Score=20.81 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=22.0
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHH
Q 035101 6 ADPEEELRWISQKVSGYVEAVLNSL 30 (73)
Q Consensus 6 ~~~d~~lr~i~~~V~sYv~~V~~tL 30 (73)
.||.+.|..+.+.+..|.+-|+..+
T Consensus 19 ~D~~G~~~~~R~~l~~YP~dl~~~~ 43 (100)
T PF13228_consen 19 YDPLGEFTALRERLAYYPEDLRLNK 43 (100)
T ss_pred ECCCchHHHHHHHHHHChHHHHHHH
Confidence 5899999999999999999988773
No 39
>KOG2956 consensus CLIP-associating protein [General function prediction only]
Probab=32.06 E-value=41 Score=28.30 Aligned_cols=17 Identities=35% Similarity=0.589 Sum_probs=14.4
Q ss_pred HHHHHHhHHHHHHHHHH
Q 035101 27 LNSLAANVPKAIVLCQV 43 (73)
Q Consensus 27 ~~tL~~sVPKAiVhcqV 43 (73)
+++-..+|=|++|+|+|
T Consensus 457 y~S~SS~VRKtaVfCLV 473 (516)
T KOG2956|consen 457 YDSTSSTVRKTAVFCLV 473 (516)
T ss_pred hcCchHHhhhhHHHhHH
Confidence 45667789999999999
No 40
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=32.06 E-value=92 Score=17.22 Aligned_cols=18 Identities=28% Similarity=0.342 Sum_probs=13.3
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 035101 9 EEELRWISQKVSGYVEAV 26 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V 26 (73)
.+.|++--+.++-|+++|
T Consensus 14 peel~~Y~~~L~~Y~~lv 31 (36)
T PF00159_consen 14 PEELAQYYAALRHYINLV 31 (36)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 456777777888888776
No 41
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=31.05 E-value=1.9e+02 Score=22.73 Aligned_cols=46 Identities=22% Similarity=0.323 Sum_probs=32.5
Q ss_pred cCCChHHHHHHHHHHHHHH-HHHHHHHH-HhHHHHHHHHHHHhHHH----HHHHHHHHHHhhh
Q 035101 5 LADPEEELRWISQKVSGYV-EAVLNSLA-ANVPKAIVLCQVEKAKE----DMLNQLYSSVNAQ 61 (73)
Q Consensus 5 ~~~~d~~lr~i~~~V~sYv-~~V~~tL~-~sVPKAiVhcqV~~aKr----~Ll~~l~~~l~~~ 61 (73)
|+.||.+ +|| +.+.+-++ +.||||. -+|+|||+ +=.+.|+.++.++
T Consensus 251 ~v~~dTe---------~Yy~~aI~~AVk~gDi~KAL--~LldEAe~LG~~~Ar~tFik~V~~k 302 (303)
T PRK10564 251 PMLNDTE---------SYFNQAIKQAVKKGDVDKAL--KLLDEAERLGSTSARSTFISSVKGK 302 (303)
T ss_pred ccCchHH---------HHHHHHHHHHHHcCCHHHHH--HHHHHHHHhCCchHHHHHHHHhhcC
Confidence 5566665 555 67777776 4699996 48999997 4567777777654
No 42
>COG3242 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.80 E-value=30 Score=21.48 Aligned_cols=10 Identities=30% Similarity=0.681 Sum_probs=8.9
Q ss_pred ChHHHHHHHH
Q 035101 8 PEEELRWISQ 17 (73)
Q Consensus 8 ~d~~lr~i~~ 17 (73)
||++||++|-
T Consensus 38 pd~~LR~~G~ 47 (62)
T COG3242 38 PDNQLRRFGG 47 (62)
T ss_pred CHHHHHHHhh
Confidence 8999999984
No 43
>PF08111 Pea-VEAacid: Pea-VEAacid family; InterPro: IPR012593 This family consists of the PEA-VEAacid neuropeptides family. These neuropeptides are isolated from the abdominal perisympathetic organs of the American cockroach. These peptides are found together with Pea-YLS-amide and Pea-SKNacid, giving a unique neuropeptide pattern in abdominal perisympathetic organs. The functions of these neuropeptides are unknown [].; GO: 0005184 neuropeptide hormone activity, 0007218 neuropeptide signaling pathway, 0005576 extracellular region
Probab=30.71 E-value=8.8 Score=17.81 Aligned_cols=9 Identities=44% Similarity=0.752 Sum_probs=6.6
Q ss_pred HHHHHHHHH
Q 035101 16 SQKVSGYVE 24 (73)
Q Consensus 16 ~~~V~sYv~ 24 (73)
|+.|.||++
T Consensus 6 gshvdsyve 14 (15)
T PF08111_consen 6 GSHVDSYVE 14 (15)
T ss_pred ccchhhhcc
Confidence 466888876
No 44
>PF15178 TOM_sub5: Mitochondrial import receptor subunit TOM5 homolog
Probab=30.52 E-value=68 Score=19.22 Aligned_cols=17 Identities=35% Similarity=0.399 Sum_probs=14.8
Q ss_pred cCCChHHHHHHHHHHHH
Q 035101 5 LADPEEELRWISQKVSG 21 (73)
Q Consensus 5 ~~~~d~~lr~i~~~V~s 21 (73)
-+|||+.-|++++.|-+
T Consensus 10 k~DPeE~k~kmR~dvis 26 (51)
T PF15178_consen 10 KMDPEEMKRKMREDVIS 26 (51)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 47999999999998865
No 45
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=30.15 E-value=46 Score=22.85 Aligned_cols=25 Identities=12% Similarity=0.347 Sum_probs=21.1
Q ss_pred HHHHHHHHHH--HhhhcHHHHHHhhcc
Q 035101 48 EDMLNQLYSS--VNAQSTAMIEELLQE 72 (73)
Q Consensus 48 r~Ll~~l~~~--l~~~e~~ql~~LL~E 72 (73)
.+|+-+|... ++..+.++|.++|+|
T Consensus 92 ~~lv~~F~~~~~l~~~eie~L~~il~~ 118 (123)
T COG3682 92 ASLVAHFAEKEKLTADEIEALKAILDE 118 (123)
T ss_pred hHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence 4667888888 999999999999885
No 46
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=30.05 E-value=1.6e+02 Score=20.97 Aligned_cols=38 Identities=11% Similarity=0.267 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHH
Q 035101 10 EELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKED 49 (73)
Q Consensus 10 ~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~ 49 (73)
+-|.||+..|++.++-+.+.+.| |-..+=-.+++....
T Consensus 2 ~if~Rl~~iv~a~~n~~~dk~ED--P~~~l~q~irem~~~ 39 (219)
T TIGR02977 2 GIFSRFADIVNSNLNALLDKAED--PEKMIRLIIQEMEDT 39 (219)
T ss_pred cHHHHHHHHHHHHHHHHHHhccC--HHHHHHHHHHHHHHH
Confidence 35889999999999999999998 766555555444443
No 47
>PRK07217 replication factor A; Reviewed
Probab=29.47 E-value=1.5e+02 Score=23.30 Aligned_cols=55 Identities=11% Similarity=0.186 Sum_probs=36.1
Q ss_pred CChHHHHHHHHHHHHH-HHHHHHHHHHhHHHHHHHH--HHHhHHHHHHHHHHHHHhhh
Q 035101 7 DPEEELRWISQKVSGY-VEAVLNSLAANVPKAIVLC--QVEKAKEDMLNQLYSSVNAQ 61 (73)
Q Consensus 7 ~~d~~lr~i~~~V~sY-v~~V~~tL~~sVPKAiVhc--qV~~aKr~Ll~~l~~~l~~~ 61 (73)
|-+.|...|+...+.. ++.=++.+..-+-+-|--| .+.+|+|+++|+++.+.+..
T Consensus 3 ~~~~~aeei~~~~s~lgvdv~~~~ie~~L~~Lv~ey~VP~~EA~rSv~~~~~~k~g~~ 60 (311)
T PRK07217 3 DLRQHAEEIHEQFSDLGVDVSVEDVEERLDTLVTEFKVPEDEARRSVTNYYLKEAGID 60 (311)
T ss_pred cHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCC
Confidence 3467888888777776 4433344444444444333 45899999999999988764
No 48
>PF08360 TetR_C_5: QacR-like protein, C-terminal region; InterPro: IPR013571 This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump []. The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites []. The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G0E_E 1JUM_A 1RPW_D 1QVT_B 2HQ5_D 1JT0_B 2DTZ_E 1JUP_D 1JT6_D 1JUS_E ....
Probab=29.07 E-value=83 Score=20.97 Aligned_cols=54 Identities=20% Similarity=0.350 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHhHH-HHHHHHHHHHHhhhcHHHHHHhhcc
Q 035101 18 KVSGYVEAVLNSLAANVPKAIVLCQVEKAK-EDMLNQLYSSVNAQSTAMIEELLQE 72 (73)
Q Consensus 18 ~V~sYv~~V~~tL~~sVPKAiVhcqV~~aK-r~Ll~~l~~~l~~~e~~ql~~LL~E 72 (73)
-+.+|.+-+...+...+.||..-|..+..+ ...++.++. |..+...-+.++|+|
T Consensus 22 KLy~~a~~~~~~i~~pl~~a~~EF~~~~~~~~ev~~~l~~-i~~~~~~~~~~ilee 76 (131)
T PF08360_consen 22 KLYGMAEHMLDDIQTPLSKAGEEFYSNQSKNPEVLEKLNE-IRRKYLEFFQKILEE 76 (131)
T ss_dssp HHHHHHHHHHHSSSGGGHHHHHHHHHHCSSSHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHcccCCHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 456777777788999999999999887533 346777666 555666566777764
No 49
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=28.47 E-value=56 Score=22.28 Aligned_cols=19 Identities=21% Similarity=0.513 Sum_probs=14.0
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 035101 9 EEELRWISQKVSGYVEAVL 27 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~ 27 (73)
|--||+|||.+-.|+....
T Consensus 65 dYnLRrIGSdLE~~iR~LL 83 (108)
T PF10664_consen 65 DYNLRRIGSDLEHFIRSLL 83 (108)
T ss_pred hhhHHHhccHHHHHHHHHH
Confidence 3468999998888876543
No 50
>PF11960 DUF3474: Domain of unknown function (DUF3474); InterPro: IPR021863 This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 126 to 140 amino acids in length. This domain is found associated with PF00487 from PFAM. ; GO: 0016717 oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water, 0055114 oxidation-reduction process
Probab=26.42 E-value=52 Score=23.17 Aligned_cols=27 Identities=26% Similarity=0.449 Sum_probs=20.5
Q ss_pred HHHHHHhHHHHHHHHHHHhHHHHHHHHHHHH
Q 035101 27 LNSLAANVPKAIVLCQVEKAKEDMLNQLYSS 57 (73)
Q Consensus 27 ~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~ 57 (73)
.+.|++.||| ||-++..-++| ..+...
T Consensus 101 L~dIraAIPk---HCf~k~~~rS~-sYv~rD 127 (136)
T PF11960_consen 101 LADIRAAIPK---HCFVKSPWRSM-SYVVRD 127 (136)
T ss_pred HHHHHhhcCh---hhcCCChHHHH-HHHHHH
Confidence 4678999999 99999999984 444433
No 51
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=26.35 E-value=1.6e+02 Score=18.98 Aligned_cols=34 Identities=21% Similarity=0.248 Sum_probs=26.6
Q ss_pred CCChHHHHHHHH--------HHHHHHHHHHHHHHHhHHHHHH
Q 035101 6 ADPEEELRWISQ--------KVSGYVEAVLNSLAANVPKAIV 39 (73)
Q Consensus 6 ~~~d~~lr~i~~--------~V~sYv~~V~~tL~~sVPKAiV 39 (73)
.+.++.+++++. .....+..|...|++.||..-+
T Consensus 69 ~~~~eF~~rVa~~~~~~~~~~a~~~~~aV~~~l~~~v~~ge~ 110 (125)
T PF10025_consen 69 FDLDEFLARVAERLGGADEDDAERLARAVFAALREAVSEGEF 110 (125)
T ss_dssp -SHHHHHHHHHHTSEETTEE-HHHHHHHHHHHHHHHS-HHHH
T ss_pred CCHHHHHHHHHHHccCCCcccHHHHHHHHHHHHHHHCCHHHH
Confidence 577888888888 7888999999999999987654
No 52
>PRK10878 hypothetical protein; Provisional
Probab=26.08 E-value=61 Score=20.11 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=18.8
Q ss_pred HHHHHHHHhhhcHHHHHHhhccC
Q 035101 51 LNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 51 l~~l~~~l~~~e~~ql~~LL~ED 73 (73)
+++-|.++...+...|++||+.+
T Consensus 12 ~~~~~~~l~~~e~~~Fe~LL~~~ 34 (72)
T PRK10878 12 FEHEYDSLSDDEKRIFIRLLECD 34 (72)
T ss_pred HHHHHhhCCHHHHHHHHHHHcCC
Confidence 56668888899999999999753
No 53
>PF09769 ApoO: Apolipoprotein O; InterPro: IPR019166 Apolipoproteins are proteins that binds to lipids. Members of this family promote cholesterol efflux from macrophage cells. They are present in various lipoprotein complexes, including HDL, LDL and VLDL. Apolipoprotein O is a 198 amino acids protein that contains a 23 amino acids long signal peptide. The apoprotein is secreted by a microsomal triglyceride transfer protein (MTTP)-dependent mechanism, probably as a VLDL-associated protein that is subsequently transferred to HDL. Apolipoprotein O is the first chondroitine sulphate chain containing apolipoprotein [].
Probab=25.51 E-value=2.1e+02 Score=19.19 Aligned_cols=31 Identities=19% Similarity=0.149 Sum_probs=25.3
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 035101 8 PEEELRWISQKVSGYVEAVLNSLAANVPKAI 38 (73)
Q Consensus 8 ~d~~lr~i~~~V~sYv~~V~~tL~~sVPKAi 38 (73)
=+.+.++++..+..|++.+.+.+....+|..
T Consensus 43 Le~~i~~~R~~~~~~~~~~~~~~~~~~~~~~ 73 (158)
T PF09769_consen 43 LEEQIRKAREFLQPYYSWAQDELNTVKSKYY 73 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568888999999999999888888887753
No 54
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=24.94 E-value=2.4e+02 Score=19.56 Aligned_cols=37 Identities=11% Similarity=0.277 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHH
Q 035101 11 ELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKED 49 (73)
Q Consensus 11 ~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~ 49 (73)
-|.||+..+++-++-+.+.+.| |-.++==.++.....
T Consensus 2 lf~Rl~~~~~a~~~~~ld~~ED--P~~~l~q~ird~e~~ 38 (221)
T PF04012_consen 2 LFKRLKTLVKANINELLDKAED--PEKMLEQAIRDMEEQ 38 (221)
T ss_pred HHHHHHHHHHHHHHHHHHhhcC--HHHHHHHHHHHHHHH
Confidence 4789999999999999999988 666665555555554
No 55
>PF08945 Bclx_interact: Bcl-x interacting, BH3 domain; InterPro: IPR015040 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Members of this entry induce apoptosis. The isoform BimL is more potent than the isoform BimEL. They form heterodimers with a number of antiapoptotic Bcl-2 proteins including Mcl-1, Bcl-2, Bcl-X(L), BFL-1, and BHRF1, but do not heterodimerise with proapoptotic proteins such as BAD, BOK, BAX or BAK. They are peripheral membrane proteins, associated with intracytoplasmic membranes. The BH3 motif is required for Bcl-2 binding and cytotoxicity. After antigen-driven expansion, the majority of T cells involved in an immune response die rapidly by apoptosis dependent on the Bcl-2 related proteins; Bim and Bax or Bak []. Bcl-xL regulates Bax and Bim is an important regulator of bcl-x deficiency induced cell death during hematopoiesis and testicular development in mice []. Bim(L) displaces Bcl-x(L) in the mitochondria and promotes Bax translocation during TNFalpha-induced apoptosis []. A potent inhibitor of antiapoptotic Bcl-2 family members, including Bcl-X(L), is AT-101 []. The immunophilin protein FKBP8 and its splice variant are Bcl-XL-interacting proteins and regulate the apoptotic signalling pathways in the RPE []. This protein is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11 []. ; PDB: 2NL9_B 2V6Q_B 3KJ0_B 3KJ1_B 3FDL_B 3D7V_B 3IO8_D 2K7W_B 2VM6_B 3IO9_B ....
Probab=24.88 E-value=74 Score=18.26 Aligned_cols=11 Identities=36% Similarity=0.568 Sum_probs=9.7
Q ss_pred HHHHHHHHHHH
Q 035101 11 ELRWISQKVSG 21 (73)
Q Consensus 11 ~lr~i~~~V~s 21 (73)
+|||||.+..+
T Consensus 23 ELRRIgDEFna 33 (40)
T PF08945_consen 23 ELRRIGDEFNA 33 (40)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHhcc
Confidence 89999998877
No 56
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=24.82 E-value=2.2e+02 Score=20.60 Aligned_cols=51 Identities=14% Similarity=0.186 Sum_probs=39.3
Q ss_pred HHHHH-HHHHHHHHHHHHHHHHhHHHHHHHHHH----HhHHHHHHHHHHHHHhhhc
Q 035101 12 LRWIS-QKVSGYVEAVLNSLAANVPKAIVLCQV----EKAKEDMLNQLYSSVNAQS 62 (73)
Q Consensus 12 lr~i~-~~V~sYv~~V~~tL~~sVPKAiVhcqV----~~aKr~Ll~~l~~~l~~~e 62 (73)
..+|| .+-..|++.....|.-.+-|.=..-++ ..-.-.|+|+|+.+|....
T Consensus 19 ~~~LG~~~~~~Y~~~l~~fl~~klsk~Efd~~~~~~L~~~~~~LHN~li~sIl~na 74 (252)
T PF12767_consen 19 QKRLGPDRWKKYFQSLKRFLSGKLSKEEFDKECRRILGRENVHLHNQLILSILKNA 74 (252)
T ss_pred HHHHChHHHHHHHHHHHHHHHhccCHHHHHHHHHHHhChhHHHHHHHHHHHHHHHH
Confidence 45666 777899999999999999988554443 3445689999999987654
No 57
>PF04091 Sec15: Exocyst complex subunit Sec15-like ; InterPro: IPR007225 Sec15 is a component of the exocyst complex involved in the docking of exocystic vesicles with a fusion site on the plasma membrane. The exocyst complex is composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84.; GO: 0006904 vesicle docking involved in exocytosis, 0000145 exocyst; PDB: 2A2F_X.
Probab=24.77 E-value=2.3e+02 Score=21.47 Aligned_cols=57 Identities=14% Similarity=0.257 Sum_probs=34.5
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHH
Q 035101 6 ADPEEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMI 66 (73)
Q Consensus 6 ~~~d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql 66 (73)
-+|.+|+ ..+..|.+.+-.+.-.++|..|--.....|=..+-+.|..-|-..+.+++
T Consensus 175 ~~ps~yi----~dli~fL~~~f~s~l~~LP~~v~~~~~~~a~~his~~l~~~Ll~~~vk~i 231 (311)
T PF04091_consen 175 GEPSDYI----NDLIQFLETTFSSTLTNLPPSVKQLVYFSACDHISESLLDLLLSDDVKRI 231 (311)
T ss_dssp -S--HHH----HHHHHHHHHHHHTTTTTSH-HHHHHHHHHHHHHHHHHHHHHHT-------
T ss_pred CCCCHHH----HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 3455554 45667777777777788898887777777777888888887777666655
No 58
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=24.69 E-value=1.3e+02 Score=16.72 Aligned_cols=17 Identities=24% Similarity=0.460 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q 035101 10 EELRWISQKVSGYVEAV 26 (73)
Q Consensus 10 ~~lr~i~~~V~sYv~~V 26 (73)
+.|++--+.++-|+++|
T Consensus 15 e~l~~Y~~~L~~Yinli 31 (36)
T smart00309 15 EDLRQYLAALREYINLI 31 (36)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 35777778888888876
No 59
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=24.66 E-value=1.3e+02 Score=16.68 Aligned_cols=18 Identities=28% Similarity=0.442 Sum_probs=13.4
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 035101 9 EEELRWISQKVSGYVEAV 26 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V 26 (73)
.+.|++--++++-|+++|
T Consensus 14 ~eel~~Y~~~L~~Yinli 31 (36)
T cd00126 14 PEELRQYLAALREYINLI 31 (36)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 457777778888888776
No 60
>PF02288 Dehydratase_MU: Dehydratase medium subunit; InterPro: IPR003208 This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.; PDB: 2D0P_B 2D0O_D 1IWP_E 1MMF_B 1NBW_B 3AUJ_B 1UC5_B 1IWB_B 1EEX_E 1DIO_B ....
Probab=24.48 E-value=92 Score=20.73 Aligned_cols=20 Identities=25% Similarity=0.242 Sum_probs=16.2
Q ss_pred cCCChHHHHHHHHHHHHHHH
Q 035101 5 LADPEEELRWISQKVSGYVE 24 (73)
Q Consensus 5 ~~~~d~~lr~i~~~V~sYv~ 24 (73)
|.++.+.+|+||+|=.-|+.
T Consensus 88 ~~~~~~~~R~iG~NAARlvK 107 (112)
T PF02288_consen 88 PLDDPETYRAIGANAARLVK 107 (112)
T ss_dssp CCS-HHHHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHHHc
Confidence 57888999999999888863
No 61
>cd09034 BRO1_Alix_like Protein-interacting Bro1-like domain of mammalian Alix and related domains. This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 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
Probab=24.47 E-value=2.9e+02 Score=20.33 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=41.0
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHH-------hHHHHH-HHHHHHhHHHHHHHHHHHHHhhhcH
Q 035101 8 PEEELRWISQKVSGYVEAVLNSLAA-------NVPKAI-VLCQVEKAKEDMLNQLYSSVNAQST 63 (73)
Q Consensus 8 ~d~~lr~i~~~V~sYv~~V~~tL~~-------sVPKAi-VhcqV~~aKr~Ll~~l~~~l~~~e~ 63 (73)
.++-+.+++..+..|++...+.+.. .+|+-+ -||+++..--.-+-++|..+...+.
T Consensus 201 ~~~liakLa~~~~~~y~~A~~~l~~~~~~~~~~~~~~w~~~v~~K~~~~~a~a~~~~a~~~~e~ 264 (345)
T cd09034 201 KLSLLARLACEAAKYYEEALKCLSGVDLETIKNIPKKWLLFLKWKKCIFKALAYYYHGLKLDEA 264 (345)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4678999999999999999998873 466654 6677777655556666666655544
No 62
>PF15335 CAAP1: Caspase activity and apoptosis inhibitor 1
Probab=24.47 E-value=71 Score=19.77 Aligned_cols=17 Identities=24% Similarity=0.503 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHhhhcH
Q 035101 47 KEDMLNQLYSSVNAQST 63 (73)
Q Consensus 47 Kr~Ll~~l~~~l~~~e~ 63 (73)
|++|+++.|+.|+.++.
T Consensus 12 r~Eml~Q~F~~l~~kkl 28 (64)
T PF15335_consen 12 RKEMLRQCFSVLKEKKL 28 (64)
T ss_pred HHHHHHHHHHHcCHHHH
Confidence 67899999999987765
No 63
>PHA02604 rI.-1 hypothetical protein; Provisional
Probab=24.03 E-value=2.6e+02 Score=19.53 Aligned_cols=44 Identities=16% Similarity=0.203 Sum_probs=32.3
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhc
Q 035101 6 ADPEEELRWISQKVSGYVEAVLNSLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQS 62 (73)
Q Consensus 6 ~~~d~~lr~i~~~V~sYv~~V~~tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e 62 (73)
+|+..+++++.+....|++ .+|.+ ...+.+.++-.+|..+|+..
T Consensus 81 ~d~~~~l~~~l~~a~~i~~--------~l~s~-----L~N~~DdI~~~~~qt~YkLt 124 (126)
T PHA02604 81 LDTIAFLDELLQEAEEIYK--------ELPSA-----LQSTLDDITGLCYQTKYKLT 124 (126)
T ss_pred cCHHHHHHHHHHHHHHHHH--------HhhHH-----HHHHHHHHHHHHHHHHHHHh
Confidence 4888899999998888887 44444 34566777888888887654
No 64
>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, func
Probab=23.08 E-value=1.6e+02 Score=20.11 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=16.8
Q ss_pred HHHhHHHHHHHHHHHHH---hhhcHHHHHHhh
Q 035101 42 QVEKAKEDMLNQLYSSV---NAQSTAMIEELL 70 (73)
Q Consensus 42 qV~~aKr~Ll~~l~~~l---~~~e~~ql~~LL 70 (73)
.|.+.++..++-|+..+ +..+..+|.+||
T Consensus 155 ~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL 186 (207)
T cd06943 155 EVESLREKVYASLEEYCRQKHPEQPGRFAKLL 186 (207)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCcccHHHHHH
Confidence 56666665555555544 334556677765
No 65
>KOG1753 consensus 40S ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=22.81 E-value=1.8e+02 Score=20.79 Aligned_cols=26 Identities=23% Similarity=0.377 Sum_probs=18.3
Q ss_pred HHHhHHHHHHHHHH----HhHHHHHHHHHH
Q 035101 30 LAANVPKAIVLCQV----EKAKEDMLNQLY 55 (73)
Q Consensus 30 L~~sVPKAiVhcqV----~~aKr~Ll~~l~ 55 (73)
++.++|||+|-.-= +.+|+++-+.|+
T Consensus 83 irqa~~kalvayyqkyvDE~skkeiKd~li 112 (145)
T KOG1753|consen 83 IRQAIAKALVAYYQKYVDEQSKKEIKDILI 112 (145)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78899999986543 256666666665
No 66
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=22.68 E-value=1.9e+02 Score=23.92 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=23.5
Q ss_pred HHHHHH-------------HHHhHHHHHHHHHHHHHhhhc
Q 035101 36 KAIVLC-------------QVEKAKEDMLNQLYSSVNAQS 62 (73)
Q Consensus 36 KAiVhc-------------qV~~aKr~Ll~~l~~~l~~~e 62 (73)
|||++| .|++|+..+|.-|++-+.-..
T Consensus 262 KAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q 301 (432)
T KOG4215|consen 262 KAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQ 301 (432)
T ss_pred HHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcC
Confidence 888875 899999999999999887665
No 67
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=22.62 E-value=2e+02 Score=17.83 Aligned_cols=62 Identities=24% Similarity=0.261 Sum_probs=32.6
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHh----HHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHh
Q 035101 7 DPEEELRWISQKVSGYVEAVLNSLAAN----VPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEEL 69 (73)
Q Consensus 7 ~~d~~lr~i~~~V~sYv~~V~~tL~~s----VPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~L 69 (73)
.|++.-..|+..-..-+..+.+.+.+. +|+.-++-.|...-..|.+.| .+=+..|.+-+++.
T Consensus 13 pP~eRw~~i~~~~k~~i~~l~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~~-~~~~~~EirGIA~~ 78 (95)
T PF15508_consen 13 PPEERWVQIAKDYKDEIRELIEVLKDLLQSFVPSGKVLDFVDKLLPHLLRYL-PQPYAEEIRGIAKA 78 (95)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHH
Confidence 355555556655555555555544444 555455666655555544443 44455555545443
No 68
>cd09242 BRO1_ScBro1_like Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Saccharomyces cerevisiae Rim20 (also known as PalA), Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Bro1 participates in endosomal trafficking. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: Snf7 in the
Probab=22.56 E-value=3.5e+02 Score=20.58 Aligned_cols=58 Identities=12% Similarity=0.113 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHh-------HHHH-HHHHHHHhHHHHHHHHHHHHHhhhcHHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSLAAN-------VPKA-IVLCQVEKAKEDMLNQLYSSVNAQSTAMI 66 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~~s-------VPKA-iVhcqV~~aKr~Ll~~l~~~l~~~e~~ql 66 (73)
++-+-+++..++.|++.+.+.+... +|+. +-|+++...--.-+-++|..+.-.+..+.
T Consensus 195 ~sliaKLa~~~~~~Y~~a~~~l~~~~~~~~~~~~~~W~~~~~~K~~~f~A~A~y~~a~~~~~~~k~ 260 (348)
T cd09242 195 ASLISKLASATANLYESCVEFLKEIQEKGISYGDPKWISLVQCKAHYYKSLAAYYHALALEAAGKY 260 (348)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHhHHhccH
Confidence 4567799999999999999998752 5665 56777776655556777777765555443
No 69
>COG1728 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.11 E-value=1.7e+02 Score=20.95 Aligned_cols=49 Identities=10% Similarity=0.233 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHhH---------------HHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHH
Q 035101 17 QKVSGYVEAVLNSLAANV---------------PKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMI 66 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sV---------------PKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql 66 (73)
++|..|=+.|..-+...| |++..|-.|.+.-+. |..|-.++-..|..|+
T Consensus 70 ~~l~~YK~lIkEFv~~ai~~~y~le~~~sfn~~g~t~~~~iVkeId~K-L~~Lt~~lm~~ek~~I 133 (151)
T COG1728 70 ENLKAYKNLIKEFVKYAIKSGYSLEESKSFNLDGRTRIFTIVKEIDDK-LADLTEELMSNEKDQI 133 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccccccccCCCceeeehhhHHhHH-HHHHHHHHHHhhHHHh
Confidence 456667666666665544 788888899988888 6667777777887776
No 70
>PF03489 SapB_2: Saposin-like type B, region 2; InterPro: IPR008138 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ].; PDB: 3BQQ_A 2RB3_B 2R0R_A 3BQP_A 2R1Q_A 1NKL_A 1L9L_A 1QDM_C 3RFI_A 4DDJ_A ....
Probab=22.07 E-value=1.3e+02 Score=15.22 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHhH-HHHH
Q 035101 17 QKVSGYVEAVLNSLAANV-PKAI 38 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sV-PKAi 38 (73)
.-|..|...+-+.|.+.+ |+.|
T Consensus 6 ~~V~~y~~~ii~~l~~~~~p~~i 28 (35)
T PF03489_consen 6 NFVDQYGPQIIQLLEKQLDPQQI 28 (35)
T ss_dssp HHHHHHHHHHHHHHHTTSTHHHH
T ss_pred HHHHHHHHHHHHHHHhcCChHHH
Confidence 457778888888877777 6665
No 71
>PF05794 Tcp11: T-complex protein 11; InterPro: IPR008862 This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the Saccharomyces cerevisiae Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants [].
Probab=22.05 E-value=3.7e+02 Score=20.60 Aligned_cols=52 Identities=23% Similarity=0.279 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHhHHH-HHHHHHHHhHHHHHHHHHHHHHhhhcHHHHHHhhcc
Q 035101 17 QKVSGYVEAVLNSLAANVPK-AIVLCQVEKAKEDMLNQLYSSVNAQSTAMIEELLQE 72 (73)
Q Consensus 17 ~~V~sYv~~V~~tL~~sVPK-AiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~LL~E 72 (73)
..-.+|.+++...|...-|. .-+.-++.+-|+.|+.-+ ......++.+.||.
T Consensus 31 ~~~~afWd~l~~el~~~~~~~~~~~~Ll~~ike~L~~ll----~~~~~~~I~e~LD~ 83 (441)
T PF05794_consen 31 TMHKAFWDALREELEQDPPDYSRLPQLLEEIKEILLSLL----PSRLRQEIEEVLDL 83 (441)
T ss_pred HHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHHHHHHhc----CHHHHHHHHHHCCh
Confidence 34478999999999998333 344567777777776544 44444456666653
No 72
>cd09249 BRO1_Rhophilin_2 Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin-2. This subfamily contains the Bro1-like domain of RhoA-binding protein, Rhophilin-2. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding protein Rhophilin-1, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-2, binds both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-2 contains an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Roles for Rhophilin-2 may include limiting stress fiber formation or increasing the turnover of F-
Probab=21.96 E-value=3.5e+02 Score=21.75 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----hHHHHH-HHHHHHhHHHHHHHHHHHH
Q 035101 12 LRWISQKVSGYVEAVLNSLAA-----NVPKAI-VLCQVEKAKEDMLNQLYSS 57 (73)
Q Consensus 12 lr~i~~~V~sYv~~V~~tL~~-----sVPKAi-VhcqV~~aKr~Ll~~l~~~ 57 (73)
+-+++..|+.|+..+.+.+.. .||+.+ -|+++..+--.=+-+++..
T Consensus 199 iAklAaqvs~~Y~~a~~al~s~~~~~~i~~~W~~~v~~K~~~f~AlA~Y~~A 250 (385)
T cd09249 199 MAQEAAKVGEVYMQVHTAMNQAPVKENIPYSWSSLVQVKAHHYNALAHYFVA 250 (385)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567779999999999998764 478765 5667666544444444443
No 73
>PF12449 DUF3684: Protein of unknown function (DUF3684) ; InterPro: IPR022155 This domain family is found in eukaryotes, and is typically between 1072 and 1090 amino acids in length.
Probab=21.66 E-value=62 Score=29.50 Aligned_cols=26 Identities=23% Similarity=0.547 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 45 KAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 45 ~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
.=++.+|+.||.+||..-. +++.+|+
T Consensus 1039 APqEd~LE~fY~~LGs~~L---SslV~E~ 1064 (1093)
T PF12449_consen 1039 APQEDILEDFYLALGSPRL---SSLVEEE 1064 (1093)
T ss_pred CCcHHHHHHHHHHhCChhh---hhhheeh
Confidence 3468899999999998765 6666664
No 74
>PF10408 Ufd2P_core: Ubiquitin elongating factor core; InterPro: IPR019474 This entry represents the most conserved part of the core region of ubiquitin conjugation factor E4 (or Ub elongating factor, or Ufd2P), running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C terminus, (IPR003613 from INTERPRO), which has ligase activity. Ubiquitin conjugation factor E4 is involved in N-terminal ubiquitin fusion degradation proteolytic pathway (UFD pathway). E4 binds to the ubiquitin moieties of preformed conjugates and catalyses ubiquitin chain assembly in conjunction with E1, E2, and E3. E4 appears to influence the formation and topology of the multi-Ub chain as it enhances ubiquitination at 'Lys-48' but not at 'Lys-29' of the N-terminal Ub moiety.; GO: 0034450 ubiquitin-ubiquitin ligase activity, 0006511 ubiquitin-dependent protein catabolic process, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 2KRE_A 3M63_A 2QIZ_A 2QJ0_A 3M62_A.
Probab=21.44 E-value=2.3e+02 Score=23.25 Aligned_cols=58 Identities=14% Similarity=0.257 Sum_probs=45.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHH------HHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSL------AANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMI 66 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL------~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql 66 (73)
++.|+.....+++|+....+|+ ...+|++.++=-+..=--++||.+-.+|-+....+|
T Consensus 488 ~~~l~~~e~~~rs~~~l~~~t~~~l~~lt~~~~~~Fl~~elv~RlA~MLn~~L~~L~Gpk~~~L 551 (629)
T PF10408_consen 488 ESQLEQAERQARSYLQLANETLKMLNYLTSEIPEPFLRPELVDRLAAMLNYNLDQLVGPKCSEL 551 (629)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-GGGGCSHHHHHHHHHHHHHHHHHHHSHHHHT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchhhhhHHHHHHHHHHHHHHHHHHcCCchhcc
Confidence 4578889999999998887764 578999988876666667899999999988776443
No 75
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=21.14 E-value=1.5e+02 Score=19.57 Aligned_cols=20 Identities=25% Similarity=0.290 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHhHHHHHHHHHH
Q 035101 22 YVEAVLNSLAANVPKAIVLCQV 43 (73)
Q Consensus 22 Yv~~V~~tL~~sVPKAiVhcqV 43 (73)
||+.+.+...+ ||.+....+
T Consensus 2 ~Fe~~~~~~~~--~k~~anwi~ 21 (148)
T PF02637_consen 2 YFEEVVKKGKN--PKLAANWIL 21 (148)
T ss_dssp HHHHHHCHSS---HHHHHHHHH
T ss_pred HHHHHHHhcCC--HHHHHHHHH
Confidence 45555444433 555554443
No 76
>PF10188 Oscp1: Organic solute transport protein 1; InterPro: IPR019332 Organic solute carrier protein 1, or Oscp1, is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red-nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein.
Probab=20.91 E-value=1.8e+02 Score=21.02 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=27.3
Q ss_pred HHHHhHHHHHHHHHHHhHHHHHHHHHHHHHhhhcHHHH
Q 035101 29 SLAANVPKAIVLCQVEKAKEDMLNQLYSSVNAQSTAMI 66 (73)
Q Consensus 29 tL~~sVPKAiVhcqV~~aKr~Ll~~l~~~l~~~e~~ql 66 (73)
.+++-||-+-++.+|..+++. +..+|..++..+-..+
T Consensus 105 ~i~~~v~~~~~~~~v~~~~~~-~~~~y~~ls~~~~~~i 141 (173)
T PF10188_consen 105 AIRDLVPDPEVQALVDEVFNR-LIEFYGKLSPGEFQLI 141 (173)
T ss_pred HHHHHccCHHHHHHHHHHHHH-HHHHHhCCCHHHHHHH
Confidence 444555556778899999987 5788998888777555
No 77
>PLN00131 hypothetical protein; Provisional
Probab=20.78 E-value=80 Score=23.51 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=19.8
Q ss_pred HHHhHHHHHHHHHHHHHhhhcHHH
Q 035101 42 QVEKAKEDMLNQLYSSVNAQSTAM 65 (73)
Q Consensus 42 qV~~aKr~Ll~~l~~~l~~~e~~q 65 (73)
+=++.-|.||+.+|..+|....+|
T Consensus 167 ldnetdrtllddlynhlydlseeq 190 (218)
T PLN00131 167 LDNETDRTLLDDLYNHLYDLSEEQ 190 (218)
T ss_pred cCccchHHHHHHHHHHHhhhhHHh
Confidence 357889999999999999776644
No 78
>PRK15039 transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional
Probab=20.67 E-value=1.7e+02 Score=18.79 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 45 KAKEDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 45 ~aKr~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
+.|..|+++|=+--|.-.+ ++.|++||
T Consensus 6 ~~k~~ll~RL~RIeGQv~g--I~~Miee~ 32 (90)
T PRK15039 6 RDKQKLKARASKIQGQVVA--LKKMLDEP 32 (90)
T ss_pred HhHHHHHHHHHHHHHHHHH--HHHHHHCC
Confidence 4567778887777777666 77887775
No 79
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=20.32 E-value=1.1e+02 Score=17.87 Aligned_cols=26 Identities=15% Similarity=0.318 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHhhhcHHHHHHhhccC
Q 035101 48 EDMLNQLYSSVNAQSTAMIEELLQED 73 (73)
Q Consensus 48 r~Ll~~l~~~l~~~e~~ql~~LL~ED 73 (73)
+.+++.+++.+...+...+.+++.+|
T Consensus 2 ~~~~~~~~~a~~~~D~~~~~~~~~~d 27 (121)
T PF13474_consen 2 EALLEEWIEAFERGDIDALLSLFSDD 27 (121)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHEEEE
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhCCC
Confidence 35788888888888888787777654
No 80
>cd09241 BRO1_ScRim20-like Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 and related proteins. This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 (also known as PalA) and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Saccharomyces cerevisiae Bro1, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Rim20 and Rim23 participate in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind comp
Probab=20.27 E-value=4e+02 Score=20.31 Aligned_cols=60 Identities=15% Similarity=0.123 Sum_probs=44.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH--HhHHHH-HHHHHHHhHHHHHHHHHHHHHhhhcHHHHHH
Q 035101 9 EEELRWISQKVSGYVEAVLNSLA--ANVPKA-IVLCQVEKAKEDMLNQLYSSVNAQSTAMIEE 68 (73)
Q Consensus 9 d~~lr~i~~~V~sYv~~V~~tL~--~sVPKA-iVhcqV~~aKr~Ll~~l~~~l~~~e~~ql~~ 68 (73)
++-+-+++..++.|++.+.+.+. +.+|+. +-|+++...-=.-+-+++..+...+.++.++
T Consensus 193 ~sliAKLa~qv~~~Y~~a~~~l~~~~~i~~~W~~~v~~K~~~f~A~A~y~~a~~~~e~~k~Ge 255 (355)
T cd09241 193 DSLIAKLAAQVSDYYQEALKYANKSDLIRSDWINHLKVKKHHFKAAAHYRMALVALEKSKYGE 255 (355)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 56788999999999999999885 445655 4557777666555778888887776655544
Done!