Query 032351
Match_columns 142
No_of_seqs 17 out of 19
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 12:57:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032351.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032351hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11594 Med28: Mediator compl 99.8 2.9E-18 6.3E-23 128.0 9.1 76 59-136 2-80 (106)
2 PF07989 Microtub_assoc: Micro 88.3 2.9 6.2E-05 29.3 6.5 46 76-121 20-73 (75)
3 PF07544 Med9: RNA polymerase 82.5 4.1 8.8E-05 28.4 5.0 28 94-121 55-82 (83)
4 PF09738 DUF2051: Double stran 78.8 5.3 0.00012 34.3 5.5 23 95-117 151-173 (302)
5 PF13094 CENP-Q: CENP-Q, a CEN 78.3 10 0.00022 28.4 6.3 41 94-134 44-84 (160)
6 PF09744 Jnk-SapK_ap_N: JNK_SA 70.3 39 0.00085 26.6 8.0 60 73-134 34-97 (158)
7 PF07798 DUF1640: Protein of u 69.4 49 0.0011 25.4 9.1 82 60-141 46-149 (177)
8 PF13863 DUF4200: Domain of un 63.0 39 0.00084 23.8 6.1 36 97-132 6-41 (126)
9 PF11577 NEMO: NF-kappa-B esse 60.2 56 0.0012 22.8 6.9 43 96-138 11-53 (68)
10 KOG3990 Uncharacterized conser 59.3 33 0.00073 30.4 6.3 27 95-121 229-255 (305)
11 KOG4083 Head-elevated expressi 59.1 38 0.00082 28.3 6.3 46 95-140 87-136 (192)
12 PF12999 PRKCSH-like: Glucosid 56.5 53 0.0012 26.7 6.6 39 95-133 129-167 (176)
13 PF07106 TBPIP: Tat binding pr 55.7 33 0.00072 25.8 5.1 47 62-109 76-127 (169)
14 PF03904 DUF334: Domain of unk 53.3 1.4E+02 0.003 25.6 8.8 71 59-129 76-151 (230)
15 PF01706 FliG_C: FliG C-termin 52.4 29 0.00062 24.6 4.0 42 33-78 54-102 (110)
16 TIGR01061 parC_Gpos DNA topois 50.2 37 0.0008 32.3 5.5 45 93-137 429-473 (738)
17 PF01920 Prefoldin_2: Prefoldi 50.0 76 0.0016 21.2 5.8 38 94-131 65-102 (106)
18 PHA02629 A-type inclusion body 49.7 38 0.00082 23.8 4.2 31 91-121 26-56 (61)
19 PRK05560 DNA gyrase subunit A; 49.6 72 0.0016 30.5 7.3 45 93-137 432-476 (805)
20 COG5509 Uncharacterized small 48.5 18 0.00039 25.8 2.5 18 95-112 36-53 (65)
21 PF07352 Phage_Mu_Gam: Bacteri 48.1 76 0.0016 23.7 5.9 43 98-140 10-52 (149)
22 PF02050 FliJ: Flagellar FliJ 47.7 77 0.0017 20.6 6.9 47 95-141 63-109 (123)
23 PF10158 LOH1CR12: Tumour supp 47.4 1.3E+02 0.0027 23.1 8.1 63 65-129 24-87 (131)
24 PF14193 DUF4315: Domain of un 47.3 34 0.00073 24.7 3.7 27 113-140 9-35 (83)
25 cd03777 MATH_TRAF3 Tumor Necro 43.4 55 0.0012 25.9 4.7 32 94-125 2-33 (186)
26 PF06133 DUF964: Protein of un 43.1 1.1E+02 0.0023 21.0 8.6 92 28-131 2-97 (108)
27 PRK09039 hypothetical protein; 42.9 1.1E+02 0.0024 26.2 6.8 47 95-141 148-194 (343)
28 PF09903 DUF2130: Uncharacteri 42.0 98 0.0021 26.0 6.2 45 94-138 2-47 (267)
29 PRK13676 hypothetical protein; 41.2 1.3E+02 0.0028 21.4 9.2 93 27-131 4-100 (114)
30 PRK02118 V-type ATP synthase s 41.1 48 0.001 30.1 4.5 83 27-119 344-431 (436)
31 PF10549 ORF11CD3: ORF11CD3 do 40.2 1.2E+02 0.0026 20.7 5.9 46 95-141 3-48 (57)
32 cd00187 TOP4c DNA Topoisomeras 39.7 61 0.0013 29.2 4.9 37 94-130 408-444 (445)
33 PF07926 TPR_MLP1_2: TPR/MLP1/ 38.6 99 0.0021 22.7 5.2 36 97-132 2-37 (132)
34 PF08285 DPM3: Dolichol-phosph 36.1 35 0.00076 24.7 2.4 24 87-110 64-87 (91)
35 cd04787 HTH_HMRTR_unk Helix-Tu 36.0 1.2E+02 0.0027 22.0 5.3 34 93-126 81-114 (133)
36 KOG3088 Secretory carrier memb 36.0 52 0.0011 29.3 3.9 25 99-123 68-92 (313)
37 PF07165 DUF1397: Protein of u 35.8 28 0.0006 28.1 2.0 24 26-49 78-101 (213)
38 smart00513 SAP Putative DNA-bi 35.4 52 0.0011 19.2 2.7 20 100-119 6-33 (35)
39 PF04568 IATP: Mitochondrial A 35.3 1.1E+02 0.0024 22.8 4.9 14 69-82 53-66 (100)
40 PF06152 Phage_min_cap2: Phage 35.3 1.2E+02 0.0026 26.3 5.9 25 111-135 337-361 (361)
41 PF14182 YgaB: YgaB-like prote 35.2 1.8E+02 0.0039 21.3 7.5 35 93-127 42-77 (79)
42 PRK15422 septal ring assembly 34.7 1.8E+02 0.004 21.3 6.3 25 110-134 48-75 (79)
43 PF13815 Dzip-like_N: Iguana/D 33.1 1.5E+02 0.0032 21.5 5.3 62 62-131 52-113 (118)
44 PF13118 DUF3972: Protein of u 32.9 1.4E+02 0.003 23.4 5.3 47 83-129 74-123 (126)
45 KOG1105 Transcription elongati 32.8 2.1E+02 0.0046 25.1 7.0 57 65-130 20-80 (296)
46 PF14131 DUF4298: Domain of un 31.3 1.6E+02 0.0034 20.8 5.1 31 100-130 2-32 (90)
47 PF06810 Phage_GP20: Phage min 30.5 2.6E+02 0.0055 21.6 7.0 45 95-139 24-78 (155)
48 PF08388 GIIM: Group II intron 30.3 62 0.0013 20.9 2.7 19 110-128 21-39 (80)
49 COG4079 Uncharacterized protei 30.2 78 0.0017 28.0 4.0 28 112-139 187-214 (293)
50 PF02870 Methyltransf_1N: 6-O- 30.2 53 0.0011 21.3 2.3 24 66-89 48-72 (77)
51 KOG2430 Glycosyl hydrolase, fa 29.9 53 0.0011 30.8 3.1 24 59-85 289-317 (587)
52 PRK12704 phosphodiesterase; Pr 29.9 1.8E+02 0.0039 26.6 6.3 21 121-141 126-146 (520)
53 PRK13182 racA polar chromosome 28.9 1.2E+02 0.0025 24.2 4.4 28 95-123 96-123 (175)
54 PF05667 DUF812: Protein of un 28.9 2.3E+02 0.005 26.7 7.0 56 61-116 401-472 (594)
55 COG4008 Predicted metal-bindin 28.5 96 0.0021 25.2 3.9 38 41-94 78-117 (153)
56 PRK00106 hypothetical protein; 27.8 2E+02 0.0043 26.8 6.3 24 119-142 139-162 (535)
57 cd04776 HTH_GnyR Helix-Turn-He 27.2 2.4E+02 0.0053 20.3 5.6 34 94-127 83-116 (118)
58 PF06755 DUF1219: Protein of u 27.0 54 0.0012 25.5 2.2 16 121-136 19-34 (114)
59 PF05278 PEARLI-4: Arabidopsis 27.0 2.6E+02 0.0057 24.3 6.6 40 94-133 203-242 (269)
60 PF02037 SAP: SAP domain; Int 26.8 1.4E+02 0.0031 17.6 3.7 20 101-120 7-34 (35)
61 PF12072 DUF3552: Domain of un 26.6 2.9E+02 0.0064 21.6 6.3 9 133-141 134-142 (201)
62 PF06273 eIF-4B: Plant specifi 26.3 47 0.001 31.1 2.1 23 90-112 364-387 (492)
63 PF04111 APG6: Autophagy prote 26.1 3.1E+02 0.0067 23.3 6.8 34 94-127 74-107 (314)
64 PRK13922 rod shape-determining 26.0 2.2E+02 0.0048 22.8 5.6 22 95-116 80-101 (276)
65 PF05565 Sipho_Gp157: Siphovir 25.8 3E+02 0.0065 21.1 6.1 40 95-134 51-90 (162)
66 cd07627 BAR_Vps5p The Bin/Amph 25.4 3.3E+02 0.0073 21.3 6.6 48 90-137 142-201 (216)
67 PF13600 DUF4140: N-terminal d 25.1 1.6E+02 0.0036 20.2 4.2 31 95-125 74-104 (104)
68 PF10018 Med4: Vitamin-D-recep 25.0 3.3E+02 0.0072 21.1 6.4 38 95-132 26-63 (188)
69 PF14389 Lzipper-MIP1: Leucine 25.0 2.3E+02 0.0049 20.0 5.0 49 63-111 26-74 (88)
70 PF02183 HALZ: Homeobox associ 24.9 64 0.0014 20.7 2.0 34 76-109 2-37 (45)
71 PF08317 Spc7: Spc7 kinetochor 24.7 2.8E+02 0.006 23.3 6.2 32 95-126 213-244 (325)
72 PF00521 DNA_topoisoIV: DNA gy 24.6 1.8E+02 0.0038 25.5 5.2 32 95-129 395-426 (426)
73 PF01496 V_ATPase_I: V-type AT 24.4 3.3E+02 0.0072 25.4 7.1 44 94-137 232-279 (759)
74 PF05529 Bap31: B-cell recepto 24.2 2.3E+02 0.0049 21.7 5.2 10 61-70 89-98 (192)
75 TIGR03319 YmdA_YtgF conserved 24.0 2.5E+02 0.0054 25.6 6.2 22 120-141 119-140 (514)
76 KOG4603 TBP-1 interacting prot 23.9 3E+02 0.0065 23.3 6.2 55 85-139 70-128 (201)
77 PF04880 NUDE_C: NUDE protein, 23.5 78 0.0017 25.4 2.6 18 96-113 36-53 (166)
78 TIGR01063 gyrA DNA gyrase, A s 23.5 2E+02 0.0042 27.7 5.6 43 94-136 430-472 (800)
79 PF06005 DUF904: Protein of un 23.4 2.6E+02 0.0057 19.4 6.8 41 95-135 22-69 (72)
80 KOG0996 Structural maintenance 23.1 2.1E+02 0.0046 30.0 6.0 48 94-141 475-522 (1293)
81 KOG3663 Nuclear factor I [Tran 23.1 96 0.0021 29.3 3.4 34 104-137 51-84 (518)
82 PF04799 Fzo_mitofusin: fzo-li 23.0 2.6E+02 0.0056 22.8 5.5 43 75-118 105-147 (171)
83 PF07052 Hep_59: Hepatocellula 22.8 76 0.0016 22.8 2.2 19 55-73 4-22 (104)
84 PRK11864 2-ketoisovalerate fer 22.6 1.5E+02 0.0033 25.5 4.3 28 81-112 263-290 (300)
85 KOG0971 Microtubule-associated 22.6 3.1E+02 0.0068 28.6 7.0 46 95-141 466-511 (1243)
86 PF11559 ADIP: Afadin- and alp 22.5 3.2E+02 0.0069 20.0 10.1 45 96-140 92-136 (151)
87 KOG3994 Uncharacterized conser 22.4 76 0.0016 28.1 2.5 21 58-78 181-203 (291)
88 PF07106 TBPIP: Tat binding pr 22.1 3.5E+02 0.0075 20.3 8.8 12 95-106 76-87 (169)
89 PRK13230 nitrogenase reductase 21.8 1.6E+02 0.0034 23.2 4.0 31 65-97 233-263 (279)
90 PF06698 DUF1192: Protein of u 21.6 2E+02 0.0043 19.7 4.0 27 90-116 20-46 (59)
91 PF01086 Clathrin_lg_ch: Clath 21.5 2.8E+02 0.006 22.5 5.4 45 93-137 111-163 (225)
92 KOG0577 Serine/threonine prote 21.3 3.6E+02 0.0079 27.2 7.0 69 58-126 542-622 (948)
93 KOG0804 Cytoplasmic Zn-finger 20.7 5.2E+02 0.011 24.6 7.6 71 58-133 332-403 (493)
94 PF11708 Slu7: Pre-mRNA splici 20.4 3.7E+02 0.0081 22.5 6.1 43 75-117 134-186 (239)
95 PHA02562 46 endonuclease subun 20.3 4.8E+02 0.011 22.4 6.9 37 90-126 298-334 (562)
96 PF15079 DUF4546: Domain of un 20.3 2.1E+02 0.0045 24.2 4.6 37 81-117 34-73 (205)
97 PF12644 DUF3782: Protein of u 20.3 2.4E+02 0.0053 17.9 5.0 35 98-132 8-43 (64)
98 PRK00888 ftsB cell division pr 20.2 2.5E+02 0.0055 20.4 4.5 34 93-126 29-62 (105)
No 1
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=99.76 E-value=2.9e-18 Score=127.99 Aligned_cols=76 Identities=24% Similarity=0.496 Sum_probs=71.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhhhhccC--CChHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032351 59 HQIDVERHARDFMEAAKKLQLYFISLQREDQ--PTEVE-MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKH 135 (142)
Q Consensus 59 hqiDVErhardFmeaAkqLq~yFi~lQr~~~--p~k~E-~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh 135 (142)
.+.+||+++.+|+|+||++++||+ |||+. ..++| +||+||++|++||.||++||.||+.+|..|+++|.|.-+.|
T Consensus 2 irt~vEq~~~~FlD~aRq~e~~Fl--qKr~~LS~~kpe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d~~~~~ 79 (106)
T PF11594_consen 2 IRTYVEQLIQSFLDVARQMEAFFL--QKRFELSAYKPEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSDAQNQH 79 (106)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 467899999999999999999998 99998 66888 99999999999999999999999999999999999998887
Q ss_pred h
Q 032351 136 I 136 (142)
Q Consensus 136 ~ 136 (142)
.
T Consensus 80 k 80 (106)
T PF11594_consen 80 K 80 (106)
T ss_pred c
Confidence 4
No 2
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=88.31 E-value=2.9 Score=29.27 Aligned_cols=46 Identities=33% Similarity=0.637 Sum_probs=30.2
Q ss_pred HHHHHHHh--hhhccCCChHHH------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 76 KLQLYFIS--LQREDQPTEVEM------LRKDIAIMEEELKAKKELIKKQERLV 121 (142)
Q Consensus 76 qLq~yFi~--lQr~~~p~k~E~------lkkeI~~le~EL~~KdELIkkh~~lI 121 (142)
||..||+. |++.......++ ||-++..|..||..+..+|....+-|
T Consensus 20 KLrI~fLee~l~~~~~~~~~~~~keNieLKve~~~L~~el~~~~~~l~~a~~~~ 73 (75)
T PF07989_consen 20 KLRIYFLEERLQKLGPESIEELLKENIELKVEVESLKRELQEKKKLLKEAEKAI 73 (75)
T ss_pred HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 78899982 332222222323 45578888888988888888777655
No 3
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 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 entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=82.49 E-value=4.1 Score=28.44 Aligned_cols=28 Identities=29% Similarity=0.494 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLV 121 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI 121 (142)
|--..+|..||+++.+|.+++.+..+.+
T Consensus 55 eeq~~~i~~Le~~i~~k~~~L~~~~~~~ 82 (83)
T PF07544_consen 55 EEQEEEIEELEEQIRKKREVLQKFKERV 82 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445789999999999999999988764
No 4
>PF09738 DUF2051: Double stranded RNA binding protein (DUF2051); InterPro: IPR019139 This entry represents transcriptional repressors which preferentially bind to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. They may control smooth muscle cell proliferation following artery injury through PDGFA repression and may also bind double-stranded RNA. They interact with the leucine-rich repeat domain of human flightless-I (FliI) protein.
Probab=78.82 E-value=5.3 Score=34.31 Aligned_cols=23 Identities=39% Similarity=0.680 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQ 117 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh 117 (142)
.|+.+...|+++|+..|+||.+|
T Consensus 151 ~L~~e~~~Lre~L~~rdeli~kh 173 (302)
T PF09738_consen 151 SLREELDELREQLKQRDELIEKH 173 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHC
Confidence 45556666666666666666665
No 5
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=78.27 E-value=10 Score=28.43 Aligned_cols=41 Identities=20% Similarity=0.307 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDK 134 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~k 134 (142)
+.|++||..++..|.+=.+-|+.-++.++.|...++++..+
T Consensus 44 ~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~~~~~ 84 (160)
T PF13094_consen 44 ELLQEEIEKEEAALERDYEYLQELEKNAKALEREREEEEKK 84 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 38999999999999999999999999999999999988876
No 6
>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.
Probab=70.32 E-value=39 Score=26.60 Aligned_cols=60 Identities=25% Similarity=0.384 Sum_probs=41.5
Q ss_pred HHHHHHHHHHhhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHh
Q 032351 73 AAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQ----RWRNDLKGQLDK 134 (142)
Q Consensus 73 aAkqLq~yFi~lQr~~~p~k~E~lkkeI~~le~EL~~KdELIkkh~~lI~----~Wq~~L~dq~~k 134 (142)
+---|++|+-+- +..=...+.|++++..|+.+..++.++=++..+.+. .|...-++...+
T Consensus 34 vLE~Le~~~~~n--~~~~~e~~~L~~d~e~L~~q~~~ek~~r~~~e~~l~~~Ed~~~~e~k~L~~~ 97 (158)
T PF09744_consen 34 VLELLESLASRN--QEHEVELELLREDNEQLETQYEREKELRKQAEEELLELEDQWRQERKDLQSQ 97 (158)
T ss_pred HHHHHHHHHHhh--hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344577777632 222234559999999999999999888777665555 888877765443
No 7
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=69.43 E-value=49 Score=25.41 Aligned_cols=82 Identities=24% Similarity=0.324 Sum_probs=50.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhhhccC---CChHHHHHHHHHHHHHHHHH-------------------HHHHHHHH
Q 032351 60 QIDVERHARDFMEAAKKLQLYFISLQREDQ---PTEVEMLRKDIAIMEEELKA-------------------KKELIKKQ 117 (142)
Q Consensus 60 qiDVErhardFmeaAkqLq~yFi~lQr~~~---p~k~E~lkkeI~~le~EL~~-------------------KdELIkkh 117 (142)
+.|+|+....|..+--+|..-...+.+.+. -..-+.|+.||..|+.+|+. =.+..+.+
T Consensus 46 k~d~e~~~~~~~a~~~eLr~el~~~~k~~~~~lr~~~e~L~~eie~l~~~L~~ei~~l~a~~klD~n~eK~~~r~e~~~~ 125 (177)
T PF07798_consen 46 KSDLENQEYLFKAAIAELRSELQNSRKSEFAELRSENEKLQREIEKLRQELREEINKLRAEVKLDLNLEKGRIREEQAKQ 125 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 578999999999888888888776665544 22233566655555555432 22345566
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhc
Q 032351 118 ERLVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 118 ~~lI~~Wq~~L~dq~~kh~~eler 141 (142)
+.+|+.=.+.+.-.+..=.+++|.
T Consensus 126 ~~ki~e~~~ki~~ei~~lr~~iE~ 149 (177)
T PF07798_consen 126 ELKIQELNNKIDTEIANLRTEIES 149 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666555555555555555543
No 8
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=62.98 E-value=39 Score=23.78 Aligned_cols=36 Identities=17% Similarity=0.420 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 97 RKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQL 132 (142)
Q Consensus 97 kkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~ 132 (142)
|.|+..+...|..|.+-|.+.++.+..+...|...-
T Consensus 6 kre~~~~~~~l~~kr~e~~~~~~~~~~~e~~L~~~e 41 (126)
T PF13863_consen 6 KREMFLVQLALDTKREEIERREEQLKQREEELEKKE 41 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 557777777777777777777777777777766543
No 9
>PF11577 NEMO: NF-kappa-B essential modulator NEMO; InterPro: IPR021063 This entry represents a conserved domain found at the N-terminal of NF-kappa-B essential modulator (NEMO) and optineurin proteins. NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation []. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini. The core domain of NEMO is a dimer which binds to two fragments of IKK []. ; PDB: 3BRT_B 3BRV_D.
Probab=60.16 E-value=56 Score=22.82 Aligned_cols=43 Identities=14% Similarity=0.237 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032351 96 LRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITE 138 (142)
Q Consensus 96 lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~e 138 (142)
|=.|...|++-|+.-..-+|..++-+..||...+.-.+.|..-
T Consensus 11 LL~EN~~LKealrQ~N~~Mker~e~l~~wqe~~~~e~~~~~~k 53 (68)
T PF11577_consen 11 LLQENQDLKEALRQNNQAMKERFEELLAWQEKQKEEREFLERK 53 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4468899999999999999999999999999888777766543
No 10
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.30 E-value=33 Score=30.35 Aligned_cols=27 Identities=26% Similarity=0.506 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLV 121 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI 121 (142)
-||+||+.|+.-|..||.+|=.-.+.|
T Consensus 229 ~lkeeia~Lkk~L~qkdq~ileKdkqi 255 (305)
T KOG3990|consen 229 KLKEEIARLKKLLHQKDQLILEKDKQI 255 (305)
T ss_pred HHHHHHHHHHHHHhhhHHHHHhhhhhh
Confidence 478888888888888888875444444
No 11
>KOG4083 consensus Head-elevated expression protein [Transcription]
Probab=59.06 E-value=38 Score=28.35 Aligned_cols=46 Identities=22% Similarity=0.232 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHhhhhhhh
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWR----NDLKGQLDKHITELE 140 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq----~~L~dq~~kh~~ele 140 (142)
-|..+...+..||+++|+++|-+...|++=. +.++.|..+-....|
T Consensus 87 ~LAr~le~~~q~L~k~daf~Ke~larlEen~~e~ykv~~eqy~~aaE~Ve 136 (192)
T KOG4083|consen 87 RLARDLEEKSQELKKQDAFYKEQLARLEENSSEFYKVTTEQYQKAAERVE 136 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 5778999999999999999999988888755 456667666554443
No 12
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=56.51 E-value=53 Score=26.67 Aligned_cols=39 Identities=23% Similarity=0.337 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLD 133 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~ 133 (142)
.+.+....+++=++.|.++|....++...|++.|.....
T Consensus 129 ~~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ 167 (176)
T PF12999_consen 129 ELEEEEEIYKEGLKIRQELIEEAKKKREELEKKLEELEK 167 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556677778888899999999988888888877665443
No 13
>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=55.74 E-value=33 Score=25.77 Aligned_cols=47 Identities=30% Similarity=0.460 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhhccC-----CChHHHHHHHHHHHHHHHHH
Q 032351 62 DVERHARDFMEAAKKLQLYFISLQREDQ-----PTEVEMLRKDIAIMEEELKA 109 (142)
Q Consensus 62 DVErhardFmeaAkqLq~yFi~lQr~~~-----p~k~E~lkkeI~~le~EL~~ 109 (142)
+++....+..+-...++...-.|.-+.. ||.+| |+..|+.|++|++.
T Consensus 76 ~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~e-l~~~i~~l~~e~~~ 127 (169)
T PF07106_consen 76 ELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEE-LREEIEELEEEIEE 127 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHH-HHHHHHHHHHHHHH
Confidence 3344455555555555555544444333 44433 55666666666543
No 14
>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=53.28 E-value=1.4e+02 Score=25.61 Aligned_cols=71 Identities=18% Similarity=0.324 Sum_probs=53.3
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHhh-hhccCCChHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 59 HQIDVERHARDFMEAAKKLQLYFISL-QREDQPTEVE----MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLK 129 (142)
Q Consensus 59 hqiDVErhardFmeaAkqLq~yFi~l-Qr~~~p~k~E----~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~ 129 (142)
...-.+.+|-||.+.+.+.+.=|+.+ |.+-.=..-| -+++||.++++|+++.-.=+|.-.+..+.|++.+.
T Consensus 76 I~ssL~eTtkdf~~~~~k~~~dF~~~Lq~~Lk~V~tde~k~~~~~ei~k~r~e~~~ml~evK~~~E~y~k~~k~~~ 151 (230)
T PF03904_consen 76 IKSSLEETTKDFIDKTEKVHNDFQDILQDELKDVDTDELKNIAQNEIKKVREENKSMLQEVKQSHEKYQKRQKSMY 151 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44578999999999999999999854 4333322222 46678999999998876668888888888888764
No 15
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=52.37 E-value=29 Score=24.59 Aligned_cols=42 Identities=26% Similarity=0.547 Sum_probs=30.5
Q ss_pred HHHHHhhcCCCccc-------hhhcccCCCCCcchhhHHHHHHHHHHHHHHHH
Q 032351 33 TALEAALLPCLPAR-------ELQAIDRSPHPSHQIDVERHARDFMEAAKKLQ 78 (142)
Q Consensus 33 ~~lEaAllpCLpar-------eLqaiDrs~hpshqiDVErhardFmeaAkqLq 78 (142)
.++-+.++.|+|.| ++.... |--.-||+..-+.|++.+|+|.
T Consensus 54 ~e~~~~il~nms~r~a~~l~~e~~~~g----~v~~~di~~Aq~~iv~~~r~l~ 102 (110)
T PF01706_consen 54 EELREKILSNMSKRAAEMLREEMEALG----PVRLSDIEEAQREIVEIVRRLE 102 (110)
T ss_dssp HHHHHHHHTTS-HHHHHHHHHHHHHH-----S--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHHhcC----CCCHHHHHHHHHHHHHHHHHHH
Confidence 36788999999999 444433 2245789999999999999985
No 16
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=50.19 E-value=37 Score=32.25 Aligned_cols=45 Identities=9% Similarity=0.175 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032351 93 VEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHIT 137 (142)
Q Consensus 93 ~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ 137 (142)
.+-|++|+.++++|++.-..++....++...|.++|.+...++-+
T Consensus 429 ~~kl~~e~~~l~~~i~~l~~iL~~~~~~~~~i~~el~~ik~kfg~ 473 (738)
T TIGR01061 429 IFELKEEQNELEKKIISLEQIIASEKARNKLLKKQLEEYKKQFAQ 473 (738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCC
Confidence 348889999999999999999999999999999999998888753
No 17
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=50.03 E-value=76 Score=21.24 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQ 131 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq 131 (142)
+.|++++..++.+++.-..-++.-.+.+..|+..|...
T Consensus 65 ~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~ 102 (106)
T PF01920_consen 65 EELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYEL 102 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36777777777777777777777777777777766543
No 18
>PHA02629 A-type inclusion body protein; Provisional
Probab=49.70 E-value=38 Score=23.81 Aligned_cols=31 Identities=39% Similarity=0.539 Sum_probs=24.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 91 TEVEMLRKDIAIMEEELKAKKELIKKQERLV 121 (142)
Q Consensus 91 ~k~E~lkkeI~~le~EL~~KdELIkkh~~lI 121 (142)
|--+.-||-|+.||.||++--|-||--++.+
T Consensus 26 s~c~ferk~iavleaelr~~metik~lekf~ 56 (61)
T PHA02629 26 SSCEFERKIIAVLEAELRKSMETIKALEKFM 56 (61)
T ss_pred chhHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445668999999999999999998766543
No 19
>PRK05560 DNA gyrase subunit A; Validated
Probab=49.57 E-value=72 Score=30.47 Aligned_cols=45 Identities=13% Similarity=0.197 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032351 93 VEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHIT 137 (142)
Q Consensus 93 ~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ 137 (142)
.+-|++|+..+.+|++.=..++..-.+++..|.++|++...++-.
T Consensus 432 ~~kL~~E~~~l~~ei~~l~~iL~~~~~l~~~i~~EL~~ikkkfg~ 476 (805)
T PRK05560 432 RDKIEDEYKELLALIADLKDILASPERLLEIIKEELLEIKEKFGD 476 (805)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCC
Confidence 348899999999999999999999999999999999998887653
No 20
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=48.50 E-value=18 Score=25.80 Aligned_cols=18 Identities=33% Similarity=0.545 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKE 112 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdE 112 (142)
+|..||+-++.|++.|+.
T Consensus 36 lLq~EIeRlkAe~~kK~~ 53 (65)
T COG5509 36 LLQAEIERLKAELAKKKA 53 (65)
T ss_pred HHHHHHHHHHHHHHhhhc
Confidence 688889999999888864
No 21
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=48.13 E-value=76 Score=23.73 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032351 98 KDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELE 140 (142)
Q Consensus 98 keI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ele 140 (142)
++|++++.++.+-+..+...-..|..|.+.-...+..-+..|+
T Consensus 10 ~ki~~l~~~~~~i~~~~~~~I~~i~~~~~~~~~~l~~~i~~l~ 52 (149)
T PF07352_consen 10 RKIAELQREIARIEAEANDEIARIKEWYEAEIAPLQNRIEYLE 52 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4688888888888888888888888887766655555555544
No 22
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=47.69 E-value=77 Score=20.62 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~eler 141 (142)
..+.++..++.++..+.+.......-...|.++.......+..+..|
T Consensus 63 ~~~~~~~~~~~~~~~~r~~l~~a~~~~k~~e~L~e~~~~~~~~~~~r 109 (123)
T PF02050_consen 63 QQQQELERLEQEVEQAREELQEARRERKKLEKLKERRREEYQQEEER 109 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567777777777777777777777777777777777776666543
No 23
>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []. The exact function of these proteins is not known.
Probab=47.43 E-value=1.3e+02 Score=23.08 Aligned_cols=63 Identities=13% Similarity=0.219 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 65 RHARDFMEAAKKLQLYFISLQREDQ-PTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLK 129 (142)
Q Consensus 65 rhardFmeaAkqLq~yFi~lQr~~~-p~k~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~ 129 (142)
=..+.|+-+|-.+|.||- +--.- ..+...|-+-|.+++.++......+..+.+++......|+
T Consensus 24 lds~~~l~Lc~R~Q~HL~--~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ae~L~ 87 (131)
T PF10158_consen 24 LDSRPVLRLCSRYQEHLN--QCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKFAEQLE 87 (131)
T ss_pred cChHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346889999999999984 21111 3344467666777777777766666666655555544443
No 24
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=47.28 E-value=34 Score=24.66 Aligned_cols=27 Identities=26% Similarity=0.222 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032351 113 LIKKQERLVQRWRNDLKGQLDKHITELE 140 (142)
Q Consensus 113 LIkkh~~lI~~Wq~~L~dq~~kh~~ele 140 (142)
=|.|-.++|..||.-|+++- .-++|+|
T Consensus 9 eieK~k~Kiae~Q~rlK~Le-~qk~E~E 35 (83)
T PF14193_consen 9 EIEKTKEKIAELQARLKELE-AQKTEAE 35 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 36788899999999999864 4456665
No 25
>cd03777 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal al
Probab=43.40 E-value=55 Score=25.89 Aligned_cols=32 Identities=9% Similarity=0.118 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWR 125 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq 125 (142)
|.++..++.+++.+.++++.|..+..+|+.-.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (186)
T cd03777 2 GLLESQLSRHDQMLSVHDIRLADMDLRFQVLE 33 (186)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 56888999999999999999999998887644
No 26
>PF06133 DUF964: Protein of unknown function (DUF964); InterPro: IPR010368 This entry consists of several relatively short bacterial and archaeal hypothetical sequences. It also includes YlbF and YmcA proteins which are involved in the formation of biofilms []. YlbF regulates sporulation prior to stage II, positively controlling the competence regulator ComK at a post-transcriptional level. It may also modulate the translation, stability or activity of ComS and may work together with YmcA to regulate community development [].; PDB: 2IAZ_C 2OEE_A 2OEQ_D 2PIH_A.
Probab=43.15 E-value=1.1e+02 Score=20.96 Aligned_cols=92 Identities=17% Similarity=0.212 Sum_probs=58.9
Q ss_pred HhHHHHHHHHhhcCCCccchhh----cccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHHHHHHH
Q 032351 28 MISCVTALEAALLPCLPARELQ----AIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIM 103 (142)
Q Consensus 28 ~~~~V~~lEaAllpCLpareLq----aiDrs~hpshqiDVErhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkkeI~~l 103 (142)
|..-..+|-.++.-|=-...+. ++..++ .+..-++-=++++.-|...|+...+.. .-..+++..+
T Consensus 2 I~~~a~eL~~~I~~s~ey~~~~~a~~~l~~d~----------e~~~l~~~f~~~q~~~~~~q~~g~~~~-~e~~~~l~~~ 70 (108)
T PF06133_consen 2 IYDKANELAEAIKESEEYKRYKAAEEALEADP----------EAQKLIEEFQKLQQELQNAQMYGKEPP-KEEIEELQEL 70 (108)
T ss_dssp HHHHHHHHHHHHHTSHHHHHHHHHHHHHHCSH----------HHHHHHHHHHHHHHHHHHHHHTTSCHH-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCHHHHHHHHHHHHHHhCH----------HHHHHHHHHHHHHHHHHHHHhhccCCc-HHHHHHHHHH
Confidence 4555566666666555544333 455555 344555555666667776777777554 5667788888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 104 EEELKAKKELIKKQERLVQRWRNDLKGQ 131 (142)
Q Consensus 104 e~EL~~KdELIkkh~~lI~~Wq~~L~dq 131 (142)
+.++.. ..+|+.+...=..|..+|.+-
T Consensus 71 ~~~l~~-~p~v~~y~~ae~~~~~ll~~i 97 (108)
T PF06133_consen 71 QEELMQ-NPVVKEYLQAEQALQDLLQDI 97 (108)
T ss_dssp HHHHHT-SHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHc-CHHHHHHHHHHHHHHHHHHHH
Confidence 888864 567777777777777777654
No 27
>PRK09039 hypothetical protein; Validated
Probab=42.92 E-value=1.1e+02 Score=26.21 Aligned_cols=47 Identities=23% Similarity=0.379 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~eler 141 (142)
.||+.++.++.+|..-.+-.+-....|..-+..|...+..-+.||++
T Consensus 148 aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~~~~~l~~ 194 (343)
T PRK09039 148 ALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQRVQELNR 194 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444555555444445556666666666666666555666665
No 28
>PF09903 DUF2130: Uncharacterized protein conserved in bacteria (DUF2130); InterPro: IPR019219 This entry, found in various hypothetical bacterial proteins, has no known function.
Probab=41.98 E-value=98 Score=26.03 Aligned_cols=45 Identities=29% Similarity=0.277 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhhhhh
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLV-QRWRNDLKGQLDKHITE 138 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI-~~Wq~~L~dq~~kh~~e 138 (142)
+.++..+...+++|+.+++.|.+-.+.. ++-.++...-++.|+.+
T Consensus 2 ~~~~~~~~e~e~~i~~~~~~Ie~lk~~~~~~s~k~~GE~lE~~~e~ 47 (267)
T PF09903_consen 2 EELKLKIKEKEEQIKDLEEQIEELKRKAEQGSTKLQGEVLEQHCEE 47 (267)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHhHHHHHHHHH
Confidence 4567788899999999999999988555 45567888889999887
No 29
>PRK13676 hypothetical protein; Provisional
Probab=41.23 E-value=1.3e+02 Score=21.38 Aligned_cols=93 Identities=20% Similarity=0.217 Sum_probs=61.4
Q ss_pred hHhHHHHHHHHhhcCCCccchhh----cccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHHHHHH
Q 032351 27 NMISCVTALEAALLPCLPARELQ----AIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAI 102 (142)
Q Consensus 27 d~~~~V~~lEaAllpCLpareLq----aiDrs~hpshqiDVErhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkkeI~~ 102 (142)
+|+....+|..++.-|=.-.++. +|+.|+ +.-.-..+|-. .|.-+-..|....+.. +...+++..
T Consensus 4 ni~d~A~eL~~aI~~s~ey~~~~~A~~~l~~d~------~a~~li~~F~~----~q~~~~~~q~~g~~~~-~e~~~~l~~ 72 (114)
T PRK13676 4 NIYDLANELERALRELPEYKALKEAKEAVKADE------EAKKLFDEFRA----LQLEIQQKQMTGQEIT-EEEQQKAQE 72 (114)
T ss_pred hHHHHHHHHHHHHHcCHHHHHHHHHHHHHHcCH------HHHHHHHHHHH----HHHHHHHHHHcCCCCC-HHHHHHHHH
Confidence 46777788999998887777665 666666 44445556633 3333333465555333 445567777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 103 MEEELKAKKELIKKQERLVQRWRNDLKGQ 131 (142)
Q Consensus 103 le~EL~~KdELIkkh~~lI~~Wq~~L~dq 131 (142)
+..++ ..++.|+.....=+.|.++|.+-
T Consensus 73 l~~~i-~~n~~i~~y~~Ae~~l~~ll~~v 100 (114)
T PRK13676 73 LGQKI-QQNELLSKLMEAEQRLSVYINDI 100 (114)
T ss_pred HHHHH-hcCHHHHHHHHHHHHHHHHHHHH
Confidence 87777 56788888888888888877654
No 30
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=41.06 E-value=48 Score=30.06 Aligned_cols=83 Identities=17% Similarity=0.131 Sum_probs=49.7
Q ss_pred hHhHHHHHHHHhhcCCCccchhhcccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHH--HHHH--
Q 032351 27 NMISCVTALEAALLPCLPARELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRK--DIAI-- 102 (142)
Q Consensus 27 d~~~~V~~lEaAllpCLpareLqaiDrs~hpshqiDVErhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkk--eI~~-- 102 (142)
|-..+...+-+.+.----+++|.+|. .+.-...+++++-|+++|.||+ +...-=+-+|+|.- +|-.
T Consensus 344 ~h~~~a~~l~~~~a~y~e~~dli~iG--------~eLs~~d~~~l~~~~~~e~~~~--~~g~~~~~~etl~~~~~~l~~~ 413 (436)
T PRK02118 344 DHGDLMNAMIRLYADSREAKEKMAMG--------FKLSNWDEKLLKFSELFESRLM--DLEVNIPLEEALDLGWKILAQC 413 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh--------hhcCHHHHHHHHHHHHHHHHhh--cCCCcccHHHHHHHHHHHHHHC
Confidence 34455555555554444445555543 1344566788999999999997 43333444555443 3221
Q ss_pred -HHHHHHHHHHHHHHHHH
Q 032351 103 -MEEELKAKKELIKKQER 119 (142)
Q Consensus 103 -le~EL~~KdELIkkh~~ 119 (142)
.+++.+.|.++|+|++.
T Consensus 414 ~~~~~~~~~~~~~~~~~~ 431 (436)
T PRK02118 414 FHPEEVGIKEQLIDKYWP 431 (436)
T ss_pred CHHHHhcCCHHHHHHhhc
Confidence 24455679999999876
No 31
>PF10549 ORF11CD3: ORF11CD3 domain; InterPro: IPR018877 This entry represents the carboxy-terminal domain from ORF11 (Q9XJS9 from SWISSPROT), one of the proteins of Pseudomonas phage D3 (Bacteriophage D3). The function of these proteins are unknown [].
Probab=40.24 E-value=1.2e+02 Score=20.66 Aligned_cols=46 Identities=30% Similarity=0.369 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~eler 141 (142)
.+..+-+.+-.|++..+++---.-+.+..| +--|.++...|..|++
T Consensus 3 s~~~e~n~ac~e~~~~K~~AS~~GrgL~~W-k~~Kp~l~~ki~~l~~ 48 (57)
T PF10549_consen 3 SLMAEYNQACAEYKKEKDIASLCGRGLNRW-KWKKPQLEQKIEELEE 48 (57)
T ss_pred cHHHHHHHHHHHHHhHHHHHHHHhHHHHHH-HHhhHHHHHHHHHHHH
Confidence 467788888899999999999999999999 7888999888888864
No 32
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=39.68 E-value=61 Score=29.17 Aligned_cols=37 Identities=24% Similarity=0.522 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKG 130 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~d 130 (142)
+-|++|+..+++|++.=..+.....+....|.++|.+
T Consensus 408 ~kL~~E~~~l~~ei~~l~~~l~~~~~~~~~i~~eL~~ 444 (445)
T cd00187 408 EKLLKELKELEAEIEDLEKILASEERPKDLWKEELDE 444 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHh
Confidence 3666777777777777777776666777888888764
No 33
>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore
Probab=38.57 E-value=99 Score=22.72 Aligned_cols=36 Identities=28% Similarity=0.407 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 97 RKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQL 132 (142)
Q Consensus 97 kkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~ 132 (142)
+.++..++.|+.+..+.+......++.=++.|..|.
T Consensus 2 ~~e~~~l~~e~~~~~~~~~~~~~~~~~~~~dl~~q~ 37 (132)
T PF07926_consen 2 ESELSSLQSELQRLKEQEEDAEEQLQSLREDLESQA 37 (132)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777777777777777777777776666666553
No 34
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=36.12 E-value=35 Score=24.74 Aligned_cols=24 Identities=29% Similarity=0.487 Sum_probs=19.7
Q ss_pred ccCCChHHHHHHHHHHHHHHHHHH
Q 032351 87 EDQPTEVEMLRKDIAIMEEELKAK 110 (142)
Q Consensus 87 ~~~p~k~E~lkkeI~~le~EL~~K 110 (142)
.|-|...+.|.+||.+-+.+|++|
T Consensus 64 nDcpeA~~eL~~eI~eAK~dLr~k 87 (91)
T PF08285_consen 64 NDCPEAAKELQKEIKEAKADLRKK 87 (91)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHc
Confidence 344667779999999999999987
No 35
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=36.01 E-value=1.2e+02 Score=22.03 Aligned_cols=34 Identities=18% Similarity=0.415 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 93 VEMLRKDIAIMEEELKAKKELIKKQERLVQRWRN 126 (142)
Q Consensus 93 ~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~ 126 (142)
.++|++.++.++++++.-..+...-..++..|..
T Consensus 81 ~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~ 114 (133)
T cd04787 81 RRLIEQRLAETERRIKELLKLRDRMQQAVSQWQQ 114 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4588999999999999999998888888888876
No 36
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.98 E-value=52 Score=29.35 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 99 DIAIMEEELKAKKELIKKQERLVQR 123 (142)
Q Consensus 99 eI~~le~EL~~KdELIkkh~~lI~~ 123 (142)
|...-++||+||.+=+||-++-+++
T Consensus 68 eL~~rqeEL~Rke~ELdRREr~~a~ 92 (313)
T KOG3088|consen 68 ELLKKQEELRRKEQELDRRERALAR 92 (313)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHhh
Confidence 3334468999999999998888877
No 37
>PF07165 DUF1397: Protein of unknown function (DUF1397); InterPro: IPR009832 This entry consists of several insect specific 27 kDa Haemolymph glycoprotein precursors. The function of this family is unknown [].
Probab=35.78 E-value=28 Score=28.10 Aligned_cols=24 Identities=21% Similarity=0.484 Sum_probs=20.6
Q ss_pred hhHhHHHHHHHHhhcCCCccchhh
Q 032351 26 MNMISCVTALEAALLPCLPARELQ 49 (142)
Q Consensus 26 ~d~~~~V~~lEaAllpCLpareLq 49 (142)
+..++||+.|-+++.|||+..+..
T Consensus 78 ~~~~~C~~~f~~~v~~Cl~~ee~~ 101 (213)
T PF07165_consen 78 PQAKECFDPFTEKVKPCLDEEEKE 101 (213)
T ss_pred HHHHHHHHHHHhhcccCCCHHHHH
Confidence 348899999999999999987554
No 38
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=35.35 E-value=52 Score=19.22 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=14.9
Q ss_pred HHHHHHHHH--------HHHHHHHHHHH
Q 032351 100 IAIMEEELK--------AKKELIKKQER 119 (142)
Q Consensus 100 I~~le~EL~--------~KdELIkkh~~ 119 (142)
.++|+++++ .|.+||+|..+
T Consensus 6 ~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~ 33 (35)
T smart00513 6 VSELKDELKKRGLSTSGTKAELVDRLLE 33 (35)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 456777777 68899988754
No 39
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=35.34 E-value=1.1e+02 Score=22.80 Aligned_cols=14 Identities=7% Similarity=0.114 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHH
Q 032351 69 DFMEAAKKLQLYFI 82 (142)
Q Consensus 69 dFmeaAkqLq~yFi 82 (142)
-|-+--+--+.+|+
T Consensus 53 ~f~krE~A~E~~Y~ 66 (100)
T PF04568_consen 53 AFGKREAAQEEQYF 66 (100)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred ccchHHHhhHHHHH
Confidence 45443333456555
No 40
>PF06152 Phage_min_cap2: Phage minor capsid protein 2; InterPro: IPR009319 This entry is represented by Bacteriophage A118, Gp4, the minor capsid protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=35.30 E-value=1.2e+02 Score=26.26 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 032351 111 KELIKKQERLVQRWRNDLKGQLDKH 135 (142)
Q Consensus 111 dELIkkh~~lI~~Wq~~L~dq~~kh 135 (142)
++.+++...+++.||+.+.+.+.+|
T Consensus 337 ~~~~~~~~~~~r~~q~~~r~~~~~~ 361 (361)
T PF06152_consen 337 DENIQKAKAKVRQQQAKYRDFIKEH 361 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4678999999999999999999887
No 41
>PF14182 YgaB: YgaB-like protein
Probab=35.18 E-value=1.8e+02 Score=21.34 Aligned_cols=35 Identities=23% Similarity=0.561 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q 032351 93 VEMLRKDIAIMEEELKAKKELIKKQ-ERLVQRWRND 127 (142)
Q Consensus 93 ~E~lkkeI~~le~EL~~KdELIkkh-~~lI~~Wq~~ 127 (142)
-..++.||..|+.+|+.=-++..+| ++.|+.++++
T Consensus 42 l~~i~~EI~~mkk~Lk~Iq~~Fe~QTeeVI~sy~~~ 77 (79)
T PF14182_consen 42 LHSIQEEISQMKKELKEIQRVFEKQTEEVIRSYQSE 77 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3478999999999999888888777 4566666653
No 42
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=34.73 E-value=1.8e+02 Score=21.28 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=16.8
Q ss_pred HHHHHHHHHHH---HHHHHHHHHHHHHh
Q 032351 110 KKELIKKQERL---VQRWRNDLKGQLDK 134 (142)
Q Consensus 110 KdELIkkh~~l---I~~Wq~~L~dq~~k 134 (142)
+++|-...+.+ -..|+..|...++|
T Consensus 48 r~~L~~en~qLk~E~~~WqerLr~LLGk 75 (79)
T PRK15422 48 REELERENNHLKEQQNGWQERLQALLGR 75 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44454444333 46899999999887
No 43
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=33.14 E-value=1.5e+02 Score=21.54 Aligned_cols=62 Identities=18% Similarity=0.269 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 62 DVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQ 131 (142)
Q Consensus 62 DVErhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq 131 (142)
-++-+..++..+|-=.=-|-+..|. .|-..+..++++++...+=+++-...+..|.+.++..
T Consensus 52 ~~dp~~~klfrLaQl~ieYLl~~q~--------~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~l 113 (118)
T PF13815_consen 52 FVDPNFLKLFRLAQLSIEYLLHCQE--------YLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKL 113 (118)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666666444445554442 3444455555555555555555555555555555443
No 44
>PF13118 DUF3972: Protein of unknown function (DUF3972)
Probab=32.85 E-value=1.4e+02 Score=23.39 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=38.5
Q ss_pred hhhhccCCChHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 83 SLQREDQPTEVE---MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLK 129 (142)
Q Consensus 83 ~lQr~~~p~k~E---~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~ 129 (142)
+|...-..+|.| +||.|+.-|++-|..=.|+.+.-.+-|..-+..|+
T Consensus 74 ~LheKvl~aKdETI~~lk~EN~fLKeAl~s~QE~y~ed~kTI~~L~~qL~ 123 (126)
T PF13118_consen 74 NLHEKVLDAKDETIEALKNENRFLKEALYSMQELYEEDRKTIELLREQLK 123 (126)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 344455567777 89999999999999999999999999988777665
No 45
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=32.82 E-value=2.1e+02 Score=25.07 Aligned_cols=57 Identities=16% Similarity=0.305 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Q 032351 65 RHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKA----KKELIKKQERLVQRWRNDLKG 130 (142)
Q Consensus 65 rhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkkeI~~le~EL~~----KdELIkkh~~lI~~Wq~~L~d 130 (142)
+.+-.|+|+-++|+.|++++ |.|++=--.|.--..+ .+|++++-..||.-|++.+..
T Consensus 20 ~n~~~~ld~l~~L~~~pvt~---------ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~ 80 (296)
T KOG1105|consen 20 KNVEAALDLLKRLKKIPVTL---------ELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDK 80 (296)
T ss_pred ccHHHHHHHHHHHHhcccHH---------HHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhc
Confidence 45567999999999999843 4444422222222222 368899999999999999864
No 46
>PF14131 DUF4298: Domain of unknown function (DUF4298)
Probab=31.27 E-value=1.6e+02 Score=20.82 Aligned_cols=31 Identities=23% Similarity=0.393 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 100 IAIMEEELKAKKELIKKQERLVQRWRNDLKG 130 (142)
Q Consensus 100 I~~le~EL~~KdELIkkh~~lI~~Wq~~L~d 130 (142)
|+.|++-++.=.+++.+-++.+..|++...+
T Consensus 2 I~eme~~y~~~~~~l~~le~~l~~~~~~~~~ 32 (90)
T PF14131_consen 2 IQEMEKIYNEWCELLEELEEALEKWQEAQPD 32 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6788888888888888888888888877654
No 47
>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length. The function of this family is unknown.; GO: 0005198 structural molecule activity
Probab=30.47 E-value=2.6e+02 Score=21.63 Aligned_cols=45 Identities=13% Similarity=0.226 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHhhhhhh
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQER----------LVQRWRNDLKGQLDKHITEL 139 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~----------lI~~Wq~~L~dq~~kh~~el 139 (142)
.+..++..++.+|+.-++-|+.-.. .|..|+...+.....|-.+|
T Consensus 24 ~~~~e~~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~~~~~~~~e~~l 78 (155)
T PF06810_consen 24 KVKEERDNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKNKTAKEEYEAKL 78 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556677777777777766666555 55566655555444444443
No 48
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=30.29 E-value=62 Score=20.88 Aligned_cols=19 Identities=37% Similarity=0.618 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 032351 110 KKELIKKQERLVQRWRNDL 128 (142)
Q Consensus 110 KdELIkkh~~lI~~Wq~~L 128 (142)
-+++|++-+..|.||-+--
T Consensus 21 ~~~~i~~LN~~lrGW~nYy 39 (80)
T PF08388_consen 21 LEELIKKLNPILRGWANYY 39 (80)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 4689999999999998753
No 49
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.24 E-value=78 Score=28.01 Aligned_cols=28 Identities=29% Similarity=0.405 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032351 112 ELIKKQERLVQRWRNDLKGQLDKHITEL 139 (142)
Q Consensus 112 ELIkkh~~lI~~Wq~~L~dq~~kh~~el 139 (142)
+|++|--+.++.|+.-|+.++-+|+.|.
T Consensus 187 rl~kkDie~L~k~R~~L~~emld~~~e~ 214 (293)
T COG4079 187 RLVKKDIETLRKHRRRLAEEMLDHIREG 214 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666778889999999999998874
No 50
>PF02870 Methyltransf_1N: 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; InterPro: IPR008332 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources []. This group of proteins are characterised by having an N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity (IPR001497 from INTERPRO).; GO: 0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A.
Probab=30.17 E-value=53 Score=21.28 Aligned_cols=24 Identities=29% Similarity=0.318 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhh-ccC
Q 032351 66 HARDFMEAAKKLQLYFISLQR-EDQ 89 (142)
Q Consensus 66 hardFmeaAkqLq~yFi~lQr-~~~ 89 (142)
.+..|-++.+||+.||-|--+ .|-
T Consensus 48 ~~~~~~~~~~qL~eYF~G~r~~~F~ 72 (77)
T PF02870_consen 48 EAPLLAEAKQQLDEYFAGERTPEFD 72 (77)
T ss_dssp CHCCHHHHHHHHHHHHHHHHS--B-
T ss_pred ccccHHHHHHHHHHHHcCCCCCCCc
Confidence 344577899999999997555 443
No 51
>KOG2430 consensus Glycosyl hydrolase, family 47 [Carbohydrate transport and metabolism]
Probab=29.94 E-value=53 Score=30.83 Aligned_cols=24 Identities=46% Similarity=0.621 Sum_probs=18.3
Q ss_pred chhhHHH-----HHHHHHHHHHHHHHHHHhhh
Q 032351 59 HQIDVER-----HARDFMEAAKKLQLYFISLQ 85 (142)
Q Consensus 59 hqiDVEr-----hardFmeaAkqLq~yFi~lQ 85 (142)
+-+||-- .||-||++ |-+||-|||
T Consensus 289 i~ldvhihkp~l~ar~~mda---llaf~pglq 317 (587)
T KOG2430|consen 289 IFLDVHIHKPMLAARGFMDA---LLAFFPGLQ 317 (587)
T ss_pred eEEEEecccchhhHhhHHHH---HHHhCcchh
Confidence 5566644 48999997 678999887
No 52
>PRK12704 phosphodiesterase; Provisional
Probab=29.89 E-value=1.8e+02 Score=26.59 Aligned_cols=21 Identities=24% Similarity=0.574 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHhhhhhhhc
Q 032351 121 VQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 121 I~~Wq~~L~dq~~kh~~eler 141 (142)
+..=.+.+.....+...+||+
T Consensus 126 Le~~~~~~~~~~~~~~~~l~~ 146 (520)
T PRK12704 126 LEKKEEELEELIEEQLQELER 146 (520)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333333444444444455554
No 53
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=28.92 E-value=1.2e+02 Score=24.20 Aligned_cols=28 Identities=18% Similarity=0.347 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQR 123 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~ 123 (142)
.|.+.|++|++.|+.|+.-|- +|.|+++
T Consensus 96 ~l~~ri~eLe~~l~~kad~vv-sYqll~h 123 (175)
T PRK13182 96 TITRRLDELERQLQQKADDVV-SYQLLQH 123 (175)
T ss_pred HHHHHHHHHHHHHHHHHhhhh-hHHHHHh
Confidence 456677777777777777664 3444444
No 54
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=28.86 E-value=2.3e+02 Score=26.66 Aligned_cols=56 Identities=30% Similarity=0.380 Sum_probs=35.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhhhccCCC----------------hHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 61 IDVERHARDFMEAAKKLQLYFISLQREDQPT----------------EVEMLRKDIAIMEEELKAKKELIKK 116 (142)
Q Consensus 61 iDVErhardFmeaAkqLq~yFi~lQr~~~p~----------------k~E~lkkeI~~le~EL~~KdELIkk 116 (142)
--|+..+.+-++++.|.+.+=.-|=.+..-+ .-..+|.+|..+++|++.|+|++++
T Consensus 401 ~~v~~s~~rl~~L~~qWe~~R~pL~~e~r~lk~~~~~~~~e~~~~~~~ik~~r~~~k~~~~e~~~Kee~~~q 472 (594)
T PF05667_consen 401 ALVEASEQRLVELAQQWEKHRAPLIEEYRRLKEKASNRESESKQKLQEIKELREEIKEIEEEIRQKEELYKQ 472 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567777777788887776643221111111 1125667888888889999988665
No 55
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=28.46 E-value=96 Score=25.19 Aligned_cols=38 Identities=39% Similarity=0.781 Sum_probs=28.8
Q ss_pred CCCccc--hhhcccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHhhhhccCCChHH
Q 032351 41 PCLPAR--ELQAIDRSPHPSHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVE 94 (142)
Q Consensus 41 pCLpar--eLqaiDrs~hpshqiDVErhardFmeaAkqLq~yFi~lQr~~~p~k~E 94 (142)
|| |.| .|+.|+-|+ ..+|++-|||-.|.++ ..+|..++
T Consensus 78 PC-plRD~~l~ri~mS~------------~EYM~lKkqLae~il~---~s~~~~e~ 117 (153)
T COG4008 78 PC-PLRDGVLNRINMSP------------EEYMELKKQLAEYILG---HSEPPVEE 117 (153)
T ss_pred Cc-cccHHHHHhcCCCH------------HHHHHHHHHHHHHHhc---cCCCcHHH
Confidence 45 444 788899888 6799999999999984 44565554
No 56
>PRK00106 hypothetical protein; Provisional
Probab=27.76 E-value=2e+02 Score=26.83 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhcC
Q 032351 119 RLVQRWRNDLKGQLDKHITELERV 142 (142)
Q Consensus 119 ~lI~~Wq~~L~dq~~kh~~elerv 142 (142)
+.++.=.+.+.....+...+||+|
T Consensus 139 eeLee~~~~~~~~~~~~~~~Le~~ 162 (535)
T PRK00106 139 KHIDEREEQVEKLEEQKKAELERV 162 (535)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444555556653
No 57
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.23 E-value=2.4e+02 Score=20.33 Aligned_cols=34 Identities=18% Similarity=0.242 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRND 127 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~ 127 (142)
+.+.+.++.++++++.-.++++.-..++..|..-
T Consensus 83 ~~l~~~~~~l~~~~~~l~~~~~~L~~~~~~~~~~ 116 (118)
T cd04776 83 EKIEKRRAELEQQRRDIDAALAELDAAEERCRER 116 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677888888888888888887777777666543
No 58
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=27.04 E-value=54 Score=25.53 Aligned_cols=16 Identities=31% Similarity=0.574 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHhhh
Q 032351 121 VQRWRNDLKGQLDKHI 136 (142)
Q Consensus 121 I~~Wq~~L~dq~~kh~ 136 (142)
++.||.+|.-++++|-
T Consensus 19 V~vWQ~llt~LL~~HY 34 (114)
T PF06755_consen 19 VEVWQQLLTYLLEQHY 34 (114)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 6789999999999994
No 59
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=26.96 E-value=2.6e+02 Score=24.25 Aligned_cols=40 Identities=23% Similarity=0.330 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLD 133 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~ 133 (142)
+..++|...+++||+.+..=++.-...|..|+.-|.+.-.
T Consensus 203 ~~~~~ELe~~~EeL~~~Eke~~e~~~~i~e~~~rl~~l~~ 242 (269)
T PF05278_consen 203 ELKKEELEELEEELKQKEKEVKEIKERITEMKGRLGELEM 242 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677777778888887777777778777777766543
No 60
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=26.78 E-value=1.4e+02 Score=17.58 Aligned_cols=20 Identities=45% Similarity=0.576 Sum_probs=13.5
Q ss_pred HHHHHHHHH--------HHHHHHHHHHH
Q 032351 101 AIMEEELKA--------KKELIKKQERL 120 (142)
Q Consensus 101 ~~le~EL~~--------KdELIkkh~~l 120 (142)
++|+++++. |.+||+|..+-
T Consensus 7 ~eLk~~l~~~gL~~~G~K~~Li~Rl~~~ 34 (35)
T PF02037_consen 7 AELKEELKERGLSTSGKKAELIERLKEH 34 (35)
T ss_dssp HHHHHHHHHTTS-STSSHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHh
Confidence 456666653 78888887653
No 61
>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
Probab=26.61 E-value=2.9e+02 Score=21.65 Aligned_cols=9 Identities=33% Similarity=0.549 Sum_probs=3.8
Q ss_pred Hhhhhhhhc
Q 032351 133 DKHITELER 141 (142)
Q Consensus 133 ~kh~~eler 141 (142)
.....+||+
T Consensus 134 ~~~~~~Le~ 142 (201)
T PF12072_consen 134 EEQQQELEE 142 (201)
T ss_pred HHHHHHHHH
Confidence 333444444
No 62
>PF06273 eIF-4B: Plant specific eukaryotic initiation factor 4B; InterPro: IPR010433 This family consists of several plant specific eukaryotic initiation factor 4B proteins.
Probab=26.32 E-value=47 Score=31.13 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=18.1
Q ss_pred CChHH-HHHHHHHHHHHHHHHHHH
Q 032351 90 PTEVE-MLRKDIAIMEEELKAKKE 112 (142)
Q Consensus 90 p~k~E-~lkkeI~~le~EL~~KdE 112 (142)
.+.+| .||++|+.|+.+|+...+
T Consensus 364 e~~~ek~lKeeI~~lk~~l~~~~~ 387 (492)
T PF06273_consen 364 ETEEEKFLKEEINALKERLEEEEA 387 (492)
T ss_pred ccccchhhhhhHHHHHHHHHhhhh
Confidence 34444 999999999999977655
No 63
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=26.13 E-value=3.1e+02 Score=23.30 Aligned_cols=34 Identities=24% Similarity=0.234 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRND 127 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~ 127 (142)
+.|.+||..++.|++..++...++.+.....+..
T Consensus 74 ~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~ 107 (314)
T PF04111_consen 74 EELDQELEELEEELEELDEEEEEYWREYNELQLE 107 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677788888888888777766666655555533
No 64
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=26.00 E-value=2.2e+02 Score=22.78 Aligned_cols=22 Identities=23% Similarity=0.379 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKK 116 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkk 116 (142)
.||+|++.|+.++..-+++.+.
T Consensus 80 ~L~~e~~~l~~~~~~~~~l~~e 101 (276)
T PRK13922 80 ELKKELLELESRLQELEQLEAE 101 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666666665555544443
No 65
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=25.80 E-value=3e+02 Score=21.05 Aligned_cols=40 Identities=25% Similarity=0.334 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDK 134 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~k 134 (142)
.+.-+|..++.|.+|=.++.|.-++.+..+++.|.+.+..
T Consensus 51 ~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL~~~m~~ 90 (162)
T PF05565_consen 51 NLEADIEAIKAEIKRLQERKKSIENRIDRLKEYLLDAMEA 90 (162)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455778888888888888889999999999998887654
No 66
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=25.43 E-value=3.3e+02 Score=21.33 Aligned_cols=48 Identities=21% Similarity=0.284 Sum_probs=36.6
Q ss_pred CChHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032351 90 PTEVEMLRKDIAIMEEELK------------AKKELIKKQERLVQRWRNDLKGQLDKHIT 137 (142)
Q Consensus 90 p~k~E~lkkeI~~le~EL~------------~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ 137 (142)
+-|-+.+++||..++.... .|.||..=+.+++..-++.|.+-++.||.
T Consensus 142 ~~K~~~~~~ei~~~e~~~~~a~~~~e~is~~~k~El~rF~~~r~~dfk~~l~~~~e~~ie 201 (216)
T cd07627 142 QEKLNSLLSELEEAERRASELKKEFEEVSELIKSELERFERERVEDFRNSVEIYLESAIE 201 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456678888877765443 57788888899999999999988887764
No 67
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=25.08 E-value=1.6e+02 Score=20.16 Aligned_cols=31 Identities=23% Similarity=0.342 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWR 125 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq 125 (142)
.|+++|..++.+++.-..-++-.+..+..|+
T Consensus 74 ~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L~ 104 (104)
T PF13600_consen 74 ELEEELEALEDELAALQDEIQALEAQIAFLQ 104 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 7777888888877777776766666666663
No 68
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 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. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=25.02 E-value=3.3e+02 Score=21.14 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQL 132 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~ 132 (142)
-+.+.|..|+.|...+|+-|+.--+.+..-++.|....
T Consensus 26 ~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 26 ENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999998877
No 69
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=24.97 E-value=2.3e+02 Score=20.04 Aligned_cols=49 Identities=20% Similarity=0.216 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHHHHHHHHHHHHHHH
Q 032351 63 VERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKK 111 (142)
Q Consensus 63 VErhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkkeI~~le~EL~~Kd 111 (142)
=|+..|...+.|-.--.+-+.--.-+.|.+..-|-+||+.+|.|+..-+
T Consensus 26 ~E~~~r~aLe~al~~~~~~~~~~~~~lp~~~keLL~EIA~lE~eV~~LE 74 (88)
T PF14389_consen 26 EEQDLRRALEKALGRSSGSLPSSPSSLPKKAKELLEEIALLEAEVAKLE 74 (88)
T ss_pred HHHHHHHHHHHHhCCCCcccCCccccCChHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555553332222101112447788888899999999976544
No 70
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=24.94 E-value=64 Score=20.71 Aligned_cols=34 Identities=18% Similarity=0.278 Sum_probs=17.7
Q ss_pred HHHHHHHhhhhccCCChHH--HHHHHHHHHHHHHHH
Q 032351 76 KLQLYFISLQREDQPTEVE--MLRKDIAIMEEELKA 109 (142)
Q Consensus 76 qLq~yFi~lQr~~~p~k~E--~lkkeI~~le~EL~~ 109 (142)
||+.=|-.|.+.+-.++.+ .|++|...|..|+..
T Consensus 2 QlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~ 37 (45)
T PF02183_consen 2 QLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQE 37 (45)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444444 666666666665543
No 71
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=24.69 E-value=2.8e+02 Score=23.29 Aligned_cols=32 Identities=25% Similarity=0.409 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRN 126 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~ 126 (142)
.+|.++..+..+++.|...+..-...++.+..
T Consensus 213 ~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~ 244 (325)
T PF08317_consen 213 ALRQELAEQKEEIEAKKKELAELQEELEELEE 244 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666666666666555555555555555543
No 72
>PF00521 DNA_topoisoIV: DNA gyrase/topoisomerase IV, subunit A; InterPro: IPR002205 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent C-terminal region in eukaryotic topoisomerase II composed of a single polypeptide. This subunit has DNA-binding capacity. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 1ZVU_A 1AB4_A 1X75_A 3NUH_A 1BJT_A 1BGW_A 2RGR_A 3KSB_B 3FOE_B 2NOV_C ....
Probab=24.65 E-value=1.8e+02 Score=25.48 Aligned_cols=32 Identities=28% Similarity=0.639 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLK 129 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~ 129 (142)
-|++|+..++.|++.=..+..+ ....|.+.|+
T Consensus 395 kL~~e~~~l~~ei~~l~~~~~~---~~~l~~~dLd 426 (426)
T PF00521_consen 395 KLQKEIKELEKEIEELEKILPK---IKDLWKKDLD 426 (426)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHC---HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhC
Confidence 5555555555555554444444 4455776663
No 73
>PF01496 V_ATPase_I: V-type ATPase 116kDa subunit family ; InterPro: IPR002490 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents the 116kDa subunit (or subunit a) and subunit I found in the V0 or A0 complex of V- or A-ATPases, respectively. The 116kDa subunit is a transmembrane glycoprotein required for the assembly and proton transport activity of the ATPase complex. Several isoforms of the 116kDa subunit exist, providing a potential role in the differential targeting and regulation of the V-ATPase for specific organelles []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015991 ATP hydrolysis coupled proton transport, 0033177 proton-transporting two-sector ATPase complex, proton-transporting domain; PDB: 2RPW_X 2NVJ_A 2JTW_A 3RRK_A.
Probab=24.39 E-value=3.3e+02 Score=25.36 Aligned_cols=44 Identities=23% Similarity=0.376 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032351 94 EMLRKDIAIMEEELK----AKKELIKKQERLVQRWRNDLKGQLDKHIT 137 (142)
Q Consensus 94 E~lkkeI~~le~EL~----~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ 137 (142)
+.++++|++++++++ ...++++++.+.+..|...+........+
T Consensus 232 ~~l~~~i~~l~~~~~~~~~~l~~~~~~~~~~l~~~~~~l~~~~~~~~~ 279 (759)
T PF01496_consen 232 KELEEEIEELEKELEELEEELKKLLEKYAEELEAWYEYLRKEKEIYEA 279 (759)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 74
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=24.24 E-value=2.3e+02 Score=21.68 Aligned_cols=10 Identities=20% Similarity=0.322 Sum_probs=7.8
Q ss_pred hhHHHHHHHH
Q 032351 61 IDVERHARDF 70 (142)
Q Consensus 61 iDVErhardF 70 (142)
.++..+++.|
T Consensus 89 ~~~~~~~~~f 98 (192)
T PF05529_consen 89 TEDQVLAKKF 98 (192)
T ss_pred hhHHHHHHHH
Confidence 6777778888
No 75
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=24.01 E-value=2.5e+02 Score=25.64 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHhhhhhhhc
Q 032351 120 LVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 120 lI~~Wq~~L~dq~~kh~~eler 141 (142)
.+..=.+.+.....+...+||+
T Consensus 119 eLee~~~e~~~~~~~~~~~le~ 140 (514)
T TIGR03319 119 NLDEKEEELEELIAEQREELER 140 (514)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333344444444445554
No 76
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=23.88 E-value=3e+02 Score=23.30 Aligned_cols=55 Identities=18% Similarity=0.283 Sum_probs=31.1
Q ss_pred hhccC-CChHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhhhh
Q 032351 85 QREDQ-PTEVE--MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLK-GQLDKHITEL 139 (142)
Q Consensus 85 Qr~~~-p~k~E--~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~-dq~~kh~~el 139 (142)
|-.|. |+-+| .|..+|..+.+.+..+..-+.--.--|..-+++|+ .++.+-|.+|
T Consensus 70 QDqF~~~~~eel~~ld~~i~~l~ek~q~l~~t~s~veaEik~L~s~Lt~eemQe~i~~L 128 (201)
T KOG4603|consen 70 QDQFDMVSDEELQVLDGKIVALTEKVQSLQQTCSYVEAEIKELSSALTTEEMQEEIQEL 128 (201)
T ss_pred HHhhcCCChHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence 44444 77666 67777777776666665555555555555555443 3444444444
No 77
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=23.55 E-value=78 Score=25.43 Aligned_cols=18 Identities=22% Similarity=0.510 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 032351 96 LRKDIAIMEEELKAKKEL 113 (142)
Q Consensus 96 lkkeI~~le~EL~~KdEL 113 (142)
||.|+.+|++||.+++.+
T Consensus 36 LkDE~RDLKqEl~V~ek~ 53 (166)
T PF04880_consen 36 LKDELRDLKQELIVQEKL 53 (166)
T ss_dssp ------------------
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 555666666666555443
No 78
>TIGR01063 gyrA DNA gyrase, A subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV.
Probab=23.49 E-value=2e+02 Score=27.68 Aligned_cols=43 Identities=16% Similarity=0.290 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHI 136 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~ 136 (142)
+-|++|+..+++|++.=..++..-.++...-.++|++...++-
T Consensus 430 ~kl~~e~~~l~~ei~~l~~iL~~~~~l~~vi~~EL~eikkkfg 472 (800)
T TIGR01063 430 EKLQEEYKELLELIADLEDILASEERVLEIIREELEEIKEQFG 472 (800)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHhC
Confidence 3888999999999999999999999888888999988888774
No 79
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=23.38 E-value=2.6e+02 Score=19.40 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032351 95 MLRKDIAIMEEE-------LKAKKELIKKQERLVQRWRNDLKGQLDKH 135 (142)
Q Consensus 95 ~lkkeI~~le~E-------L~~KdELIkkh~~lI~~Wq~~L~dq~~kh 135 (142)
+|+.||..|+++ -..-.+=..+-..--..|+.-|...++|-
T Consensus 22 ~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~~LL~kl 69 (72)
T PF06005_consen 22 LLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLRSLLGKL 69 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 455555555553 22222222333344568999999888763
No 80
>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]
Probab=23.09 E-value=2.1e+02 Score=29.99 Aligned_cols=48 Identities=23% Similarity=0.313 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 032351 94 EMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 94 E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~eler 141 (142)
+-++++|-.++.||.-..+=+.++...++.-+..|++.+.+|.+.+-+
T Consensus 475 ~~~~~e~~~~ekel~~~~~~~n~~~~e~~vaesel~~L~~~~~~~~~~ 522 (1293)
T KOG0996|consen 475 EGIREEIEKLEKELMPLLKQVNEARSELDVAESELDILLSRHETGLKK 522 (1293)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677788888888888888888888888899999999999887654
No 81
>KOG3663 consensus Nuclear factor I [Transcription]
Probab=23.05 E-value=96 Score=29.29 Aligned_cols=34 Identities=32% Similarity=0.585 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032351 104 EEELKAKKELIKKQERLVQRWRNDLKGQLDKHIT 137 (142)
Q Consensus 104 e~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ 137 (142)
+||-+.||||...--++=|.|-..|-.-|.|-|+
T Consensus 51 ~EEravkdELl~ekpEvKqKWASRLLaKlrKDIr 84 (518)
T KOG3663|consen 51 DEERAVKDELLNEKPEVKQKWASRLLAKLRKDIR 84 (518)
T ss_pred hHHHHHHHHHhccchHHHHHHHHHHHHHHHhhcc
Confidence 5677888888888888888899888877777664
No 82
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=22.99 E-value=2.6e+02 Score=22.79 Aligned_cols=43 Identities=21% Similarity=0.320 Sum_probs=23.0
Q ss_pred HHHHHHHHhhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 75 KKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQE 118 (142)
Q Consensus 75 kqLq~yFi~lQr~~~p~k~E~lkkeI~~le~EL~~KdELIkkh~ 118 (142)
+.|...|-+|-..--- ...-|+.||+.|+.|+..=++++.+-+
T Consensus 105 qeL~~tf~rL~~~Vd~-~~~eL~~eI~~L~~~i~~le~~~~~~k 147 (171)
T PF04799_consen 105 QELSSTFARLCQQVDQ-TKNELEDEIKQLEKEIQRLEEIQSKSK 147 (171)
T ss_dssp -----HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566544332111 112578888888888888777766543
No 83
>PF07052 Hep_59: Hepatocellular carcinoma-associated antigen 59; InterPro: IPR010756 This family represents a conserved region approximately 100 residues long within mammalian hepatocellular carcinoma-associated antigen 59 and similar proteins. Family members are found in a variety of eukaryotes, mainly as hypothetical proteins.
Probab=22.80 E-value=76 Score=22.75 Aligned_cols=19 Identities=26% Similarity=0.497 Sum_probs=15.7
Q ss_pred CCCcchhhHHHHHHHHHHH
Q 032351 55 PHPSHQIDVERHARDFMEA 73 (142)
Q Consensus 55 ~hpshqiDVErhardFmea 73 (142)
.+-..++||+.|-+.|||.
T Consensus 4 ~~qT~~~d~DkhM~~YIE~ 22 (104)
T PF07052_consen 4 TAQTGQRDVDKHMMKYIEE 22 (104)
T ss_pred cccccchhHHHHHHHHHHH
Confidence 4456789999999999985
No 84
>PRK11864 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional
Probab=22.63 E-value=1.5e+02 Score=25.51 Aligned_cols=28 Identities=25% Similarity=0.309 Sum_probs=17.3
Q ss_pred HHhhhhccCCChHHHHHHHHHHHHHHHHHHHH
Q 032351 81 FISLQREDQPTEVEMLRKDIAIMEEELKAKKE 112 (142)
Q Consensus 81 Fi~lQr~~~p~k~E~lkkeI~~le~EL~~KdE 112 (142)
||.+|.||.-+.+| +|+.++++..++=|
T Consensus 263 ~l~~q~Rf~~L~~~----~~~~~q~~vd~~~~ 290 (300)
T PRK11864 263 YLKLQGRFKHLTEE----EIKGLQEEIDEMWE 290 (300)
T ss_pred HHhhccchhcCCHH----HHHHHHHHHHHHHH
Confidence 55689999877644 35555555544433
No 85
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=22.60 E-value=3.1e+02 Score=28.55 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 032351 95 MLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELER 141 (142)
Q Consensus 95 ~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~eler 141 (142)
.|.++|++||+=-..-++|+.-..++--.-+++| |++.-|+.||++
T Consensus 466 lLeetv~dlEalee~~EQL~Esn~ele~DLreEl-d~~~g~~kel~~ 511 (1243)
T KOG0971|consen 466 LLEETVGDLEALEEMNEQLQESNRELELDLREEL-DMAKGARKELQK 511 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhHHHHHHH
Confidence 6677788887766666777777776666666665 566678888764
No 86
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=22.46 E-value=3.2e+02 Score=20.04 Aligned_cols=45 Identities=18% Similarity=0.287 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032351 96 LRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLDKHITELE 140 (142)
Q Consensus 96 lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ele 140 (142)
+..+...++.+++.-..-+|...+-++.=++.+......|.+|+-
T Consensus 92 ~~~~~~~l~~~~~~~~~~~k~~kee~~klk~~~~~~~tq~~~e~r 136 (151)
T PF11559_consen 92 AEEKERQLQKQLKSLEAKLKQEKEELQKLKNQLQQRKTQYEHELR 136 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444455555555555555555555555566666666666653
No 87
>KOG3994 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.35 E-value=76 Score=28.05 Aligned_cols=21 Identities=33% Similarity=0.515 Sum_probs=18.2
Q ss_pred cchhhHHHH--HHHHHHHHHHHH
Q 032351 58 SHQIDVERH--ARDFMEAAKKLQ 78 (142)
Q Consensus 58 shqiDVErh--ardFmeaAkqLq 78 (142)
|+.+|+||- +.+||-+||.+=
T Consensus 181 See~eiErekL~akFI~~A~eiC 203 (291)
T KOG3994|consen 181 SEEGEIEREKLAAKFILAAREIC 203 (291)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHH
Confidence 678888888 999999999864
No 88
>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=22.09 E-value=3.5e+02 Score=20.30 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=4.4
Q ss_pred HHHHHHHHHHHH
Q 032351 95 MLRKDIAIMEEE 106 (142)
Q Consensus 95 ~lkkeI~~le~E 106 (142)
.+..+|..|++|
T Consensus 76 ~ld~ei~~L~~e 87 (169)
T PF07106_consen 76 ELDAEIKELREE 87 (169)
T ss_pred HHHHHHHHHHHH
Confidence 333333333333
No 89
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=21.81 E-value=1.6e+02 Score=23.21 Aligned_cols=31 Identities=19% Similarity=0.089 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhccCCChHHHHH
Q 032351 65 RHARDFMEAAKKLQLYFISLQREDQPTEVEMLR 97 (142)
Q Consensus 65 rhardFmeaAkqLq~yFi~lQr~~~p~k~E~lk 97 (142)
..+..|.++|+.+-.-.. +|+-.|+-++.|+
T Consensus 233 ~~a~~y~~La~ell~~~~--~~~~~~~~~~~~~ 263 (279)
T PRK13230 233 EISNIFRELAEAIYENNT--GTIPNPLEEEEID 263 (279)
T ss_pred HHHHHHHHHHHHHHhcCC--CCCCCCCCHHHHH
Confidence 346789999998766432 5777788888765
No 90
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=21.63 E-value=2e+02 Score=19.71 Aligned_cols=27 Identities=33% Similarity=0.404 Sum_probs=16.3
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 90 PTEVEMLRKDIAIMEEELKAKKELIKK 116 (142)
Q Consensus 90 p~k~E~lkkeI~~le~EL~~KdELIkk 116 (142)
+.-.+-|.+-|+.|+.|+.|=..-|.+
T Consensus 20 ~lSv~EL~~RIa~L~aEI~R~~~~~~~ 46 (59)
T PF06698_consen 20 LLSVEELEERIALLEAEIARLEAAIAK 46 (59)
T ss_pred hcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556667777777777665555443
No 91
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=21.52 E-value=2.8e+02 Score=22.49 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=33.6
Q ss_pred HHHHHH-------HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032351 93 VEMLRK-------DIAIM-EEELKAKKELIKKQERLVQRWRNDLKGQLDKHIT 137 (142)
Q Consensus 93 ~E~lkk-------eI~~l-e~EL~~KdELIkkh~~lI~~Wq~~L~dq~~kh~~ 137 (142)
++.+|+ +|++. ++|-+.|.|++++-.+-|..|.+.-..++.+++.
T Consensus 111 ~e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~ 163 (225)
T PF01086_consen 111 PEAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKK 163 (225)
T ss_dssp TTHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446665 34433 3455677889999999999999999999988775
No 92
>KOG0577 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=21.26 E-value=3.6e+02 Score=27.25 Aligned_cols=69 Identities=25% Similarity=0.318 Sum_probs=45.7
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHhhhhccCCChHHHHHHHHH----HHHHHHH--------HHHHHHHHHHHHHHHHH
Q 032351 58 SHQIDVERHARDFMEAAKKLQLYFISLQREDQPTEVEMLRKDIA----IMEEELK--------AKKELIKKQERLVQRWR 125 (142)
Q Consensus 58 shqiDVErhardFmeaAkqLq~yFi~lQr~~~p~k~E~lkkeI~----~le~EL~--------~KdELIkkh~~lI~~Wq 125 (142)
+|+.++|+-|++--..-||++---++-|+.+..+--+.-||+.. .+++||. .|++-+++|++-++.-+
T Consensus 542 khqa~~ekeak~~~a~EkKfqq~i~~qqkk~l~~~~e~qkkeYK~~KE~~KeeL~e~~stPkrek~e~l~~qKe~Lq~~q 621 (948)
T KOG0577|consen 542 KHQAIGEKEAKAASAEEKKFQQHILGQQKKELKAYLEAQKKEYKLNKEQLKEELQENPSTPKREKAEWLLRQKENLQQCQ 621 (948)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHH
Confidence 47788888888877778888888777777766444343333322 3455554 57777777777776655
Q ss_pred H
Q 032351 126 N 126 (142)
Q Consensus 126 ~ 126 (142)
.
T Consensus 622 a 622 (948)
T KOG0577|consen 622 A 622 (948)
T ss_pred H
Confidence 3
No 93
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=20.66 E-value=5.2e+02 Score=24.57 Aligned_cols=71 Identities=17% Similarity=0.282 Sum_probs=0.0
Q ss_pred cchhhHHHHHHHHHH-HHHHHHHHHHhhhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 58 SHQIDVERHARDFME-AAKKLQLYFISLQREDQPTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRNDLKGQLD 133 (142)
Q Consensus 58 shqiDVErhardFme-aAkqLq~yFi~lQr~~~p~k~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~~L~dq~~ 133 (142)
|-+.+.|++.-+.-. --.-+..|| +..-.....++-+..+++.+-+.-.....++..++..|++.|+++.+
T Consensus 332 Sqr~y~e~~~~e~~qsqlen~k~~~-----e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~E 403 (493)
T KOG0804|consen 332 SQRKYYEQIMSEYEQSQLENQKQYY-----ELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEERE 403 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHH-----HHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 94
>PF11708 Slu7: Pre-mRNA splicing Prp18-interacting factor; InterPro: IPR021715 The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain.
Probab=20.45 E-value=3.7e+02 Score=22.51 Aligned_cols=43 Identities=37% Similarity=0.548 Sum_probs=28.9
Q ss_pred HHHHHHHHhhhhccC--------CChHHHHHHHHHHHHHHHHH--HHHHHHHH
Q 032351 75 KKLQLYFISLQREDQ--------PTEVEMLRKDIAIMEEELKA--KKELIKKQ 117 (142)
Q Consensus 75 kqLq~yFi~lQr~~~--------p~k~E~lkkeI~~le~EL~~--KdELIkkh 117 (142)
.+||.|=.-.+++.. ||+.|+|+++...=+++++. |..|+.|+
T Consensus 134 ~~lq~FAWea~~kg~~~~hl~AnPT~~E~l~k~~~~kk~~~~~~~k~~ll~kY 186 (239)
T PF11708_consen 134 EKLQRFAWEAAKKGGLDVHLQANPTKAELLRKEFKEKKEELKEEKKQSLLEKY 186 (239)
T ss_pred HHHHHHHHHHHhccCCceeeeeCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456777665565544 99999999988776666554 44555543
No 95
>PHA02562 46 endonuclease subunit; Provisional
Probab=20.32 E-value=4.8e+02 Score=22.44 Aligned_cols=37 Identities=11% Similarity=0.374 Sum_probs=26.2
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 90 PTEVEMLRKDIAIMEEELKAKKELIKKQERLVQRWRN 126 (142)
Q Consensus 90 p~k~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~ 126 (142)
|.+.+.|...|..++.+++.=++.|....+.+..+.+
T Consensus 298 ~~~~~~l~d~i~~l~~~l~~l~~~i~~~~~~~~~~~~ 334 (562)
T PHA02562 298 PDRITKIKDKLKELQHSLEKLDTAIDELEEIMDEFNE 334 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455678888888888888777777766666665443
No 96
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=20.30 E-value=2.1e+02 Score=24.25 Aligned_cols=37 Identities=30% Similarity=0.400 Sum_probs=25.9
Q ss_pred HHhhhhccCCChHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 032351 81 FISLQREDQPTEVE---MLRKDIAIMEEELKAKKELIKKQ 117 (142)
Q Consensus 81 Fi~lQr~~~p~k~E---~lkkeI~~le~EL~~KdELIkkh 117 (142)
|-++..+-..++.- -||.|..+.++||+.|-|=||.-
T Consensus 34 yKgvKqeGpftk~G~T~eLkNeLREVREELkEKmeEIKQI 73 (205)
T PF15079_consen 34 YKGVKQEGPFTKTGGTQELKNELREVREELKEKMEEIKQI 73 (205)
T ss_pred hhhhhhcCCccCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555544443 68889999999999998877643
No 97
>PF12644 DUF3782: Protein of unknown function (DUF3782); InterPro: IPR024271 This functionally uncharacterised family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.
Probab=20.27 E-value=2.4e+02 Score=17.86 Aligned_cols=35 Identities=23% Similarity=0.416 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Q 032351 98 KDIAIMEEELKAKKE-LIKKQERLVQRWRNDLKGQL 132 (142)
Q Consensus 98 keI~~le~EL~~KdE-LIkkh~~lI~~Wq~~L~dq~ 132 (142)
++|..++++|+.-.+ |.+...+.|..+-+.|..--
T Consensus 8 ~~i~a~~e~l~~~~~~lt~e~~~~l~~~~~al~~~~ 43 (64)
T PF12644_consen 8 DEIMATKEELEELEERLTKEDKKRLEEYIDALGARW 43 (64)
T ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHh
Confidence 377777887777666 88888888887777766543
No 98
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=20.23 E-value=2.5e+02 Score=20.38 Aligned_cols=34 Identities=6% Similarity=-0.047 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032351 93 VEMLRKDIAIMEEELKAKKELIKKQERLVQRWRN 126 (142)
Q Consensus 93 ~E~lkkeI~~le~EL~~KdELIkkh~~lI~~Wq~ 126 (142)
-..++.+++.+++|++....=..+-.+.|..|++
T Consensus 29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3467788888888877666656666666777765
Done!