Query 040074
Match_columns 148
No_of_seqs 13 out of 15
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 04:51:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040074.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040074hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11594 Med28: Mediator compl 97.4 0.00022 4.9E-09 53.9 4.0 63 80-142 10-80 (106)
2 PF07989 Microtub_assoc: Micro 78.7 3.6 7.8E-05 28.8 3.7 39 89-127 20-73 (75)
3 PF13094 CENP-Q: CENP-Q, a CEN 73.1 11 0.00024 28.1 5.3 46 95-140 39-84 (160)
4 PF13863 DUF4200: Domain of un 70.2 17 0.00037 25.5 5.5 38 103-140 6-43 (126)
5 PF07165 DUF1397: Protein of u 66.2 5.6 0.00012 32.0 2.6 27 25-51 76-102 (213)
6 PF04201 TPD52: Tumour protein 59.5 29 0.00062 28.1 5.5 46 99-144 31-84 (162)
7 PHA02629 A-type inclusion body 56.8 18 0.00039 25.6 3.5 28 101-128 30-57 (61)
8 KOG3663 Nuclear factor I [Tran 53.6 17 0.00037 34.1 3.8 51 93-143 30-84 (518)
9 cd00187 TOP4c DNA Topoisomeras 53.6 19 0.00041 32.3 3.9 39 98-136 406-444 (445)
10 PRK09039 hypothetical protein; 53.5 36 0.00079 29.0 5.5 50 98-147 145-194 (343)
11 TIGR01061 parC_Gpos DNA topois 53.2 13 0.00028 35.1 3.0 45 98-142 428-472 (738)
12 PF14131 DUF4298: Domain of un 47.9 52 0.0011 23.3 4.7 31 106-136 2-32 (90)
13 PF12999 PRKCSH-like: Glucosid 47.2 43 0.00094 27.2 4.8 36 100-135 128-163 (176)
14 PF04799 Fzo_mitofusin: fzo-li 45.5 47 0.001 27.0 4.7 33 90-122 107-145 (171)
15 COG1390 NtpE Archaeal/vacuolar 44.0 74 0.0016 25.5 5.6 52 89-140 44-96 (194)
16 PF05667 DUF812: Protein of un 43.9 27 0.00059 32.5 3.5 28 98-125 448-475 (594)
17 PF01920 Prefoldin_2: Prefoldi 42.8 74 0.0016 21.2 4.7 39 98-136 63-101 (106)
18 PF07544 Med9: RNA polymerase 41.4 18 0.00039 25.2 1.6 45 81-125 24-80 (83)
19 PF00521 DNA_topoisoIV: DNA gy 40.7 38 0.00082 29.4 3.7 44 89-135 382-426 (426)
20 cd00632 Prefoldin_beta Prefold 39.7 99 0.0021 21.7 5.1 39 98-136 64-102 (105)
21 PRK12704 phosphodiesterase; Pr 39.2 79 0.0017 28.7 5.6 30 118-147 117-146 (520)
22 KOG0971 Microtubule-associated 37.7 67 0.0015 33.1 5.3 49 98-147 463-511 (1243)
23 PF07106 TBPIP: Tat binding pr 37.5 63 0.0014 24.2 4.1 31 87-117 53-85 (169)
24 PRK05560 DNA gyrase subunit A; 37.4 58 0.0013 31.0 4.7 58 85-142 417-475 (805)
25 TIGR03319 YmdA_YtgF conserved 37.3 90 0.0019 28.3 5.7 37 112-148 105-141 (514)
26 cd08811 CARD_IPS1 Caspase acti 36.9 15 0.00032 27.1 0.6 12 40-51 26-37 (84)
27 PF03938 OmpH: Outer membrane 34.4 46 0.001 23.9 2.8 47 69-115 20-68 (158)
28 PF01086 Clathrin_lg_ch: Clath 33.4 1.1E+02 0.0024 24.6 5.1 39 105-143 124-163 (225)
29 TIGR01062 parC_Gneg DNA topois 33.3 59 0.0013 31.2 4.1 44 99-142 426-469 (735)
30 PF08614 ATG16: Autophagy prot 32.9 96 0.0021 24.0 4.5 37 98-134 117-153 (194)
31 PF13094 CENP-Q: CENP-Q, a CEN 32.2 2.1E+02 0.0046 21.2 6.5 46 101-146 38-83 (160)
32 PF12072 DUF3552: Domain of un 32.1 1.6E+02 0.0034 23.1 5.7 17 131-147 126-142 (201)
33 PRK00106 hypothetical protein; 31.7 1.2E+02 0.0026 28.1 5.7 19 129-147 143-161 (535)
34 COG4079 Uncharacterized protei 31.5 74 0.0016 28.2 4.1 28 118-145 187-214 (293)
35 TIGR01063 gyrA DNA gyrase, A s 31.5 58 0.0012 31.0 3.7 45 98-142 428-472 (800)
36 PF04880 NUDE_C: NUDE protein, 30.4 34 0.00073 27.5 1.7 18 105-122 15-32 (166)
37 PF12004 DUF3498: Domain of un 29.4 18 0.00039 33.4 0.0 33 98-130 445-477 (495)
38 PF07926 TPR_MLP1_2: TPR/MLP1/ 29.3 1.6E+02 0.0035 21.5 5.0 34 103-136 2-35 (132)
39 PF14182 YgaB: YgaB-like prote 29.3 1.2E+02 0.0026 22.3 4.3 33 100-132 43-76 (79)
40 PF07352 Phage_Mu_Gam: Bacteri 28.7 1.9E+02 0.0041 21.5 5.4 43 104-146 10-52 (149)
41 PF04568 IATP: Mitochondrial A 28.5 75 0.0016 23.7 3.1 22 125-146 72-93 (100)
42 PF11221 Med21: Subunit 21 of 28.2 60 0.0013 24.4 2.6 54 81-134 76-134 (144)
43 PHA02562 46 endonuclease subun 28.1 1.9E+02 0.0042 24.7 5.9 47 90-136 162-213 (562)
44 PF10158 LOH1CR12: Tumour supp 27.7 85 0.0018 24.0 3.4 52 79-130 25-82 (131)
45 PF08647 BRE1: BRE1 E3 ubiquit 27.5 2.3E+02 0.0049 20.1 5.4 45 102-147 50-94 (96)
46 PF11172 DUF2959: Protein of u 27.2 74 0.0016 26.6 3.2 32 95-136 76-107 (201)
47 PF09738 DUF2051: Double stran 26.9 51 0.0011 28.4 2.3 16 98-113 113-128 (302)
48 KOG4083 Head-elevated expressi 26.9 1.9E+02 0.0041 24.4 5.5 47 99-145 85-135 (192)
49 PF07964 Red1: Rec10 / Red1; 26.7 1.3E+02 0.0027 29.4 5.0 38 98-135 634-673 (706)
50 PRK02119 hypothetical protein; 25.9 2.3E+02 0.0049 19.6 5.4 26 110-135 22-47 (73)
51 KOG4031 Vesicle coat protein c 25.6 1.6E+02 0.0035 25.1 5.0 33 111-143 125-157 (216)
52 PF09124 Endonuc-dimeris: T4 r 25.3 81 0.0018 21.6 2.6 30 93-126 12-48 (54)
53 PF03735 ENT: ENT domain; Int 25.1 38 0.00083 23.8 1.0 33 116-148 23-55 (73)
54 PRK13979 DNA topoisomerase IV 25.0 67 0.0015 31.7 3.0 64 79-142 410-491 (957)
55 PF15642 Tox-ODYAM1: Toxin in 24.5 1.1E+02 0.0024 27.8 4.0 37 108-144 131-167 (385)
56 cd05295 MDH_like Malate dehydr 23.8 47 0.001 30.1 1.6 37 81-124 75-115 (452)
57 PF05529 Bap31: B-cell recepto 23.6 1.6E+02 0.0034 22.4 4.2 13 134-146 166-178 (192)
58 PF10446 DUF2457: Protein of u 23.5 30 0.00064 32.2 0.3 27 35-61 205-237 (458)
59 PF10280 Med11: Mediator compl 23.4 46 0.001 24.3 1.2 36 64-112 37-74 (117)
60 PF15619 Lebercilin: Ciliary p 23.3 2.9E+02 0.0064 22.1 5.8 48 98-145 20-70 (194)
61 KOG0804 Cytoplasmic Zn-finger 23.1 2E+02 0.0044 27.2 5.5 52 87-138 349-402 (493)
62 KOG3204 60S ribosomal protein 23.1 1.7E+02 0.0037 24.6 4.6 37 106-142 147-183 (197)
63 PF08232 Striatin: Striatin fa 23.0 2.8E+02 0.0061 20.9 5.4 41 101-141 29-69 (134)
64 PF13815 Dzip-like_N: Iguana/D 22.8 1.4E+02 0.0031 21.5 3.7 39 98-136 74-112 (118)
65 PF13815 Dzip-like_N: Iguana/D 22.7 2.2E+02 0.0047 20.6 4.6 38 98-135 81-118 (118)
66 PF04111 APG6: Autophagy prote 22.5 2.4E+02 0.0052 23.9 5.4 19 101-119 75-93 (314)
67 KOG3990 Uncharacterized conser 22.0 2.5E+02 0.0055 25.1 5.6 22 100-121 228-249 (305)
68 PRK14872 rod shape-determining 21.7 1.2E+02 0.0025 26.9 3.5 30 91-120 57-87 (337)
69 PF02050 FliJ: Flagellar FliJ 21.5 2.4E+02 0.0051 18.2 6.3 49 98-146 60-108 (123)
70 cd03777 MATH_TRAF3 Tumor Necro 21.3 1.5E+02 0.0033 23.3 3.8 32 100-131 2-33 (186)
71 PF07957 DUF3294: Protein of u 21.1 2.2E+02 0.0049 24.1 5.0 41 99-139 6-47 (216)
72 PRK13454 F0F1 ATP synthase sub 20.7 4E+02 0.0087 20.5 6.1 44 98-141 63-106 (181)
73 PF10549 ORF11CD3: ORF11CD3 do 20.3 2.9E+02 0.0063 18.8 5.3 45 102-147 4-48 (57)
74 PF05384 DegS: Sensor protein 20.3 66 0.0014 25.5 1.6 49 81-129 80-130 (159)
75 PF07798 DUF1640: Protein of u 20.1 2.9E+02 0.0063 21.1 5.0 34 81-114 54-97 (177)
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=97.38 E-value=0.00022 Score=53.85 Aligned_cols=63 Identities=27% Similarity=0.405 Sum_probs=54.5
Q ss_pred ccCCCCccchhhhhh---hhh-----hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074 80 SDDFPPPLDHQKLYF---RLT-----IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN 142 (148)
Q Consensus 80 ~rDFmeaakklqlYF---~lq-----~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~ 142 (148)
+--|...|+....|| |+. -+..++.||..+.+||--|++|++||.-.|..|++.|-|.-+.|.
T Consensus 10 ~~~FlD~aRq~e~~FlqKr~~LS~~kpe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~d~~~~~k 80 (106)
T PF11594_consen 10 IQSFLDVARQMEAFFLQKRFELSAYKPEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLSDAQNQHK 80 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 356888899988888 332 667789999999999999999999999999999999998877764
No 2
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=78.66 E-value=3.6 Score=28.76 Aligned_cols=39 Identities=33% Similarity=0.621 Sum_probs=24.1
Q ss_pred hhhhhh---hhhh------cc------chhhhHHHHHHHhhhhHHHHHHHHHHH
Q 040074 89 HQKLYF---RLTI------VK------EPRHEIDAMEEELKIKDELVQKQEKVI 127 (148)
Q Consensus 89 klqlYF---~lq~------~e------~lrkeIa~mEeELk~KdELi~kq~kli 127 (148)
||++|| +|+. .+ .|+-++..|..||+.+..++.+..+-|
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 789999 6761 11 355566666666666666666555433
No 3
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=73.11 E-value=11 Score=28.11 Aligned_cols=46 Identities=26% Similarity=0.296 Sum_probs=38.7
Q ss_pred hhhhccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 040074 95 RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDK 140 (148)
Q Consensus 95 ~lq~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~k 140 (148)
.+...+.|++||..+|..|..-.+-|+.=++=++.|..+++++..+
T Consensus 39 ~~~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~~~~~ 84 (160)
T PF13094_consen 39 NLHQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREEEEKK 84 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4446678999999999999988888888888888888888888776
No 4
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=70.21 E-value=17 Score=25.47 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=31.2
Q ss_pred hhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 040074 103 RHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDK 140 (148)
Q Consensus 103 rkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~k 140 (148)
|+|+..+...|..|.+-+.+.+..+..+++.|+..-..
T Consensus 6 kre~~~~~~~l~~kr~e~~~~~~~~~~~e~~L~~~e~~ 43 (126)
T PF13863_consen 6 KREMFLVQLALDTKREEIERREEQLKQREEELEKKEQE 43 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888888999999999999988888888888765443
No 5
>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=66.21 E-value=5.6 Score=31.96 Aligned_cols=27 Identities=19% Similarity=0.437 Sum_probs=22.8
Q ss_pred hhHHHHHHHHhhhhhcccCcchHHHhh
Q 040074 25 EIEDMIACVNVMDDALLPCLTELDLNK 51 (148)
Q Consensus 25 ~~~Dm~acV~~leaaLLPCLpareLqa 51 (148)
.+...+.|+..+-+++.|||++.|..-
T Consensus 76 k~~~~~~C~~~f~~~v~~Cl~~ee~~~ 102 (213)
T PF07165_consen 76 KRPQAKECFDPFTEKVKPCLDEEEKEI 102 (213)
T ss_pred hhHHHHHHHHHHHhhcccCCCHHHHHH
Confidence 356789999999999999999987543
No 6
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=59.49 E-value=29 Score=28.14 Aligned_cols=46 Identities=28% Similarity=0.442 Sum_probs=33.8
Q ss_pred ccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHH--------HHHHHhhhhhh
Q 040074 99 VKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKE--------LRDRLDKHNAE 144 (148)
Q Consensus 99 ~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~ke--------Lkdql~kH~~E 144 (148)
.++||.|++..|||+.+=...+---+|-..+|++. |+.-+.|+...
T Consensus 31 ~eeLr~EL~KvEeEI~TLrqvL~aKer~~~eLKrkLGit~l~elkqnlskg~~~ 84 (162)
T PF04201_consen 31 REELRSELAKVEEEIQTLRQVLAAKERHCAELKRKLGITPLSELKQNLSKGWHD 84 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHCCchHHHHHHHHHHHhHh
Confidence 46899999999999987776666666666677654 47777776543
No 7
>PHA02629 A-type inclusion body protein; Provisional
Probab=56.80 E-value=18 Score=25.56 Aligned_cols=28 Identities=29% Similarity=0.355 Sum_probs=23.1
Q ss_pred chhhhHHHHHHHhhhhHHHHHHHHHHHH
Q 040074 101 EPRHEIDAMEEELKIKDELVQKQEKVIQ 128 (148)
Q Consensus 101 ~lrkeIa~mEeELk~KdELi~kq~kliq 128 (148)
--||-|+++|.||+.--|-|+--+|..+
T Consensus 30 ferk~iavleaelr~~metik~lekf~e 57 (61)
T PHA02629 30 FERKIIAVLEAELRKSMETIKALEKFME 57 (61)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3488999999999999998887777653
No 8
>KOG3663 consensus Nuclear factor I [Transcription]
Probab=53.65 E-value=17 Score=34.10 Aligned_cols=51 Identities=27% Similarity=0.341 Sum_probs=36.4
Q ss_pred hhhhh--hccchhhhHHH--HHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 040074 93 YFRLT--IVKEPRHEIDA--MEEELKIKDELVQKQEKVIQELKKELRDRLDKHNA 143 (148)
Q Consensus 93 YF~lq--~~e~lrkeIa~--mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ 143 (148)
+|.|| +-+-.+|-=.. .+||--+||||...--.+-|.|-..|-..|.|-|.
T Consensus 30 wfnlqarkrkyfkkhekrMsk~EEravkdELl~ekpEvKqKWASRLLaKlrKDIr 84 (518)
T KOG3663|consen 30 WFNLQARKRKYFKKHEKRMSKDEERAVKDELLNEKPEVKQKWASRLLAKLRKDIR 84 (518)
T ss_pred hhhHHHHHHHHHHHHHhhhchhHHHHHHHHHhccchHHHHHHHHHHHHHHHhhcc
Confidence 56777 22333332222 37888899999988888889999999888888764
No 9
>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=53.58 E-value=19 Score=32.28 Aligned_cols=39 Identities=18% Similarity=0.285 Sum_probs=33.9
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
..+.|++|++.+++|++.=..+.....++.+-|.++|++
T Consensus 406 e~~kL~~E~~~l~~ei~~l~~~l~~~~~~~~~i~~eL~~ 444 (445)
T cd00187 406 EREKLLKELKELEAEIEDLEKILASEERPKDLWKEELDE 444 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHh
Confidence 567888999999999998888888888899999999874
No 10
>PRK09039 hypothetical protein; Validated
Probab=53.45 E-value=36 Score=29.03 Aligned_cols=50 Identities=22% Similarity=0.347 Sum_probs=33.0
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELER 147 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELER 147 (148)
-.+.||..|+.+|++|..-.+-.+.+..-|...+..|..-+..-+.||+|
T Consensus 145 qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~~~~~l~~ 194 (343)
T PRK09039 145 QIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQRVQELNR 194 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666666666666655555666666777777777777666777765
No 11
>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=53.22 E-value=13 Score=35.10 Aligned_cols=45 Identities=16% Similarity=0.249 Sum_probs=37.9
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN 142 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~ 142 (148)
..+.|++|++.+++|++.-..++....++.+-|++||++=..|+-
T Consensus 428 e~~kl~~e~~~l~~~i~~l~~iL~~~~~~~~~i~~el~~ik~kfg 472 (738)
T TIGR01061 428 DIFELKEEQNELEKKIISLEQIIASEKARNKLLKKQLEEYKKQFA 472 (738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhC
Confidence 456788899999999999999998888888889999888777664
No 12
>PF14131 DUF4298: Domain of unknown function (DUF4298)
Probab=47.90 E-value=52 Score=23.26 Aligned_cols=31 Identities=23% Similarity=0.305 Sum_probs=27.0
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 106 IDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 106 Ia~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
|..||+-+.-=.+++.+-++.++.|++-..+
T Consensus 2 I~eme~~y~~~~~~l~~le~~l~~~~~~~~~ 32 (90)
T PF14131_consen 2 IQEMEKIYNEWCELLEELEEALEKWQEAQPD 32 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7889999999999999999999999886543
No 13
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=47.18 E-value=43 Score=27.18 Aligned_cols=36 Identities=36% Similarity=0.535 Sum_probs=26.0
Q ss_pred cchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 040074 100 KEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELR 135 (148)
Q Consensus 100 e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLk 135 (148)
+.+.++...+++-+++|.++|+.-++...+|++.++
T Consensus 128 ~~~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~ 163 (176)
T PF12999_consen 128 EELEEEEEIYKEGLKIRQELIEEAKKKREELEKKLE 163 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445556777788888899998887777666665543
No 14
>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=45.49 E-value=47 Score=27.00 Aligned_cols=33 Identities=30% Similarity=0.407 Sum_probs=20.8
Q ss_pred hhhhh-hhh-----hccchhhhHHHHHHHhhhhHHHHHH
Q 040074 90 QKLYF-RLT-----IVKEPRHEIDAMEEELKIKDELVQK 122 (148)
Q Consensus 90 lqlYF-~lq-----~~e~lrkeIa~mEeELk~KdELi~k 122 (148)
|...| ||. ....|..||+.|+.++..-+.+..+
T Consensus 107 L~~tf~rL~~~Vd~~~~eL~~eI~~L~~~i~~le~~~~~ 145 (171)
T PF04799_consen 107 LSSTFARLCQQVDQTKNELEDEIKQLEKEIQRLEEIQSK 145 (171)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34467 665 5667788888888887766555443
No 15
>COG1390 NtpE Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]
Probab=43.99 E-value=74 Score=25.53 Aligned_cols=52 Identities=10% Similarity=0.190 Sum_probs=42.1
Q ss_pred hhhhhh-hhhhccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 040074 89 HQKLYF-RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDK 140 (148)
Q Consensus 89 klqlYF-~lq~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~k 140 (148)
...-+| +.+++.+..+....=...++.+..+....+++|+.|-+.+++.|..
T Consensus 44 ~~~~~~~~~~~ea~~~~~~iis~A~le~r~~~Le~~ee~l~~~~~~~~e~L~~ 96 (194)
T COG1390 44 AIEEILRKAEKEAERERQRIISSALLEARRKLLEAKEEILESVFEAVEEKLRN 96 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 345566 6677777777766666899999999999999999999999988753
No 16
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=43.91 E-value=27 Score=32.50 Aligned_cols=28 Identities=43% Similarity=0.597 Sum_probs=22.4
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEK 125 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~k 125 (148)
..+.+|.+|..+++|++.|+|++++=.+
T Consensus 448 ~ik~~r~~~k~~~~e~~~Kee~~~qL~~ 475 (594)
T PF05667_consen 448 EIKELREEIKEIEEEIRQKEELYKQLVK 475 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667888999999999999998766333
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=42.84 E-value=74 Score=21.19 Aligned_cols=39 Identities=31% Similarity=0.486 Sum_probs=24.7
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
..+.|.++++.++++++.-..-++.-.+-+..|++.|+.
T Consensus 63 ~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~ 101 (106)
T PF01920_consen 63 AIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYE 101 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667777777777666555555555556666666654
No 18
>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=41.39 E-value=18 Score=25.18 Aligned_cols=45 Identities=27% Similarity=0.406 Sum_probs=26.1
Q ss_pred cCCCCccchhhhhh-hhh-----------hccchhhhHHHHHHHhhhhHHHHHHHHH
Q 040074 81 DDFPPPLDHQKLYF-RLT-----------IVKEPRHEIDAMEEELKIKDELVQKQEK 125 (148)
Q Consensus 81 rDFmeaakklqlYF-~lq-----------~~e~lrkeIa~mEeELk~KdELi~kq~k 125 (148)
.||..++..++.=| ... ..+.-..+|..+|+++..|.+++++-+.
T Consensus 24 kd~~~~~~~lk~Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~ 80 (83)
T PF07544_consen 24 KDLDTATGSLKHKLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKE 80 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555666565554 211 3444455777777777777777666543
No 19
>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=40.73 E-value=38 Score=29.43 Aligned_cols=44 Identities=20% Similarity=0.294 Sum_probs=28.8
Q ss_pred hhhhhh-hhhhccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 040074 89 HQKLYF-RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELR 135 (148)
Q Consensus 89 klqlYF-~lq~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLk 135 (148)
.+++|. .....+.|.+|++.+++|++.=..+..+ +.+-|.++|+
T Consensus 382 ~m~L~~LT~~e~~kL~~e~~~l~~ei~~l~~~~~~---~~~l~~~dLd 426 (426)
T PF00521_consen 382 SMPLRRLTKEEIEKLQKEIKELEKEIEELEKILPK---IKDLWKKDLD 426 (426)
T ss_dssp TSBGGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHC---HHHHHHHHHH
T ss_pred hchHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhC
Confidence 344443 3336667778888888877766555555 6677888875
No 20
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=39.65 E-value=99 Score=21.67 Aligned_cols=39 Identities=13% Similarity=0.308 Sum_probs=23.0
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
..+.|.+.+..++.+++.-+.=++.=.+-+.+|++.|+.
T Consensus 64 a~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~l~~ 102 (105)
T cd00632 64 ARTELKERLETIELRIKRLERQEEDLQEKLKELQEKIQQ 102 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566667777777665555555555555566655543
No 21
>PRK12704 phosphodiesterase; Provisional
Probab=39.25 E-value=79 Score=28.73 Aligned_cols=30 Identities=20% Similarity=0.460 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Q 040074 118 ELVQKQEKVIQELKKELRDRLDKHNAELER 147 (148)
Q Consensus 118 ELi~kq~kliq~w~keLkdql~kH~~ELER 147 (148)
+-+.++++-++.-++++.....+...+||+
T Consensus 117 ~~Le~re~eLe~~~~~~~~~~~~~~~~l~~ 146 (520)
T PRK12704 117 KELEQKQQELEKKEEELEELIEEQLQELER 146 (520)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333344444444444444455555554
No 22
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=37.69 E-value=67 Score=33.06 Aligned_cols=49 Identities=20% Similarity=0.323 Sum_probs=39.9
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELER 147 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELER 147 (148)
++..|+.+|+.||+--.+-+.|+.-+..+--.+++|| |++.-|+.||++
T Consensus 463 kVklLeetv~dlEalee~~EQL~Esn~ele~DLreEl-d~~~g~~kel~~ 511 (1243)
T KOG0971|consen 463 KVKLLEETVGDLEALEEMNEQLQESNRELELDLREEL-DMAKGARKELQK 511 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhHHHHHHH
Confidence 6778888999999888888889988888877777776 567778888864
No 23
>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=37.47 E-value=63 Score=24.19 Aligned_cols=31 Identities=23% Similarity=0.326 Sum_probs=16.4
Q ss_pred cchhhhhhhhhhc-cc-hhhhHHHHHHHhhhhH
Q 040074 87 LDHQKLYFRLTIV-KE-PRHEIDAMEEELKIKD 117 (148)
Q Consensus 87 akklqlYF~lq~~-e~-lrkeIa~mEeELk~Kd 117 (148)
..|.++||-.|.. +. -..|+..|..+++...
T Consensus 53 ~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~ 85 (169)
T PF07106_consen 53 YGKQKIYFANQDELEVPSPEELAELDAEIKELR 85 (169)
T ss_pred ecceEEEeeCccccCCCCchhHHHHHHHHHHHH
Confidence 4678999976622 21 2224555555544433
No 24
>PRK05560 DNA gyrase subunit A; Validated
Probab=37.43 E-value=58 Score=30.99 Aligned_cols=58 Identities=12% Similarity=0.122 Sum_probs=46.3
Q ss_pred Cccchhhhhh-hhhhccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074 85 PPLDHQKLYF-RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN 142 (148)
Q Consensus 85 eaakklqlYF-~lq~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~ 142 (148)
++.=.++||- +-...+.|++|++.+.+|++.-..++..-.+++.-|.+||++=..++-
T Consensus 417 ~~IL~m~L~~LT~~e~~kL~~E~~~l~~ei~~l~~iL~~~~~l~~~i~~EL~~ikkkfg 475 (805)
T PRK05560 417 QAILDMRLQRLTGLERDKIEDEYKELLALIADLKDILASPERLLEIIKEELLEIKEKFG 475 (805)
T ss_pred HHHHHhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhC
Confidence 4445566665 333577889999999999999999999999999999999998777664
No 25
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=37.33 E-value=90 Score=28.35 Aligned_cols=37 Identities=30% Similarity=0.519 Sum_probs=17.7
Q ss_pred HhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcC
Q 040074 112 ELKIKDELVQKQEKVIQELKKELRDRLDKHNAELERV 148 (148)
Q Consensus 112 ELk~KdELi~kq~kliq~w~keLkdql~kH~~ELERV 148 (148)
+|..|.+-+.++++-++.-.+++.....+...+||++
T Consensus 105 ~Le~ke~~L~~re~eLee~~~e~~~~~~~~~~~le~~ 141 (514)
T TIGR03319 105 NLEKKEKELSNKEKNLDEKEEELEELIAEQREELERI 141 (514)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333344444444444445555555555566653
No 26
>cd08811 CARD_IPS1 Caspase activation and recruitment domain (CARD) found in IPS-1. Caspase activation and recruitment domain (CARD) found in IPS-1 (Interferon beta promoter stimulator protein 1), also known as CARDIF, VISA or MAVS. IPS-1 is an adaptor protein that plays an important role in interferon induction in response to viral infection. It is crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. The CARD of IPS-1 associates with the CARDs of two RNA helicases, RIG-I and MDA5, which bind viral DNA in the cytoplasm during the initial stage of intracellular antiviral response, leading to the induction of type I interferons. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homo
Probab=36.89 E-value=15 Score=27.12 Aligned_cols=12 Identities=50% Similarity=0.908 Sum_probs=8.7
Q ss_pred cccCcchHHHhh
Q 040074 40 LLPCLTELDLNK 51 (148)
Q Consensus 40 LLPCLpareLqa 51 (148)
-||||++.|=..
T Consensus 26 ~LpCLT~~Dqe~ 37 (84)
T cd08811 26 YLPCLTASDQEE 37 (84)
T ss_pred ccccCchhhHHH
Confidence 489999987433
No 27
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=34.38 E-value=46 Score=23.94 Aligned_cols=47 Identities=15% Similarity=0.177 Sum_probs=29.3
Q ss_pred cccchhhccccccCCCCccchhhhhh-hhh-hccchhhhHHHHHHHhhh
Q 040074 69 VQPAVETELQASDDFPPPLDHQKLYF-RLT-IVKEPRHEIDAMEEELKI 115 (148)
Q Consensus 69 hqidVEr~~hA~rDFmeaakklqlYF-~lq-~~e~lrkeIa~mEeELk~ 115 (148)
.-||+++=+..|..+-.+-++++-.| ..+ .-+..++++..+.++|..
T Consensus 20 a~Vd~~~v~~~~~~~k~~~~~l~~~~~~~~~~l~~~~~el~~~~~~l~~ 68 (158)
T PF03938_consen 20 AVVDVDKVFQESPAGKDAQAKLQEKFKALQKELQAKQKELQKLQQKLQS 68 (158)
T ss_dssp EEE-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred EEeeHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788887777777777777777777 444 444455555555555444
No 28
>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=33.36 E-value=1.1e+02 Score=24.65 Aligned_cols=39 Identities=21% Similarity=0.403 Sum_probs=30.8
Q ss_pred hHHHHH-HHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 040074 105 EIDAME-EELKIKDELVQKQEKVIQELKKELRDRLDKHNA 143 (148)
Q Consensus 105 eIa~mE-eELk~KdELi~kq~kliq~w~keLkdql~kH~~ 143 (148)
+|+... ++-+.|.+++.+=++-|..|.+....++.+++.
T Consensus 124 ~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~ 163 (225)
T PF01086_consen 124 RIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKK 163 (225)
T ss_dssp TSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444433 445678899999999999999999999988765
No 29
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit, proteobacterial. 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=33.31 E-value=59 Score=31.16 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=31.2
Q ss_pred ccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074 99 VKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN 142 (148)
Q Consensus 99 ~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~ 142 (148)
+..+++|++.+++|.+.-.+|+....++.+--++||++-.+++-
T Consensus 426 ~~~i~~E~~~l~~e~~~l~~~L~~~~~~~~~i~~el~~~~~~~g 469 (735)
T TIGR01062 426 EHAIIDEQSELEKERAILEKILKSERELNQLVKKEIQADATKYG 469 (735)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhC
Confidence 45567778888887777777777777776666777777666653
No 30
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 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 []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=32.93 E-value=96 Score=23.95 Aligned_cols=37 Identities=27% Similarity=0.367 Sum_probs=25.7
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKEL 134 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keL 134 (148)
....|+++++.++++++-.++-|+...+.++-.++|+
T Consensus 117 ~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~ 153 (194)
T PF08614_consen 117 RLAELEAELAQLEEKIKDLEEELKEKNKANEILQDEL 153 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666777777777777777777777777766665
No 31
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=32.20 E-value=2.1e+02 Score=21.25 Aligned_cols=46 Identities=17% Similarity=0.354 Sum_probs=35.0
Q ss_pred chhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 040074 101 EPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELE 146 (148)
Q Consensus 101 ~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELE 146 (148)
...+-|+.+++|++.-....++-.+-|+..++-.+..-..-..+.+
T Consensus 38 ~~~~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~~~~ 83 (160)
T PF13094_consen 38 ANLHQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREEEEK 83 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5667888999999888888888888888888887776655444443
No 32
>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=32.13 E-value=1.6e+02 Score=23.09 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=7.2
Q ss_pred HHHHHHHHhhhhhhhhc
Q 040074 131 KKELRDRLDKHNAELER 147 (148)
Q Consensus 131 ~keLkdql~kH~~ELER 147 (148)
.+++..-......+||+
T Consensus 126 ~~e~~~~~~~~~~~Le~ 142 (201)
T PF12072_consen 126 EEELEELIEEQQQELEE 142 (201)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333333344445554
No 33
>PRK00106 hypothetical protein; Provisional
Probab=31.70 E-value=1.2e+02 Score=28.14 Aligned_cols=19 Identities=32% Similarity=0.476 Sum_probs=8.4
Q ss_pred HHHHHHHHHHhhhhhhhhc
Q 040074 129 ELKKELRDRLDKHNAELER 147 (148)
Q Consensus 129 ~w~keLkdql~kH~~ELER 147 (148)
.-++++.....+...+||+
T Consensus 143 e~~~~~~~~~~~~~~~Le~ 161 (535)
T PRK00106 143 EREEQVEKLEEQKKAELER 161 (535)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3333333334444455555
No 34
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.55 E-value=74 Score=28.23 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 040074 118 ELVQKQEKVIQELKKELRDRLDKHNAEL 145 (148)
Q Consensus 118 ELi~kq~kliq~w~keLkdql~kH~~EL 145 (148)
+|++|--..++.|+..|+.++-+|+.|.
T Consensus 187 rl~kkDie~L~k~R~~L~~emld~~~e~ 214 (293)
T COG4079 187 RLVKKDIETLRKHRRRLAEEMLDHIREG 214 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666777889999999999999999874
No 35
>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=31.50 E-value=58 Score=31.05 Aligned_cols=45 Identities=13% Similarity=0.287 Sum_probs=38.2
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN 142 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~ 142 (148)
..+.|++|++.+++|++.-..++....++..-..+||++=..++-
T Consensus 428 e~~kl~~e~~~l~~ei~~l~~iL~~~~~l~~vi~~EL~eikkkfg 472 (800)
T TIGR01063 428 EREKLQEEYKELLELIADLEDILASEERVLEIIREELEEIKEQFG 472 (800)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHHhC
Confidence 467788999999999999999999888888888888888777664
No 36
>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=30.39 E-value=34 Score=27.46 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=13.0
Q ss_pred hHHHHHHHhhhhHHHHHH
Q 040074 105 EIDAMEEELKIKDELVQK 122 (148)
Q Consensus 105 eIa~mEeELk~KdELi~k 122 (148)
..+.||+||.-|+.|...
T Consensus 15 RnalLE~ELdEKE~L~~~ 32 (166)
T PF04880_consen 15 RNALLESELDEKENLREE 32 (166)
T ss_dssp HHHHHHHHHHHHHHHHHC
T ss_pred HhHHHHHHHHHHHHHHHH
Confidence 457889999777777544
No 37
>PF12004 DUF3498: Domain of unknown function (DUF3498); InterPro: IPR021887 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 433 to 538 amino acids in length. This domain is found associated with PF00616 from PFAM, PF00168 from PFAM. This domain has two conserved sequence motifs: DLQ and PLSFQNP. ; PDB: 3BXJ_B.
Probab=29.37 E-value=18 Score=33.35 Aligned_cols=33 Identities=33% Similarity=0.432 Sum_probs=0.0
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQEL 130 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w 130 (148)
.||+||||-+.|-.-+..|..+|+-|+|=|.-+
T Consensus 445 vEeELrre~~~m~~~~~~kqrii~aQ~~~i~~L 477 (495)
T PF12004_consen 445 VEEELRREHAEMQAVLDHKQRIIDAQEKRIAAL 477 (495)
T ss_dssp ---------------------------------
T ss_pred hhhhhhhhHHHHhcccccchHHHHHhhhhcccc
Confidence 567788888888888888999999999877654
No 38
>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=29.30 E-value=1.6e+02 Score=21.52 Aligned_cols=34 Identities=24% Similarity=0.438 Sum_probs=17.7
Q ss_pred hhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 103 RHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 103 rkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
+++|..++.+++...+.+...+.-++..+..|+.
T Consensus 2 ~~e~~~l~~e~~~~~~~~~~~~~~~~~~~~dl~~ 35 (132)
T PF07926_consen 2 ESELSSLQSELQRLKEQEEDAEEQLQSLREDLES 35 (132)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555555555555444444444443
No 39
>PF14182 YgaB: YgaB-like protein
Probab=29.28 E-value=1.2e+02 Score=22.31 Aligned_cols=33 Identities=33% Similarity=0.476 Sum_probs=25.6
Q ss_pred cchhhhHHHHHHHhhhhHHHHHHH-HHHHHHHHH
Q 040074 100 KEPRHEIDAMEEELKIKDELVQKQ-EKVIQELKK 132 (148)
Q Consensus 100 e~lrkeIa~mEeELk~KdELi~kq-~kliq~w~k 132 (148)
..++.||+.|..+|+.--++..+| +.+|+.++.
T Consensus 43 ~~i~~EI~~mkk~Lk~Iq~~Fe~QTeeVI~sy~~ 76 (79)
T PF14182_consen 43 HSIQEEISQMKKELKEIQRVFEKQTEEVIRSYQS 76 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346779999999999888888887 457777664
No 40
>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=28.65 E-value=1.9e+02 Score=21.53 Aligned_cols=43 Identities=16% Similarity=0.151 Sum_probs=26.2
Q ss_pred hhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 040074 104 HEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELE 146 (148)
Q Consensus 104 keIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELE 146 (148)
++|+.+..++..-...++.+-.-|+.|-..-...+.+-+..|+
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 3566666666666666677777777776655555555444443
No 41
>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=28.48 E-value=75 Score=23.65 Aligned_cols=22 Identities=23% Similarity=0.693 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHhhhhhhhh
Q 040074 125 KVIQELKKELRDRLDKHNAELE 146 (148)
Q Consensus 125 kliq~w~keLkdql~kH~~ELE 146 (148)
.-|..+++.|+++...|..+|+
T Consensus 72 EqL~~Lk~kl~~e~~~~~k~i~ 93 (100)
T PF04568_consen 72 EQLKKLKEKLKEEIEHHRKEID 93 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555444444443
No 42
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 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. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=28.17 E-value=60 Score=24.38 Aligned_cols=54 Identities=24% Similarity=0.253 Sum_probs=34.2
Q ss_pred cCCCCccchhhhhh-hhh----hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Q 040074 81 DDFPPPLDHQKLYF-RLT----IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKEL 134 (148)
Q Consensus 81 rDFmeaakklqlYF-~lq----~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keL 134 (148)
+|+...+|.+-..- +|- .++.=.+.|..+++|++...+-.+.--+--..|.+.+
T Consensus 76 ~dIi~kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v 134 (144)
T PF11221_consen 76 TDIIRKAKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQV 134 (144)
T ss_dssp HHHHHHHHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77888888877766 666 4555567899999999877654443333333333333
No 43
>PHA02562 46 endonuclease subunit; Provisional
Probab=28.12 E-value=1.9e+02 Score=24.66 Aligned_cols=47 Identities=13% Similarity=0.266 Sum_probs=23.2
Q ss_pred hhhhhhhh-----hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 90 QKLYFRLT-----IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 90 lqlYF~lq-----~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
+..|..++ ....++.+|+.++.++.....-++...+.+...++.+..
T Consensus 162 ~~~~~~~~~~~k~~~~e~~~~i~~l~~~i~~l~~~i~~~~~~i~~~~~~~~~ 213 (562)
T PHA02562 162 ISVLSEMDKLNKDKIRELNQQIQTLDMKIDHIQQQIKTYNKNIEEQRKKNGE 213 (562)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 55555444 233455556666555555544444444444444444333
No 44
>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=27.71 E-value=85 Score=24.00 Aligned_cols=52 Identities=8% Similarity=0.014 Sum_probs=34.9
Q ss_pred cccCCCCccchhhhhhhhh------hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHH
Q 040074 79 ASDDFPPPLDHQKLYFRLT------IVKEPRHEIDAMEEELKIKDELVQKQEKVIQEL 130 (148)
Q Consensus 79 A~rDFmeaakklqlYF~lq------~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w 130 (148)
.||.|.--+-.+|-||++. ....|-+-|..||.++-.....+..+.|.+-..
T Consensus 25 ds~~~l~Lc~R~Q~HL~~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ 82 (131)
T PF10158_consen 25 DSRPVLRLCSRYQEHLNQCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKF 82 (131)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3489999999999999665 445666667777777665555555444444333
No 45
>PF08647 BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR013956 BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions [].
Probab=27.48 E-value=2.3e+02 Score=20.05 Aligned_cols=45 Identities=22% Similarity=0.381 Sum_probs=33.4
Q ss_pred hhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Q 040074 102 PRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELER 147 (148)
Q Consensus 102 lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELER 147 (148)
..+.+++|.-|++.-.-++.|...+|...+. +...+-.-+.++||
T Consensus 50 ~mr~~d~l~~e~k~L~~~~~Ks~~~i~~L~~-~E~~~~~~l~~~Ek 94 (96)
T PF08647_consen 50 AMRSKDALDNEMKKLNTQLSKSSELIEQLKE-TEKEFVRKLKNLEK 94 (96)
T ss_pred HHHhHHHHHHHHHHHHHHHHHhHHHHHHHHH-HHHHHHHHHHHhhc
Confidence 3567888999999999999999999988876 44444444555554
No 46
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=27.19 E-value=74 Score=26.64 Aligned_cols=32 Identities=25% Similarity=0.385 Sum_probs=24.7
Q ss_pred hhhhccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 95 RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 95 ~lq~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
+-...+.++.-|+.+|+ ...-|+.+|.+||..
T Consensus 76 s~~~A~~V~~RI~~vE~----------Va~ALF~EWe~EL~~ 107 (201)
T PF11172_consen 76 SEDAAEEVSDRIDAVED----------VADALFDEWEQELDQ 107 (201)
T ss_pred HHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHH
Confidence 33477888889988885 456789999999863
No 47
>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=26.95 E-value=51 Score=28.43 Aligned_cols=16 Identities=25% Similarity=0.430 Sum_probs=8.3
Q ss_pred hccchhhhHHHHHHHh
Q 040074 98 IVKEPRHEIDAMEEEL 113 (148)
Q Consensus 98 ~~e~lrkeIa~mEeEL 113 (148)
-++.|+..+..|||.+
T Consensus 113 qvd~Lkd~lee~eE~~ 128 (302)
T PF09738_consen 113 QVDLLKDKLEELEETL 128 (302)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4455555555555543
No 48
>KOG4083 consensus Head-elevated expression protein [Transcription]
Probab=26.92 E-value=1.9e+02 Score=24.38 Aligned_cols=47 Identities=17% Similarity=0.263 Sum_probs=35.9
Q ss_pred ccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHH----HHHHHHHhhhhhhh
Q 040074 99 VKEPRHEIDAMEEELKIKDELVQKQEKVIQELK----KELRDRLDKHNAEL 145 (148)
Q Consensus 99 ~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~----keLkdql~kH~~EL 145 (148)
.-.|+.+...|+.+|+-+|++++-|--=|++=. |+++.|.++-....
T Consensus 85 ~~~LAr~le~~~q~L~k~daf~Ke~larlEen~~e~ykv~~eqy~~aaE~V 135 (192)
T KOG4083|consen 85 AARLARDLEEKSQELKKQDAFYKEQLARLEENSSEFYKVTTEQYQKAAERV 135 (192)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999999988887755 45566666655443
No 49
>PF07964 Red1: Rec10 / Red1; InterPro: IPR012491 Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localises to the synaptonemal complex in Saccharomyces cerevisiae and the analogous structures (linear elements) in Schizosaccharomyces pombe []. This family is currently only found in fungi. ; GO: 0007059 chromosome segregation, 0007131 reciprocal meiotic recombination
Probab=26.71 E-value=1.3e+02 Score=29.40 Aligned_cols=38 Identities=32% Similarity=0.511 Sum_probs=33.0
Q ss_pred hccchhhhHHHHHHHhh--hhHHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELK--IKDELVQKQEKVIQELKKELR 135 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk--~KdELi~kq~kliq~w~keLk 135 (148)
-...|++-|++.-+||. |=.||=+|..+|+.+.|+-.+
T Consensus 634 FSneL~~KI~IIN~ELNnKI~kELSeKYQ~LF~eLQ~sFq 673 (706)
T PF07964_consen 634 FSNELIRKISIINEELNNKIMKELSEKYQRLFKELQKSFQ 673 (706)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 67889999999999996 568999999999999996443
No 50
>PRK02119 hypothetical protein; Provisional
Probab=25.89 E-value=2.3e+02 Score=19.55 Aligned_cols=26 Identities=27% Similarity=0.380 Sum_probs=13.2
Q ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHH
Q 040074 110 EEELKIKDELVQKQEKVIQELKKELR 135 (148)
Q Consensus 110 EeELk~KdELi~kq~kliq~w~keLk 135 (148)
|.-+..=++.|-+|.+-|...+..|+
T Consensus 22 E~tie~LN~~v~~Qq~~id~L~~ql~ 47 (73)
T PRK02119 22 ENLLEELNQALIEQQFVIDKMQVQLR 47 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334445555556655555555443
No 51
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.58 E-value=1.6e+02 Score=25.13 Aligned_cols=33 Identities=27% Similarity=0.454 Sum_probs=27.0
Q ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 040074 111 EELKIKDELVQKQEKVIQELKKELRDRLDKHNA 143 (148)
Q Consensus 111 eELk~KdELi~kq~kliq~w~keLkdql~kH~~ 143 (148)
++=|.|-||+.|-+|=|..|-+...++++|-+.
T Consensus 125 ~sek~k~ElrekAkKelddwy~~~~ek~~k~~~ 157 (216)
T KOG4031|consen 125 ASEKLKEELREKAKKELDDWYDQQNEKLEKTKA 157 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344677899999999999999988888887653
No 52
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=25.30 E-value=81 Score=21.59 Aligned_cols=30 Identities=37% Similarity=0.463 Sum_probs=20.8
Q ss_pred hh-hhhhccchhhhHHHHHH------HhhhhHHHHHHHHHH
Q 040074 93 YF-RLTIVKEPRHEIDAMEE------ELKIKDELVQKQEKV 126 (148)
Q Consensus 93 YF-~lq~~e~lrkeIa~mEe------ELk~KdELi~kq~kl 126 (148)
-| ||++.+| |+.|.+ +-.+|.+|++.-+|=
T Consensus 12 ~FSRl~k~eM----iaem~~~G~~y~~~~tK~~Lvk~fkKq 48 (54)
T PF09124_consen 12 WFSRLTKPEM----IAEMDSYGFEYNEKDTKAQLVKIFKKQ 48 (54)
T ss_dssp HHHTS-HHHH----HHHHHHTT----TTS-HHHHHHHHHHH
T ss_pred HHHhcCHHHH----HHHHHHhCCcCCccccHHHHHHHHHHH
Confidence 46 8887776 677777 788899998876553
No 53
>PF03735 ENT: ENT domain; InterPro: IPR005491 This entry represents a protein regulator which is able to repress transcription, possibly via its interaction with a multi protein chromatin re-modeling complex that modifies the chromatin. Its interaction with BRCA2 suggests that it may play a central role in the DNA repair function of BRCA2 []. ; PDB: 1UZ3_B 1UTU_B 2FMM_E.
Probab=25.05 E-value=38 Score=23.81 Aligned_cols=33 Identities=36% Similarity=0.525 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcC
Q 040074 116 KDELVQKQEKVIQELKKELRDRLDKHNAELERV 148 (148)
Q Consensus 116 KdELi~kq~kliq~w~keLkdql~kH~~ELERV 148 (148)
...|-..+++||...+++|.=--+.|.++|.||
T Consensus 23 qg~lsweke~lLt~Lr~~L~IS~e~H~~~l~~~ 55 (73)
T PF03735_consen 23 QGPLSWEKEKLLTELRKELNISDEEHREELRRA 55 (73)
T ss_dssp HSS--HHHHHHHHHHHHHTT--HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence 333666788888888888888888888888764
No 54
>PRK13979 DNA topoisomerase IV subunit A; Provisional
Probab=25.05 E-value=67 Score=31.71 Aligned_cols=64 Identities=17% Similarity=0.242 Sum_probs=43.0
Q ss_pred cccCCCCccchhhhhhhhh------------------hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 040074 79 ASDDFPPPLDHQKLYFRLT------------------IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDK 140 (148)
Q Consensus 79 A~rDFmeaakklqlYF~lq------------------~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~k 140 (148)
+|.+=-+|-+.|.-+|.++ -.+.|.+|.+.+.++.+.-.+++....++.+-.++||++-..|
T Consensus 410 ~s~~~~~a~~~l~~~f~~s~~qa~aIl~mrL~~Lt~le~~kl~~E~~eL~~~I~~l~~iL~~~~~l~~vi~~EL~eik~k 489 (957)
T PRK13979 410 SSKSKKDASENLIEKFGFTDEQAEAILELMLYRLTGLEIVAFEKEYKELEKLIKKLTKILSSEKELLKVIKKELKEVKEK 489 (957)
T ss_pred cCCCHHHHHHHHHHHhCCCHHHHHHHHhCcHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 4455556666777777553 3345666677777777777777777777777788888877766
Q ss_pred hh
Q 040074 141 HN 142 (148)
Q Consensus 141 H~ 142 (148)
+-
T Consensus 490 yg 491 (957)
T PRK13979 490 YG 491 (957)
T ss_pred hC
Confidence 54
No 55
>PF15642 Tox-ODYAM1: Toxin in Odyssella and Amoebophilus
Probab=24.47 E-value=1.1e+02 Score=27.79 Aligned_cols=37 Identities=30% Similarity=0.401 Sum_probs=29.9
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 040074 108 AMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAE 144 (148)
Q Consensus 108 ~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~E 144 (148)
.-||+|.+|.+.|..|-+++-..+-||+.+.+--...
T Consensus 131 q~ee~Le~k~~~is~qL~~~~~~r~EL~~~~~~l~~Q 167 (385)
T PF15642_consen 131 QHEEALEKKKEDISRQLQVIPKHRVELKQKQDDLTKQ 167 (385)
T ss_pred HHHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHH
Confidence 3488999999999999999999888888776544433
No 56
>cd05295 MDH_like Malate dehydrogenase-like. These MDH-like proteins are related to other groups in the MDH family but do not have conserved substrate and cofactor binding residues. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subgroup are uncharacterized MDH-like proteins from animals. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=23.81 E-value=47 Score=30.07 Aligned_cols=37 Identities=22% Similarity=0.311 Sum_probs=25.7
Q ss_pred cCCCCccchhhhhhhhh----hccchhhhHHHHHHHhhhhHHHHHHHH
Q 040074 81 DDFPPPLDHQKLYFRLT----IVKEPRHEIDAMEEELKIKDELVQKQE 124 (148)
Q Consensus 81 rDFmeaakklqlYF~lq----~~e~lrkeIa~mEeELk~KdELi~kq~ 124 (148)
.||+|- .++||++| +++|+ .+|+|-|.+|.|+-+.++
T Consensus 75 ~~f~e~---~~~yyg~~s~m~~~~~~----~i~~en~~~~~~~~~e~~ 115 (452)
T cd05295 75 NEFLEY---AESYYGITSSMMSEEMT----VIAEENLETHIEVEKEEE 115 (452)
T ss_pred HHHHHH---HHHHhCccccccHHHHH----HHHHHhHHHHHHHHHHHH
Confidence 577775 58999888 33332 367888988887765554
No 57
>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=23.61 E-value=1.6e+02 Score=22.44 Aligned_cols=13 Identities=38% Similarity=0.733 Sum_probs=5.4
Q ss_pred HHHHHhhhhhhhh
Q 040074 134 LRDRLDKHNAELE 146 (148)
Q Consensus 134 Lkdql~kH~~ELE 146 (148)
|++++.+...|+|
T Consensus 166 lk~el~~~~~~~~ 178 (192)
T PF05529_consen 166 LKKELEKKEKEIE 178 (192)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444443
No 58
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=23.46 E-value=30 Score=32.18 Aligned_cols=27 Identities=26% Similarity=0.440 Sum_probs=21.0
Q ss_pred hhhhhcccCcchHHHhhh------cCCCCCCCC
Q 040074 35 VMDDALLPCLTELDLNKA------IMPDFEAPL 61 (148)
Q Consensus 35 ~leaaLLPCLpareLqa~------idp~~~~~l 61 (148)
.||+|.+-||-+|-..+- |||.|-.|=
T Consensus 205 PLE~AY~Scle~Rr~~K~~~iPQDIDPSFPtSD 237 (458)
T PF10446_consen 205 PLEAAYISCLEARRREKHIPIPQDIDPSFPTSD 237 (458)
T ss_pred hHHHHHHHHHHHHHHcCCCCCCCCCCCCCCCCC
Confidence 688999999999887654 888776553
No 59
>PF10280 Med11: Mediator complex protein ; InterPro: IPR019404 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 Med11 of the Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3R84_S 3RJ1_O.
Probab=23.38 E-value=46 Score=24.35 Aligned_cols=36 Identities=28% Similarity=0.400 Sum_probs=24.8
Q ss_pred CCCCCcccchhhccccccCCCCccchhhhhh-hhh-hccchhhhHHHHHHH
Q 040074 64 FDEPAVQPAVETELQASDDFPPPLDHQKLYF-RLT-IVKEPRHEIDAMEEE 112 (148)
Q Consensus 64 s~~pshqidVEr~~hA~rDFmeaakklqlYF-~lq-~~e~lrkeIa~mEeE 112 (148)
.+.++..-.++. |+ .-|| .|. ....||++|..|++-
T Consensus 37 ~~~~~~k~~f~~--~~-----------~~f~~~L~~V~~~Lr~qI~~L~e~ 74 (117)
T PF10280_consen 37 QDPESSKEAFES--AT-----------SEFFSTLSSVEVELRRQIKYLEEV 74 (117)
T ss_dssp --TGGGHHHHHH--HH-----------HHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CcchhHHHHHHH--HH-----------HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334555566666 54 4567 666 777899999999986
No 60
>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease
Probab=23.29 E-value=2.9e+02 Score=22.13 Aligned_cols=48 Identities=29% Similarity=0.464 Sum_probs=31.4
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHH---HHHHHHHHhhhhhhh
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQEL---KKELRDRLDKHNAEL 145 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w---~keLkdql~kH~~EL 145 (148)
....+..+|+.+.-|.++=..+-.+|+|-|..+ ..+|-.-+..|+.|+
T Consensus 20 ~l~elq~~l~~l~~ENk~Lk~lq~Rq~kAL~k~e~~e~~Lpqll~~h~eEv 70 (194)
T PF15619_consen 20 ELAELQRKLQELRKENKTLKQLQKRQEKALQKYEDTEAELPQLLQRHNEEV 70 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 344556666666777777777777777777555 556666666676664
No 61
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=23.13 E-value=2e+02 Score=27.21 Aligned_cols=52 Identities=27% Similarity=0.441 Sum_probs=32.6
Q ss_pred cchhhhhh--hhhhccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 040074 87 LDHQKLYF--RLTIVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRL 138 (148)
Q Consensus 87 akklqlYF--~lq~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql 138 (148)
...++-|| .++....|..+-..+|.+-|+-....++.-.-+..|+|+|+++.
T Consensus 349 len~k~~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~ 402 (493)
T KOG0804|consen 349 LENQKQYYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEER 402 (493)
T ss_pred HHhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566788 56677777777777777766655555444444556666665543
No 62
>KOG3204 consensus 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis]
Probab=23.07 E-value=1.7e+02 Score=24.59 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=29.4
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 040074 106 IDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHN 142 (148)
Q Consensus 106 Ia~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~ 142 (148)
++.+||+.|.|.++--.++|-+...++..+.-..|-|
T Consensus 147 tatLEeKRKeK~~~~y~kKkql~kl~~~Aekn~~kki 183 (197)
T KOG3204|consen 147 TATLEEKRKEKAKIHYQKKKQLMRLRKQAEKNVEKKI 183 (197)
T ss_pred HHHHHHHHhHhhhhhHHHHHHHHHHHHHHHHHHHHhH
Confidence 5889999999999998888777777777666655554
No 63
>PF08232 Striatin: Striatin family; InterPro: IPR013258 This domain is associated with the N terminus of striatin. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (IPR001680 from INTERPRO) repeat domain []. It acts as a scaffold protein [] and is involved in signalling pathways [, ].
Probab=23.01 E-value=2.8e+02 Score=20.88 Aligned_cols=41 Identities=22% Similarity=0.269 Sum_probs=36.1
Q ss_pred chhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 040074 101 EPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKH 141 (148)
Q Consensus 101 ~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH 141 (148)
+++--|+-+|-|.|.-.-|-+...|=|.-+...||....|.
T Consensus 29 EmkarIa~LEGE~r~~e~l~~dL~rrIkMLE~aLkqER~k~ 69 (134)
T PF08232_consen 29 EMKARIAFLEGERRGQENLKKDLKRRIKMLEYALKQERAKY 69 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46788999999999999999999999999999998887774
No 64
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=22.80 E-value=1.4e+02 Score=21.55 Aligned_cols=39 Identities=15% Similarity=0.313 Sum_probs=28.1
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRD 136 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkd 136 (148)
.-+.|-..+..++++++...+-+++-++.++.+..+++.
T Consensus 74 ~q~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~ 112 (118)
T PF13815_consen 74 CQEYLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKK 112 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667778888888887777777777777777766654
No 65
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=22.68 E-value=2.2e+02 Score=20.62 Aligned_cols=38 Identities=21% Similarity=0.406 Sum_probs=27.4
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELR 135 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLk 135 (148)
..+.+..++..+.++.+.-...++++..-+...++|+|
T Consensus 81 ~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~k 118 (118)
T PF13815_consen 81 QLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKESK 118 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 45667777777777777777777777777777777764
No 66
>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=22.53 E-value=2.4e+02 Score=23.92 Aligned_cols=19 Identities=42% Similarity=0.541 Sum_probs=8.7
Q ss_pred chhhhHHHHHHHhhhhHHH
Q 040074 101 EPRHEIDAMEEELKIKDEL 119 (148)
Q Consensus 101 ~lrkeIa~mEeELk~KdEL 119 (148)
.+.+||..+|+|++..++.
T Consensus 75 ~l~~el~~le~e~~~l~~e 93 (314)
T PF04111_consen 75 ELDQELEELEEELEELDEE 93 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444555555544444433
No 67
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.04 E-value=2.5e+02 Score=25.11 Aligned_cols=22 Identities=27% Similarity=0.462 Sum_probs=18.0
Q ss_pred cchhhhHHHHHHHhhhhHHHHH
Q 040074 100 KEPRHEIDAMEEELKIKDELVQ 121 (148)
Q Consensus 100 e~lrkeIa~mEeELk~KdELi~ 121 (148)
--|+.||+.++.-|.-||.+|-
T Consensus 228 ~~lkeeia~Lkk~L~qkdq~il 249 (305)
T KOG3990|consen 228 QKLKEEIARLKKLLHQKDQLIL 249 (305)
T ss_pred HHHHHHHHHHHHHHhhhHHHHH
Confidence 3477899999999999998774
No 68
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=21.68 E-value=1.2e+02 Score=26.89 Aligned_cols=30 Identities=23% Similarity=0.104 Sum_probs=25.3
Q ss_pred hhhhhhh-hccchhhhHHHHHHHhhhhHHHH
Q 040074 91 KLYFRLT-IVKEPRHEIDAMEEELKIKDELV 120 (148)
Q Consensus 91 qlYF~lq-~~e~lrkeIa~mEeELk~KdELi 120 (148)
+.||+|. .-+.||+|++.|++++....++.
T Consensus 57 ~~y~~L~~EN~~Lk~Ena~L~~~l~~~e~l~ 87 (337)
T PRK14872 57 SHALVLETENFLLKERIALLEERLKSYEEAN 87 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7899888 55789999999999998876663
No 69
>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=21.49 E-value=2.4e+02 Score=18.16 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=28.8
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELE 146 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELE 146 (148)
.....+++|..++.++..+.+......+=...|.+....+...+..+..
T Consensus 60 ~i~~~~~~~~~~~~~~~~~r~~l~~a~~~~k~~e~L~e~~~~~~~~~~~ 108 (123)
T PF02050_consen 60 AIQQQQQELERLEQEVEQAREELQEARRERKKLEKLKERRREEYQQEEE 108 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666777777776666555555555555566655555555555543
No 70
>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=21.28 E-value=1.5e+02 Score=23.33 Aligned_cols=32 Identities=13% Similarity=0.146 Sum_probs=26.6
Q ss_pred cchhhhHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 040074 100 KEPRHEIDAMEEELKIKDELVQKQEKVIQELK 131 (148)
Q Consensus 100 e~lrkeIa~mEeELk~KdELi~kq~kliq~w~ 131 (148)
+.+...+..+++.+..+++.|.++++-|+...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (186)
T cd03777 2 GLLESQLSRHDQMLSVHDIRLADMDLRFQVLE 33 (186)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677888899999999999999998887654
No 71
>PF07957 DUF3294: Protein of unknown function (DUF3294); InterPro: IPR012917 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of mitochondrial ribosomal proteins, which appears to be fungal specific [].
Probab=21.10 E-value=2.2e+02 Score=24.09 Aligned_cols=41 Identities=17% Similarity=0.394 Sum_probs=26.5
Q ss_pred ccchhhhHHHHHHHhhhhHHHHHH-HHHHHHHHHHHHHHHHh
Q 040074 99 VKEPRHEIDAMEEELKIKDELVQK-QEKVIQELKKELRDRLD 139 (148)
Q Consensus 99 ~e~lrkeIa~mEeELk~KdELi~k-q~kliq~w~keLkdql~ 139 (148)
-+.|+++|+.+++-.+--+.||.| .+.|++-|-+-.|.+.+
T Consensus 6 le~Lk~qV~~L~~lV~KQs~lIskTGq~vlelQv~~~K~~~~ 47 (216)
T PF07957_consen 6 LEELKKQVDELQALVKKQSKLISKTGQQVLELQVKKQKRDVN 47 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467888888887666555555544 45566667666666553
No 72
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=20.74 E-value=4e+02 Score=20.55 Aligned_cols=44 Identities=14% Similarity=0.098 Sum_probs=30.3
Q ss_pred hccchhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 040074 98 IVKEPRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKH 141 (148)
Q Consensus 98 ~~e~lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH 141 (148)
+.+..++++...|+-..--.++.+..++.+..++++-..-+++-
T Consensus 63 R~~~I~~~l~~Ae~~~~eA~~~~~eye~~L~~Ar~EA~~ii~~A 106 (181)
T PRK13454 63 RQGTITNDLAAAEELKQKAVEAEKAYNKALADARAEAQRIVAET 106 (181)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666667777777766667777777777777777665555443
No 73
>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=20.32 E-value=2.9e+02 Score=18.78 Aligned_cols=45 Identities=18% Similarity=0.178 Sum_probs=33.8
Q ss_pred hhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhc
Q 040074 102 PRHEIDAMEEELKIKDELVQKQEKVIQELKKELRDRLDKHNAELER 147 (148)
Q Consensus 102 lrkeIa~mEeELk~KdELi~kq~kliq~w~keLkdql~kH~~ELER 147 (148)
+..|...+=-|++...++----=|.+..| |--|.++...+..|++
T Consensus 4 ~~~e~n~ac~e~~~~K~~AS~~GrgL~~W-k~~Kp~l~~ki~~l~~ 48 (57)
T PF10549_consen 4 LMAEYNQACAEYKKEKDIASLCGRGLNRW-KWKKPQLEQKIEELEE 48 (57)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHhHHHHHH-HHhhHHHHHHHHHHHH
Confidence 44455555567777777777778899999 8888888888888764
No 74
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=20.29 E-value=66 Score=25.47 Aligned_cols=49 Identities=14% Similarity=0.259 Sum_probs=40.9
Q ss_pred cCCCCccchhhhhhhhh--hccchhhhHHHHHHHhhhhHHHHHHHHHHHHH
Q 040074 81 DDFPPPLDHQKLYFRLT--IVKEPRHEIDAMEEELKIKDELVQKQEKVIQE 129 (148)
Q Consensus 81 rDFmeaakklqlYF~lq--~~e~lrkeIa~mEeELk~KdELi~kq~kliq~ 129 (148)
+++-+.|+.+|+-..+- .++.||+.-+.+|-.|+.-.+.|.+-+.|+-.
T Consensus 80 k~AYe~A~~lQ~~L~~~re~E~qLr~rRD~LErrl~~l~~tierAE~l~sq 130 (159)
T PF05384_consen 80 KEAYEEAHELQVRLAMLREREKQLRERRDELERRLRNLEETIERAENLVSQ 130 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567888888888333 88999999999999999999999998888644
No 75
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=20.08 E-value=2.9e+02 Score=21.15 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=17.2
Q ss_pred cCCCCccchhhhhh-hhh---------hccchhhhHHHHHHHhh
Q 040074 81 DDFPPPLDHQKLYF-RLT---------IVKEPRHEIDAMEEELK 114 (148)
Q Consensus 81 rDFmeaakklqlYF-~lq---------~~e~lrkeIa~mEeELk 114 (148)
-.|..+.-.|+... .+. ..+.|++||+.++.+|+
T Consensus 54 ~~~~a~~~eLr~el~~~~k~~~~~lr~~~e~L~~eie~l~~~L~ 97 (177)
T PF07798_consen 54 YLFKAAIAELRSELQNSRKSEFAELRSENEKLQREIEKLRQELR 97 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555554 222 33445566666655544
Done!